exchange reactions of urea inclusion compounds

Exchange Reactions of Urea Inclusion Compounds

thesis presented to the University of London in partial fulfillment of

the requirem ents for the degree of Doctor of Philosophy.

University College London,

Departm ent of Chemistry,

Christopher Ingold Laboratories,

20, Gordon Street

London WC1H OAJ

Presented by

Arjuman Khan

ProQuest Number: 10797806

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ABSTRACT

U rea inclusion compounds (UICs) consist of a u rea Tiost’

fram ew ork th a t forms hexagonal channels w ith in w hich ‘guest’

molecules (organic molecules) can be included. They have a typical

chiral space group of P 6X22 w ith lattice p aram eters a = b = 8.23 A, and

c = 11.017 A. This project investigates exchange reactions of UICs of

the type shown below:

uA A(1)+ub B(UIC) => uA A(UIC) + oB B(l)

In these exchange reactions, the guest species A and B are

CnH 2n+2 , (c = 10-15), CH16B r2, C10H 20C12, ch iral alcohols and chiral

brom oalkanes. I t h as been shown from XH NMR analysis, th a t w ith a

polycrystalline sam ple of a u rea inclusion compound, exchange

betw een alkanes and halogenoalkanes occurs w ith a preference for

longer chain molecules.

D etailed single crystal X-ray diffraction experim ents w ith single

crystal UICs fu lly im m ersed in liquid guest provided concrete and

more detailed evidence for the exchange occurring w ith in a single

crystal.

Exchange reactions w ith partia lly im m ersed single crystals were

also investigated. Liquid was shown to be expelled ou t from th e top

(exposed) end of the crystal. X-ray diffraction d a ta showed two sets of

layer lines characteristic of two guest species sim ultaneously p resen t

in th e UIC.

Solid solution form ation for two guest species w as a ttem pted by

cocrystallisation. DSC and powder X-ray diffraction resu lts showed

2

th a t th e po ten tial for solid solution form ation depends crucially on the

crystal s tru c tu re of th e UIC.

The m ain resu lts obtained from th is study is th a t guest species

are able to en te r and leave the u rea channels v ia an exchange process

w ith th e preference for long chain a lkanes displacing sho rte r chain

ones. In m ost u rea inclusion compounds solid solution form ation

(homogeneous m ixture) by cocrystallisation or v ia exchange is

impossible. T here is, however, firm evidence from th e exchange

reactions th a t two guest species can be p resen t in th e sam e u rea

inclusion compound in the form of macroscopic dom ains

(heterogeneous m ixture).

3

ACKNOWLEDGMENTS

I w ould first and foremostly like to thank m y supervisor Dr

S.T.Bramwell for his continual support and encouragem ent throughout

the project. I w ould also like to express m y appreciation for the time

and effort he pu t tow ards guiding and advising m e through the write

up of m y thesis. I w ould also like to acknowledge Professor Kenneth

H arris for his suggestions and ideas and also for the use of the

diffractometer at Birmingham. Special thanks to Professor Truter for

her guidance and help in familiarising me w ith the X-ray rotation

camera. I w ould also like to acknowledge Dr Sella for his useful

discussions, M ark Field for helping me w ith his com puting skills,

Maria C hristofi, Vanessa Chen and all of m y group.

Finally I w ould like to show m y appreciation to m y M um and

Dad for their moral support and m y Brother and Sister for being

patient w ith me especially near to completion of m y thesis.

4

CONTENTS

ABSTRACT 2

ACKNOW LEDGMENTS 4

LIST OF FIGURES 10

LIST OF TABLES 17

CHAPTER 1: INTRODUCTION

1.1 Inclusion Com pounds 22

1.2 Urea Inclusion C om pounds 25

1.2.1 Substances that form urea inclusion com pounds 25

1.2 2 The host structure in urea inclusion com pounds 28

1.2.3 The guest structure in urea inclusion com pounds 30

1.2.4 Crystallography of urea inclusion com pounds 33

1.2.5 Thermodynamic stability in urea inclusion com pounds 35

1.2.6 The "sliding m ode' in urea inclusion com pounds 37

1.2.7 Applications of urea inclusion compounds 38

1.3 Previous W ork on Urea Inclusion C om pounds Relevant to 39

th is Study

1.3.1 Phase transitions in alkane urea inclusion com pounds 39

1.3.2 Stability of alkane urea inclusion com pounds 41

1.3.3 Thermal anomalies in alkane urea inclusion com pounds 45

1.4 a,co-Dibromoalkane Urea Inclusion Com pounds 49

5

1 .51,6-Dibromohexane Urea Inclusion C om pound 51

1.6 Background to Aims of the Present W ork 53

1.6.1 Exchange reactions of urea inclusion com pounds 53

1.6.2 Solid solution formation in urea inclusion com pounds 54

CHAPTER 2: THEORY OF THE EXPERIMENTAL TECHNIQUES

2.1 Introduction 57

2.2 Optical Exam ination using the Polarising M icroscope 58

2.3 X-ray D iffraction Studies 60

2.3.1 In troduction 60

2.3.2 Powder X-ray diffraction 65

2.3.3 Single crystal X-ray diffraction using a ro ta tion cam era 66

2.3.4 Construction of a reciprocal lattice grid 69

2.4 D ifferential Scanning Calorim etry (DSC) 70

2.5 N uclear M agnetic Resonance 71

2.6 O ptical Activity 75

CHAPTER 3: EXPERIMENTAL PREPARATION AND

CHARACTERISATION OF PURE UREA INCLUSION COM POUNDS

3.1 Introduction 78

3.2 D etails of the Preparation of the Urea Inclusion C om pounds 79

used in th is w ork

3.3 Characterisation of Incom m ensurate Urea Inclusion 80

Com pounds

3.3.1 X-ray powder diffraction 80

3.3.2 Single crystal X-ray diffraction 84

6

3.3.3 D ifferential scanning calorim etry

3.3.4 N uclear m agnetic resonance

88

88

CHAPTER 4: EXCHANGE REACTIONS W ITH POLYCRYSTALLINE

UREA INCLUSION COM POUNDS

4.2 Expt 1: The Experim ental Investigation of the Exchange w ith a 102

C10H20C12(UIC) (w ith n = 10,11,12,13,14 and 15)

4.3 Expt 2: The Experimental Investigation of the Percentage 104

Exchange Between a Series of Q H ^^ U IC ) and C8H16Br2(l) and

CnH2n+2(UIC) and C10H20C12(1)

4.4 Expt 3: An Experim ent to M onitor the Mass changes of the 106

UIC R esulting from the Exchange Between CnH2n+2(l) and

C8H16Br2(UIC) and CnH2n+2(l) w ith C10H20C12(UIC)

4.5 Expt 4: The Experim ental Investigation of the Percentage 108

Exchange betw een C8H16Br2(UIC) and D ifferent M olar Ratios of

CHAPTER 5: EXCHANGE REACTIONS WITH FULLY IMMERSED

UREA INCLUSION COM POUND SINGLE CRYSTALS

5.2 An Experiment to Investigate the Percentage Exchange 127

Betw een C8H16Br2(UIC) and CnH2n+2(l)

5.3 Investigation of the Rate of the Exchange Reaction Between 129

C8H16Br2(UIC) and C15H32(1) by Single Crystal X-ray D iffraction.

4.1 Introduction 101

Series of CnH2n+2(l) and C8H16Br2(UIC), and CnH 2n+2(l) w ith

C15H32(l):C8H16Br2(l).

4.6 Sum m ary and Further D iscussion 110


5.4 Sum m ary and Further D iscussion 132

7

CHAPTER 6: EXCHANGE REACTIONS WITH PARTIALLY

IMMERSED UREA INCLUSION COMPOUND SINGLE CRYSTALS


6.2 Exchange Reactions Characterised by NMR Analysis 141

6.2.1 1,8-Dibromooctane UIC exchanged w ith pen tadecane from 141

the w atch glass

6.2.2 Self exchange of 1,8-dibromooctane from th e w atch glass 144

6.2.3 Both ends of th e crystal im m ersed in liquid guests 145

6.2.4 1,8-Dibromooctane exchanged w ith pen tadecane from th e 146

capillary tube

6.2.5 ‘S e lf’exchange from th e capillary tube 147

6.2.6 Repetition of the exchange reaction using th e sam e UIC 148

crystal

6.2.7 A ttem pted exchange w ith a te tragonal u rea crystal and 148

C15H32(1) from the w atch glass

6.3 Single Crystal X-ray Diffraction Studies 149

6.3.1 Exchange of 1,8-dibromooctane w ith pen tadecane from th e 149

w atch glass

6.3.2 Exchange of decane w ith pentadecane from th e w atch glass 151

6.3.3 ‘S e lf exchange w ith pentadecane from th e w atch glass 152

6.3.4 ‘S e lf exchange w ith decane from th e w atch glass 152

6.4 Summary and Further Discussion 153

CHAPTER 7: EXCHANGE REACTIONS WITH CHIRAL GUEST

SPECIES


7.2 Expt 1: (R/S) 2-dodecanol guest 168

7.3 Expt 2: (R/S) 2-decanol guest 170

8

7.4 Expt 3: (R/S) 2-brom otridecane 172

7.5 Expt 4: (R/S) 2-bromodecane 174

7.6 Use of chiral sh ift reagents 175

7.7 Sum m ary and Discussion 176

CHAPTER 8: SOLID SOLUTION FORM ATION IN UREA

INCLUSION COM POUNDS


8.2 Expt 1 :1,6-dibromohexane :l,6-dichlorohexane UIC 180

8.3 Expt 2 :1,8-Dibromooctane: Decane UIC 183

8.4 Expt 3: Valeric A nhydride UIC:Undecane UIC 185

8.5 Sum m ary and D iscussion 185

CHAPTER 9: SUMMARY AND CONCLUSION 192

APPENDIX: DETAILS OF CALCULATIONS AND 196

EXPERIMENTAL DATA

REFERENCES 209

9

LIST OF FIGURES

CHAPTER 1

Figure 1.1: Molecules that form the host structures belonging to type II.

Figure 1.2: A diagram representing the basic host structure of the UIC

w hen view ed along the tunnel axis.

Figure 1.3: The three diagram s above represent the urea molecule in

different conformations where (a) is the urea molecule in the planar

conformation (b) is an illustration of the side view of a urea molecule and

(c) is the construction of a unit cell of the urea inclusion com pound

showing the six levels w ith the urea molecule on its side.

Figure 1.4: Representation of the incom m ensurate m odulation of the guest

structure w ith respect to the host substructure w here (a) represents the

basic structure w ithout the m odulation due to the host substructure (b)

result w ith m odulation of the host substructure and (c) True structure

(guest +modulation).

Figure 1.5: Single crystal XRD oscillation photograph recorded at room

tem perature for decane urea inclusion com pound from ref 53.

Figure 1.6: Schematic two-dimensional representation of a urea inclusion

com pound, viewed perpendicular to the tunnel axis.

Figure 1.7: Representation of the urea structure w here (a) the herringbone

arrangem ent of the guest molecules and (b) the orthorhom bic distortion

from ref 31.

Figure 1.8: Powder X-ray diffraction for n-hexadecane urea betw een 296 K

and 46 K from ref 44.

Figure 1.9: The variation of mole ratio (m) of urea + n-alkane adducts w ith

the num ber of carbon atoms in the alkane (n) from ref 114.

Figure 1.10: Differential therm ogram s of urea and a series of urea-n-

10

paraffin adducts from ref 108.

Figure 1.11: M orphology of the 1,6-dibromohexane UIC from ref 57.

Figure 1.12: Guest repeat vs num ber of carbons for a,co-dibromoalkanes in

urea from ref 114.

Figure 1.13: High resolution solid state 13C NMR spectra of (a) 1,8-

dichlorooctane urea inclusion com pound (b) n-decane urea inclusion

com pound (c) sample 1; (d) sample 2; (e) sample 3 from ref 115.

Figure 1.14: Phase diagram for a solid solution.

Figure 1.15: Eutectic phase diagram.

CHAPTER 2

Figure 2.1: The polarising microscope from ref 117.

Figure 2.2: Figure 2.2: X-ray emission from a m etal surface producing

sharp transitions and featureless Bremstrahlung background.

Figure 2.3: Diagram to show the function of a pow der X-ray

diffractometer from ref 118.

Figure 2.4: Crystal m ounted on a goniometer head by m eans of nail

varnish accurately aligned w ith its c-axis coinciding w ith the rotation axis

of the camera from ref 117.

Figure 2.5: Geometry of the rotation photograph which shows the

diffraction of X-ray from sets of lattice planes which satisfy the Bragg

equation in the crystal producing Bragg reflections on the film.

Figure 2.6: A construction of a hexagonal reciprocal lattice grid.

Figure 2.7: Schematic representation of the DSC apparatus.

Figure 2.8: Energy levels in a hydrogen nucleus in a magnetic field.

CHAPTER 3:

Figure 3.1: Pow der X-ray diffractograms of urea inclusion com pounds

11

Figure 3.2: X-ray diffractogram of 1,8-dibromooctane UIC

Figure 3.3: X-ray diffractogram of Urea in the tetragonal phase

Figure 3.4: Single crystal X-ray diffraction rotation photograph recorded

for pentadecane UIC at room tem perature. The crystal was rotated about

its c-axis.

Figure 3.5: Bernal Chart used to calculate the c-param eter of the host

lattice in the UIC and also used to index the single crystal rotation

photograph of the UIC.

Figure 3.6: Single crystal X-ray diffraction pattern recorded on a AXIS IIC

diffractometer for 1,8-dibromooctane UIC at room tem perature. The

single crystal was rotated about its c-axis.


for tetragonal urea at room tem perature. The single w as rotated about its

c-axis.

Figure 3.8: m W /m g versus tem perature DSC curve for hexadecane UIC.

Figure 3.9: m W / m g versus tem perature DSC curve for pentadecane

UIC.

Figure 3.10: m W /m g versus tem perature DSC curve for 1,8-

dibromooctane UIC.

Figure 3.11:13C NMR spectrum of 1,8-dibromooctane UIC.

Figure 3.12:13C NMR spectrum of pentadecane UIC.

Figure 3.13: NMR spectrum of pentadecane UIC.

Figure 3.14: NMR spectrum of 1,8-dibromooctane UIC.

CHAPTER 4

Figure 4.1: *H NMR spectrum for the exchange of C14H30(1) w ith

C8H 16Br2(UIC). The spectrum shows 81 (1) % incorporation of C14H 30(1) into

the UIC.

12

Figure 4.2: A graph to show the percentage incorporation of a series of

alkanes(l) into 1,8-dibromooctane UIC.

Figure 4.3: A graph to show the percentage incorporation of a series of

alkanes(l) into 1,10-dichlorodecane UIC.

Figure 4.4: A graph to show the percentage incorporation of 1,8-

dibromooctane(l) into alkane UICs.

Figure 4.5: A graph to show the percentage incorporation of 1,10-

dichlorodecane into alkane UICs.

Figure 4.6: A graph to show the relationship betw een the percentage

incorporation of a series of alkanes into 1,8-dibromooctane UIC w ith the

experimental and expected mass changes.

Figure 4.7: A graph to show the relationship betw een the percentage

incorporation of a series of alkanes into 1,10-dichlorodecane UIC w ith the

experimental and expected mass changes.

CHAPTER 5

Figure 5.1: A graph to represent the relationship of the expected and

experimental mass changes w ith the percentage incorporation of a series

of alkanes into 1,8-dibromooctane UIC.

Figure 5.2: ]H NMR spectrum of the exchange of 1,8-dibromooctane from

the UIC w ith dodecane(l). The spectrum shows that 63 (2) % exchange of

dodecane w ith 1,8-dibromooctane UIC.

Figure 5.3: A graph to show the percentage exchange of a series of

alkanes(l) w ith single crystals of 1,8-dibromooctane UICs.

Figure 5.4: Single crystal X-ray diffraction rotation photograph of pure

1,8-dibromooctane UIC recorded at room tem perature.

Figure 5.5: Single crystal X-ray diffraction rotation photograph of

pentadecane UIC recorded at room tem perature.

13


at room tem perature after one day of the exchange betw een

dibromooctane in the UIC w ith pentadecane(l).


at room tem perature after two days of the exchange between



at room tem perature after three days of the exchange between



at room tem perature after four days of the exchange betw een



at room tem perature after five days of the exchange betw een


CHAPTER 6

Figure 6.1: Experimental apparatus designed to study the exchange

reactions. The photographs show a single crystal of dibromooctane UIC

w ith one end of the crystal placed in a capillary sealed w ith wax and the

other end im m ersed into a pool of pentadecane(l). The photograph was

taken after 24 hr s.

Figure 6.2: A graph to show the rate of exchange betw een 1,8-

dibromooctane UIC and pentadecane(l).

Figure 6.3: Single crystal X-ray diffraction pattern recorded on a R-AXIS

IIC diffractometer for 1,8-dibromooctane UIC at room tem perature before

exchange. The single crystal was rotated about its c-axis.

Figure 6.4: Single crystal X-ray diffraction pattern recorded on a R-AXIS

14

IIC diffractometer for the exchange of 1,8-dibromooctane from the UIC

w ith pentadecane (1) after 24 hrs at room tem perature. The single crystal

was rotated about its c-axis.

Figure 6.5: Magnified image of the low angle region of figure 6.4 showing

the presence of the guest reflections characteristic of both the guest

species after the exchange process.

Figure 6.6: Magnified image of the (3 0 0) and (2 1 0) guest reflections from

figure 6.4 showing their relative intensities.

Figure 6.7: *H NMR spectrum of the exchange of 1,8-dibromooctane from

the UIC w ith pentadecane (1). The spectrum shows that there is almost

complete exchange w ith < 10 % 1,8-dibromooctane rem aining in the UIC.

Figure 6.8: Single crystal X-ray diffraction pattern recorded on a AXIS IIC

diffractometer for the exchange of 1,8-dibromooctane in the UIC w ith

pentadecane (1) at room tem perature after a week. The single crystal was

rotated about its c-axis.

Figure 6.9: Magnified diffraction pattern of the low angle region of figure

6.8 showing the presence of guest reflections m ainly characteristic of

pentadecane guest species.

Figure 6.10: Single crystal X-ray diffraction photograph recorded for pure

decane UIC at room tem perature. The single crystal was rotated about its

c-axis.

Figure 6.11: Single crystal X-ray diffraction photograph recorded at room

tem perature for the exchange of decane in the UIC w ith decane (1). The

single crystal was rotated about its c-axis.

CHAPTER 8

Figure 8.1: Hom ogeneous mixture

Figure 8.2: Heterogeneous m ixture

15

Figure 8.3: Single crystal X-ray diffraction rotation photograph of pure

1.6-dibromohexane UIC. The crystal was rotated about its c-axis.

Figure 8.4: mW / m g versus tem perature DSC curve for 25:75 1,6-

dibromohexane UIC, (reproduced twice).

Figure 8.5: mW / m g versus tem perature DSC curve for 100:0 1,6-

dibromohexane (red):l,6-dichlorohexane (UIC), 25: 75 1,6-dibromohexane:

1.6-dichlorohexane (UIC) (blue), and 0:100 1,6-dibromohexane: 1,6-

dichlorohexane (green) (UIC).

Figure 8.6: X-ray diffractogram representing the different prepared ratios

of the 1,6-dibromohexane: 1,6-dichlorohexane (UIC) w here red = 100 %

1.6-dibromohexane UIC, green = 75 % 1,6-dibromohexane UIC, blue = 50

% 1,6-dibromohexane UIC, black = 25 % 1,6-dibromohexane UIC, and

pink = 100 % 1,6-dichlorohexane UIC.

Figure 8.7: NMR spectrum of an attem pt to prepare 25:75 1,8-

dibromooctane : decane UIC

16

LIST OF TABLES

CHAPTER 1

Table 1.1: A selection of guest molecules which form inclusion

com pounds w ith urea.

Table 1.2: The offset Ag along the tunnel axis betw een the centre of masses

of guest molecules in adjacent channels.

Table 1.3: Hydrocarbons that form urea adducts from ref 25.

Table 1.4: Non-adducting hydrocarbons w ith urea from ref 25.

Table 1.5: The enthalpy of formation from tetragonal urea and gaseous

hydrocarbon and the m ean increment per CH2 unit for several alkanes

from ref 94.

Table 1.6: cg and Ag for basic guest structure of a,co-dibromoalkane urea

inclusion com pounds from ref 52.

CHAPTER 2

Table 2.1: The seven crystal systems w ith the cell param eters and angles.

Table 2.2: Representation of the nuclear spin quantum num bers of the

commonly occurring nuclide.

Table 2.3: Chemical shift values for the listed functional groups that are

used in this study.

Table 2.4: N atural abundance data for the commonly occurring nuclide.

17

CHAPTER 3

Table 3.1: Data for the length of the guest molecules and the num ber of

urea molecules required for the series of alkanes.

Table 3.2: Data for the length of the guest molecules and the num ber of

urea molecules required for the series of substituted alkanes.

Table 3.3: (h k 1) reflections of hexadecane UIC at 151 K.

Table 3.4: (h k 1) reflections for the hexadecane UIC obtained from this

study.

Table 3.5: (h k 1) reflections, observed and calculated 20 values for the

pentadecane UIC.

Table 3.6: (h k 1) reflections, observed and calculated 20 values for 1,8-

dibromooctane UIC.

Table 3.7: (h k 1) reflections, observed and calculated 20 values for pure

tetragonal urea.

Table 3.8: Listings of (h k 1) reflections of pentadecane UIC and its

corresponding 2 sin0 values.

Table 3.9: (h k 1) reflections and 2 sin0 values for the 1,8-dibromooctane

UIC.

CHAPTER 4

Table 4.1: The percentage incorporation that occurred w ith Q H ^ l ) and

C8H 16Br2(UIC) in series 1 and CnH2n+2(l) and C10H 20C12(UIC) in series 2.

Table 4.2: Percentage incorporation of C8H 16Br2(l) into CnH2n+2(UIC) in

series 1 and the percentage exchange data for C10H20C12(1) into

CnH 2 n+2(UIC) in series 2.

Table 4.3: Data obtained for the percentage incorporation, the

experimental and expected mass changes for the exchange process that

occurred w ith CnH2n+2(l) and C8H 16Br2(UIC) guest species

18

Table 4.4: Data obtained for the experimental and expected m ass changes

and the percentage incorporation for the exchange process that occurred

w ith Q H ^ ^ l) and C10H20C12(UIC) guest species.

Table 4.5: The percentage incorporation of C15H32(1) and C8H 16Br2(l) into

the UIC after the exchange process (± 5% w ithin experim ental error).

Table 4.6: Guest periodicities (Cg) of alkane UIC determ ined from

equation 3.1, decomposition tem peratures of the even n-paraffins and

their (AHd) values from ref 108.

CHAPTER 5

Table 5.1: The initial mass, final mass and the change in m ass for the

exchange process w ith a series of CnH2n+2(l) guest species into a

C8H 16Br2(UIC).

Table 5.2: The percentage incorporation, expected m ass change and the

experimental mass change for the exchange process w ith a series of

CnH2n+2(l) w ith C8H 16Br2(UIC).

CHAPTER 6

Table 6.1: Percentage ratio of guest species present in the capillary tube,

crystal and watch glass for the exchange reaction w ith C8H 16Br2(UIC) and

c 15h 32(1)-Table 6.2: M easurem ents of the rate of exchange betw een C8H 16Br2(UIC)

and C15H32(1).


crystal and watch glass after the exchange reaction in the following

reaction I C8H 16Br21 C8H 16Br21 C15H321.


crystal and watch glass of the exchange reaction w ith

19

C15H32IC8H 16Br2| —

Table 6.5: Table to represent the exchange reaction w ith

C8H 16Br21 C8H 16Br2

Table 6.6: Exchange reaction that occurred w ith a pure urea crystal and

C15H32(1).

CHAPTER 7

Table 7.1: Mass of crystal, concentration and specific rotation values of the

exchange process described in experiment 1. L iterature value for [a]d =

244.5° from refl52.

Table 7.2: Mass of the liquid in the capillary tube concentration and

specific rotation values of the exchange process described in experiment

1.

Table 7.3: Specific rotation values of the racemic m ixture for the exchange

process described in experiment 1.

Table 7.4: Mass of crystal, concentration and specific rotation values of the

exchange process described in experiment 2. [a]d reported in literature =

138.8° from ref 153.

Table 7.5: Mass of liquid in the capillary tube, concentration and specific

rotation values of the exchange process described in experim ent 2.

Table 7.6: Specific rotation values of the racemic m ixture for the exchange

process described in experiment 2.

Table 7.7: Mass of the crystal, concentration and specific rotation values of

the exchange process described in experiment 3.

Table 7.8: Mass of the liquid in the capillary tube concentration and


3.

Table 7.9: Specific rotation values for the racemic m ixture for the

20

exchange process described in experiment 3.

Table 7.10: Mass of the crystal, concentration and specific rotation values

of the exchange process described in experiment 4.

Table 7.11: Mass of the liquid in the capillary tube, concentration and


4.

Table 7.12: Specific rotation values of the racemic m ixture for the

exchange process described in experiment 4.

CHAPTER 8

Table 8.1: Ratio of guest molecules used for solid solution formation in

1,6-dibromohexane: 1,6-dichlorohexane UIC.

Table 8.2: Ratio of guest species in the starting the final solutions for 1,6-

dibromoohexane: 1,6-dichlorohexane UIC.

Table 8.3: Relative ratios of 1 ,8-dibromooctane and decane guest species

present in the UIC.

21

CHAPTER 1

INTRODUCTION

1.1 Inclusion Compounds

The molecular im prisonm ent of one molecule by another has

been of great interest in science since the early 19th century. The

discovery of clathrate com pounds (now recognised as inclusion

compounds) dates back to Davy1 and Faraday2 w ho prepared and

analysed the first chlorine clathrate hydrate, and Clemm3 and W ohler4

w ho prepared the first quinol clathrate. M ylius5 suggested that on

crystallisation of a volatile material w ith quinol it was possible to

entrap the former w ithin the latter w ithout any direct interactions

betw een the two molecules, this was attributed to an im prisoning

action. It was not until the tw entieth century that these com pounds

were actually confirmed to be inclusion com pounds, w hen in 1945 and

1947 Powell and Palin6 and Palin and Powell7 characterised them by X-

ray diffraction studies. It was later suggested by Powell8 that this type

of chemical combination should be know n by the term 'clathrate'

compounds.

The first urea inclusion com pound w as accidentally discovered

by Bengen in 1940, while analysing fats in milk, using urea. A small

quantity of urea was added to milk and soon after the fat precipitated

on the surface. In betw een the fat and the milk there appeared another

layer, which was assum ed to be an emulsion. Octanol w as added to

the m ixture to destroy the emulsion but it still rem ained leaving

crystals on the barrier of the bottom layer. It w as later found that the

emulsion was calcium phosphate. The experiment w as repeated under

a microscope in the absence of the milk. A drop of octanol from a

syringe was added to the urea and crystals grew w hich Bengen nam ed22

and differently shaped from those included w ithin the channels of

urea15,16. In 1954, X-ray diffraction studies by Lenne13 showed the

thiourea tunnel structure to be topologically similar to the urea tunnel

structure, but w ith a larger cross-section. Consequently, there is a

greater selectivity to accommodate large guest molecules in the

channels of thiourea. For example thiourea can accommodate guests

such as ferrocene, cyclohexane and its derivatives and other

organometallic guests. Selenourea is also categorised as type II host

com pound. It has not been studied to such an extent as the urea and

thiourea host structures, due to its toxicity17. The molecules that form

these host structures are shown in fig. 1.1

h2n nh2 h2n nh2 h2n nh2

O S Se

urea thiourea selenourea

Figure 1.1: Molecules that form the host structures belonging to type II inclusion compounds.

Quinol clathrates form a series of com pounds w ith certain

volatile com ponents of the general type M = H2S, S 0 2, H C 0 2H, HC1,

HBr, CH3OH, and CH3CN. The quinol molecules C6H 4(OH)2M, link

through hydrogen bonds at approxim ately the tetrahedral angle to the

C-O bond, to form a three dimensional cage. The available space

m akes it possible to arrange a second identical cage which

interpenetrates the first. There are no direct linkages betw een the

molecules of the two cages and are inseparable w ithout breaking the

hydrogen bonds that exist betw een them. W hen M = S 0 2 the clathrate

24

an adduct. It was also found that the adduct could be dissolved in

solvents. The experiment was repeated w ith other organic com pounds

for example, ethers, aldehydes and carboxylic acids in place of octanol,

which also produced crystals. This new phenom enon was term ed

'urea addition com pounds'9,10 by Bengen and w as potential m ethod for

the separation of long chain hydrocarbons from short chain ones. The

first publication of this work was in 1949 by Bengen and Schlenk11.

Inclusion com pounds consists of guest species contained in

cavities in a host structure. The cavities can be of m any kinds such as

isolated cages, interconnecting cages, linear non-intersecting tunnels

or interlayer spacing. The guest species m ay be atomic, molecular or

ionic. There are two kinds of inclusion compounds: A type I inclusion

com pounds has a host lattice which stays intact if the guest molecule is

replaced or rem oved completely. The m ain inclusion com pounds of

this kind are zeolites. These com pounds contain em pty channels that

allow the access of guest molecules to and from the channels. They are

w idely used in the petroleum industry, zeolite ZSM-5 catalyses the

production of ethyl benzene from benzene and ethylene12. Another

example specific to this class of com pounds is the P-quinol clathrate. A

type II inclusion com pound has a host fram ework that collapses on the

rem oval of its guest. Examples of such host structures are urea,

thiourea and selenourea. Urea inclusion com pounds have hexagonal

channels that form spirals of either right handed or left handed

chirality depending on the w ay the crystal is formed. These helices

form the walls of the urea host tunnel and include the guest molecules

such as octanol within. The absence of the guest species in the urea

tunnels or even the presence of gaps, will result in destabilisation of

the host structure w ith respect to the pure tetragonal urea13,14. Since

1947 it has been know n that thiourea also forms crystalline inclusion

com pounds that incorporate guest molecules that are som ewhat larger

23

com pound is firmly retained in spite of the volatility of the sulphur

dioxide in the free state bu t S 0 2 is readily liberated by any process

which destroys the fram ework8.

1.2 Urea Inclusion C om pounds

1.2.1 Substances that form urea inclusion com pounds

Urea forms inclusion com pounds w ith a large variety of organic

guest molecules for example alkanes, halogenoalkanes, alcohols,

ethers, esters, carboxylic acids and ketones. The potential for forming a

urea inclusion com pound w ith a particular guest is governed by a

num ber of factors including the degree of branching of the guest

molecule and on its chain length. The m ethod for predicting the

optim um host:guest ratio is given by Rennie and H arris18 and for a

given hom ologous series there is a linear relationship betw een the

chain length of the guest molecule and the num ber of ureas required

to enclose one mole of guest18,19,20. Bengen and Schlenk11, Schlenk19 and

Bengen10 showed that the form ation of urea inclusion com pounds can

occur w ith alkanes, ethers alcohols, ketones carboxylic acids and esters

so long as the chain length was greater than six cabon atoms.

Zim m erschied et al11 carried out experiments to determ ine the range of

linear com pounds that form urea adducts. A qualitative precipitation

m ethod was used w here several drops of the hydrocarbon were added

to a saturated solution of the hydrocarbon. They show ed that only the

linear hydrocarbons formed precipitates w here n-hexane showed a

slight precipitate and there was no evidence for a precipitate in

heptane. These observations defined the lower limit of adduct

form ation under these test conditions. Cycloalkanes, isoparaffins and

aromatic classes show ed no precipitate, hence did not form an adduct

w ith urea. Zimmerschied et al21 also carried out calorimetric

25

m easurem ents to calculate the num ber of moles of urea required w ith

respect to a particular alkane guest molecule. They added small

portions of hydrocarbon to a m ixture of urea and m ethanol until the

tem perature ceased to rise. They found that for an undecane guest

molecule 9.5 moles of urea were required and for a hexadecane guest

molecule 11 moles of urea were required. M onobe and Yokoyama22

prepared a urea inclusion com pound of polyethylene of molecular

w eight 59 000 which suggested that there was no upper chain length

limit for n-alkane guest. Radell et al23 in 1961 reported that urea

inclusion com pounds can form w ith alkynes and alkenes and in 1964

he reported that at term inal positions of the chain there is greater

tolerance w ith regards to the choice of substituents24. Thus,

com pounds w ith terminally halogenated end groups and carboxylic

acid end groups form stable adducts. How ever due to the

crossectional diam eter of the urea being betw een 5.1 - 5.9 A limited

branching is possible. A very bulky substituent on a molecule will not

allow it to fit into the inclusion cavities and m ethyl groups at non

term inal positions are acceptable but not larger substituents. It has

been reported by Schliesser and Flitter25 that cyclic alkane urea

inclusion com pounds are possible, provided that the guest species

contains a long chain alkane. Some examples of guest species that

form urea inclusion com pounds are listed in table 1.1 on page 27.

26

Guest example

n-alkanes

n-substituted alkanes

alcohols

ethers

aldehydes

carboxylic acidsOH

anhydrides

alkenes

O O

'O

alkynes

Table 1.1: A selection of guest molecules which form inclusion compounds with urea.

27

1.2.2 The host structure in urea inclusion com pounds

The general structure type of the urea inclusion com pounds was

established by H erm ann and Schlenk19,26,27 w ho determ ined the

structure of hexadecane urea inclusion com pound by single crystal

diffraction. They showed the structure to be hexagonal at room

tem perature w ith six urea molecules per unit cell having a chiral space

group P6122 or P652228,29 and lattice param eters a = b = 8.20 A c = 11.1

A. This structure was confirmed by Smith30,31 w ho found it to be

consistent w ith most urea inclusion com pounds, w ith lattice

param eters a = b = 8.24 A c = 11.0 A. More recently H arris and

Thomas28 determ ined the lattice param eters of the hexadecane urea

inclusion com pound to be a = b = 8.227 A c = 11.017 A which showed

to be consistent w ith those originally reported.

The typical structure of a urea inclusion com pound is show n in

figure 1.2 on page 29. The urea molecules are linked by hydrogen

bonds so as to form interpenetrating helices, w hich results in a lattice

having hexagonal channels of infinite length and its guest molecules

contained in the channels32,33,. The helices, of which three urea

molecules form the boundary to each channel, m ay have a screw axes

of either sense, either a right handed or left handed, which is

dependent on the crystal growth, and in any particular single crystal,

the same chirality exists.

Figure 1.3 on page 30 shows a view of the structure along the c-

axis. Proceeding along the c-axis there are six levels (six dom ains

differing only in orientation by 60 rotation about the channel axis) at

which the urea molecules can be situated before the cycle is repeated.

At any one level the urea molecules occupy three of the six vertices of

the hexagonal channel. In only one of these three does the oxygen

atom of the carbonyl group project into the channel; in the other two

planes the urea skeletons are tangential to the walls of the cavity.

28

Figure 1.2: A diagram representing the basic host structure of the FIC when viewed along the tunnel axis.

29

H HI

■NV HNN

\lcII

0 0

(a) (b)

level 1

level 2

level 3

level 4

level 5

Figure 1.3: The three diagrams above represent the urea molecule in different conformations where (a) is the urea molecule in the planar conformation (b) is an illustration of the side view of a urea molecule and (c) is the construction of a unit cell of the urea inclusion compound showing the six levels with the urea molecule on its side.

1.2.3 The guest structure in urea inclusion com pounds

The long chain guest molecules occupy the hexagonal tunnels of

the urea host structure that is illustrated in figure 1.2. An im portant

structural issue in urea inclusion com pounds is the relationship betw een

the guest and host periodicities cg and ch respectively in the channel. The

periodicity of the guest structure along the c-axis may be different to that

30

of the host. Urea inclusion com pounds are classified as 'incom m ensurate',

if there are no sufficiently small integers n for w hich nch = m Cg18,34'35/36'37 for

example in the 1,8-dibromooctane urea inclusion com pound the

coefficients are irrational that is to say that n / m = 16.03 / 11.017 = 1.455

w here the num erator is the length of the guest species and the

denom inator represents the length of the urea host. If how ever the host

and the guest are 'com m ensurate', then the coefficient m and n in mcg and

nch are equal to a rational number. Thus for a com m ensurate 2,9-

decanedione inclusion com pound there are three guest molecules for

every four repeats of the urea helix therefore the relationship is 3cg = 4ch

Similarly for 2,10 undecanedione urea inclusion com pound the

relationship is 2cg = 3ch Most of the conventional urea inclusion

com pounds possess the incom m ensurate type arrangem ent though there

are examples in the literature of com m ensurate system s38,39'40'41,42 in

addition to those m entioned above such as 1,6-dibromohexane and 1,6-

dichlorohexane urea inclusion compound.

For an incom m ensurate inclusion com pound the host and the

guest subsystems are not in structural registry w ith each other. Due to

host-guest interactions each subsystem will exert an incom m ensurate

m odulation upon the other subsystem. H arris and Thomas28 and H arris43

discussed the idea that the host substructure consists of a basic host

structure, which experiences an incom m ensurate m odulation arising

from its interaction w ith the guest species. This m odulation has the same

periodicity as the basic guest structure. Similarly, the guest substructure

comprises of a basic structure that is subjected to an incom m ensurate

m odulation arising from its interaction w ith the host. This is show n in

figure 1.4.

31

Host = Basic structure ( ch) + m odulation ( cg)

Guest = Basic structure ( cg) + m odulation ( ch )

For any one subsystem , the exam ple figure 1.4 uses the guest structure,

(a) Basic structure

-t i i(b) modulation

Dis p la cem en t along c

(c)True structure (Basic structure + m odulation)

• • • • •

Figure 1.4: Representation of the incommensurate modulation of the guest structure with respect to the host substructure where (a) represents the basic structure without the modulation due to the host substructure (b) result with modulation of the host substructure and (c) True structure (guest +modulation).

32

The commensurate and incom m ensurate urea inclusion

com pounds are distinguished using theoretical calculations18,34,35,36 by

observing the relative fluctuations in the host-guest interaction energies

w ith translation of one substructure w ith respect to another along the

channel axis. W hen a set of n guest species w ith periodicity p are moved

through the channels of urea, the average host-guest interaction energy

per guest molecule is monitored. If the fluctuations are small then this is

attributed to incom m ensurate behaviour, how ever if they are sufficiently

large this is attributed to comm ensurate behaviour. The large regular

fluctuations in the comm ensurate urea inclusion com pounds occur

because there is a tendency for the guest substructure to 'lock' into the

host substructure at intervals along the channel axis.

1.2.4 C rystallography of urea inclusion com pounds

Single crystal X-ray studies show that in an incom m ensurate

system the inclusion com pound gives two distinguishable diffraction

patterns; one due the basic host structure and one from the guest

structure. The diffraction patterns comprise of layer lines that characterise

the periodicities of the host and the guest substructure along the channel.

W ith the exception of (h k 0), these layers can be classified as either host

(h) or guest (g) guest layer lines w ith the understanding that each pattern

contains contributions from the other substructure arising from the

m odulation28,44. For the majority of urea inclusion com pounds the basic

urea host structure rem ains invariant regardless of the guest species

which m eans that the basic host diffraction pattern is the same for

different inclusion com pounds (apart from h k 0). The structure belongs

to the hexagonal crystal system and has a chiral space group P6a22 and

lattice param eters a = b = 8.227 A, c = 11.017 A. In general the rotation

photographs for the urea inclusion com pounds, show that the guest

molecules are closely packed along the urea channels17,31,45,46,47 and exhibit

33

sufficient positional ordering to allow an average three-dimensional

lattice to be defined despite the fact that there is substantial dynamic

disorder of the guest molecules at room tem perature48'4930,51'52. There is

diffuse scattering which provides information about the local structural

details of the guest molecules included in the urea host fram ework and

discrete scattering between the host layer lines that is attributed to three

dimensional ordering of the guest. The spacing of layer lines is dependent

upon the periodicity of the guest structure. Figure 1.5 is an X-ray

oscillation photograph of a typical urea inclusion com pound namely

decane urea inclusion com pound 3 which illustrates the positions of the

host and guest layer lines.

(hk 3)hm 2)„^"(hk 1)h (hk 0) — (hk I ) h — (hk 2)h C l(hk 3)h ^

O

•(hk 2)g(hk 1)g

.(hk 7)g ■(hk 2)g

Figure 1.5: Single crystal XRD oscillation photograph recorded at room temperature for decane urea inclusion compound from ref 53.

Referring to the figure, at low 29 angles betw een the h layer lines,

(which are observed as sharp well defined Bragg reflections) for example

the (h k l)hand (h k 2)h the guest layer lines are present and comprise of

diffuse or discrete scattering or both depending on the ordering of the

guest molecules in the channels.

In general the basic guest structure m ay be of lower sym m etry than

the host. The periodicity, c, along the channel axis calculated from the

spacing between these layer lines is close to the predicted length of the

guest molecule in their extended linear conformation.

34

1.2.5 Therm odynam ic stability in urea inclusion com pounds

In general short chain guest molecules do not form stable urea

inclusion com pounds, as there is insufficient interaction energy betw een

the host and guest. Once a sufficient length is exceeded the complexation

energy will be large enough to form a stable inclusion com pound. In

alkane urea inclusion com pounds the equilibrium vapour pressure

m easurem ents of the alkanes indicate that the enthalpy of complexation

increases by approxim ately 2.4 kcal mol'1 for each m ethylene group

added to the linear chain20,54,55. For alkanes and urea in m ethanol solutions,

this value is closer to 1.6 Kcal mol'1 per CH2 group21. This increases the

stabilisation energy per methylene group which m eans that long chain

guest molecules can tolerate a larger degree of branching than the lower

homologues.

The ordering of guest molecule in a urea tunnel differ for different

guest molecules. Figure 1.6 illustrates the arrangem ent of the guest

molecule in an incom m ensurate urea inclusion com pound along the c-

axis.

Tun ne l axis

Guest moleculeH ost tunnel

Figure 1.6: Schematic two-dimensional representation of a urea inclusion compound, viewed perpendicular to the tunnel axis.

The param eter Ag is assigned as the offset of the guest ordering in one

channel w ith respect to its surrounding channels and corresponds to the

optim um interaction betw een the guest molecules in the adjacent

35

channels. The values of Ag for the different families of inclusion

com pounds are listed in the table 1.2.

Urea inclusion compounds Ag (A)

n-alkane UICs 0

a,co-dibromoalkane UICs S / 3carboxylic acid anhydride UICs 0

heptanoic anhydride UICs 2.3

diacyl peroxide UICs 4.6

Table 1.2: The offset Ag along the tunnel axis between the centre of masses of guest molecules in adjacent channels.

Table 1.2 shows that for the offset Ag for alkanes is zero, how ever for the

a,G)-dibromoalkanes it is dependent on the chain length. Studies w ith

inclusion com pounds containing differently functionalised n-alkane

guests have show n that the m ode of interchannel ordering depends

critically upon the nature and position of these functional groups37'47,49,56.

Possible explanations for non-zero Ag values include57.

(i) Guest-guest interactions in neighbouring channels.

(ii) An indirect interaction betw een guest molecules in neighbouring

channels, transm itted via their m utual interaction w ith the urea

molecules in the channel wall (including the possibility of bulky

substituents in guest molecules distorting the channel wall).

(iii) Kinetic factors related to crystal growth.

Schlenk58,59,60,61,62 dem onstrated that the inclusion of chiral guest

molecules into the urea channels can also occur bu t depends on the

chirality of the host structure. Recent studies by Yeo and H arris63,64

involved com putational investigations w here the study of the m inim um

36

host-guest interaction energies between the chiral urea host and chiral 2-

brom otridecane and 2-bromotetradecane guest molecules w ere carried

out. In incom m ensurate systems w ithin a given tunnel of the urea

inclusion com pound each guest molecule experiences a different

environm ent w ith respect to the host structure. The m inim um host-guest

interaction energy was determ ined as a function of distance over one unit

cell of host in the 2-bromoalkane urea inclusion com pound. The results

showed, that in a urea inclusion com pound w ith a chiral space group

P6j22 there is a preference for the R enantiom er and was show n to be

favoured in all six positions along the tunnel.

1.2.6 The 's lid ing m ode' in urea inclusion com pounds

The m otion of guest species along the c-axis of the urea channels

can be explained by the incom m ensurate intergrow th nature of the urea

inclusion compounds. Incommensurate urea inclusion com pounds

contain two regular interpenetrating sublattices65,66,67 and require more

than three lattice vectors to define their structural periodicity. The two

substructures are incom m ensurate in only one direction (c-direction) and

therefore have four lattice vectors a, b, q and c2 w here a and b are the

same for both the host and the guest substructures, and cx and c2 are

lattice vectors for the host and the guest substructures respectively along

the incom m ensurate c-axis. The inclusion com pounds are examples of

aperiodic crystals which, in addition to their three acoustic m odes (low

energy vibrational modes) have other zero energy modes. The zero

energy m ode in the urea inclusion com pound arises from relative shifts of

the two substructures along the com m ensurate direction which is

referred to as the 'sliding m ode'67,68,69. The shift of the substructure along

the incom m ensurate axis comprise of both longitudanal and transversal

displacem ent of the atoms. Schmicker et al69 reported the 'sliding m ode' as

a combination of the m ovem ent of the host and guest w ith respect to one

37

another and a so called 'phason ' type of m odulation of the two

subsystem s which collectively causes the m ovem ent of the atoms along

the channels70. Brillouin scattering was used to study the 'sliding m ode' in

heptadecane urea inclusion com pound69. Another inclusion com pound,

dioctanoyl peroxide urea, was studied for the observation of the 'sliding

m ode' bu t the latter was found to be absent. This discrepancy was

explained as an effect of 'p inning ' of the sublattices by im purities69. Smart

et al50 suggested that the lack of three dim ensional ordering in the

heptadecane urea inclusion com pound reduces the effect of 'p inning '

which allows the sliding m ode to be observed at energies accessible in the

Brillouin scattering zone. For the dioctanoyl peroxide urea inclusion

com pound there is both one dimensional and three dim ensional ordering,

which enhances the 'p inning ' effects, therefore the 'sliding m ode' cannot

be observed in the Brilluion scattering zone. Heilm an et al68,71 studied a

similar 'sliding m ode' in Hg3.§ AsF6by neutron diffraction.

1.2.7 A pplications of urea inclusion com pounds

Urea inclusion com pounds have been used industrially for the

separation of straight chain alkanes from branched and cyclic organic

compounds. Zimmerschied et al21 showed in their report that the

separation of unbranched hydrocarbons from complex petroleum

fractions is m ade possible by the use of urea. This was carried out by the

stirring of oil (a m ixture of the hydrocarbons) w ith urea dissolved in

methanol. The adduct was washed w ith 2,2,4-trimethylpentane, filtered

and decom posed in water, which was then distilled in order to remove

the 2,2,4-trimethylpentane. Schlenk and H olm an72 and Cason et al73

reported the separation of carboxylic acids using urea. Schlenk and

Holm an72 studied a num ber of carboxylic acids w here they carried out

experiments to separate binary m ixtures of these acids. The carboxylic

38

acids were heated and added to a solution in m ethanol and allowed to

crystallise at room tem perature. This deposited crystalline urea

complexes which was filtered and dried. The yields of the carboxylic acid

in the complex and that in the filtrate w ere calculated. W hite74

investigated the use of urea inclusion com pounds as hosts for addition

polym erisation reactions. The butadiene urea complex w as form ed at -55

°C in a low concentration of m ethanol and then acted as a seed to

nucleate the grow th of the urea inclusion complex that contains the

m onom er molecules. They also reported that polym erisation occurs

readily w hen the urea complex is irradiated w ith high energy electrons.

Furtherm ore, urea inclusion com pounds also have the potential for

utilizing its chiral nature in the separation of racemic m ixtures58,59'60,61.

1.3 Previous Work on Urea Inclusion Compounds Relevant to this

Study

1.3.1 Phase transitions in alkane urea inclusion compounds

Phase transitions for the alkane UIC have been studied and it is

found that on lowering the tem perature, the UICs undergo a phase75 76 77 78 79 80 i itransition to the orthorhombic p h a s e accompanied by a change in

the dynamics of the included guest m olecule47,49,81,82,83,84. The phase

transition is show n to increase on increase in chain length of the included

guest molecule. Eukao et al85 reported for the alkane (CnH 2n+2) UICs the

transition tem peratures to range from 110 K (n = 10) to 160 K (n = 20) and

220 K (n = 40). W elberry and Mayo78 showed that for the hexadecane urea

inclusion com pound there is a phase transition at approxim ately 147 K

from a hexagonal (high tem perature ) to orthorhom bic (low tem perature)

phase This was investigated by X-ray diffraction, w ith diffraction

patterns resolved at 295 K and low tem peratures betw een 130-150 K. The

strong diffuse scattering due to the guest species in the urea inclusion

39

com pounds has been investigated using a Monte Carlo Sim ulation which

showed that, at tem peratures just above the phase transition there are

quite large domains of the orthorhombic herringbone structure. This is

illustrated shown in figure 1.7. At low tem peratures the alkanes are m uch

more ordered for which there is an expansion of the frame work in

directions parallel to the plane of the alkane and contraction in the

perpendicular direction which is indicative of an orthorhom bic phase.

Harris et alu in another report studied the phase transitions of the

hexadecane urea inclusion compound. They showed betw een 151 K and

149 K evidence for a change occurring in the peak w idth as a result of a

phase transition. This is illustrated in figure 1.8 and is consistent w ith that

reported by the other authors.

CD

(a)

7

7 H /o ------------Y -(b

(b)

Figure 1.7: Representation of the urea structure where (a) The herringbone arrangement of the guest molecules and (b) the orthorhombic distortion from ref 31.

40

7=120 K

7 = 147 K

\ ____

JV*.7=134 K

\ ________/V.

JL.

2 B (degrees)

7=149 K.

7=296 K

403020100

Figure 1.8: Powder X-ray diffraction for n-hexadecane urea between 296 K and 46 K from ref 44.

The structural changes of the UICs that w ere caused by the phase

transitions were reported the same for the alkane and a,o>dibromoalkane

UIC. Yeo et a f6 however observed a more complicated change in the low

tem perature phase for the 1,10-dicarboxylic acid urea inclusion

com pound and Shannon et a f7 reported a two phase transition on cooling

heptanoic anhydride urea inclusion compound.

1.3.2 Stability of alkane urea inclusion compounds

As w ith all inclusion compounds, structural compatibility between

the host and the guest substructures of alkane urea inclusion com pounds

are of necessity in order to confer stability. A detailed study of the factors

that control adduct form ation in alkane urea inclusion com pounds were

by Schliessler and Flitter25 who carried out experim ents on a large range

41

of hydrocarbons. The results are sum m arised in table 1.3 and 1.4

respectively for adducting and non-adducting urea inclusion compounds.

n-octacosane

n-tridecane n-hexatriacontane

n-tridecene 1-phenyleicosane

n-tetradecane 1 -cy clohexyleicosane

n-hexacosane 1-cyclopentylgeneicosane

Table 1.3: Hydrocarbons that form urea adducts from ref 25

n-pentane 2-phenyleicosane

n-hexane 17-phenyl triacontane

2,2,4 trimethylpentane 1-cyclohexyloctane

4, methyltridecane 2-cy clohexyleicosane

3-ethyltetracosane 9-cy clohexyleicosane

5-n-butyldocosan 1,4-di-n-decylcyclohexane

9-n-butyldocosane 1-a-napthylpentadecane

11-n-butyldocosane 1-a-decalylpentadecene

4-n-hexyldocosane 1-a-nhexadecylhydrindene

5-ethyl-5-(2-ethylbutyl)-octadecane 1-a-n-hexadecylhydrindane

phenyloctane l-cyclopentyl-2-hexadecyclopentane

Table 1.4: Non-adducting hydrocarbons with urea from ref 25.

As show n from table 1.3, adduct form ation occurs w ith guest

molecules that do not contain substituents in the m iddle of the chain A

m ethyl group on the m iddle of an n-C13 chain show n in table 1.4 inhibits

crystalline complex formation. Other contributing factors to the stability

of these inclusion com pounds have been discussed in section 1.2.5.

Distances betw een adjacent guest molecules in any one channel also

contribute to the overall stability of the inclusion com pound as explained

below.

42

It has been reported by Rennie and H arris34 that the repeat distance

of the guest molecules (cg) is slightly less than the length of the alkane in

the type of extended, linear conformation that it m ust adopt to fit w ithin

the space available inside the urea channel. Gilson and McDowell88,89 and

Connor and Blears90 concluded that the hydrocarbon molecules were able

to rotate more or less freely about their longitudinal axis and were able to

flex and twist the hydrocarbon chain. A detailed com puter sim ulation by

Souaille et al91,92 on the dynamic properties in the nonadecane UIC showed

that the interactions betw een adjacent guest species in the tunnels,

influences the translational and re-orientational m otion of the guest

species. Solid state nuclear magnetic resonance confirmed that the guest

molecules pack w ithin Van der Waals contact radii along the channel

axis93. The m easured values of cgin the inclusion com pound is typically ca

0.5 A shorter than the predicted van der Waals length of the guest

molecules in their extended linear conformation47. Plausible explanations

for the shortening effects include, coiling of the guest molecule; tilting of

the guest molecules away from the tunnel axis, side by side stacking of

the end groups of adjacent guest molecules w ithin the tunnel and van der

W aals overlap of the neighbouring guest molecules in the tunnel18,34,35.

Laves et a f4 reported the distance betw een the term inal carbon atoms of

the successive alkane molecules in the same channel as being 0.374 nm,

which is shorter than the norm al Van der Waals distance for a CH3 group

of 0.41 nm. This shortening effect was also observed by Parsonage et al54

and was used to explain the therm odynam ic anomalies that occur in

inclusion compounds. They explained that if a gap is present betw een the

alkane molecules, the strong attractive host-guest interactions w ould be

wasted. They also suggested that an equilibrium betw een the CH3—CH3

distance is reached w hen the host-guest potential energy is minimised

that is w hen the repulsive force betw een the ends of the guest molecules

balance the attractive force of the urea that tends to 'suck' the molecules

43

together. Parsonage et al showed that the CH3—CH 3 interaction potential

energy is m inim ized w hen the CH3—CH3 distance is 0.375 nm , w hich was

show n to be in good agreement w ith the X-ray observation of Laves et al94.

It has been proposed by m any authors that the m ain proportion of

the alkane guest (CH2)n exists essentially only in the all trans

conformation but there is a small degree of distortion at the term inal

groups of the alkane. There is however discrepancy am ongst the authors

on the degree of distortion 45'95,96'97'98/"'100. On the basis of 13C NMR studies,

2H NMR studies and MD simulations the alkanes CH3(CH2)nCH3 w ith

n = 5-8 have been show n to contain (15-30 %) gauche bonds at the ends of

the alkane chains. Others have claimed that there is a m uch smaller

degree of gauche end group present. IR spectroscopy of the m ethyl

rocking m odes at low tem perature phases of urea inclusion com pounds,

suggests the gauche end group concentration to be 5 % both at 298 K and

90 K. Laves et a f4 and Lenne et al101 have investigated the relationship

betw een cg and n, where n is the num ber of carbon atom s in the alkane.

This study was carried out by calculating the length of the alkane chains

by X-ray diffraction and plotting a graph of cg against n. They concluded

that n converges to a linear relationship as n increases. The formula

derived for alkane urea inclusion com pound is:

cg = 1.26n + 2.48 Aequation 1.1

The graph, in figure 1.9 of cg vs c shows that the hexadecane point

deviates from the best fit linear correlation, w hich indicates a

com m ensurate system, whereas those lying on the line were

representative of an incom m ensurate system. The hexadecane molecule

before inclusion has a length of 23.1 A. and w hen in a constrained

environm ent, as in the inclusion adduct an apparent shortening is

44

observed to 22.6 A. Lenne et alm, Shannon et al57 and Forst et alw2,76

suggested that the discrepancy between the experim ental cg and the value

predicted on the basis of the Van der Waals length can be accounted for

by the repulsive interactions between adjacent molecules w ithin the

channel. Smith found that the chain was able to contract presum ably by

some slight rotation about the internal C-C bonds.

£

R \0 12 14 \t> 1» 20 22 240 471

Figure 1.9: The variation of mole ratio (m) of urea +n-alkane adducts with the number of carbon atoms in the alkane (n) from ref 114.

1.3.3 Thermal anomalies in alkane urea inclusion compounds

The stability of an inclusion com pound can be attributed to a

num ber factors. This includes hydrogen bonding betw een adjacent urea

molecules and Van der Waals forces betw een the urea molecules

themselves and betw een the urea molecules and the hydrocarbon guest

molecules. The formation of the complex m ay be represented as follows:

complex (s) = urea (s) +hydrocarbon (1)

equation 1.2

The heats of form ation of inclusion com pounds for this process from

solid urea and pure hydrocarbon rely partly on the differences in the

45

hydrogen bond energy between those in the tetragonal phase of urea and

those in the adduct. They also rely on the differences in the Van der

Waals forces present betw een the reactants and product.

The concept of stability in urea inclusion com pounds w as

investigated by Redlich et al20. Experiments w ere carried out to m easure

the decomposition pressures of the urea adducts. They found that the

Gibbs free energy of decomposition, AG, increased approxim ately

linearly w ith chain length at 298.15 K. The following m athem atical

relationship described in equation 1.3 for the Gibbs free energy was

derived from their results.

AG / {kj (mol.guest)’1 = -9.11 + 1.59n for n-alkanes

equation 1.3

W here n is the num ber of carbon atoms in the guest molecule.

Zimmerscheid et al21 determ ined the corresponding enthalpy of form ation

of the n-alkane adducts, and a typical value is 1.6 Kcal per CH2 group,

which is close to the value for the Van der Waals interaction and is found

to be a fairly good fit to the straight line. The expression for AH is given

in equation 1.4

AH / {kj (mol.guest)’1} = -10.23 + 11.74n

equation 1.4

Table 1.5 outlines the m ean increment of enthalpy per CH2 unit 5 for

several n-alkanes.

46

Alkane CH3(CH2) CH3

n = 5-14

AHfg / (KJ (mol.guest)'1 8 / (KJ (mol.guest)'1

5 66.9

6 82.0 15.1

7 95.8 13.8

8 106.3 10.5

10 128.4 11.1

14 169.0 10.2

Table 1.5: The enthalpy of formation from tetragonal urea and gaseous hydrocarbon and the mean increment per CH2 unit for several alkanes from ref 109.

The heat capacity m easurem ents carried out on the alkane urea

adducts shows a regular increase in AS of decom position w ith n, which

suggests that molecular m otion in the complex is m ore restricted for

longer chain molecules. For the adducts of the four even alkanes listed in

table 1.5 the decomposition tem perature T, change in enthalpy AH and

the entropy AS all vary linearly w ith chain length (n). Specific heat

capacity m easurem ents were carried out by Pem berton and

Parsonage103,104, Cope and Parsonage105 and Gannon and Parsonage106 w ith

pure hydrocarbons. These experiments show ed transitions that occur at a

few degrees below their m elting tem peratures. This is due to the rotation

and reorientation of the molecules about their longitudinal axis.

Pem berton et al1M carried out similar experiments on both the

corresponding straight chain urea adducts and a substituted hydrocarbon

adduct namely, 2-methyl pentadecane. They concluded from the results

that the transitions were partly due to the m otion and interactions of the

guest molecules in adjacent channels. This was verified by the fact that

the decom position of 2-methyl pentadecane adduct show ed a transition

at a higher tem perature than the unsubstituted urea adducts. The

presence of the new CH3 group in the 2-methyl pentadecane effects this

transition because the m ethyl group inhibits the m ovem ent of the guest

molecules. Furtherm ore the transition tem peratures of the adducts are

47

about one half the m elting tem peratures of the corresponding pure

hydrocarbons. This was explained by Parsonage et al in term s of the

potential energy betw een the axis of two parallel long chain molecules

which is proportional to r"5. The distance betw een the guest molecules in a

urea adduct and a pure alkane are 8.230 A and 4.6 A respectively,

therefore the transition tem perature in the adduct is expected to be lower

than that of the pure paraffin.

u rea

1 0

12 '

20

2-1

•28

S A M P L E B L O C K T E M P E R A T U R E C C )

Figure 1.10: Differential thermograms of urea and a series of urea-n-

paraffin adducts from ref 108.

Figure 1.10 illustrates the decom position tem peratures of the urea

adducts as a function of chain length and in a later report by Ahm ad et

al107 decomposition tem peratures reported for the UICs ranged from 378

K (n = 10) to 409 K (n = 30) (where n represents the num ber of carbon

48

atoms in the guest molecule), which were in close aggreem ent to those of

McAdie. McAdie108 and Parsonage and Stavely109 suggested in their report

that w hen the pure hydrocarbon melts the interm olecular interactions are

broken by the potential of the term inal m ethyl groups and the vibrational

and rotational energies of the whole molecule. In the urea adducts there

are host-guest interactions which cause restricted m otion in the channels.

W hen the guest molecules obtain enough energy to freely rotate (in three

dimensions), this enables them to escape out from the tunnels for which

the hexagonal lattice breaks dow n and rearranges to the tetragonal form.

1.4 (X,co-Dibromoalkane Urea Inclusion Compounds

A series of a,co-dibromoalkane inclusion com pounds Br(CH2)nBr

were prepared and studied w ith n ranging from 7 to 10. These particular

inclusion com pounds possess the conventional urea host structure

(hexagonal sym m etry at room tem perature) apart from w hen n = 6 which

has a comm ensurate monoclinic structure.

The X-ray diffraction patterns for all the a,o)-dibromoalkane urea

inclusion com pounds (except that of the 1,6-dibromohexane inclusion

complex) contain the same general features w here the host lattice

comprise of sharp discrete reflections that are generally m ore intense than

those of the guest reflections. The general ordering of the guest molecules

show n by X-ray diffraction studies are different to those of the pure

alkane urea inclusion compounds. Features that are only characteristic to

the a,co-dibromoalkanes are intense broad diffuse bands that are m ainly

observed betw een the third and the fourth layer lines of the host lattice.

The chain lengths and the Ag values have been reported by Smart57

for the a,G>dibromoalkane urea inclusion com pounds from n = 7-10 as

show n in table 1.6.

49

Br (CH2)nBr n = 7 n = 8 n = 9 n = 10

cg / A 14.1 15.5 17.4 18.1

A g / A 4.65 5.13 5.79 6.03

Table 1.6: cg and Ag for basic guest structure of c^co-dibromoalkane urea inclusion compounds from ref 57.

a,oD ibrom oalkanes exhibit three dimensional ordering, Ag = cg / 3,

w here cg denotes the periodic repeat distance and Ag denotes the offset

along the tunnel axis betw een the positions of the guest species in

adjacent channels (see section 1.2.5). Harris et alno discussed the steric

influence on the offset, Ag, in a,o>dibromoalkane urea inclusion

compounds. The bulky brom ine substituent interacts extremely strongly

w ith the channel walls of the urea in comparison to interactions of m ethyl

group present in an alkane inclusion compound. X-ray diffraction studies

show that, for the 1,6-dibromohexane inclusion com pound, the brom ine

distorts the urea channels and will possibly have similar influence on the

conventional incom m ensurate systems. Furtherm ore the experimental

evidence supports the idea that the functional group is a contributing

factor in the ordering of the guest. The interaction of the guest molecule

w ith m ore than one functional group in each adjacent channel leads to

the optim um value of Ag to be dependent on the repeat distance, c .

H ow ever Ag will be constant w ith interactions w ith just one functional

group111. It has been further suggested that for guests of short chain

length, interactions w ith m any functional groups in the different channels

is probable, whereas for long chain guest molecules interactions will only

occur w ith one neighbour. This theory does not appear to hold for the

acid anhydride family49, for which relatively short guest molecules have

been show n to have a constant Ag = 0. The reason for this difference is

possibly due to the carboxylic anhydride urea inclusion com pound

adopts the all trans conformation. This conform ation m ay lead to long

50

range dipole-dipole interaction between guest molecules in adjacent

channels which prom ote the inter tunnel ordering w ith Ag = 0. The same

argum ent can be applied to the ketone urea inclusion com pound38.

1.5 1,6-Dibromohexane Urea Inclusion C om pound

The structure of 1,6-dibromohexane urea inclusion com pound has

been reported different to that of the conventional a,co-dibromoalkane

urea inclusion com pound in that there is a com m ensurate relationship

betw een the host and guest substructures57,112,113,114. The oscillation

photograph for 1,6-dibromohexane urea inclusion com pound reported by

Smart57 showed that the host and guest layer lines were present as one set

of lines indicative of the commensurate nature of the urea inclusion

compound. The structure is monoclinic w ith space group P21 / n, w ith

lattice param eters a = 8.45 A, b = 10.95 A, c = 13.62 A, a = y = 90°, P =

92.5°. The external crystal m orphology of the 1,6-dibromohexane urea

inclusion com pound is a truncated pyram id57 as show n in figure 1.11,

which is different to the conventional needle like urea inclusionj 113,114com pounds

%%

%*

%N

%S

✓*

✓✓

✓*

✓*

©

J<

*<

**

*✓

S*

%%

*%

%

Figure 1.11: Morphology of the 1,6-dibromohexane UIC from ref 57.

The commensurate nature of the 1,6-dibromohexane urea inclusion

com pound is evident from figure 1.12 w here the cg values are

extrapolated for the incommensurate a,co-dibromoalkane urea inclusion

51

ocom pound from a predicted value cg = 12.8 A for the fully staggered 1,6-

dibromohexane guest molecule. The graph shows that there is a

shortening of the 1,6-dibromohexane guest molecule by 1.8 A from 12.8 A to 11.0 A which allows the guest molecule to lock into the host. The

deviation from the straight line confirms that the periodicities of the host

and guest substructures are based on the same lattice (i.e. they are

commensurate) and the crystal sym m etry of the composite inclusion

com pound is described by a single three dimensional monoclinic space

group.

Another significant difference is that the 1,6-dibromohexane urea

inclusion com pound contains a gauche conformation at each end of the

molecule. In contrast mainly trans end groups exist in the conventional Br

(CH2)nBr UIC w ith only a small fraction (5-14 %) of gauche end group.

<

UsO

Number of carbons

Figure 1.12: Guest repeat vs number of carbons for a,co-dibromoalkanes in urea from ref 114.

52

1.6 Background and Aims of the Present W ork

1.6.1 Exchange reactions of urea inclusion com pounds

M ahdyarfar and H arris115 found evidence for the m igration of a

second guest molecule into the channels of a urea inclusion

compound. The experiment w as carried out using 1,8-dichlorooctane

UIC and n-decane UIC. Single crystals of 1,8-dichlorooctane UICs

w ere im m ersed in liquid n-decane inside a closed bottle (sample 1)

and left at room tem perature for five days. Two other sam ples were

prepared in the same w ay as sam ple 1: sam ple 2 w as ground and

im m ersed in liquid n-decane at room tem perature while sample 3 was

left at 0 °C for 5 days. The three sam ples w ere then filtered and

collected, and high resolution solid state 13C NMR spectra were

recorded for each of the three samples. The authors have show n from

the spectra in figure 1.13 that the liquid alkane had entered the

channel. The spectral evidence suggested that for the ground crystals

of 1,8-dichlorooctane UIC the process for the decane to enter the

channels of urea w as more rapid, relative to that of the unground

samples. This was presum ably due to a larger contact area between

the liquid and the solid phases. M ahdyarfar and H arris115 furtherm ore

concluded that the tem perature dictated the kinetics of the exchange.

Consequently, the exchange that occurred at 0 °C was comparatively

slower to the one that had occurred at room tem perature. In spectrum

e there arose an additional peak at 8 45.2 w hich w as not present

initially in the pure 1,8-dichlorooctane UIC. The implications of this is

the presence of two intermolecular environm ents in the UIC one at 5

45.7 which is assigned to the ( CH2 Cl C l ) and the other at 8 45.2

due to the ( CH2C1 CH3).

The evidence obtained from the experim ent carried out by

M ahdyarfar and Harris showed an interesting area of study. The m ain

53

aim of this project was therefore to develop the exchange reactions

further in order to understand the mechanism, w hether the exchange

occurs w ithout disruption to the host fram ew ork and also its

utilisations.

( e )

1 _

( c )

l A i j»>

(a)

45.0 40.0 35.0 30.0 25.05 /ppm

20.0 15.0

Figure 1.13: High resolution solid state 13C NMR spectra of (a) 1,8- dichlorooctane urea inclusion compound (b) n-decane urea inclusion compound (c) sample (d)sample 2; (e) sample 3 from ref 115.

1.6.2 Solid solution formation in urea inclusion compounds

There are two limiting possibilities of the types of systems that

could form a system where two guest species are completely miscible

in the solid state or both guest species are immiscible The two cases

are described below. The simplest form of a solid solution system is

one that shows complete miscibility in both solid and liquid state116.

The m elting point of A is depressed by the addition of B and that

54

of B is increased by the addition of A. At low tem peratures a single phase

solution exists. At high tem peratures, a single phase liquid solution

exists. At interm ediate tem peratures, a two phase region of solid solution

exists. This is show n in figure 1.14.

TLiquid

L + SS

TO.ASolid solutions

Pure A Pure BComposition

Figure 1.14: Phase diagram for a solid solution.

Figure 1.15 represents the phase diagram of eutectic system w ith partial

solid solution formation.

Liquid

Liquid +

Solid ATLiquid

+ Solid BTE

Solid A + Solid B

Pure BCompositionPure A

Figure 1.15: Eutectic phase diagram.

55

Consider two component liquid of composition w. W hen it is cooled it

enters the two phase region labeled 'liquid + solid B'. Almost pure

solid begins to come out of solution and the rem aining liquid becomes

richer in A. Further cooling results in more solid formation. The liquid

phase becomes progressively richer in A. Point Q is know n as the

eutectic point. The liquid at the eutectic composition freezes at this

single tem perature, and w hen the solid w ith the eutectic composition

melts it forms a liquid of the same composition. Solutions to the right

of Q deposit B as they cool and solutions to the left of Q deposits A.

In this work a series of experiments were carried out on urea

inclusion com pounds w here in chapter 2 the back ground theory to the

experimental techniques are discussed, following the characterisation

of pure urea inclusion com pounds in chapter 3. Chapter 4 introduces

this new concept of exchange where experiments were carried out on

polycrystalline samples of a variety of inclusion com pounds in order to

understand the fundam entals of the exchange processes. The

subsequent chapters 5, 6 and 7 carried out m ore advanced experiments

related to the exchange process where single crystal urea inclusion

com pounds were used.

Solid solution formation of two guest species in a urea inclusion

com pound was the initial aim to the project w here the interest was to

prepare the solid solution of the urea inclusion com pound and to

study its phase transitions. This is discussed in chapter 8 and explains

details of the criterions for solid solution formation.

56

CHAPTER 2

THEORY OF THE EXPERIMENTAL TECHNIQUES

2.1 Introduction

A num ber of techniques were used for characterisation of the urea

inclusion com pounds, namely; optical exam ination using a polarising

microscope, pow der X-ray diffraction, single crystal X-ray diffraction,

nuclear magnetic resonance, optical polarim etry and differential scanning

calorimetry.

X-ray pow der diffraction was used to identify the form ation of a

urea inclusion com pound and single crystal X-ray diffraction was carried

out before and after the exchange process to observe relative changes in

intensities of reflections, which m ay be indicative of the exchange

process. Further characterisation by nuclear magnetic resonance gave

figures for the percentage exchange (defined in the appendix) that

occurred w ithin the urea inclusion compounds. The relative ratio for each

guest species present in the urea inclusion com pound was calculated

from the relative integrals obtained from the solution *H NMR spectrum.

NMR w ith chiral shift reagents and optical polarim etry w ere carried out

on urea inclusion com pounds that contained chiral guest molecules in the

attem pt that the shift reagent w ould estimate the chiral selectivity.

Optical polarim etry was used to identify w hether the guest species in the

urea inclusion com pound was of the R or S configuration and also to

determ ine the degree of resolution after the exchange process. Specific

rotation m easurem ents obtained in this study were com pared w ith the

literature data for the optically pure enantiom er to determ ine the

resolution of the guest species in the urea inclusion compound.

Differential scanning calorimetry was m ost useful for the characterisation

of the urea inclusion compounds. It was used for comparison of the

57

decom position tem peratures of the urea inclusion com pounds and the

urea obtained in this study to that reported in the literature. Further uses

w ere for the detection of solid solution form ation in urea inclusion

com pounds which showed characteristic shifts in the pow er versus

tem perature DSC curve.

All the techniques m entioned above are discussed individually

below.

2.2 Optical Exam ination using the Polarising M icroscope

The polarising microscope117118 enables exam ination of crystals in

plane polarised light w ith observations of the effect that the crystal has on

the plane of polarisation. Figure 2.1 shows the construction of a typical

polarising microscope.

Ocular

Bertrand lens

Analyser

Accessory plates

Objective

I Rotating stage

Converging lens

[ I Polariser

» 1

I_______ J C

Mirror

Figure 2.1:The Polarising microscope from ref 117.

The analyser and polariser both polarise the light that passes through

them, w ith their polarising directions at right angles to one another.

W hen a crystal is observed w ith both the polariser and analyser in place

the crystal is said to be between crossed polars. In the absence of a crystal

58

the field observed between crossed polars is uniform ly dark. The electric

vector of light entering the microscope from the polariser vibrates at right

angles to the vibration direction of the analyser and the observed field

does not illuminate. In the presence of a crystal a small am ount of light

does pass through and the observed field is not completely blacked out.

The explanation for this phenom enon is as follows.

Polarised light that enters the crystal can be resolved into two

perpendicular vectors. The behaviour of these rays on passing through a

crystal is show n by means of a geometric construction know n as an

indicatrix. This is an ellipsoid whose dimension in any direction from the

centre is proportional to the refractive index of the light vibrating along

that direction. The behaviour of light as it passes through the crystal

depends on the shape of the section of the indicatrix perpendicular to its

direction of travel. The vibrations of the electric field interact m ore

strongly in one direction than in another which causes the differences in

the refractive indices along the different vibration directions, thus giving

rise to the different speeds of light through the crystal.

Anisotropic crystals in general have an ellipsoidal indicatrix.

Crystals of the cubic system are isotropic and w hen the microscope stage

is rotated between crossed polars these crystals rem ain uniformly dark

implying that light passes through w ith all the vibration directions

equally affected. A uniaxial indicatrix has two of its principal axes equal

and the third can be larger or smaller than the other two. The crystal

systems that adapt this indicatrix are the hexagonal, trigonal and

tetragonal. A biaxial indicatrix is a triaxial ellipsoid having its three

m utually perpendicular semi-axes equal to the three principal indices of

refraction of a biaxial crystal. Biaxial crystals belong to the orthorhombic

monoclinic or triclinic crystal system. An anisotropic crystal displays

extinction w hen the vibration directions of the polars coincide w ith a

principal vibration direction in the crystal. W hen the microscope stage is

59

rotated through 45° components of the light along different axes of the

indicatrix propagate at different speeds and the plane of polarisation is

altered hence the brightness of light is at a maxim um. The colour show n

by the crystal in this bright position depends on the difference betw een

the refractive indices or birefringences (A n) and the thickness of the

crystal; the product of the two quantities is called the retardation. As the

crystal is turned at 90° from its starting position the crystal again displays

extinction.

The criterion for the selection of a single crystal for X-ray

diffraction is the observation of uniformity in brightness at any point

during rotation of the crystal. Defects in the crystal such as splitting,

obvious twinning, occlusions and satellites can be observed. Occlusion

appears as small bubbles in the crystal, tw inning and satellites are present

as separate entities attached to the crystal so w hen the stage is rotated

there will contain regions in it that appear brighter or not so bright.

2.3 X-ray D iffraction Studies

2.3.1 Introduction

The production of X-rays118 involves the bom bardm ent of high

energy electrons w ith a m etal surface. The electrons decelerate as they

plunge into the m etal and generate radiation w ith a continuous range of

wavelengths called Bremstrahlung. Peaks in the spectrum in figure 2.2

arise from the collisions of the incoming electrons w ith those in the inner

shells of the atoms.

60

Figure 2.2: X-ray emission from a metal surface producing sharp transitions and featureless Bremstrahlung background.

A collision expels an electron from the inner shell and a higher

energy electron falls into the vacancy, emitting the excess energy as an X-

ray photon. The most common target m aterial used in this study is

copper. The three components of the em itted radiation are Kttl/ Ka2 and Kp

w here the electronic decay occurs from the 2p—> Is and 3p—» Is orbitals

respectively. The Kp and the Ka2 radiations are filtered leaving the line

having a wavelength of 1.54 A, which is the radiation for the diffraction

from lattice planes in crystals. This diffraction phenom enon was

explained geometrically by Bragg et al120,ul w ho considered an X-ray beam

striking a set of lattice planes in a crystal. They found that the

requirem ent of a reflection at a crystal lattice plane was that the distances

travelled by waves reflected from successive planes to differ by a whole

num ber of wavelengths. The condition for this to occur is show n in

equation below

2d sinG = nX

w here d is the interplanar spacing, X is the w avelength of the X-

rays, 0 is the angle of incidence and n is an integer. In general n is taken

as 1 as it can be absorbed into the miller indices (see below). All crystals

61

m ay be described by atoms arranged in a repetitive three dimensional

pattern which is know n as a unit cell. If each repeat unit of this pattern

which m ay be an atom or a group of atoms is taken as a point then a three

dimensional point lattice is created. Thus by neglecting the complicated

structure of atoms surrounding each point and considering the points

alone one arrives at a series of points in space w hich form the foundation

on which the crystal is built. They are characterised in term s of their unit

cell dimensions into seven possible crystal systems; these are show n in

table 2.1. If there are lattice points only at the corners of the unit cell then

the unit cell is said to be primitive. The monoclinic, orthorhombic,

tetragonal and cubic system can also have lattice points at the centre of

the faces, or the m iddle of the body in addition to at the corners of the

unit cell. These are said to be centered unit cells. In addition to the seven

prim itive lattices there are seven centered lattices that in total constitute

the fourteen Bravais lattices. Each lattice type is represented by a lattice

symbol P, I, F, C w here these symbols denote prim itive, body centred face

centred and centred respectively. A combination of the sym m etry

elements, possibly w ith these 14 lattices leads to 230 distinct

crystallographic space groups. Knowledge of the space group and the

assymmetric unit allows generation of the entire structure122,123,124,125.

System Axial relation Angular relation

cubic a = b = c a = P = y = 90°

tetrahedral a = b * c a = p = y = 90°

orthorhombic a *b * c a = p = y = 90°

hexagonal a = b * c a = P = 90° Y = 1 2 0 °

trigonal a = b * c a = p = y ^ 90°

monoclinic a * b * c a = y = 90° p ^ 90°

triclinic a * b * c a * P * y * 90°

Table 2.1: The seven crystal systems with the cell parameters and angles.

62

The lattice planes in a crystal are labelled using Miller indices. For

a three dimensional unit cell three indices are required and by convention

are labeled h, k, 1 where h, k and 1 are integers, positive, negative or zero.

The Miller indices are inversely related to fractional coordinates w ithin

the unit cell of the lattice plane. The intercept along the x direction gives

h, along the y gives k and along z gives 1. If x = V£ then h = 2. The

separation of planes is know n as the d-spacing and is denoted d ^ . The

relationship betw een the d-spacing and lattice param eters can be

determ ined geometrically but is dependent upon the crystal system. For a

hexagonal crystal the d spacing for any set of planes is given by the

formula below.

1 = 4 h 2 +hk+k2 + l2d i n 2 23 a c

The am ount or intensity of X-ray scattering from each lattice plane

is different and is dependent upon the position of the atom s in the unit

cell. This can be explained by assum ing that the contribution of any atom

to the reflected wave is proportional to the num ber of electrons it contains

or alternatively, to the atomic num ber (Z). This assum ption holds for

reflections of low order where the angle w ith w hich the rays are scattered

is extremely small. It ceases to be even approxim ately true w hen

reflections of higher order are considered. For small angles of scattering

the diffracted waves from the greater proportion of the electrons will be

in the same phase and the total am plitude will be nearly Z times that of a

single electron. However, at greater angles of scattering the wavelets

diffracted by the separate electrons give less support to each other (i.e

they will be out of phase w ith each other) and the effect is greatly

reduced. The relationship below defines how the scattering factor f relates

to the electron distribution.

63

f = am plitude of scattering by the electron cloud am plitude of scattering by a single point electron

The scattering from individual atoms combines to give a diffracted ray.

The intensity in a specified direction (h k 1) can be described in term s of

the structure factor, F. For example w hen considering a face centered

cubic unit cell there are atoms at the corner and at faced centred

positions. For the (1 0 0) plane the atoms at the edge will scatter the X-

rays in phase because their phase difference will be 2n radians bu t w ith

the atom half w ay between the (10 0) plane their phase difference will be

n radians. Half way between the planes the reflected ray will be out of

phase. For the (2 0 0) plane the phase difference is 2tt radians and hence

they scatter in phase. There is therefore an effect of destroying the first

reflection and in fact every reflection of odd order, while they strengthen

the intensity of even order reflections. W hen successive planes parallel to

a face are identical w ith regards their actions on the X-rays, their

reflections dim inish regularly in intensity as their order increases. If this

regularity is absent, it implies that the successive planes are different w ith

regards spacing or constitution. The relationship of the phase difference 8

betw een atoms at the origin and a position w ith a fractional co-ordinates

(x, y, z) is given by:

8 = 2n (hx + ky +lz)

The sum m ation over the j atoms in the unit cell gives the structure factor

F.

F ^ = 2 fj (cos8 + i sin5)

The intensity of the diffracted beam I ^ is proportional to I F ^ 12

64

Thus the intensity of the diffracted X-rays depends crucially on the

relative position of the atoms. Other factors that contribute to intensities

of reflections are geometrical, for example the Lorentz factor. This has not

been discussed, as it is not directly relevant to our studies.

The proceeding section 2.3.2 discusses Pow der X-ray diffraction

w ith polycrystalline samples of the urea inclusion com pound and section

2.3.3 includes X-ray diffraction studies w ith single crystals of the urea

inclusion compounds.

2.3.2 Pow der X-ray diffraction

X-ray diffractograms118 from pow der samples are recorded w ith

intensity as a function of diffraction angle, 20. The inform ation obtained

from these patterns is derived from sam ples of random orientation in the

crystallites. The pow der diffractometer uses an X-ray detector (counter),

essentially a Gieger-M uller tube to m easure the position of the diffracted

beams. The ground sample is rotated about its axis O w ith a detector

travelling on the circumference of the circle centred at O as show n in

figure 2.3. Diffractometers are typically operated such that they set to

scan betw een required angular limits. The signal from the counter is

recorded in regular steps of 20. Hence, w henever the angle of the

incidence beam satisfies the Bragg equation a strong signal is detected.

The 0 values for the various reflections can be read from the resulting

diffractogram and the d-spacing is calculated from the reflecting planes.

65

Specim enSlit

system

Sourceslit

Receiving slit

.Counter

Figure 2.3: Diagram to show the function of a powder X-ray diffractometer

adapted from ref 118.

2.3.3 Single crystal X-ray diffraction using a rotation camera

A rotation camera typically uses a nickel filtered Cu Ka radiation

(wavelength 1.54 A) where the selected crystal is m ounted on a

goniometer head in preparation for the collection of X-ray photographic

data. A goniometer head consists of a set of arcs at right angles to each

other. The crystal is attached to the pin of the goniom eter head by means

of a fine glass fibre. The fibre is attached to the p in by blue-tac. The fibre

tip is then finely coated w ith nail varnish and is then brought up to the

crystal that adheres to the fibre in the required orientation. The crystal

m ust be accurately aligned, and setting photographs are carried out in

order to obtain this accurate alignment. The film holder is locked onto the

camera so that the crystal lies at the centre of the cameras cylindrical axis;

the X-rays are switched on and the crystal is m ade to oscillate continually

through 360° by the camera motor. This is illustrated in figure 2.4.

66

__2\TCamerarotationaxis

Crystal

Figure 2.4: Crystal mounted on a goniometer head by means of nail varnish which is accurately aligned with its c-axis coinciding with the rotation axis of the camera from ref 117.

The X-ray beam is perpendicular to the rotation axis and every

time the Bragg condition is satisfied a reflection occurs. If we consider the

rotation photograph (see introduction) the zero layer line is seen to arise

from the reflections of the incident X-ray beam by sets of planes parallel

to the axis of rotation of the crystal. As the crystal rotates about its c-axis,

the family of h k 0 planes will produce the zero layer reflections as

successive set of planes are brought into position that satisfy the Bragg

equation. While these reflections are occurring other planes not parallel to

the axis of rotation will also be satisfying the Bragg equation. This results

in the production of cones by general h k 1 planes as show n in figure 2.5.

Each cone has a different value of n in the Bragg equation and is

produced by a family of planes h k n (where n = 1 in this discussion).

Therefore the film in the X-ray camera will contain spots in straight lines

corresponding to diffraction from one set of planes and each spot appears

on the cone n whenever a set of planes h k n satisfies the Bragg equation.

From this set of data the unit cell dimension of the c axis of the urea host

fram ework and also that of the guest molecules can be immediately

determ ined. A reciprocal lattice grid described in section 2.3.4 enables the

67

indexing of these reflections. Using Bragg's Law the d-spacing betw een

the lattice planes can be calculated.

Single crystal X-ray diffraction experiments were also carried out at

Birmingham University (though the majority of the single crystal work

was at UCL) on a R-AXIS-IIC area image detector diffractometer using

Mo-Koq radiation126. The operating conditions for the rotating anode

source was 56 KV, 124 mA. This particular diffractometer uses rotating

anode source and two image plates for collecting the X-ray data. The two

image plates are coupled together such that one plate is m oved into

position for data collection and the second is positioned for scanning by a

laser beam. M easurements are hence recorded by scanning the plate w ith

the laser and after the image plate has been read the plates are rotated by

90° w here the image plate is exposed to an erasing lamp.

C ry sta

X - r a y beam

Fil m

Figure 2.5: Geometry of the rotation photograph which shows the diffraction of X-ray from sets of lattice planes which satisfy the Bragg equation in the crystal producing Bragg reflections on the film.

68

2.3.4 Construction of a reciprocal lattice grid

The position of intensity maxima (reflection) in the diffraction

pattern of a crystal can be understood in term s of a lattice that is

reciprocal to the direct lattice of the crystal. Direct space describes the

crystal and the corresponding crystal lattice. The unit cell of a crystal

lattice is defined by basic vectors a, b, c w hich are in tu rn defined by

lengths a, b, c and angles a , p, y respectively. For every direct lattice it is

possible to construct a reciprocal lattice. It is a set of vectors in reciprocal

space represented as points, which describe a family of lattice planes. In

this case the basic vectors are a*, b*, c* w ith lengths a*, b*, c* and angles

a*, P*, y*.

The concept of reciprocal lattice is used to describe the relationship

betw een crystal structure and diffraction spectra. To construct a

reciprocal lattice, any point of the real lattice is taken as an origin, from

which lines are draw n perpendicular to all sets of lattice planes, where

the reciprocal vectors a*, b* c* are norm al to ( b, c), (a, c), ( a, b ) planes

respectively of the direct crystal lattice. The relationship betw een the

direct and the reciprocal unit cells depends on the particular crystal

system. For example in a hexagonal unit cell a = b ^ c , a = P = 90° y = 120°

in real space but in reciprocal space the unit cell lengths are inversely

related to that in real space. The angles in reciprocal and real space lattice

are always related in such a w ay that a + a* = 180°, P + p* = 180°, y + y* =

180°, so in the hexagonal case a *, p* are also 90° and their reciprocal axes

are parallel bu t y* = 180° -120° = 60°. In cases w here all the angles are 90°

then a = P = y=oc* = P* = y* = 90°, and the corresponding pairs of real and

reciprocal axes are parallel i.e a I I a*, b I I b*, c I I c* . In order for the

construction of a reciprocal lattice grid the cell param eters of the unit cell

are required and for the UICs described in this thesis the unit cells

69

param eters are such that a = b = 8.22 A c = 11.011 A. The distance d* in

reciprocal space is therefore equal to 1 /d from the origin of a reciprocal

lattice where the reciprocal axis is in the direction that is perpendicular to

the set of planes. The dimensions of the reciprocal lattice will be A'1, or

reciprocal Angstrom, but for the purpose of interpretation of diffraction

data d* = X / d, w here X is the wavelength of the x-rays used. Therefore

the unit of d* is dimensionless reciprocal units (r.u). A reciprocal lattice

grid can be constructed w hen a large num ber of sets of planes are

considered, a three dimensional array of points builds up and this is

known as the reciprocal lattice grid. Figure 2.6 on page 77 is a

representation of a hexagonal reciprocal grid using chrom ium radiation,

and a scale of 1 cm = 0.1 r.u. The interplanar spacing a* is given by a* = X

/ a => 2.29 / 8.22 cos30° = 0.322 A and the interplanar spacing b* is given

by b* = X / b = 0.322 A w here in both cases a = b = 8.22 A and the

wavelength of chrom ium radiation = 2.29 A.

2.4 D ifferential Scanning Calorim etry (DSC)

Differential Scanning Calorim etry127 is a technique that studies the

difference in the heat that flows to a sample pan and a reference at a

certain tem perature. Figure 2.7 shows the general set up of a typical DSC

apparatus.Gas out

umance

Sensor amplifier

Recorder

Programmer

Figure 2.7: Schematic representation of the DSC apparatus.

70

The heat is supplied from the same source to the sam ple contained

in a pan and similarly to the reference in its pan (normally alum inium

pans are used) and the tem perature difference At is m easured. The

tem perature difference is converted to a pow er difference AP using a

calibration software. The DSC curve has AP as the ordinate and

tem perature as the abscissa. The tem perature of the sam ple and the

reference are the same until some therm al event occurs such as melting,

decom position or a change in structure. Endothermic peaks are observed

in the DSC curve, which is indicative of the absorption of m ore pow er, by

the sample. This causes the sample tem perature to lag behind if the

change is an endotherm ic change or lead if the change is exothermic. In

the former case the sample remains at this tem perature until the event is

completed and then increases rapidly to catch up w ith the tem perature

required by the program m er.

2.5 Nuclear Magnetic Resonance

NMR is a technique used to investigate the structure of molecules

and is observable because certain nuclei behave like tiny spinning bar

m agnets 128/129 130. Nuclei such as ^ 13C, 19F and 31P have nuclear spin values

of Vi. Certain other nuclei that are im portant in organic chem istry have a

nuclear spin value of zero and therefore have no nuclear resonance

signals; these include 12C and 160 . Table 2.2 lists the spin quantum num ber

of the commonly occurring nuclides.

71

I Nuclide

0 12c , 16o

% 'H, 13C, 15N, 19F, 29Si, 31P

1 2h , 14n

3 /2 “B ^ N a fC l, 37C1,

5 /2 17o , 27A1,

3 10B

Table 2.2: Representation of the nuclear spin quantum numbers of the commonly occurring nuclide.

W hen a proton is placed in a uniform m agnetic field, it has two

orientations w ith respect to the field; a low energy orientation in which

the nuclear m agnet is aligned w ith the field and of high energy

orientation in which it is aligned against the field. The transition betw een

these two states occurs on absorption of a quantum of suitable

electromagnetic radiation hu. This is illustrated in figure 2.8.

AE

Figure 2.8: Energy levels in a Hydrogen nucleus in a magnetic field.

A typical magnetic field strength used for NMR is 9.4 T and the required

frequency of radiation is 400 MHz which falls in the radiofrequency

region of the electromagnetic spectrum. In order to induce NMR

transitions a radio frequency field is required. The resonance frequency is

also dependent upon the chemical environm ent that the nucleus is

present in and therefore signals due to the different nuclei will be in

different regions in the spectrum and this is know n as the chemical shift.

72

There are two permitted orientations of the proton when it is placed in a magnetic field. This causes the nuclei to flip from the lower energy level to the upper one.

The protons in the different chemical environm ents will hence resonate at

different frequencies and will therefore show signals at different chemical

shifts. The contributions to the chemical shifts are strongly dependent on

the electron density around the nucleus; the larger the electron density

the greater the shielding and the smaller the chemical shift, 5. Chemical

shifts are m easured relative to TMS (tetramethylsilane) w hich is defined

to have a zero chemical shift. The twelve protons of the TMS being

chemically equivalent all resonate at the same value of the applied field

and therefore give rise to a single line. Table 2.3 below lists the chemical

shift values for the functional groups used in this study.

Functional group ~ Chemical shift ( 8)

C- CH3 (methyl proton) 0.9

R- CH2-C 1.4

C-CH-OH 3.9

C-CH2-Br 3.5

Table 2.3: Chemical shift values for the listed functional groups that are used in this study.

Natural abundance

'H 99.985

2H 0.015

13c 1.108

14n 99.63

15n 0.37

17o 0.037

19f 100

29Si 4.7031p 100.0

Table 2.4: Natural abundance data for the commonly occurring nuclide.

73

The natural abundances of commonly occurring nuclides are listed

in table 2.4. From the table it can be seen that 13C is a dilute spin species

and hence it is unlikely to contain more than one 13C nucleus in a given

molecule. Therefore it is unnecessary to take into account the 13C-13C spin

coupling w ithin a molecule. Protons, how ever are 100 % abundant spin

species and a molecule is likely to contain m any of them. In a 13C NMR

spectrum proton decoupling is required due to the protons being 100 %

abundant species and therefore will couple w ith 13C nucleus. Decoupling

involves irradiation of protons at its resonance frequency by a stronger

radio frequency (coj and sim ultaneously is observed by the norm al

observing radio frequency (co2) and the carbon nucleus is spin decoupled

to a singlet. The spin decoupling is regarded as arising from rapid

transitions betw een those two possible spin states of the proton and the

carbon nuclei.

Chiral shift reagents were used in this w ork to study the

enantiomeric purity of a chiral m ixture131,132. Param agnetic shift reagents

are useful for structure elucidation and in the presence of a param agnetic

m etal it selectively binds to the polar group of one enantiom er which

results in a perturbation of the chemical shift of that particular

enantiom er in the NMR spectrum, separating the two signals. The

splitting is often more pronounced for the proton closest to a polar group.

In the case of an alcohol the proton next to the OH group has a chemical

shift value of 5 ~ 3.9. W hen the Eu metal in the complex binds to an

alcohol it reversibly coordinates to the OH group, and the local field due

to the param agnetic europium ion helps to spread out the spectrum.

74

CH3(CH2)4CH2OH + Eu (Fod)^—► CH3(CH2)4CH2HO------Eu(Fod)3

An example of a chiral shift reagent is Eu(Fod)3. Europium ions

causes dow n field shifts in the spectra w hereas praseodym ium for

example can be used to cause upfield shifts.

2.6: Optical Activity

The optical activity of a substance can be detected and m easured

using a device know n as a polarim eter133. The instrum ent consists of a

light source, two polarising lenses and betw een the lenses a tube to hold

the substance that is being examined for optical activity. These are

arranged such that the light passes through one of the lenses (polariser),

then the tube then the second lens (analyser). The function of the lens is to

tu rn the ordinary light whose vibrations are in all possible planes into

plane polarised light where the vibration direction is in one plane only.

This is carried out by passing the light through a lens m ade of polaroid or

a nicol prism. Hence if w hen the sample is placed in the tube it does not

effect the plane of polarisation and light transm ission is still at a

m axim um the substance is said to be optically inactive. If the substance

how ever rotates the plane of polarisation the analyser is rotated to

conform w ith this new plane if light transmission is to be a m axim um and

the substance is said to be optically active. If the rotation of the plane is to

the right (clockwise) the substance is dextrorotary and if the rotation is to

the left (anticlockwise) the substance is levorotatory. The am ount of

rotation is dependent upon how m any molecules the light encounters in

passing through the tube. This implies that the rotation of a specific

optically active com pound will depend on the length of the tube and its

concentration. The light will encounter twice as m any molecules in a tube

20 cm long as in a tube 10 cm long and the rotation will be twice as large.

75

The specific rotation is related to the length of the tube and the

concentration as described in the equation below.

Specific rotation [a]d = observed rotation (degrees)Length (dm) x g / ml

76

|-2 0

0

~3

0 0—

h

4 0

*T5

0 0

CHAPTER 3

EXPERIMENTAL PREPARATION AND

CHARACTERISATION OF PURE UREA INCLUSION

COMPOUNDS

3.1 Introduction

Since the early discovery m ade by Bengen9,10'11 of the urea

com pounds there have been two main m ethods described in the

literature for their preparation, that of McAdie108 in 1962 and that of

Harris et alno. In McAdie's method, urea is dissolved in m ethanol and

the guest species is added at room tem perature to form a two phase

mixture. The m ixture is heated to 65 °C and then placed in a preheated

dew ar, at 65 °C for slow crystallisation. If the carbon chain of the guest

species exceeds about ten carbons, isopropyl alcohol or t-amyl alcohol

is added to dissolve it, such that a hom ogenous m ixture is formed. The

Harris m ethod is the same except the guest is added to the urea in

m ethanol at 48 °C. The McAdie m ethod was used in this study because

it was found to produce better quality crystals and the Bragg peak

characteristic of the guest species in the pow der X-ray diffraction

pattern was more apparent (see section 3.2.1). The details of the

preparation is given in the next section. The urea inclusion com pounds

in this w ay were characterised by pow der X-ray diffraction, single

crystal X-ray diffraction, DSC and nuclear magnetic resonance. These

m ethods are discussed in section 3.2.1, 3.2.2, 3.2.3 and 3.2.4

respectively. Further experimental details are discussed in later

chapters.

78

3.2: D etails of the Preparation of the Urea Inclusion C om pounds

used in th is w ork

In this w ork relative am ounts of urea w ith respect to the guest

species were calculated and m easured accurately. Urea (4.99 g) was

dissolved in m ethanol at room tem perature until a saturated solution

was obtained. The pentadecane guest species (1.5 g) w as added to the

mixture, which was heated to 65 °C in a w ater bath. Fetterly134 tested a

large num ber of solvents for the recrystallisation of the UICs and

found that isobutyl alcohol, t-butyl alcohol and t-amyl alcohol are not

included into the channels to any appreciable extent. In this work

isopropanol or t-amyl alcohol was added until the solution was

homogeneous. The beaker that contained the solution was rem oved

from the w ater bath and was placed in a pre-heated dew ar to

crystallise slowly.

In order to calculate the relative am ounts of urea and guest to

form the urea inclusion compound, the guest molecular length was

calculated using bond length data tabulated in the appendix and

assum ing a tetrahedrally coordinated carbon. It w as then assum ed

that, w ith six urea molecules per unit cell one urea molecule w ould

occupy 11 / 6 = 1.833 A of space along the c-axis. Hence the ratio of

urea to guest can be calculated. The details of this calculation is given

in the appendix.

An alternative m ethod was to use the linear m athematical

relationship between the molecular length and the num ber of carbon

atoms given in chapter 1, section 1.3.2. Table 3.1 and 3.2 lists the

num ber of urea molecules required for each guest molecule and their

corresponding periodicities calculated from the bond length data and

the derived linear relationship.

79

Guest molecule Chain length

obtained from

bond length data

Chain length from

equation 1.1

Molar ratio of

host:guest

decane 15.3 15.08 8.36

undecane 16.58 16.34 9.04

dodecane 17.83 17.60 9.73

tridecane 19.08 18.86 10.41

tetradecane 20.33 20.12 11.09

pentadecane 21.58 21.38 11.77

Table 3.1: Data for the length of the guest molecules and the number of urea molecules required for the series of alkanes.

Guest molecule Chain length (A) Literature value Molar ratio of

urea: guest

1,8-dibr omooctane 16.03 15.5 8.7

1,10-dichlorodecane 17.89 9.8

1,6-dibromohexane 13.5 12.8 7.4

1,6-dichlorohexane 12.9 7.0

Table 3.2: Data for the length of the guest molecules and the number of urea molecules required for the series of substituted alkanes.

3.3 Characterisation of Incommensurate Urea Inclusion Compounds

3.3.1 X-ray powder diffraction

Figure 3.1 on page 90 shows X-ray diffractograms of a series of

alkane UIC from decane to hexadecane UIC and figure 3.2 on page 91

is an X-ray diffractogram of pure dibromooctane UIC. The patterns

show that the general structure of all the alkane UIC are the same.

These results may be compared to those previously reported in the

literature. Smith30 carried out prelim inary examinations of n-

hydrocarbon adducts of various chain lengths C8-C50 by the pow der

80

m ethod and found that they all had similar structures that contained

negligible am ounts of pure crystalline urea. H arris et alu has studied

the hexadecane UIC in detail and found from single crystal studies

that the hexagonal param eters for the inclusion com pound were a = b

= 8.2266 (9) A, c = 11.017 (2) A, a = p = 90°, y = 120°. On the basis of

these cell param eters they indexed the majority of the peaks in the

pow der pattern excluding the Bragg reflection at 20 = 3.9° that was

characteristic of the guest periodicity. Table 3.3 lists the (h k 1)

reflections.

20 / ° h k 1 Intensity of thereflections

12.55 1 0 0 m20.525 1 0 2 m21.90 1 1 0 s23.35 1 1 1 m25.30 2 0 0 s26.60 2 0 1 s27.525 1 0 3 s

Table 3.3 (h k 1) reflections of hexadecane UIC at 151 K.

In general, guest reflections are present in the diffractogram at

low diffraction angles. In figure 3.1 the Bragg peaks characteristic of

the guest reflections were identified in the region of 20 < 5°. It was also

observed w hen going from hexadecane to tridecane UIC that there was

a shift in the Bragg reflection to higher 20 angles. This was due to the

progressive increase in the d-spacings of the guest molecules w ith

increase in chain length which was calculated from the Bragg equation.

The d-spacings obtained from this w ork w ere consistent w ith those

previously recorded by Harris and Thomas28.

In this study the hexdecane UIC was indexed as show n in table

3.4 using the TREOR indexing program and the results w ere in close

agreem ent w ith those obtained from the literature for the hexadecane

81

UIC.

Crystal A B C Alpha Beta Gamma volumesystemhexagonal 8.2204 8.2204 11.0119 90.000 90.000 120.000 644.43

h k 1 20 (obs.) 20(calc.) A03.869

1 0 0 12.410 12.423 - 0.0131 0 1 14.794 14.805 - 0.0111 0 2 20.379 20.374 0.0061 1 0 21.584 21.603 - 0.0191 1 1 23.076 23.078 - 0.0032 0 0 24.980 24.995 - 0.0152 0 1 26.281 26.291 - 0.0101 1 2 27.042 27.050 - 0.0081 0 3 27.300 27.313 - 0.0141 1 3 32.680 32.682 - 0.0022 1 0 33.267 33.269 - 0.0022 1 1 34.262 34.278 - 0.0161 0 4 34.914 34.914 0.0002 1 2 37.164 37.160 0.0051 1 4 39.369 39.360 0.0102 1 3 41.583 41.580 0.0032 2 0 44.025 44.026 - 0.0002 2 1 44.822 44.827 -0.0043 1 0 45.927 45.924 0.0033 1 1 46.721 46.699 0.021

Table 3.4: (h k 1) reflections for the hexadecane UIC obtained from this study.

The Bragg reflection at 3.869° which w as not indexed on the

basis of the hexagonal unit cell was characteristic of the hexadecane

guest. Harris et al44 quoted this reflection to be at 20 = 3.9° which is

consistent w ith 20 = 3.898° obtained from this study.

The Miller indices for pentadecane UIC and 1,8-dibromooctane

UIC are given in table 3.5 and 3.6 respectively.

82

Crystalsystem A B C Alpha Beta Gammahexagonal

h k

8.2245 8.2245

1 20 (obs.)

11.0152 90.00

20 ( calc.)

90.00 120.00

delta (20)1 0 0 12.413 12.417 -0.0041 0 2 20.359 20.366 -0.0071 1 0 21.589 21.592 -0.0031 1 1 23.062 23.067 -0.0052 0 0 24.988 24.983 0.0062 0 1 26.281 26.278 0.0031 0 3 27.305 27.304 0.0012 1 1 34.275 34.261 0.0152 0 3 35.090 35.073 0.0171 1 4 39.349 39.345 0.0042 1 3 41.574 41.562 0.0122 2 0 44.003 44.002 0.0011 1 6 54.705 54.708 -0.003

Table 3.5: (h k 1) reflections, observed and calculated 20 values for the pentadecane UIC.

Crystalsystem

A B C Alpha Beta Gamma

hexagonal 8.2371 8.2371 11.0232 90.00 90.00 120.00

h k 1 20 (obs) 20 (calc) delta (20)1 0 2 20.388 20.345 -0.0061 1 0 21.558 21.559 -0.0011 1 1 23.037 23.034 0.0032 0 0 24.961 24.944 0.0182 0 1 26.288 26.239 0.0491 0 3 27.296 27.279 0.0182 1 1 34.241 34.209 0.0331 0 4 34.793 34.873 -0.0792 0 3 35.075 35.032 0.0431 1 4 39.339 39.305 0.0342 1 3 41.546 41.507 0.0392 2 0 43.901 43.932 -0.0312 2 1 44.702 44.733 -0.0311 1 5 46.672 46.694 -0.0221 1 6 54.665 54.657 0.0083 2 0 56.197 56.156 0.0413 3 0 68.236 68.262 -0.0026

Table 3.6: (h k 1) observed and calculated 20 values for 1,8-dibromooctane UIC.

The pow der pattern of pure urea in figure 3.3 on page 92 was

used to identify the pure urea impurities that rem ained in the UIC

after its preparation. Caron and Donohue135 reported that the urea in

its pure phase has cell param eters a = b = 5.662 A, c = 4.716 A, a = p = y = 90°. From this work using single crystal X-ray diffraction studies c =

4.712 A, which is also in close agreement w ith the literature reports.

Table 3.7 below lists the 20 angles and its Miller indices.

Crystal A B C Alpha Beta Gammasystem__________________________________________________________________tatragonal

h k

5.6538 5.6538

1 20 (obs)

4.7090 90

20 (calc)

90 90

Delta(20)0 0 1 18.802 18.809 -0.0071 1 0 22.229 22.218 0.0111 0 1 24.566 24.583 -0.0171 1 1 29.249 29.280 -0.0312 0 0 31.619 31.624 -0.0052 0 1 37.065 37.061 0.0040 0 2 38.199 38.192 0.0072 1 1 40.417 40.459 -0.0421 0 2 41.493 41.512 0.0291 1 2 44.658 44.657 0.0012 2 0 45.355 45.331 0.024

Table 3.7 : (h k 1) reflections, observed and calculated 20 values for pure tetragonal urea.

3.3.2 Single crystal X-ray diffraction

The single crystal X-ray diffraction photograghs w ere taken on

an rotation camera using chromium radiation (X = 2.29 A) and copper

radiation (k = 1.54 A). The chromium radiation was used for the

pentadecane UIC and pure urea whereas for all the other UICs copper

radiation was used. Figure 3.4 on page 93 is a single crystal X-ray

diffraction pattern of the pentadecane UIC. The spots on the

photograph are Bragg reflections and correspond to reciprocal lattice

points which are produced by the diffraction of X-rays from sets of

lattice planes. The first row of spots is known as the zero layer line and

84

comprise of reflections from the (h k 0) set of planes in the crystal

w here in this particular layer line the (h k 0) reflections are common to

both 'h ' and 'g ' diffraction patterns. Other rows of spots in the

diffraction pattern are called the first, second, th ird layer lines e.t.c.

and are produced from the scattering of X-rays from the (h k 1) planes.

The guest layer lines (h k l)g lie in between the host layer lines (h k l)h

and their separation is characteristic of the guest. In general, the guest

reflections m ay contain a contribution from the host and vice versa.

Harris and Thomas28 calculated the structure factor for the Ti'

reflections and found there to be guest contribution w hen 1 was zero

but not w hen 1 was non zero. They initially assum ed, in their

calculation, that the channels were in the form of a long cylinder that

contained guest molecules w ith no periodicity w ith respect to the host

structure. This gave the result that there was no contribution in X-ray

scattering to (h k 0) from the guest molecules. This results from the fact

that the guest has the same periodicity as the host only in the a-b

plane. A second situation considered by Harris and Thomas was a

m odulated guest substructure w ith respect to the host structure.

U nder such circumstances, it was found that the host reflections w ith

non-zero 1 values w ould in general contain a scattering contribution

from the guest electron density. There is also a contribution to the

guest reflections arising from the incom m ensurate perturbations to the

basic host structure. However, the incom m ensurate m odulation to the

basic guest structure constitutes a relatively small structural

perturbation and therefore the basic host structure largely accounts for

the relative intensities of the host reflections.

In this work the c param eter for the host lattice was also

calculated from the Bernal chart shown in figure 3.5 on page 94. The

value that corresponded to the spacing betw een the zero and the first

layer line was obtained directly from the vertical axis in the Bernal

85

chart. This gave a value of 2 sin0 = 0.205 and w ith the application of

Bragg's law the length of the c-axis was determ ined as 11.17 A which

was consistent w ith the literature data. The same procedure was

applied to the guest reflections, for example the guest layer lines for

pentadecane are close to the centre of the two host layer lines which

indicates a large repeat distance calculated as 20.58 A which is

consistent to that reported in the literature.

The Bernal chart was also used to index the diffraction pattern.

The chart was superim posed onto the X-ray photograph and the two

were viewed together against a lighted screen. The distance (2 sinO)

betw een successive layer lines was directly obtained from the Bernal

chart. The x-axis on the Bernal chart represents the horizontal distance

betw een a reciprocal lattice point and the rotation axis through the

origin. Assignments of the (h k 1) reflections w ere m ade to the zero

layer line which used the reciprocal lattice grid show n in chapter 2 and

the X-ray data was compared w ith the literature indexing data for

hexadecane UIC. For example a reflection falling at a distance 0.86 r.u

from the origin w ould equal 8.6 cm on the reciprocal lattice grid (1 cm

= 0.1 r.u). The corresponding (h k 1) values w ere determ ined by

placing a ruler at the origin w ith one end held stationary. The other

end was moved through its curvature on the grid and the (h k 0)

values that coincided w ith the distance, 8.6 cm from the origin were

recorded. This procedure was repeated for all the reflections. Table 3.8

lists reflections from the zero layer line of the pentadecane UIC and the

corresponding Miller indices.

86

2 sinG Miller indices Intensities of the reflections

0.33 (10 0) s0.56 (110) s0.65 (0 2 0) s0.80 urea w0.86 (210) s0.97 (3 0 0) m1.13 (13 0) s

Table 3.8: Listings of (h k 1) reflections of pentadecane UIC and its corresponding 2 sinG values.

The (h k l)h values and the cell param eters obtained from the

hexadecane UIC by Harris et alu were substituted into the formula for

the calculation of the d-spacing of a hexagonal unit cell. The 2 sinG

value (d-spacings) obtained for each (h k l)h reflection w ere consistent

w ith those obtained from the X-ray photographs. As show n in table 3.8

some urea was present in the sample, how ever this w as only a small

amount.

The rotation photograph of 1,8-dibromooctane UIC shown in

figure 3.6 on page 93 was also indexed by direct comparison of the

pentadecane UIC and the (h k 1) values are listed in table 3.9.

2 sinG Miller indices Intensity of the reflections

0.37 (110) s0.44 (0 2 0) s0.58 (210) w0.66 (3 0 0 ) m0.78 (13 0) m

Table 3.9: (h k 1) reflections and 2sin0 values for the 1,8-dibromooctane UIC.

A rotation photograph of urea in the pure phase w as also taken

using chrom ium radiation. It was superim posed on to the pentadecane

UIC in order to identify the (h k 1) reflections due to any urea that was

still present in the pentadecane UIC. Figure 3.7 on page 95 is an X-ray

87

diffraction pattern of the pure tetragonal urea w ith cell param eters

a = b = 5.662 A, c = 4.712, A a = p = y = 90°.

3.3.3 D ifferential scanning calorimetry

Thermal DSC investigations of the UICs w ere carried out on a

Shim adzu DSC-50 instrument. The principal of the DSC was discussed

in chapter 2. The mW / m g versus tem perature DSC curve in figure 3.8

on page 96 illustrates the thermal anomalies that occur in the

hexadecane UIC. The sharp peak at 138 °C was assigned to the m elting

of the pure urea and the transition at ~ 122 °C was assigned to the

decomposition of the hexadecane UIC. Figure 3.9 and figure 3.10 on

pages 96 and 97 shows the thermal decomposition of the pentadecane

and 1,8-dibromooctane UICs respectively. The decomposition of the

pentadecane urea inclusion compound occurs at ~ 119 °C. In the 1,8-

dibromooctane UIC the transition at 96.8 °C corresponds to the

decomposition of 1,8-dibromooctane UIC. From previous reports136'137

the decompositions and phase transition tem peratures are chain length

dependent hence the highest tem perature is observed for hexadecane.

The results obtained for the pentadecane UIC and the hexadecane UIC

supports the results of Pemberton et al5i and McAdie108 w ho reported

the decomposition tem peratures of 109 °C and 105 °C for the

hexadecane and pentadecane UICs respectively.

3.3.4 N uclear m agnetic resonance

Solid state 13C NM R

Harris et alns reported a 13C NMR spectrum of the decane UIC

which was m easured on a Bruker MSL 300 machine. As this technique

is not used elsewhere in the thesis it is not described in detail. Figure

3.11 and figure 3.12 on page 98 represents the spectra for the

pentadecane UIC and 1,8-dibromooctane UIC respectively. The

assignm ents m ade in the spectrum of the pentadecane UIC were

consistent w ith those reported by Harris et al4i. The spectrum of 1,8-

dibromooctane UIC in figure 3.12 varies slightly due to the presence of

the brom ine group in the UIC.

aH NM R

Figure 3.13 and figure 3.14 on pages 99 and 100 are NMR

spectra of the pure pentadecane UIC and the pure 1,8-dibromooctane

respectively. The spectra were rim on a VXR-400 machine using TMS

(tetram ethyl silane) as the reference. The NMR spectra w ere used to

characterise the percentages of guest molecules present after the

exchange reaction.

89

ID

UCD

sI

+0rH

0 0 ' 0

LO3

13vD

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ld■;dj

13

LOm

13m

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90

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re

3.1:

Pow

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y di

ffrac

togr

ams

of ur

ea

inclu

sion

com

poun

ds

2-Th

eta

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ale

in

r-j

in

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s«s1(J2 t •3 ►» 2 krn©u3on£

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91

2-Th

eta

- Sc

ale

egJSa."«cou>£JCS

eg£0 62MO+*u1"52 A n

3DU

0 0 ’Qie •£d;j 00' 0

92

Figure 3.4: Single crystal X-ray diffraction rotation photograph recorded for pentadecane UIC at room temperature. The single crystal was rotated about its c-axis.

Figure 3.6: S ingle crystal X-ray diffraction pattern recorded on a R-AXIS IIC diffractometer for 1,8 dibromooctane UIC at room temperature. The single crystal was rotated about its c-axis.

93

i

/

10 cOS

y5

Siu'£JS

£ ££ Z © ©t ■=© s*3 DX

i fr ■=u C . O C£ o'*■* '-C £ « « “ US On « © 05 — U 05© ts** b ■c ho vor. o® "Si t =05 on-a v© « E -S£ .£ OS.. ol/~, *•

■gSi on U 3

.1 S*05

94

m ■

Figure 3.7: Single crystal X-ray diffraction rotation photograph recorded for tetragonal urea at room temperature. The single was rotated about its c-axis.

95

D S Cm W _0.00

10.00

- 100.00 0.00 100.00TempfCJ

Figure 3.8: mW / mg versus temperature DSC curve for hexadecane UIC

DSCmWO.OC

-40. OC

-50.OC

- 100.00 0.00 100.00TempfC]

Figure 3.9: mW / mg versus temperature DSC curve for pentadecane UIC

D SC

0.00

- 10.00

- 20 . 00;

- 3 0 . 0 0

- 100.00 0.00 1 00.00T e m p [ C l

Figure 3.10: mW / mg versus temperature DSC curve for 1,8-dibromooctane UIC

97

H3CCH2(C&2),iCH2CH3

IP

K .

H 2N C O N H 2

1 JL—1------ r~1 0 0 8 0

PPM

I40

I— 20

—I----’---- 1--- -----1—160 140 120 60

Figure 3.11:13 C NMR spectrum of pentadecane UIC

0 6 p OC

BrCH2(CH2)6CH2Br

06

1 60 1 40 120 80100 4060 20P P M

Figure 3.12:13 C NMR spectrum of 1,8-dibromooctane UIC

98

— co

Figu

re

3.13:

*H

NMR

spec

trum

of

Pent

adec

ane

UIC

B rCH

^CH

^CH

j CH^

CH^

CH, C

H^C

IL

U<pa

V

100

&\

/—

CLCL

—in

— IX)

—r -

— co

CD

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3.14:

*H

NMR

spec

trum

of 1,

8-di

brom

ooct

ane

UIC

CHAPTER 4

EXCHANGE REACTIONS WITH POLYCRYSTALLINE UREA

INCLUSION COMPOUNDS

4.1 Introduction

The first report for the exchange reaction w as reported by

M ayhdafar and H arris115 and is explained in detail in chapter 1. They

show ed that w hen a polycrystalline sample of 1,8-dichlorooctane UIC is

placed into a solution of decane an exchange occurs betw een the two

guest species. The aim of this study is to investigate the exchange

reactions further using different UICs and guest species in the liquid

phase.

This chapter discusses the exchange reactions of poly crystalline 1,8-

dibromooctane UIC as one series of experiments (series 1) and

poly crystalline 1,10-dichlorodecane UIC as another series of experiments

(series 2). In both series the guest species was exchanged w ith a series of

n-alkanes from the liquid phase. However, in one of the experiments for

each series, the 1,8-dibromooctane and the 1,10-dichlorodecane was

initially in the liquid phase and the alkane guest species was in the UIC.

The following experiments that were carried out:

♦ Expt 1: The Experimental Investigation of the Percentage Exchange

w ith a Series of CnH 2n+2(l) and C8H 16Br2(UIC) and CnH2n+2(l) and

C10H 20C12(UIC) w ith n = 10,11,12,13,14 and 15.

♦ Expt 2: The Experimental Investigation of the Percentage Exchange

Between a series of CnH 2n+2(UIC) and C8H 16Br2(l) and CnH 2n+2(UIC) and

101

C10H20C12(1).

♦ Expt 3: An Experiment to Monitor the Mass changes of the UIC

Resulting from the Exchange between C8H 16Br2(UIC) and CnH2n+2(l) and

C10H20C12(UIC) and Q H ^ l ) (n = 11-15).

♦ Expt 4: The Experimental Investigation of the Percentage Between

C8H 16Br2(UIC) and Different Molar Ratios of C15H32(1): C8H 16Br2(l).

4.2 Expt 1: The Experimental Investigation of the Percentage Exchange

with a Series of CnH2n+2(l) and C8H16Br2(UIC), and CnH2n+2(l) (with n = 10,

11,12,13,14 and 15).

The aim of this experiment was to estimate the degree of exchange

as a function of chain length of the incoming alkane CnH 2n+2(l). It involved

the exchange of different chain length alkanes ranging from decane to

pentadecane w ith C8H 16Br2(UIC) in one series of experiments (series 1)

and C 10H 20C12(UIC) in a different series of experiments (series 2). The 1,8-

dibromooctane UIC or 1,10-dichlorodecane UIC w ere prepared by the

m ethod described in chapter 3.

1,8-Dibromooctane UIC (0.2595 g) or for the 1,10-dichlorodecane

UIC (0.2074 g) were finely ground w ith a pestle and m ortar. The ground

sam ples were transferred into a 150 m l beaker w here alkane (= 6.6 m l for

series 1 and = 6 ml for series 2 representing 100 times excess) was added

to the UIC. The beaker that contained the reactants w as left on the bench

at room tem perature for 5 days, to allow for the exchange to occur. The

sam ple was filtered and washed w ith 2,2, tri-m ethyl pentane (3 ml) to

rem ove the free decane that rem ained on the surface. It w as left under

vacuum for 2 hrs in the buchner funnel and w as then placed in a

desiccator over night to ensure complete dryness. The dried sample was

re-weighed the next day and the new masses w ere recorded. Each

102

exchange was carried out in exactly the same w ay and w as repeated once

to ensure reproducibility. The averages of the percentage incorporation

for the two experiments were recorded in the table 4.1. The percentage

exchange was determ ined by XH NMR and the m ethod of calculation is

described in the appendix. The volumes of Q H ^ ^ l) guest species

required for the exchange process both in series 1 and series 2 w ere not

expected to depend on n, due to the fact that in every exchange process

each CnH2n+2(l) guest species occupies the same volum e in the urea tunnels.

The experimental conditions for the two processes and the m ethod for

calculating the am ount of alkane required for each exchange is also

tabulated in the appendix.

Figure 4.1 on page 119 shows the NMR spectrum of the

exchange for C14H30(1) w ith C8H 16Br2(UIC). The results for the percentage

exchange betw een the guest species in series 1 and 2 are tabulated below

in table 4.1 and is also represented in the form of a bar chart in figure 4.2

and figure 4.3 on pages 120 and 121 respectively.

The results clearly show a preference for exchange w ith the longer

alkane guest molecule. The bar graphs in figure 4.3 of the individual

alkanes indicated a gradual decline of incorporation into the

C8H 16Br2(UIC) from C15H32 to C10H20 guest species w ith a 90 % exchange

w ith C15H32(1) and C8H 16Br2(UIC) in comparison to a 5 % exchange betw een

C10H20(1) and C8H 16Br2(UIC) guest species.

103

n Percentage incorporation Percentage incorporation of

of Q H ^ l ) in series 1 C A . J ! ) in series 2

C8H16Br2(UIC) C10H mC12(UIC)

10 5(1) 16 (1)

11 21 (3) 18(1)

12 63 (5) 19(4)

13 70(2) 36(4)

14 81 (4) 63(2)

15 90 (4) 80 (3)

Table 4.1: The percentage incorporation that occurred with C^H^O) and C8H16Br2(UIC) in series 1 and and C10H20C12(UIC) in series 2.

The bar chart in figure 4.2 from series 2 show ed that the percentage

incorporation of C10H20(1) CnH22(l) and C12H24(1) w as betw een 15-20 %

whereas the percentage incorporation of the C13H 26(1), C14H 28(1) and

C 15H30(1) guest species into the C10H20C12(UIC) ranged from betw een 35-

80%.

In a further experiment (not reported in detail here) it w as

established that for the replacement of 1,8-dibromooctane w ith

pentadecane, the reaction was complete after three days. This m otivated

the choice of five days as an appropriate reaction time for the above

reaction.


Between a Series of CnH2n+2(UIC) and C8H16Br2(l) and Q H ^ttJIC ) and

C10H20C12(1)

This experiment was designed to test the hypothesis that in the

exchange process the same percentage exchange values determ ined in

experim ent 1 could be obtained starting from CnH2n+2(UIC) w ith

104

C8H 16Br2(l) in the liquid phase. The experimental m ethod and the

calculation for the am ounts of guest required w as the sam e as that

described in section 4.2. C8H 16Br2(UIC) (0.2 g) was used for each exchange

experim ent w ith ~ 5.5 m l of C8H 16Br2(l) required for precisely a 100 fold

excess. In the case of series 2, CnH2n+2(UIC) (0.2 g, ~ 7.45 ml of alkane) was

used for each exchange experiment. The experimental conditions are

sum m arised in the appendix. For each series of experiments the volume

of liquid used was the same for the individual alkanes, as expected for the

reasons discussed in section 4.2. The results for the exchange reactions for

both the series of experiments are show n in table 4.2 below.

n Percentage Percentage

incorporation (%) incorporation (%)

of C8H 16Br2(l) into of C10H20C12(1) into

Q H ^O JIC ) in C M C ) in

series 1 series 2

10 89 (3) 55(7)

11 67 (9) 38 (1)

12 41 (6) 34(2)

13 17(1) 16 (1)

14 7(1) 16 (2)

15 >1 % 3(1)

Table 4.2: Percentage incorporation of C8H16Br2(l) into C^H^dJIC) in series 1 and the percentage exchange data for C10H20C12(1) into CnH2n+2(UIC) in series 2.

The results show that the percentage incorporation of the C8H 16Br2(l) into

the CnH2n+2(UIC) decreases w ith increase in chain length of the alkane

guest molecule. For example on exchange betw een C8H 16Br2(UIC) and

C15H30(1) there was < 1 % incorporation. In series 2, the results show that

105

the C10H 20C12(1) replaced the smaller guest species to a greater extent than

it d id w ith the larger guest species. The results for the both the series of

experiments is illustrated in figure 4.4 and 4.5 on pages 122 and 123

respectively in the form of a bar graph.

4.4 Expt 3: An Experiment to Monitor the Mass Changes of the UIC

Resulting from the Exchange Between CnH2n+2(l) and C8H16Br2(UIC) and

CnH2n+2(l) with C10H20C12(UIC)

The aim of this experiment was to m easure the change in mass

upon exchange of C8H 16Br2(UIC) w ith the CnH 2n+2(l) guest species. This

w as carried out to confirm the results of experim ent 1, that the rate of

exchange increases as a function of chain length.

A finely ground sample of the 1,8-dibromooctane UIC (0.295 g) or

1,10-dichlorodecane (0.2074 g) was placed into a 150 m l beaker at room

tem perature. The alkane (= 6.6 ml for series 1 and = 6 m l for series 2 with

both series in 100 times excess) was added to the UIC in the beaker and

w as left on the bench for 5 days. After 5 days the UIC was dried under

vacuum which used the same m ethod as explained in chapter 3. The

sam ple was then weighed and the experimental data was recorded with

the m ethod for calculating the required masses in the appendix.

Table 4.3 and 4.4 lists the results for the percentage incorporation of

the CnI i2n+2(UIC) guest species and expected m ass changes for both series

of experiments. The graph in figure 4.6 and 4.7 on pages 124 and 125

represents the data for both the experimental and expected m ass changes

for each of the series of experiments (calculated from the results of

experiment 1).

106

n Percentage Experimental Expected change

incorporation (%) change in mass (g) in mass (g)

10 5 (1) 0.003 (2) 0.002

11 21 (3) 0.0092 (3) 0.0083

12 63 (5) 0.0248 (1) 0.0243

13 70 (2) 0.0306 (2) 0.0267

14 81 (4) 0.0331 (3) 0.0304

15 90 (4) 0.0370 (2) 0.0334

Table 4.3: Data obtained for the percentage incorporation, the experimental and

expected mass changes for the exchange process that occurred with CnH2n+2(l) and

C8H16Br2(UIC) guest species.

n Percentage Experimental Expected mass

incorporation (%) mass change (g) change (g)

10 16 (1) 0.0002 (3) 0.0019

11 18 (1) 0.0006 (3) 0.0020

12 19 (4) 0.0031 (4) 0.0021

13 36 (4) 0.0037 (2) 0.0036

14 63 (2) 0.0060 (2) 0.0061

15 80 (3) 0.0065 (2) 0.0074

Table 4.4:Data obtained for the experimental and expected mass changes and the percentage incorporation for the exchange process that occurred with Q H ^G ) and C10H20C12(UIC) guest species.

It can be seen that the results for series 1 are highly consistent, and show

that the exchange is reproducible to a high degree of accuracy. The results

obtained for series 2 of experiments were not as conclusive in that the

expected and the experimental mass changes for n = 10 and 11 did not

show consistency (see also figure 4.7).

107


Betw een C8H16Br2(UIC) and D ifferent M olar Ratios of C15H32(1):

C8H16Br2(l).

The aim of this experiment was to carry out exchange reactions

w ith different concentrations of the C15H32(1) guest species which

exchanged w ith C8H 16Br2(UIC). This was designed to test the hypothesis

that the percentage exchange depended upon the concentration of the

guest in the liquid phase.

1,8-Dibromooctane UIC (0.05 g) was finely ground w ith a pestle

and m ortar and added to a 150 m l beaker that contained 7.5 %

pentadecane (0.0996 ml) and 92.5 % 1,8-dibromooctane (1.07 ml). The

relative volumes of pentadecane w ith respect to the 1,8-dibromooctane in

the solution were calculated as explained in the appendix. The mixture

was left at room tem perature on the bench for five days. The contents of

the beaker was then filtered under vacuum and dried for two hours. The

crystals were then transferred into a sample vial and placed in a

dessicator overnight to ensure complete dryness of the crystals.

A whole range of concentrations for the C15H32(1) guest species were

used which ranged from 7.5 % to 100 %. The ratios of concentrations and

volumes of C15H32(1) guest species w ith respect to the C8H 16Br2(UIC) for

each experiment were calculated as shown in the appendix.

The ratios of C15H32 w ith respect to the C8H 16Br2(UIC) guest species

present after the exchange process are tabulated in table 4.5.

108

Concentrations of

C15H32(1) used (%)

Percentage of C15H32

present in the UIC (%)

Percentage of C8H 16Br2

present in the UIC (%)

7.5 37 63

15.5 39 61

23.8 42 58

32.7 71 29

42.4 66 33

52.3 74 26

63.1 78 22

74.5 85 15

86.8 92 8

100 94 6

Table 4.5: The percentage incorporation of C15H32(1) and C8H16Br2(l) into the UIC after the exchange process (± 5% within experimental error).

The equilibrium between the different concentrations of the guest species

is expressed in the form of a chemical equation. The equation reads as

follows:

uaA(1) + uB B(UIC) «=> uA (UIC) + ubB(1)

Equation 4.1

W here A = pentadecane B = 1,8-dibromooctane. The results clearly show

that the percentage exchange is correlated w ith the concentration of the

guest in the liquid phase. However this is not entirely consistent w ith

other results as discussed in section 4.6.

109

4.6 Sum m ary and Further D iscussion

The results for the experiments in sections 4.2, 4.3, have all shown

that there was a preference for exchange if the incoming guest species was

of a longer chain length than that already present in the UIC. For

example, in experiment 1 in section 4.2 the exchange of C10H 20C12 w ith

C10H 22 (1) was show n to be unfavourable w ith only a 16 (1) % exchange in

comparison to a 80 (3) % incorporation w ith the C15H 32 guest species.

Experiment 2 in section 4.3 (replacement of CnH 2n+2(UIC) with

C8H 16Br2(l)) showed that even w ith an excess volum e of C8H 16Br2(l) guest,

it was unable to replace the C15H32 from the UIC. The bar graph in section

4.3 showed > 1 % exchange in the C15H32(UIC) but as the length of the

CriH2n+2 guest species was decreased, the percentage exchange w ith the

C8H 16Br2(l) guest species increased.

The results from experiment 3 in section 4.4 supported these

results, in that the experimental mass changes correlated well w ith the

expected change calculated from the percentage exchange found in

experiment 1. W hen the C15H32(1) guest species was exchanged with

C8H 16Br2 guest species the experimental mass difference w as 0.0370 g and

the expected m ass was 0.0334 g. The same experim ent for the C10H 20C12

was carried out but was not as conclusive w ith the C10H22 and CnH24 guest

species.

The results obtained from experiment 4 in section 4.5 show ed that

as the concentration of the C15H32(1) increased the percentage exchange

increased.

We now discuss therm odynam ic and kinetic factors that controlled

the state of the equilibria using examples of experim ent 1 and 2 in section

4.2 and 4.3. In experiment 1 there was a 90 (4) % exchange of the C15H32

however, w hen the experiment was reversed as described in the second

110

experiment, the C8H 16Br2(l) exchanged w ith the C15H32 w ith > 1 %

exchange. In experiment 1 the exchange was observed to be a rapid

process but in experiment 2 this was not the case. In the case of

experiment 1 the C15H32(1) was in excess and the equilibrium w ould have

favoured the formation of the C15H32(UIC). However, in experim ent 2,

C8H 16Br2(l) was in excess but the equilibrium still apparently rem ained in

favour of the C15H32(UIC). The most plausible explanation of this

observation was that the process described in experim ent 2 was largely

kinetically controlled, had the experiment been left for a longer period of

time the exchange may have been a more likely favored process. The

analogous experiments for the C10H20C12(UIC) system were not as

conclusive. In experiment 1 for the C15H32(1) exchange, the reaction gave a

80 (2) % incorporation. However experiment 2 gave only a 3 (1) %

exchange. The results of experiment 4 show ed a correlation betw een the

degree of exchange and the concentration in the liquid phase. This is

consistent w ith either kinetic or therm odynam ic control.

These results m ay be related to other studies of the therm odynam ic

and kinetic stabilities of UICs. The ability of UICs to undergo exchange

m ay be related to the'sliding m ode'67'68,69. It is expected that the general

stability of UICs prim arily govern the exchange of the guest species

through the channels, where the CnH2n+2(l) guest species enter into the

channels along the incommensurate axis and the C8H 16Br2 slides through

the channels leaving via the other exit. The factors that affect the

therm odynam ic stability of the UIC are discussed below and are used to

explain the extent of the exchange process and the limitations.

• Short chain guest species do not form inclusion compounds.

Hollingsworth and H arris114 suggested that it was partly due to their

111

higher volatility and due to it being a short chain guest molecule it

contains a low binding energy in comparison to longer chian guests.

• A dduct formation is also dependent upon the energy of formation of

the host and the guest molecules. The shorter chain guest molecules (C

> 6) have less contact w ith the urea host (i.e. host-guest interaction).

Consequently the urea molecules are not able to gain the necessary

stabilization from their interaction w ith the included species to form a

stable UIC114. Thermodynamic studies carried out by Pemberton and

Parsonage54 and McAdie108 have provided an insight to the relative

stabilities of the UIC. Parsonage and Pem berton have reported the

observation of gradual transitions w ith increase in chain length for the

even paraffins, C10H 22 C12H26, C14H30, CI6H34 and C20H42 and one odd

paraffin C15H 32. McAdie carried out differential therm al analysis on the

even urea adducts ranging from C10H22 to C28H58 and found that the

C10H 22 (UIC) is marginally unstable at room tem perature and the

decomposition tem perature for the UICs draw closer to the urea

endotherm as a function of chain length. The progressive increase in

the decomposition tem perature of the UICs w ith increasing chain

length is given in table 4.6 w ith an estimate of the heat of

decomposition (A Hd). Experiments were also carried out on pure

hydrocarbons and tested for adduct formation w ith urea by Shannon et

al36 in one publication and Schleisser and Flitter25 in another. They

found that the stability of the UIC to increase w ith increase in chain

length. Bengen and Schlenk11, Schlenk138 and Bengen10 found that the

optim um num ber of carbons was six which w as unbranched or slightly

branched.

112

Guest molecule Chain length (A) Decomposition

temperature of

UICs (°C)

AFId (Kcal mol"1 of

urea)

decane 15.08 ± 0.1 81.5 ±1.1 9.9

undecane 16.34 ± 0.1

dodecane 17.60 ± 0.1 91.2 ±1.7 13.4

tridecane 18.86 ± 0.1

tetradecane 20.12 ± 0.1 101.7 ±2.3 18.7

pentadecane 21.38 ± 0.1

Table 4.6: Guest periodicities (Cg) of alkane, UIC decomposition temperatures of the even n-paraffins and their (A Hd) values from ref 108.

• For alkanes and urea in m ethanol the enthalpy of complexation is

reported to be 1.6 kcal mol"1 per CH2 group21. The increase in

stabilisation on progressive addition of methylene groups to the alkane

chain guest molecules implies greater stability in the UIC139.

• The general requirem ent for any favourable process is one where the

Gibbs free energy is exothermic140,141. The therm odynam ic properties of

the adducts of urea were studied by Redlich et al20. For the lower

molecular w eight guest substances the change in Gibbs free energy

(AG) for the guest substance in the vapour state was carried out by the

m easurem ents of the decomposition pressure. For the higher molecular

weight guest molecules equilibrium studies were carried out. It was

found that AG per mole of urea was found to increase approximately

linearly w ith chain length (owing to an increase in the host-guest

interactions). The features that dom inate the exchange processes are the

guest-guest and host-guest interactions in the UIC and the enthalpy of

the reaction. Brustolon et alli2 showed that the host-guest and the guest-

guest interactions are largely affected by the dynamic behaviour,

113

functional groups that were present on the guest species and the

ordering of the guest species in the UIC. As a consequence AH is

dom inated by the identity of the guest species in the urea channels.

Previous studies143'144,145 suggest that the rotational m otion of the guest

species around the tunnel axis and the change in conformations of the

chain is uncorrelated. Brustolon et alul studied different types of UIC to

test the importance of molecular interactions betw een the guest species.

Experimental evidence obtained from EPR studies suggests that guest-

guest interchannel interactions are im portant in the case of dicarboxylic

acid guest species which give rise to strong intermolecular hydrogen

bonding betw een the carboxylic acid groups. Another possible reason

for restricted m otion m ay also be caused by the m otion of the urea host

lattice. Heaton et al have studied the dynamic properties of urea

molecules in nonadecane / (2H4) UIC by pow der146 and single crystal X-

ray diffraction147. From this work they showed that there occur 180°

jum ps of the urea molecules about their C = 0 axis and is also evident in

the pure crystalline urea form above am bient tem peratures. This also

includes simultaneous rotation about the C-N axis.

In order to understand the m echanism for exchange process the

exchange between the C10H22 (1) and that of the C8H 16Br2 is discussed

below.

In the determ ination of a favourable exchange process the first

factor to be considered are the chain lengths of C10H 22(1) and C8H 16Br2

guest molecules, which in this case are of comparable length.

In the exchange reactions the C8H 16Br2(UIC) w ere prepared

carefully and exact ratios of urea molecules w ith respect to the C8H 16Br2

molecules were calculated. For a C10H22(1) molecule the am ount required

to fit into a C8H 16Br2 host fram ework was calculated. Therefore, in these

114

particular exchange processes because the C10H 22 (1) was adopted to fit into

the C8H 16Br2(UIC) host framework the length of the guest molecule was

irrelevant as the actual num ber of host-guest interactions were not

altered.

Among other affects point num ber 4 is the m ost important. A

proposal was m ade that was related to the idea of bulky substituents

hindering molecular motion. Fukao et aZ48 reported the offset value for

alkanes as Ag = 0 and Harris et alno reported for the dihalogenoakanes an

offset of Ag = Cg / 3 which was different to that of the alkanes. They

suggested the guests' functional groups interacted significantly w ith more

than one functional group in each adjacent channel, hence distorting the

channel walls. This implied that the optim um value of Ag was dependent

on the periodic repeat distance (Cg). Evidently, the identity and position

of the functional group are relevant factors. Short chain guest molecules

for example 1,8-dibromooctane m ay contain m any interacting neighbours

whereas for longer guests this is unlikely and just one interacting

neighbour m ay be expected. It was suggested by Aliev et allu and others110

the possibility that the a,co-dibromoalkane guest species were more

spatially constrained in comparison to the alkane guest species which

perhaps limited the rotation at the ends of the molecule. Smart et al148

showed by Raman spectroscopy that there w as a percentage of the

brom ine end group in the gauche conformation which interchanges to the

trans form which m ay inhibit the exchange process.

The literature reports provide useful information which m ay be

used to help explain the results obtained in this study. The C8H 16Br2 guest

molecule m ay be considered a short chain alkane, w ith C10H22(1) guest

molecule of similar length. Strong interactions already exist between more

than one of the guest species in the adjacent channels in the C8H 16Br2(UIC).

115

Therefore the exchange w ith C10H 22(1) was a less favoured process. There

are no bulky substituents present on the C10H22(l)molecule (the m ethyl

group at the ends are not as bulky as the brom ine group) to compensate

for the interactions that occur between a C8H 16Br2 guest species and that of

another C8H 16Br2 guest species in adjacent channels.

In view of the above discussion of a system w here predom inantly

no exchange occurred, a system w here the exchange w as highly favoured

is also considered. The experiment involved w as the exchange betw een

C15H32(1) and C8H 16Br2(UIC). Similarly in this system the length of the

C15H32(1) molecule is not im portant as the chain length is adopted to fit into

the C8H 16Br2(UIC) framework, in this case less C15H32(1) guest species are

required to be accommodated into the channels of urea. After the

completion of the exchange the guest-guest interactions in the adjacent

channels were m uch reduced but m ore so, there were stronger host-guest

interactions due to less gaps between the adjacent guest species which

w ould cause the structure to destabilise.

Experiment 1 in section 4.2 has show n that the forw ard reaction

was favourable which implies that the change in enthalpy upon exchange

is m ore exothermic. The m ost plausible explanation for this positive result

was the presence of stronger host-guest interactions in the C15H32(UIC).

The guest-guest interactions in the same and adjacent channels however,

favoured the C8H 16Br2(UIC) formation. This w as due to relatively strong

interactions that exists betw een two adjacent C8H 16Br2 species in the same

and in adjacent channels in comparison to the w eaker interactions

betw een the CnH2n+2 species, but even still the experiments show ed there to

be more affinity for the C15H 32 than C8H 16Br2 in the UIC. In these particular

exchange reactions the entropy did not show a great significance in the

determ ination of the state of the exchange process. Implications and

116

suggestions were m ade to the possible effects that the entropy m ay have

on such systems bu t were not as conclusive as expected.

A high entropy state is a consequence of random ness or disorder in

a system. The disorder in the C8H 16Br2(UIC) w ould be expected to be

greater than that in the C15H 32(UIC), bu t w as inhibited by the strong guest-

guest interactions of the C8H 16Br2 guest species. The hindrance in the

molecular m otion of the guest species in the urea channels is influenced

by a num ber of constraints that the guests in the UIC experience. In

addition to the strong guest-guest interactions there are also hydrogen

bonded chains of guest species in a channel, that have their motions

strongly correlated. There also exist strong interactions betw een the guest

species and the channel walls. In the C15H32(UIC) the guest-guest

interactions in the adjacent channels were som ewhat w eaker than the

C8H 16Br2(UIC). This however is counteracted by a lower degree of

disorder and random ness due to the longer chain C15H32 guest species.

From the evidence obtained from the experiments in section 4.2 and the

literature discussions the entropy seemed m ore likely to favour the

C8H 16Br2(UIC).

In sum m ary, the three elements that control the exchange reaction

were:

♦ Host-guest interactions

♦ Guest-guest interactions

♦ The entropy of a system

It has been explained that the last two elements have shown to

favour the C8H 16Br2(UIC) formation and only one nam ely the host-guest

interactions, favour the C15H32(UIC). The experiment however has shown

a preference for the C15H32(1) molecule to exchange w ith the C8H 16Br2 guest

molecule in the UIC, which indicates that the host-guest interactions

117

dom inate the exchange process by far. In conclusion, the experiments

w ere m ost favourable w ith the longer chain alkanes and the results shows

a progressive increase in the percentage incorporation w hen proceeding

from C10H22(1) through to the C15H32(1) guest molecule.

118

119

Figu

re

4.1:

*H NM

R sp

ectru

m

for

the

exch

ange

of

Ci4H

3o(l)

with

CgH

^Br^

UIC

). sp

ectru

m

show

s 81

(1) %

inco

rpor

atio

n of

Ci

^Cl)

into

the

UIC

.

Figu

re

4.2:

A gr

aph

to sh

ow

the

perc

enta

ge

inco

rpor

atio

n of

a

seri

es

of

alka

nes(

l)

into

1,8-

dibr

omoo

ctan

e U

IC

120

98

Figu

re

4.3:

A

grap

h to

show

th

e pe

rcen

tage

in

corp

orat

ion

of

a se

ries

of

al

kane

s(l)

in

to

1,10

-d

ich

loro

dec

ane

UIC

0) _ O) Cm o *3C flj

o o> - Q .a> tr a o

o c

------- ----- r

r

----- ——----w—j

imgj

BB&Bm

121

Figu

re

4.4:

A gr

aph

to sh

ow

the

perc

enta

ge

inco

rpor

atio

n of

l,8-d

ibro

moo

ctan

e(l)

into

alka

ne

UIC

s

122

Figu

re

4.5:

A

grap

h to

show

th

e p

erce

nta

ge

inco

rpor

atio

n of

1,

10-

dic

hlo

rod

ecan

e in

to

a se

ries

o

fal

kane

U

ICs

<u -

S’ IC TOo o

Q. « tr a o

ac

Figu

re

4.6:

A gr

aph

to sh

ow

the

rela

tion

ship

be

twee

n th

e p

erce

nta

ge

inco

rpor

atio

n of

a

seri

es

of

alka

nes

into

1,

8-d

ibro

moo

ctan

e UI

C wi

th

the

exp

erim

enta

l an

d ex

pec

ted

m

ass

cha

ng

es.

2cQ) T3E 0i_ O0 0Q_ Q_X X0 0♦ ■

<UO)c

<u0)O)ro-*-*c<uo<vQ .

■'tf- uO CO UO CMo CO o CN od o d o d

d d

(6 ) a 6 u e ip s s e iu

124

Figu

re

4.7:

A gr

aph

to re

pre

sen

t th

e re

lati

onsh

ip

betw

een

the

per

cen

tage

in

corp

orat

ion

of

a

seri

es

of

alka

nes

into

1,

10-d

ich

loro

dec

ane

UIC

with

th

e ex

per

imen

tal

and

exp

ecte

d

mas

s ch

an

ges

2c<D ■oE a;\_ oQ) CDQ. Q.X Xa; CD♦ ■

oCD

O00

Oco

o

o00

oCN

O

OCO CNCO o00

co(0s—Oo.ooc0O)(0

■*->c0Ov-0a.

oo oo oo oo ooo

oo oo oo

(6) aBueip sseiu

125

CHAPTER 5

EXCHANGE REACTIONS WITH FULLY IMMERSED UREA

INCLUSION COMPOUND SINGLE CRYSTALS

5.1 Introduction

In the previous chapter the exchange reactions were carried out on

polycrystalline samples of the UICs, where it was observed that the

pentadecane exchanges w ith the 1,8-dibromooctane UIC w ith

approxim ately a 95 % exchange after five days. In this chapter single

crystal X-ray studies, which is a more powerful technique, is used to

m onitor the exchange process, where small changes in the structure upon

exchange m ay be observed in the rotation photograph. The reason for the

choice of pentadecane exchanging w ith 1,8-dibromooctane UIC in this X-

ray study is that, in this system the exchange is very high (as established

from the results of chapter 4) and the scattering of X-rays by a bromine

group is large, hence it is a prom inent feature in the diffraction pattern.

The crystals for this experiment were selected using a polarising

microscope (see section 2.2). In the case of 1,8-dibromooctane UIC they

were approxim ately 0.5 cm long needles that required great care when

handling them and were slightly broader than the average alkane UIC

crystal. The experiments in this chapter are described below.

A series of exchange reactions w ith different alkanes in the liquid

phase ranging from decane to pentadecane were carried out, w ith single

crystals of the 1,8-dibromooctane UIC. The exchange was m onitored by

m easuring the change in m ass of the UICs before and after the exchange

process and by *H NMR. An advantage for the use of the 1,8-

dibromooctane UIC is that in the mass change experiments, due to the

126

large difference in the mass of a brom ine atom in com parison to that of a

carbon atom there will be a significant difference in the initial and final

masses upon exchange. This allows for an accurate determ ination of the

percentage exchange in the UIC. The second experim ent involves a 'five

day' single crystal X-ray diffraction study using pentadecane(l) and 1,8-

dibromooctane UIC. The 1,8-dibromooctane crystal w as im m ersed into a

solution of pentadecane and each day the crystal was rem oved and a

diffraction pattern was recorded. In this w ay the changes in structure of

the UIC could be observed.

5.2 An Experiment to Investigate the Percentage Exchange Between

C8H16Br2(UIC) and CnH2n+2(l)

The aim of this experiment was to m easure the percentage

exchange in the UIC w hen the C8H 16Br2(UIC) guest w as replaced by the

guest- K was carried out to test the hypothesis that the

percentage incorporation increases w ith an increase in chain length.

Percentage exchange was determ ined by m easuring m ass changes and

also by NMR. A single crystal of C8H 16Br2 (UIC) w ith m ass of about 4

m g (accurately weighed for each exchange experim ent on a sartarius

microbalance) was fully im m ersed into an excess liquid of C15H 32(1) (~ 1

ml; 1000 times excess). The liquid that contained the crystal was left at

room tem perature on the bench for five days, to allow for exchange to

occur. After five days the crystal was filtered and w ashed in the way

described in section 3.1. The experimental conditions for the experiment

can be found in the appendix. At the end of the experim ent the final mass

was recorded. The mass readings for each exchange w ere taken three

times and the m ean and standard deviations are quoted in table 5.1.

127

Initial mass of 1,8-

dibromooctane

UIC (mg)

Final mass (mg) Change in mass

(mg)

10 5.405 (1) 5.207 (3) 0.198 (3)

n 5.113 (6) 4.872 (7) 0.241 (9)

12 3.570 (3) 3.22 (2) 0.350 (4)

13 3.567 (2) 3.128 (7) 0.439 (7)

14 2.984 (6) 2.634 (8) 0.35 (1)

15 4.405 (1) 3.815 (7) 0.590 (7)

Table 5.1: The initial mass, final mass and the change in mass for the exchange process with CnH2n+2(l) guest species into a C8H16Br2(UIC).

The results obtained from this experiment show im m ediately that the

change in mass increases w ith an increase in the chain length of the guest

species. The graph in figure 5.1 on page 134 shows that an approxim ately

linear relationship exists between the m ass changes and the chain length

of Q H ^ ^ l) guest species.

After completion of the exchange reactions the same crystals were

dissolved in deuterated m ethanol and were characterised by JH NMR in

the w ay described in the appendix. This was carried out in order to

compare the expected mass change calculated from the percentage

incorporation (see appendix) obtained from lH NMR w ith the mass

change obtained in this experiment.

The results for the percentage incorporation of the CnH2n+2(l) guest

species into the channels of the C8H 16Br2(UIC) single crystals are recorded

in table 5.2.

128

C nH 2n+2(l) Percentage

incorporation (%)

Expected mass

change (mg)

Experimental

mass change (mg)

10 24 (6) 0.206 0.198 (3)

11 30 (1) 0.231 0.241 (9)

12 63 (2) 0.332 0.350 (4)

13 77 (2) 0.402 0.439 (7)

14 81 (3) 0.354 0.35 (1)

15 95 (1) 0.560 0.59 (7)

Table 5.2: The percentage incorporation expected mass change and the experimental mass change of the exchange process of CnH2n+2(l) with C8H16Br2(UIC).

The results show a good agreem ent and confirm that the percentage

incorporation is indeed dependent upon the length of the guest species.

For example w hen C12H26(1) was exchanged w ith C8H 16Br2 in the UIC there

was a 63 (2) % incorporation in comparison to the 95 (1) % exchange with

the C15H32(1) and the C8H 16Br2 guest species. The NMR spectrum for

C12H26(1) exchanging w ith C8H 16Br2 in the UIC is show n in figure 5.2 on

page 135 and the bar graph in figure 5.3 on page 136 illustrates the results

show ing the percentage incorporation for the whole series of alkanes.

5.3 Investigation of the Rate of the Exchange Reaction Between

C8H16Br2(UIC) and C15H32(1) by Single Crystal X-ray Diffraction.

This experiment was designed to observe changes in the crystal

structure and crystal integrity caused by the incoming C15H32(1) guest

species into the C8H 16Br2(UIC) in the exchange process.

A single crystal of 1,8-dibromooctane UIC (0.212 mg) w as placed

into a 150 ml beaker that contained pentadecane (0.55 ml, 10000 times

excess) and was left for five days to allow for exchange to occur. Each day

129

the crystal w as rem oved from the beaker and m ounted on a goniometer

head using blu-tac. It was then placed on the X-ray cam era where the

single crystal X-ray diffraction rotation photograph w as recorded. Further

reference w ith regards to this technique is described in chapter 2. After

having carried out the m easurem ents the blu-tac was rem oved from the

crystal, and the latter was placed back into the beaker that contained the

C15H 32(1). This process was repeated five times, once a day for five days.

The X-ray rotation photographs were indexed as described in chapter 3

and the changes observed in the intensities of the reflections before and

after the exchange of the guest species were recorded. The crystal was

dissolved in deuterated methanol and characterised by NMR to obtain

the percentage exchange that had occurred w ith the C15H32(1) and the

C8H 16Br2(UIC) as described in the appendix. The calculation for the

relative am ount of C15H32(1) required is also show n in the appendix.

Rotation photographs for the pure C8H 16Br2(UIC) and the

C15H 32(UIC) are show n in figure 5.4 and figure 5.5 on page 137. Two (h k 1)

reflections that showed a significant change in the intensities upon

exchange were the (2 1 0) and the (3 0 0) reflections, which are labeled in

the X-ray diffraction pattern in figure 5.4 and figure 5.5. Figure 5.4 shows

that in the pure C8H 16Br2(UIC) the (3 0 0) reflection is relatively weaker

w ith respect to the (2 1 0) reflection and figure 5.5 shows that in the pure

C i5H32(UIC) the (3 0 0) reflection is almost comparable w ith the intensity of

the (2 1 0) reflection. The relative intensities of these two reflections may

be com pared w ith respect to one another as a function of time.

Day 1

Figure 5.6 on page 138 shows that for day 1 of the exchange, there

is a significant change in the relative intensities of the (2 1 0) and the

130

(3 0 0) reflections. On comparison of the intensities of the pure

C8H 16Br2(UIC), the (2 1 0) reflection is relatively stronger and the (3 0 0) is

relatively weaker. The diffuse bands characteristic of the C8H 16Br2 guest

species are still present, though much w eakened in intensity. This

indicates the continued presence of the C8H 16Br2 guest in the UIC.

Day 2

The X-ray pattern in figure 5.7 on page 138 obtained from day 2 of

the exchange show a slight increase in the intensity of the (2 1 0)

reflection. The diffuse bands characteristic of the C8H 16Br2 guest species

are still present although their relative intensities are significantly

reduced.

Day 3

The X-ray pattern in figure 5.8 on page 139 for day 3 of the

experim ent shows evidence for a slight increase in the mosaicity of the

crystal and the diffuse bands due to the C8H 16Br2 guest species are no

longer apparent in the rotation photograph.

Days 4 and 5

The rotation photographs for days 4 and 5 in figure 5.9 and figure

5.10 on page 139 respectively shows a slight increase in decomposition to

the structure after day 3. After the third day in a repeat experiment there

was a 97 % (obtained from lH NMR) exchange of pentadecane® into the

1,8-dibromooctane UIC suggesting that the exchange w as complete after

three days.

131


The results obtained from this chapter are consistent w ith those

reported in chapter 4. The experiment in section 5.2 shows that the

percentage incorporation increases w ith an increase in chain length of the

incoming guest species. Thus the exchange reaction w ith the C10H22(1)

guest species and C8H 16Br2(UIC) guest species gave only a 24 (6) %

incorporation whereas the exchange w ith the C15H32(1) .and C8H 16Br2(UIC)

guest species occurred w ith 95 (1) % incorporation. The NMR data

supports the results of the experiment in section 5.2 w here the

experimental m ass changes are consistent w ith those expected from the

NMR analysis.

The X-ray studies on the exchange reactions of C15H32(1) with

C8H 16Br2(UIC) provide an insight into the m echanism of the exchange. The

two m ain reflections that reflected the exchange are the (2 1 0) and the

(3 0 0) reflections. From the oscillation photographs of the pure UIC the

(2 1 0) reflection is characteristic of the C15H32(UIC) and the (3 0 0)

reflection m ore so of the C8H 16Br2(UIC). On incorporation of the C15H32(1)

guest species into the C8H 16Br2(UIC) after the first day the diffuse bands

characteristic of the C8H 16Br2 guest species were significantly weakened in

intensity. The (2 1 0) reflection increased in intensity in the X-ray structure

factor which was most likely due to the entrance of the C15H32(1) into the

tunnels. The (3 0 0) reflection, which was a relatively strong reflection in

the pure C8H 16Br2(UIC) was significantly weaker after the first day of the

exchange process. The changes in the reflections w ere therefore attributed

to the incorporation of the new guest species and the relative intensities of

the two reflections in the final product are consistent w ith those present in

the pure C15H32(UIC). The X-ray diffraction studies of the 'five day'

experim ent suggested that the exchange was complete after the third day.

132

This was also confirmed in an experiment on pow der samples, which is

not reported in detail here.

The overall conclusion from the X-ray study w as that the exchange

process occurs betw een the two guest species w ith only a slight loss in the

integrity of the crystal. The C15H32(1) guest species was able to enter into

the urea channels and displace the C8H 16Br2(UIC) guest species w ithout

major disruption to the host framework. The mechanism for the exchange

process of how the guest species enter and leave the channels has not

been determ ined in this chapter, however, will be investigated through

experiments in the forthcoming chapter.

133

Figu

re

5.1:

A gr

aph

to re

pre

sen

t th

e re

lati

onsh

ip

of

the

exp

ecte

d

and

exp

erim

enta

l m

ass

chan

ges

wit

h

the

per

cen

tage

in

corp

orat

ion

of

a se

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134

135

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t g p ^ M ^BjWp agiiSBg

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136

Figure 5.4: Single crystal x-ray diffraction rotation photograph of pure 1,8 dibromooctane UIC recorded at room temperature.

Figure 5.5: Single crystal x-ray diffraction rotation photograph of pentadecane UIC recorded at room temperature.

137

Figure 5.6: Single crystal x-ray diffraction rotation photograph recorded at room temperature after one day of the exchange between dibromooctane in the UIC with pentadecane (1).

( 3 0 0 ) ( 2 1 0 )

\ /

Figure 5.7: Single crystal x-ray diffraction rotation photograph recorded at room temperature after two days of the exchange between dibromooctane in the UIC with pentadecane (1).

138

( 3 0 0 ) ( 2 1 0 )

\ /

Figure 5.8: Single crystal X-ray diffraction rotation photograph recorded at room temperature after three days of the exchange between dibromooctane in the UIC with pentadecane (1).

Figure 5.9: Single crystal X-ray diffraction rotation photograph recorded at room temperature after four days of the exchange betw een dibromooctane in the UIC with pentadecane(l).

Figure 5.10: Single crystal X-ray diffraction rotation photograph recorded at room temperature after five days of the exchange between dibromooctane in the UIC with pentadecane (1).

139

i

CHAPTER 6

EXCHANGE REACTIONS WITH PARTIALLY IMMERSED

UREA INCLUSION COMPOUND SINGLE CRYSTALS

6.1 Introduction

The last two chapters described the exchange reactions on

poly crystalline and single crystal UICs that w ere fully immersed in the

exchanging liquid guest. The results were consistent w ith the idea that

guest species could literally pass along the channels of the UIC w ithout

disruption to the overall crystal structure. This process could potentially

be used for practical separation of molecular m ixtures. In order to test this

idea an exchange reaction was carried out on a single crystal of 1,8-

dibromooctane UIC which was partially immersed into liquid pentadecane.

The experimental set up is shown in figure 6.1 on page 160 and is

described in detail later. After approxim ately 1 h r liquid w as observed to

have collected in the capillary tube. This is a surprising effect and the

experiments in this chapter are designed to investigate it further. Three

m ain types of experiments were carried out using the different pathw ays

for the entrance of the potential guest (s) in the liquid phase into the UIC.

These are listed below.

(i) The crystal im m ersed into the liquid guest from the bottom end

(ii) The crystal imm ersed into the liquid guest from the top end.

(iii) Both ends of the crystal immersed into liquid guest

In addition to the above experiments the kinetics of one particular

140

system was studied in order to understand the reaction as a function of

time (section 6.2.1). X-ray diffraction studies on selective system s were

carried out and are discussed in section 6.3.

In this chapter, the following shorthand notation is used to

represent the experiments:

l u l v l w l => I X | Y | Z |

In this notation U, V, W, X, Y, Z are chemical species. | u |

represents liquid U in the capillary tube; IV | represents the UIC in the

capillary tube; IW | represents liquid W in the watch glass. Then

IX IY IZ I represents the corresponding arrangem ent of chemical species

after the exchange. For example I — I C8H 16Br21C15H321 represents a

situation w ith the capillary tube em pty (no U), the UIC of C8H 16Br2 guest

(V), and C15H 32(1) in the watch glass (W).

6.2 Exchange Reactions Characterised by NMR Analysis

6.2.1 1,8-Dibromooctane exchanged with pentadecane from the watch

glass

I — I C8H 16Br21C15H321 => IC15H 32/ C8H 16Br21C15H32 / C8H 16Br21C15H 321

This experiment tests the idea that C15H32(1) is able to enter the UIC

channels from the bottom end of the crystal, replacing the C8H 16Br2 from

the UIC which leaves via the other end of the crystal.

The UIC was prepared in the usual m anner to that described in

chapter 3. A crystal was selected and examined under the polarising

microscope to confirm that it was a single crystal. The apparatus was set

141

up as shown in figure 6.1. One end of the crystal was placed in a small

capillary tube that was adapted to accommodate the crystal and w as held

in a vertical position by m eans of wax. The other end of the crystal

pro truded from the capillary tube and was im m ersed into a know n guest

liquid (~ 0.1 ml) contained in a watch glass. The capillary tube that

contained the crystal was attached vertically to a clamp stand holder by

m eans of scotch tape. The watch glass rested on a second clamp stand

holder that was attached to the same clamp stand in a position directly

beneath the crystal. The crystal was left to stand on the bench at room

tem perature until liquid was observed at the top of the capillary tube. The

time span for the whole experiment was on average, 2-3 hr s. The

apparatus was dism antled and the analysis of the solution in the watch

glass and that in the capillary tube was carried out by lH NMR. In both

cases the liquids were dissolved in deuterated chloroform.

Characterisation of the crystal which was dissolved in deuterated

m ethanol was also carried out by lH NMR.

Table 6.1 shows the NMR results for the percentage exchange

that occurred in the crystal and the ratio of guest species present in the

capillary tube and watch glass. The capillary tube that was originally

em pty was found to be filled w ith a significant am ount of liquid which

w hen characterised showed to be rich in C8H 16Br2( l) .

Capillary tube Crystal Watch glass

pentadecane (%) 93 (10) 93 (10) 100

1,8-dibromooctane (%) 7(10) 7(10) 0

Table 6.1: Percentage ratio of guest species present in the capillary tube, crystal and watch glass for the exchange reaction with C8H16Br2(UIC) and C15H32(1).

142

The result suggest that the C8H 16Br2(l) was displaced from the

crystal and w as exchanged by the C15H32 that had entered the crystal.

The absence of the C8H 16Br2(l) in the watch glass suggests that

C8H 16Br2(l) leaves only via the opposite end to that which w as im m ersed

in C 15H32(l).

Next a kinetic study of the same reaction was perform ed. The same

apparatus was set up as shown in previous experiment (section 6.2.1).

However in this experiment the rate of reaction was monitored.

M easurem ents of the height of liquid in the capillary tube after every five

m inutes were noted. This was directly obtained by placing a narrow strip

of card that was perm anently fixed to the tube and after every five m inute

intervals the height of the liquid was m arked on the card. At the end of

the experiment the apparatus was dism antled and the height of each

m ark was m easured w ith a ruler.

The results are recorded in table 6.2 and is presented graphically in

figure 6.2 on page 161. The graph resembles a sigmoid curve and, it can

be deduced that between (0-130 min) the crystal is said to be in an

incubation period, where no liquid is observed to have passed through

the crystal into the capillary tube. The crystal at the end of the incubation

period was observed to have changed from an almost transparent crystal

to an opaque one. After 130 m in the liquid is seen to collect in the

capillary tube, and this process continued for 200 minutes.

143

Time (min) Distance(mm)0 060 0120 0125 0130 0135 0.5(7)140 0.5(7)145 0.5(7)150 1.2(2)155 1.2(2)160 1.2(2)165 1.3(4)170 1.8(4)175 2.0(6)180 2.0(6)185 2.0(6)190 2.1(4)195 2.2(3)200 2.2(3)

Table 6.2: Measurements of the rate of exchange between C8H16Br2(UIC) and C1SH„(1).

6.2.2 Self exchange of 1,8-dibromooctane from the watch glass

I — I C8H 16Br21 C8H 16Br21 => | C8H 16Br21 C8H 16Br21 C8H 16Br21

The experiment w as designed to test the idea that a guest species in

the liquid state could exchange w ith an identical guest in the UIC. The

experimental procedure is the same to that previously discussed. It was

found that liquid collected in the capillary tube, although only after

several days. NMR analysis confirmed this liquid to be 1,8-

dibromooctane. The results show that the exchange occurs even w ith the

same guest species entering the UIC as that already present. The

C8H 16Br2(l) exchanges w ith the C8H 16Br2(UIC) which leaves the crystal and

the liquid collects in the capillary tube.

144

6.2.3 Both ends of the crystal im m ersed in liqu id guest

I C 8H 16B r 2 I C 8H 16B r 2 I C 15H 32 I = > I C 8H 16B r 2 / C 15H 32 I C 8H 16B r 2 / C 15H 32 I C 15H 32 I

This experiment tests if the C15H32(1) can enter the crystal from the

bottom end while competing w ith the incoming C8H 16Br2(l) which enters

from the top end of the crystal. The experimental details are the same to

that described in the experiment in section 6.2.1 w ith a small modification

in that both ends of the crystal were im m ersed into a potential liquid

guest. The C8H 16Br2(l) was added to the capillary tube using a syringe and

the bottom end of the crystal is imm ersed in C15H32(1) contained in a watch

glass. The results are show n in table 6.3 below.

Capillary tube Crystal (%) Watch glass

(%) (%)pentadecane (%) 73(6) 71 (4) 96 (4)

1,8-dibromooctane (%) 27 (3) 29 (4) 4(3)

Table 6.3: Percentage ratio of guest species present in the capillary tube, crystal and watch glass after the exchange reaction in the following reaction | C8H16Br21 C8H16Br21 C15H321.

The results indicate that there is a preference for the C15H32 in the

UIC and that even though there were two guest species entering the

crystal the C15H 32(1) m anaged to displace the C8H 16Br2 from the (UIC). This

result provides strong evidence that the C15H32(1) passes through the

crystal into the capillary tube and dom inates the exchange process.

The NMR results of the liquid in the w atch glass showed that

there was only 4 (3) % of C8H 16Br2(l) present in comparison to the 96 (4) %

of C15H32. This result implies that nearly all the species entering the

channels enter from the same end and all the leaving species will leave

from the other end. There is no apparent random translation of guest

145

w here one C8H 16Br2(l) leaves from one end and another from the other end

of the channel.

6.2.41,8-Dibromooctane exchanged w ith pentadecane from the capillary

tube

I C,5H321 C8H 16Br21 — U IC15H 321 C15H 3 2/C 8H 16Br21CI5H32 /C 8H 16Br21

The C8H 16Br2(UIC) in this experiment w as im m ersed from its top

end into C15H32(1) guest. The experimental procedure in this particular

experiment differed slightly from the experim ent in section 6.2.1. After 5-

7 days (which is m uch longer than 200 m in of section 6.2.1) small drops of

liquid were observed in the watch glass, underneath the crystal. The

crystal, liquid in the capillary tube, and the liquid in the w atch glass were

analysed individually by 2H NMR. The solvent that w as used to dissolve

the crystal was deuterated m ethanol and for the liquids, deuterated

chloroform.

Capillary tube Crystal Watch glass

quantity of pentadecane 100 98 (6) 89 (4)

present (%)

quantity of 1,8- 0.00 2(6) 11 (4)

dibromooctane present

(%)

Table 6.4: Percentage ratio of guest species present in the capillary tube, crystal and watch glass of the exchange reaction with | C15H321 C8H16Br21 — I.

The results in table 6.4 highlight that the exchange is able to occur

from both the extreme ends of the crystal. W hen the crystal was

im m ersed into liquid guest from the bottom end of the crystal, liquid was

146

observed to have collected at the top. W hen im m ersed from the top end,

liquid was found to have collected in the watch glass The results from the

NMR spectra show that C15H32(1) is able to displace the C8H 16Br2 from

the crystal almost completely, w ith a percentage incorporation of 98 (6) %.

These results are consistent w ith the other set of results in the

previous section which were that the guest species leave the tunnel in an

ordered m anner and depart via the other end from which the incoming

guest species had entered.

6.2.5 'Self 'exchange from the capillary tube

I C8H 16Br21 C8H 16Br | — | =» | C8H16Br21 C8H 16Br21 C8H 16Br21

The C8H 16Br2(l) was imm ersed from the top end of the crystal and

liquid guest was observed to collect in the watch glass. The experimental

procedure was the same to that previously discussed. In this experiment

the transport of liquid from the capillary tube into the watch glass took

several days. The results of the experiment are tabulated in table 6.5.

Crystal analysis: => pure 1,8-dibromooctane

Liquid in the capillary tube: => pure 1,8-dibromooctane

Liquid in the watch glass pure 1,8-dibromooctane

Appearance of crystal before exchange

=>

clear, almost a single crystal.

Appearance of crystal after exchange

=>

opaque in appearance.

Table 6.5: Table to represent the exchange reaction with I C,H16Br21 C,HltBrJ — | .

In this particular exchange the collection of C8H 16Br2(l) into the

w atch glass was at a slower rate than that w ith the C15H 32(1) entering from

147

the top end.

6.2.6 Repetition of the exchange reaction using the same UIC crystal

I - 1 C8H 16Br21C15H321 => I C8H 16Br2/C 15H321 C8H 16Br2/C 15H321C15H321

The apparatus was set up in the usual m anner C8H 16Br2(UIC) was

exchanged w ith C15H 32(1). After each exchange process the liquid that was

collected in the capillary tube was rem oved and the exchange was

repeated w ith the same crystal. This process w as repeated eight times

after which the crystal became the consistency of slush. The C8H 16Br2

crystal after all the exchange reactions was opaque in appearance, and

tender.

6.2.7 Attempted exchange with a tetragonal urea crystal and C15H32 from

the watch glass

I — I urea IC15H321 => I — I urea I C15H321

In this experiment a pure crystalline urea crystal was set up for the

exchange reaction and was imm ersed into C15H32(1). The purpose was to

confirm that the transport of the liquid could only occur in a UIC. The

results are show n in table 6.6 below.

Crystal analysis => pure urea

Liquid in capillary tube =» empty capillary

Liquid in the watch glass => pentadecane

Table 6.6: Exchange reaction that occurred with a pure urea crystal and C15H32(1).

The results show ed that after 4 days there w as no liquid collected in the

capillary tube due to the presence of urea in its pure tetragonal form.

148

6.3 Single Crystal X-ray D iffraction Studies

The experiments in section 6.2 suggest strongly that liquid guest

can be transported through the crystal. Single X-ray diffraction m ay be

used to provide m inute details of any changes in the crystal structure that

accompany this process. In this section the exchange reactions of partially

im m ersed single crystals are studied by single crystal X-ray diffraction. A

num ber of systems were studied, however m uch attention was draw n

tow ards the exchange reaction w ith C8H 16Br2 in the UIC and C15H32(1).

Each system is discussed individually below w ith close attention to the

changes in intensities of reflections in the oscillation photographs which

m ay be related to the exchange process.

6.3.1 Exchange of 1,8-dibromooctane w ith pentadecane from the watch

glass.

I — I C8H 16Br21C15H321 => | C15H32/C 8H 16Br21 C15H 32/C 8H 16Br21C15H 321

This experiment (unlike those of the forthcoming sections) was

carried out at the Chemistry Departm ent, University of Birmingham, in

order to utilise the R-AXIS IIC diffractometer (described in section 2.3.3 )

that proved to be an ideal instrum ent for this work. The exchange

reaction was carried in the same m anner as that show n in figure 6.1. After

the transport of liquid was complete, the apparatus was dism antled,

traces of wax w ere removed from the crystal using methanol, and the

crystal was m ounted on the goniometer of the R-AXIS IIC diffractometer.

The X-ray diffraction pattern of a single crystal of pure 1,8-

dibromooctane UIC before and after the exchange is illustrated in figure

6.3 and figure 6.4 on page 162 respectively. Figure 6.3 shows the

characteristic discrete reflections and diffuse bands of the 1,8-

dibromooctane guest species. Figure 6.4 shows the X-ray diffraction

149

pattern of the same crystal as that in figure 6.3 after a 24 hr exchange w ith

pentadecane(l). It shows new discrete layer lines and streaks present in

the UIC in addition to those originally present. Figure 6.5 on page 163 is

the same X-ray pattern as that shown in figure 6.4 except that it shows an

enlarged picture of the low angle region w here details of the guest

reflections can be seen more clearly. From calculations of guest repeat

distances it can be confidently stated that the new discrete spots and

diffuse bands are characteristic of the pentadecane guest species present

in the same UIC. The layer lines of the pentadecane guest species are

closer to the centre than those of 1,8-dibromooctane owing to its larger

repeat distance. The layer lines characteristic of the C8H 16Br2 is also

present, although the relative intensity is significantly reduced. The

presence of two separate guest reflections in the same UIC is indicative of

ordered macroscope domains for each guest species. Also from the figure

it is clear that the exchange process is not associated w ith any significant

loss in integrity of the crystal; only a slight increase in the mosaicity of the

crystal during the exchange process is evident. Figure 6.6 on page 163

shows an enlarged picture of the (3 0 0) and (2 1 0) reflections after the

exchange, which is consistent w ith the results to the five day reaction in

section 5.3 of the fully im m ersed single crystal. In the X-ray pattern of the

pure C8H 16Br2 (UIC) the (3 0 0) reflection is of strong intensity relative to

the weak (2 1 0) reflection. Upon exchange w ith the pentadecane the (2 1

0) reflection becomes significantly stronger and the (3 0 0) reflection

becomes only slightly stronger bu t weaker than the (2 1 0) reflection. The

changes in intensities of these reflections w ere discussed previously in

section 5.3. It is difficult however to extract further information from the

X-ray patterns of how m uch exchange occurred. The NMR for the

exchange is show n in figure 6.7 on page 164 w here the crystal was

150

dissolved in deuterated m ethanol shows that there was < 10 % 1,8-

dibromooctane rem aining in the UIC after one day of the exchange.

The same experiment was repeated w ith another crystal of

C8H 16Br2(UIC) which was immersed into C15H 32(1). The experim ent w as left

for a week to allow for exchange. Figure 6.8 on page 165 shows that even

after a week there is only slight disruption to the host framework. Figure

6.9 on page 165 is an enlarged view of the low angle region of the UIC

after the exchange. The guest layer lines due to the C15H32 are prom inent

features in the X-ray pattern but those of the C8H 16Br2 are present only as

very w eak intensity diffuse bands. The ’H NMR spectra of the UIC crystal

show ed there to be < 2 % of C8H 16Br2 present in the crystal.

6.3.2 Exchange of decane with pentadecane from the watch glass

I— I c 10h 22 I c 15h 32 I => I c 15h 32/ c 10h 22 I c 15h 32/ c 10h 22 I c 15h 32 I

This experiment was designed to test the exchange of one alkane

for another. This and the forthcoming experiments all used a rotation

camera at UCL. The experiment was carried out using the same apparatus

to that shown in figure 6.1 on page 160. After the liquid was show n to

have collected in the capillary tube the apparatus w as dism antled and the

wax rem oved from the crystal using methanol. The crystal was m ounted

on the goniometer and the X-ray data w as recorded on the X-ray film

using the rotation camera (described in section 2.3.3). The X-ray

photograph for the C10H22(UIC) contains diffuse and discrete scattering

betw een the layer lines. The diffuse bands represent one-dimensional

ordering and the discrete spots are attributed to three-dimensional

ordering. The pure C10H 22(UIC) contains the same basic host reflections as

the C15H32 (UIC). On incorporation of the C15H32 the discrete spots that

were originally present in the C10H 22(UIC) disappear and the diffuse

151

bands significantly decrease in intensity. This structural change supports

the view of exchange of decane for pentadecane has occurred.

6.3.3 'Self' exchange with pentadecane from the watch glass

I— IC15H321C15H321 => I C]5H321C15H321C15H321

In this experiment the apparatus was set up as in figure 6.1 and the

experimental procedure for the exchange experim ent including collection

of the X-ray data was the same as that described in section 6.3.2. The

emphasis, however of this experiment was to detect any change in the

general ordering of the guests w ithin the channels or disruption to the

host fram ework on incorporation of the same guest species into the UIC

channels.

The rotation photograph after the exchange showed no significant

difference in structure to the one before the exchange.

6.3.4 'Self' exchange with decane from the watch glass

I— I c 10h 22 I c 10h 22 I => I c 10h 22 I c 10h 22 I c 10h 22 I

The experimental details were the same as those previously

reported and is the same as the experiment described in section 6.3.3

except using different alkane guests. Figure 6.10 on page 166 shows the

UIC before exchange. The X-ray pattern in figure 6.11 on page 166 shows

the UIC after exchange. There is strong evidence for severe disorder to the

structure and development of rings at lower angles which indicates

decomposition. The Bragg peaks due to the host lattice are m uch larger

than that usually observed which is a consequence of the developm ent of

a polycrystalline sample. There are also diffuse bands observed in the

pattern which represent one dimensional ordering in the urea channels.

This observation is surprising in that there is evidence for decomposition

152

and also the UIC shows one dimensional ordering.


It has been successfully shown that exchange reactions can occur in

UICs, where the potential incoming guest species can displace the existing

guest species from the channels w ithout severe disruption to the host

framework. The pathw ay by which the guest species enter and leave the

channels is not clearly identified, however the m ost plausible explanation

which is suggested from the X-ray data and other results is that the liquid

enters from one end and leaves from the other. One m ay envisage two

physical processes that facilitate the exchange reactions. These are

capillarity and chemical stability. In the systems that have been studied

both factors do not necessarily work together in any one particular

system. In addition to this there is a third subtle factor that could also aid

the process; that is the wax that is used to seal the crystal inside the

capillary tube. Very little is known at this stage about all three factors;

hence further experiments are needed in order to reach firm conclusions

as to the extent to which the wax, for example, plays a role. There are

however plausible suggestions discussed below based on the results

obtained from this work.

Chemical stability applies to systems w here a physical change

occurs and the outcome is such that the chemical species obtained will be

the m ore therm odynam ically stable one. For example in section 6.2.1 the

preferred inclusion com pound is clearly that of C15H 32. It is thus likely that

C i5H32(UIC) is m ore therm odynam ically stable than the C8H 16Br2(UIC).

The guest-guest interactions, host-guest interactions and host-host

interactions influence the stability of the UIC as explained in detail in

chapter 4. Following the discussions in chapter 4 the intermolecular forces

153

(i.e. bond strength) betw een a C15H 32 species and urea is stronger than the

intermolecular forces betw een a C8H 16Br2 species and urea. This leads to

the suggestion that there is a preference for the C15H32 which causes the

C8H 16Br2 to be forced out of the channels. Another factor influencing the

stability is the entropy. This increases w hen the m otion or random ness of

the guests in the inclusion com pound increases. W hen a system has more

order then it is said to have low entropy hence a less stable UIC. In this

study however the host-guest interactions appear to dom inate m ost of the

exchange process. There have been some systems w here the guest in the

inclusion com pound and the exchanging guest have been the same

(section 6.2.2 and 6.2.5). For chemical stability to be active, there initially

needs to be some kind of concentration gradient to cross over and in some

systems this does not occur. The most plausible explanation as to how the

liquid rises up the crystal w ithout a chemical driving force is capillarity

effects. Capillarity is a surface phenom enon and is crucial w ith regards to

this study. Liquids tend to rise up a capillary due to surface tension and

the interactions between the liquid and the walls of the capillary. They

adapt a shape that minimises their surface area and maximise the num ber

of species in the bulk, however this is opposed by the force of gravity.

W hen a glass capillary is im m ersed in a liquid it has a tendency to adhere

to the walls w here the energy will be at its m inim um and it will cover

m ost of the wall. As the liquid creeps up the inside wall it has the effect of

curving the surface of the liquid inside the wall. The curvature implies

that the pressure beneath the meniscus is less than the atmospheric

pressure by 2y/r w here r is the radius of the tube. The pressure outside

the tube is P the atmospheric pressure but inside the tube under the

curved surface it is P-2y/r. The excess external pressure forces the liquid

up the tube until pressure equilibrium is m aintained. This is observed in

154

these experiments. The proposed pathw ay for the exchange that occurs

via capillary action is as follows. The guest species in the inclusion

com pound protrude from the crystal causing the m erging of these guest

species w ith the free guest species in the watch glass. Simultaneously, at

the top end of the crystal there are guest species protruding from the

crystal which is a high-energy situation. Any system in general will be

stable in a state of low energy so hence the liquid at the top will tend to

wet the outsides of the crystal and at the same time sucking up the liquid

from the watch glass through the crystal. The liquid will still continue to

rise out through the crystal wetting the outsides of the crystal wall, and

eventually producing a curved surface. The capillary tube (which is just

an extension of the crystal in this sense) will now take over and force the

liquid up the tube via capillary rise and will continue do so until the

pressures inside and outside the capillary tubes are equal. Another

possible suggestion is that the liquid at the bottom will climb up the sides

of the crystal through the wax and collect in the tube, and at the same

time the guest species protrude from the top, w et the sides of the crystal,

and suck up liquid through the crystal eventually form ing a curved

surface.

The second experiment in section 6.2.1 is the study of the kinetics of

the exchange reaction. The incubation period of the reaction suggests that

the inclusion com pound before the exchange m ay have the ends of the

tunnel closed up so that the C8H 16Br2 species can be enclosed tightly

w ithin the channels. In this incubation stage the ends of the tunnels are

possibly being rearranged in such a m anner to provide access to the

incoming C15H32 species. Incorporation of this guest species causes defects

to the structure where the degree of imperfection is reflected by an

increase in w idth of single crystal X-ray diffraction spots. After

155

approxim ately two and half-hours the liquid appears to pass though the

channels of the inclusion com pound and out into the capillary tube. The

liquid continues to rise up the tube due to capillary action until an

equilibrium is m aintained betw een the chemical forces due to movement

in the UIC channels, the mechanical force, and gravity.

The third experiment in section 6.2.2 ('self' exchange) poses a

num ber of questions for w hy the reaction occurred. The efficiency of an

exchange process depends on the properties of the UIC and the external

environment. The im portant factor is the difference in chemical potentials

of two guest species at the two ends of the crystal. In this the liquid is seen

to travel up the crystal against the strong force of gravity that supposedly

opposes the reaction which leads to the suggestion that capillarity plays a

significant role. The rate for the exchange how ever has show n to be much

slower than in the case where C15H32(1) replaced C8H 16Br2 from the UIC.

The C8H 16Br2 vs C15H32 took ~3 hrs whereas the C8H 16Br2 vs C8H 16Br2 took

several days.

The results from the experiment in section 6.2.3 w here the crystal

w as im m ersed into two liquid guests from both ends shows that there

was a preference for C15H32 in the UIC. After the exchange the crystal was

characterised and shown to contain 71 (4) % of the C15H32. The exchange

process showed that the entrance of the C8H 16Br2(l) from the capillary was

a m inor process. The C15H32(1) dominates the access into the channels as

can be seen by the contents of the liquid in the w atch glass. There is also a

possibility that the speed of entry of the C15H 32(1) into the channels was

m uch faster than that of the C8H 16Br2(l) because of the bulky bromine

atoms which m ay im pede the transport.

The experiment in section 6.2.4 illustrates that the exchange process

can occur from either end of the crystal held in a vertical position. It was

156

shown in section 6.2.1 that the C15H 32(1) can enter from the bottom end of

the crystal, but this experiment showed that it could also enter from the

top end of the crystal, and pass through the crystal into the w atch glass.

The same experiment was also repeated for the C8H 16Br2(l) and also

showed to be successful. Thus exchange is a property of UICs. It is likely

that the guest species enter and leave the channels in an ordered m anner

and the motion of the guest species in the channel is in one direction only.

If the entrance of the guest species is from the bottom end of the crystal

then their exit is from the other end. This is evident from the experim ent

in section 6.2.1, that after the exchange the C8H 16Br2(l) w as only present in

the capillary tube.

The control experiment in section 6.2.7 confirms reports149 150 that

w ithout a guest species the urea species does not form hexagonal

structure, therefore does not allow the passagew ay for any liquid alkane

or halogenoalkane to pass through.

In summary:

♦ Capillarity effects are dom inant in cases w here the incoming guest is

the same to that present in the inclusion compound.

♦ Chemical stability is the driving force of the exchange reactions w hen

the incoming guest species is different and forms a m ore stable UIC to

that already present in the UIC. This has also been show n as a result in

chapter 4 (polycrystalline samples). There is however a possibility that

capillarity is also involved in the process bu t if anything it helps the

exchange. Further investigation of its mechanism requires further

studies (see chapter 9).

♦ From the experiments w here the liquid enters the crystal from the

capillary tube (section 6.2.4) and is then transported to the w atch glass,

the process is shown to take a longer period of time (5-7 days). This

157

result leads to the idea that the role of the wax m ay not be significant

as, if the wax was playing a large part in facilitating the exchange then

the time for the transport of the liquid through from the capillary into

the watch glass w ould be the same as that of the experiment in section

6.2.1. W ith regards to the 'se lf exchange experiments (section 6.2.2 and

6.2.5 ), the transport of the liquid through the crystal also took several

days and therefore its seems unlikely that the wax w as a dom inating

factor. Recent results from Mr J.Houseley151 show that the wax can play

a role in the exchange. This suggests that m inute details of how the

experiment was perform ed are im portant, for example the quantity of

wax used.

Single crystal X-ray diffraction was a technique that provided

indisputable evidence for the occurrence of the exchange process. The

single crystal X-ray diffraction patterns that w ere recorded at

Birmingham University using the R-AXIS IIC diffractometer showed

beyond doubt that the exchange had occurred, by the presence of

reflections from both guests in the recorded data. The X-ray results

obtained from the rotation camera at UCL provided some information

about the exchange process for example changes in intensity before and

after exchange, but the appearance of new layer lines characteristic of the

entrance of the new guest upon exchange is not clearly visible due to the

limitations of the instrument.

The X-ray diffraction experiments carried out at Birmingham

University showed only slight disruption to the host structure. In

contrast, the I — IC10H221C10H221 (section 6.3.4) exchange process showed

severe dam age to the inclusion compound. This result m ore im portantly

confirmed the fact that even w ith a 'se lf exchange process the potential

incoming guest species does enter the channels, of the UIC rather than

158

travelling up the sides of the crystal. From the X-ray pattern there is

strong evidence of a complete structural change to the host framework

which can only arise from the entrance of the guest species into the UIC

causing the disruption. There are however other plausible m eans of liquid

guest collecting in the capillary tube, for example travelling up the sides

of the crystal as explained, bu t our studies suggest that in any exchange

reaction the m ain pathw ay is through the crystal. Further studies are

currently being carried out to investigate the extent to which the liquid

travels up the sides of the capillary.

159

Figure 6.1: Experimental apparatus designed to study the exchange reactions. The photograph shows a single crystal of dibromooctane UIC with one end of the crystal placed in a capillary tube sealed with wax and the other end immersed in a pool of pentadecane (1). The photograph was taken after 24 hrs.

160

Figu

re

6.2:

A gr

aph

to sh

ow

the

rate

of

ex

chan

ge

betw

een

1,8-

dib

rom

ooct

ane

UIC

and

pen

tad

eca

ne(

l)

o

ooCM

OO

CM lOCM •<- O

(ujiu) eoueisip

I6l

<b

i H k l l K j

<h fa 4fa

Figure 6.3: S in g le crystal X-ray d iffraction pattern recorded on a R-AXIS IIC diffractometer for 1,8 dibromooctane UIC at room temperature before exchange. The single crystal was rotated about its c-axis.

:V/,

Figure 6.4: S in g le crystal X-ray d iffraction pattern recorded on a R-AXIS IIC d i f f r a c to m e te r for the e x c h a n g e o f 1,8 d ib r o m o o c t a n e from the U IC w ith pentadecane (1) after 24 hrs at room temperature. The s ingle crystal w as rotated about its c-axis.

162

Figure 6.5: M agnified image of the low angle region of figure 6.4 show ing the presence of guest reflections characteristic of both guest species after the exchange process.

Figure 6.6: M agnified image of the (3 0 0) and (2 1 0) guest reflections from figure 6.4 show ing their relative intensities.

163

Figure 6.8: Single crystal X-ray diffraction pattern recorded for the exchange of 1,8 dibromooctane in the UIC with pentadecane (1) at room temperature after a w eek using a AXIS IIC diffractometer. The single crystal was rotated about its c-axis.

Figure 6.9: M agnified diffraction pattern of the low angle region of figure 6.8 show ing the presence of guest reflections mainly characteristic of the pentadecane guest species.

165

Figure 6.10: Single crystal X-ray diffraction photograph recorded for pure decane UIC at room temperature. The single crystal was rotated about its c-axis.

Figure 6.11: Single crystal x-ray diffraction photograph recorded at room temperature for the exchange of decane in the UIC with decane (1). The single crystal was rotated about its c-axis.

CHAPTER 7

EXCHANGE REACTIONS WITH CHIRAL GUEST SPECIES

7.1 Introduction

The exchange reactions studied so far have been w ith achiral guest

molecules and have shown to be a prom ising technique for separation

purposes on a macroscopic level. This chapter exploits the chiral nature of the

host fram ework where the exchange reactions are carried out w ith chiral

guest species which, in the future could become a practical m ethod for

separation of racemic mixtures. The systems that were studied were racemic

m ixtures of 2-bromodecane, 2-bromotridecane, 2-decanol, and 2-dodecanol, in

each case exchanging w ith decane UICs. The experiments were carried out in

the same w ay as described in chapter 6 w ith the UICs partly im m ersed into

the liquid phase of a potential guest contained in a w atch glass. However in

this case all the liquids were racemic mixtures. For each racemic mixture two

successive exchange experiments were carried out, firstly to remove the

alkane from the UIC and replace it w ith the chiral guest, and secondly to

collect some chiral guest in the capillary tube in order to determ ine its optical

purity. The UIC crystal, the liquid collected in the capillary tube and the

liquid in the watch glass after the exchange, were all characterised by optical

polarimetry. Chiral shift reagents in *H NMR w ere attem pted for

characterisation of the UIC but unfortunately the shift reagents failed to work.

The exchange reactions for all the different systems and the optical

rotation m easurem ents were perform ed in the same way, as described in the

following section.

167

7.2 Expt 1 (R/S) 2-dodecanol guest

I. I — I C,0H221 R /S I => IC10H22 R/S I R /S / C10H221 R /S I .

II. I — I R /S / CjoH jj | R /S I => I R /S /C 10H221 R /S I R/S I .

O H

The decane UIC w as prepared using the same m ethod to that described

in chapter 3 and the experimental procedure for the exchange process was as

described in section 6.2.1. The exchange w as carried out twice on the same

crystal. The crystal was first im m ersed into the racemic m ixture and the

exchange was allowed to occur to displace the decane from the UIC and

collect into the capillary tube. The liquid in the capillary tube w as syringed

out and the exchange was repeated. The aim of this successive exchange was

to collect the chiral guest species in the capillary tube in order to determine

w hether a pure enantiom er can be obtained via exchange through the UIC

crystal. This was only feasible if the exchange was repeated. The decane was

assum ed to be largely displaced from the UIC in the first exchange, and

rem oved from the capillary tube. The repetition of the exchange allowed for

more of the racemic m ixture to enter into the crystal hence displacing the

chiral guest already present in the UIC which w as again collected into the

capillary tube. The crystal, liquid in the capillary tube and the watch glass

were characterised by optical polarim etry using a polarim eter 2000 as

described below. The m ethod for calculating the concentrations and specific

rotations is described in the appendix.

To perform polarim etry a single crystal of 2-dodecanol UIC (0.237 mg)

(after exchanging w ith the decane from its UIC) was dissolved in m ethanol (2

ml) in a 2 ml volumetric flask. The polarim eter cell was rinsed w ith methanol

168

in order to remove any impurities that it contained. The polarim eter was

referenced to zero using the methanol. To do this m ethanol w as added to the

cell, ensuring that it contained no air bubbles. It w as placed in the polarimeter

and w as referenced to zero. The cell was then em ptied of the m ethanol and

the procedure w as repeated to check the accuracy of the referencing. Having

referenced the polarim eter the cell was dried w ith a heat gun in order to

rem ove any traces of m ethanol that were present. The sample was then

transferred from the volumetric flask into the cell and placed into the

polarimeter. Once the reading had stopped fluctuating the value of the

rotation was recorded. This was repeated three times by taking the cell out

from the polarim eter and placing it back in again, in order to obtain an

average of the three readings and was carried out for all the chiral guest

molecules that were used.

The results in table 7.1 suggest that the crystal had separated the

racemic m ixture into one pure enantiomer. It shows that two of the crystals

rotate the polarised light in an anticlockwise direction and one in the

clockwise direction The values for the specific rotations correlated well with

those reported in the literature. The liquid in the capillary tube provided a

very crude result in that even after two sucessive exchange reactions there

w ere still im purities present in the m ixture causing errors in the data. The

NMR suggested that there were long chain hydrocarbons present in the

sample, therefore suspecting the presence of wax and possibly decane.

169

Repeat. 1 Repeat.2 Repeat.3

mass of crystal 0.121 (3) 0.0319 (3) 0.129 (3)

(mg)

concentration^ / 6.65 x 10'3 1.59 x 10'3 6.43 x 10‘3

ml)

a (-) 0.014 (2) (+) 0.004 (2) (-) 0.017 (2)

[a]d (-) 230 (30) (+) 250 (130) (-) 260 (30)

Table 7.1: Mass of crystal, concentration and specific rotation values of the exchange process described in experiment. Literature value for [a]d = 244.5° from ref 152


mass of liquid 0.193 (3) 0.251(3)

(mg)

concentration(g/ 9.65 x 10'3 0.01255

ml)

a (+) 0.006 (2) (+) 0.006 (2)

[a]d (+) 60 (20) (+) 50 (20)

Table 7.2: Mass of the liquid in the capillary tube, concentration and specific rotation values of the exchange process described in experiment 1.

Repeat. 1 Repeat.2 Repeat3

a 0.00 0.00 0.00

[a]d 0-00 0.00 0.00

Table 7.3: Specific rotation values of the racemic mixture for the exchange process described in experiment 1.

7.3 Expt 2: (R/S) 2-decanol

The experiment was carried out using the same m ethod as that

described in experiment 1 in section 6.2.1 except using a racemic m ixture of 2-

decanol. The reaction scheme shown in 7.2 is also applied to this experiment

and the experiments to follow. The decane UIC w as partly im m ersed into a

170

solution of 2-decanol and two successive exchange reactions w ere carried out

on the UIC inorder to collect one of the forms of the chiral guest species in the

capillary tube.

The optical rotation m easurem ents in table 7.4 for the crystal are fairly

consistent w ith those reported in the literature and suggest that resolution of

the chiral mixture has occurred. One w ould expect the enantiomeric form (R

or S) that is included into the UIC to be dependent on w hether the crystal is

P6522 or P6122. In the table two readings are recorded as negative which

suggest that the guest in the UIC rotates the plane of polarised light in the

anti-clockwise direction and the third reading is positive which suggests that

the light is rotated in a clockwise sense. The results from table 7.5 are not

conclusive due to the fact that there is wax and decane in the guest m ixture as

indicated from the NMR spectra. The specific rotation values for the liquid

in the watch glass w ere zero as expected because both the enantiom ers were

present in a 50:50 m ixture which implies that rotation of light occurs in

opposite directions bu t by the same amount.


mass of crystal 0.049 (3) 0.0568 (3) 0.0573(3)

(mg)

concentration^ / 2.45 x 10'3 2.84 x 10'3 2.85 x 10'3

ml)

a (-) 0.016 (2) (-) 0.005 (2) (+) 0.004 (2)

K (-) 650 (80) (-) 180 (70) (+) 140 (70)

Table 7.4: Mass of crystal, concentration and specific rotation values of the exchange process described in experiment 2. [a]d reported in literature = 138.8° from ref 153.

171

Repeat. 1 Repeat.2 Repeat.3mass of liquid 0.212 (3) 0.263 (3) 0.241 (3)

(mg)

concentration 0.0106 0.01315 0.01205

(g /m l)

a (+) 0.008 (2) (+) 0.008 (2) (-) 0.007 (2)

[ala (+) 40 (10) (+) 60.(20) (-) 60 (20)

Table 7.5: Mass of liquid in the capillary tube, concentration and specific rotation values of the exchange process described in experiment 2.


a 0.000 0.000 0.000

[a]d 0.000 0.000 0.000

Table 7.6: Specific rotation values of the racemic mixture for the exchange processdescribed in experiment 2.

7.4 Expt 3: (R/S) 2-brom otridecane

The experiment was carried out in the same m anner to that described

in section 6.2.1 w ith two successive exchange reactions, hoping to collect

either the R or the S enantiomer in the capillary tube. The exchange involved

the practical immersion of decane UIC crystal into a racemic m ixture of 2-

brom otridecane w ith the collection of decane in the capillary tube which was

then em ptied out. A second exchange was then carried out to allow chiral

liquid guest to collect in the capillary tube. Optical rotation m easurem ents

were carried out on the liquid in the capillary tube, liquid in the watch glass

and the crystal and the results are illustrated in tables 7.7, 7.8 and 7.9.

172


mass of crystal 0.1485 (3) 0.0938 (3) 0.0862 (3)

(mg)

concentration(g/ 7.43 x 10'3 4.69 x 10'3 4.311 x 10'3

ml)

a (-) 0.006 (2) (-) 0.006 (2) (-) 0.006 (2)

[aid (-) BO (30) (-) 130 (40) (-) 140 (50)

Table 7.7: Mass of the crystal, concentration and specific rotation values of the exchange process described in experiment 3.


mass of liquid 0.224 0.216

(mg)

concentration(g/ 0.0112 0.0108

ml)

a (+) 0.004 (2) (+) 0.003 (2)

M d (+) 40 (20) (+) 30 (20)

Table 7.8: Mass of the liquid in the capillary tube concentration and specific rotation values of the exchange process described in experiment 3.


a 0.00 0.00 0.00

[a]d 0.00 0.00 0.00

Table 7.9: Specific rotation values of the racemic mixture for the exchange process described in experiment 3.

For this experiment there were no literature reports for the specific rotation

values of this guest, hence no comparisons were m ade. All three results for the

UIC crystal were consistent w ith one another. The specific rotation values for

all the selected crystals were negative. The specific rotation values for the

liquid in the capillary tube did not provide conclusive results for reasons

173

discussed previously.

7.5 Expt 4: (R/S) 2-brom odecane

In this experiment a racemic m ixture of 2-bromodecane w as used and

the experiment was carried out as that explained in section 6.2.1. The decane

UIC was immersed from the bottom end into a solution of 2-bromodecane and

two successive exchange reactions were carried out. The optical polarim etry

measurements were recorded for the crystal and the two liquids in the usual

way.

The results are shown in tables 7.10, 7.11 and 7.12. The results obtained

for all three crystals were comparable w ithin experim ental error. There is

however no literature reports for their specific rotation. The results from the

liquid in the capillary tube suggest that chirality does exist in the liquid and

the evidence from the NMR strongly suggests that there are hydrocarbon

impurities present, consequently giving inaccurate polarim etry results.


mass of crystal 0.0743 (3) 0.0591 (3) 0.0651 (3)

(mg)

concentration(g/ 3.72 x 10'3 2.96 x 10'3 3.3 x 10'3

ml)

a (-) 0.003 (2) (-) 0.003 (2) (-) 0.004 (2)

[a]d (-) 80 (50) (-) 100 (70) (-) 120 (60)

Table 7.10: Mass of the crystal, concentration and specific rotation values of the exchange process described in experiment 4.

174


mass of liquid 0.211 (3) 0.211 (3) 0.235 (3)

(mg)

concentration(g/ 0.0105 0.0105 0.0118

ml)

a (-) 0.014 (2) (+) 0.004 (2) (-) 0.004 (2)

(-) 130 (20) (+) 40 (20) (-) 30 (20)

Table 7.11: Mass of the liquid in the capillary tube, concentration and specific rotation values of the exchange process described in experiment 4.


a 0.00 0.00 0.00

[a]. 0.00 0.00 0.00

Table 7.12: Specific rotation values of the racemic mixture in the exchange process described in experiment 4.

7.6 Use of chiral sh ift reagents

The results obtained for the liquid expelled from the crystal into the

capillary tube for all four experiments described in this chapter were

unreliable. In view of these results chiral shift reagents were attem pted to

resolve the enantiomers in order to determine the ratio of R and S present. The

two chiral shift reagents used in these experiments w ere Eu(fod)3 and Pr(fod)3

(the structure of fod is show n at the end of this section). The binding of the

chiral ligand to the m etal centre of the shift reagent results in a reagent which

in principal can resolve the resonances of the enantiomers. The Eu(fod)3

induces dow n field shifts and the Pr(fod)3 induces up field shifts. The

experiment was carried out in the following way: Firstly a racemic m ixture of

pure 2-decanol was attem pted as a reference, to see w hether the separation of

the two enantiomers occur and to obtain an idea of the quantity of shift

175

reagent required to observe a splitting in the signals, especially that of the

proton attached to the carbon containing the hydroxyl group. The alcohol was

dissolved in deuterated chloroform using the standard technique. The *H

NMR spectrum of the sample was run first w ith only the chiral alcohol and

then the NMR sample tube was rem oved from the sam ple cham ber and a

speck of the chiral shift reagent was added to it. The spectrum was recorded

again in the presence of the chiral shift reagent. The addition of the chiral shift

reagent continued in similar quantities, w ith the hope of observing a splitting

in the signal at 5 = 3.761. However, the *H NMR spectrum show ed no splitting

of the signal at 6 = 3.761. Instead the spectrum show ed that there was

preferential binding of the m etal centre to the w ater that w as contained in the

deuterated solvent at 5 = 1.574, which caused a splitting of this particular

signal. Further addition of the shift reagent caused severe broadening of the

signals in the spectrum. Several attem pts were m ade to resolve the 2-decanol

using smaller quantities of shift reagent, bu t no success was achieved using

this m ethod, hence was not further studied.

.0 = C/ C(CH3)3M \ *C

° ~ C\ f 2 c f 2c f 3

M(fod),

7.7 Sum m ary and D iscussion

A given UIC crystal either contains a right handed or a left handed

helices. The potential for the separation of racemic m ixtures using the chiral

urea tunnel structure is determ ined by the extent to which the interactions

between a host tunnel of given chirality differs for two enantiomers. The

176

polarim etry results obtained from this chapter suggest that the UIC is able to

selectively include one form either the R or the S after the exchange process.

The early w ork of Schlenk58,59,60'61,62 also shows that there is a significant host-

guest chiral recognition between the urea tunnel structure and the chiral guest

molecule. In experiment 1 in section 7.2 when 2-dodecanol was exchanged

w ith decane in the UIC, [a]d = 230° which correlated well w ith the literature

value of [a]d = 244.5°152. Experiment 2 in section 7.3 also show ed results for the

UIC crystal in good agreem ent w ith the literature, the experimental [a]d for

one experiment gave 138.12° and the literature reported 138.8°153. The [a]d

values obtained for the liquid in the capillary tube in all four experiments

however were completely inconsistent w ith the literature values. The evidence

from the *H NMR suggests that there were hydrocarbon im purities present

which effected the mass of the sample and consequently the specific rotation.

This therefore implies that there is a possibility that the liquid collected in the

capillary tube contains one pure enantiomer bu t the results were affected by

these impurities. Yeo and Harris63 carried out com putational investigations on

2-bromotridecane and 2-bromotetradecane molecules w ithin the urea tunnel

structure. They showed that the same enantiomer of the guest molecule is

preferred for all positions along the tunnel. From this recent article it can be

confidently said that there is preferred inclusion of only one of the

enantiomeric forms of the chiral guest molecule. In another report Yeo and

Harris64 carried out computational investigations which predicted that there is

a significant chiral preference for the R enantiom er of the 2-bromoalkanes

w ithin P6j22 urea tunnel structure and S enantiom er for the 2-bromoalkanes

of the P6522 tunnel structure. This effect however is not observed in the 2-

brom oundecane, they found that there is a restricted range of positions at

which the S or the R enantiom er is preferred w ithin the UIC. From the results

obtained by Yeo and Harris the spiral arrangem ents of the urea molecules i.e

177

w hether it is only right handed spirals or only left handed spirals can be

applied to each 2-bromoalkane UIC crystal used in the chiral exchange

processes in this study.

The polarim etry results and the results obtained from the chiral shift

reagents in NMR for the liquid collected in the capillary tube were

inconclusive. Hence this requires further studies and possibly alternative

m eans to m easure the resolution of the enantiomers. Another m ethod is also

required for the crystal in addition to polarim etry m easurem ents in order to

confirm these results.

178

CHAPTER 8

SOLID SOLUTION FORMATION IN UREA INCLUSION

COMPOUNDS

8.1 In troduction

Solid solution formation in UICs was the first area of study in this

research project prior to the exchange reactions described in chapters 4-7.

The interest was geared towards the study of their phase transitions and

the effects that two guest species in the UIC as a solid solution would

have on these transitions. However due to the solid solution formation

being largely unsuccessful it was abandoned as an avenue of research.

Nevertheless some interesting results were obtained. This chapter

describes solid solution formation by cocrystallisation of two starting

m ixtures of the UICs (liquid guest dissolved in urea in m ethanol in the

liquid phase) in incom m ensurate and com m ensurate systems. A solid

solution is a hom ogeneous mixture (see figure 8.1) of two different species

at the molecular scale, contrary to this is a heterogeneous m ixture which

is a mechanical m ixture of crystallites at the macroscopic level. This is

further illustrated in figure 8.2 which shows separate dom ains of crystals

A and B in the same sample. The reason for this w ork was to investigate

w hether two guest species were able to be contained in the same unit cell

of the UIC implying a solid solution and then to further study their phase

transitions. The difference betw een the two forms of the UIC is the nature

of the ordering of the guest species w ith respect to the host structure (see

section 1.2.5).

179

Figure 8.1: Homogeneous mixture Figure 8.2: Heterogeneous mixture

The incom m ensurate systems were w ith 1,8-dibromooctane

UIC:decane UIC, 1,8 dichlorooctane U IG alkane UIC (Cn, C14, C15) and

valeric anhydride UIC: undecane UIC. The com m ensurate system used

was 1,6-dibromohexane UIC:l,6-dichlorohexane UIC. Section 8.2

discusses the comm ensurate system and the proceeding sections discuss

the incom m ensurate systems.

8.2 Expt 1 :1,6-Dibromohexane :l,6-dichlorohexane UIC.

In this experiment starting mixtures of 1,6-dibromohexane and 1,6-

dichlorohexane dissolved in a solution of urea in m ethanol in the liquid

phase were cocrystallised. The individual solutions of 1,6-dibromohexane

UIC and 1,6-dichlorohexane UIC were prepared in the standard way

described in chapter 3 and the ratios of each guest species used for each

experim ent are listed in table 8.1 below. The example of the 25 % 1,6-

dibromohexane UIC is used to dem onstrate how the experiment was

carried out. Prepared solutions of 1,6-dibromohexane UIC (25 %, 0.375 g)

and 1,6-dichlorohexane UIC (75 %, 0.554 g) w ere mixed together into one

beaker at 65 °C until a homogenous m ixture had formed. The beaker that

contained the solution of the UIC was then allowed to crystallise slowly in

a preheated dewar. The calculation of the percentage ratios is shown in

the appendix. Figure 8.3 on page 188 is a single crystal X-ray diffraction

rotation photograph of pure 1,6-dibromohexane UIC. The photograph

180

illustrates that there is one layer line which is attributed to both host and

guest reflections and is a characteristic feature of com m ensurate systems.

1,6-dibromohexane UIC ( % ) 1,6-dichlorohexane UIC ( % )

0 100

25 75

50 50

75 25

100 0

Table 8.1: Ratio of guest molecules used for solid solution formation in 1,6- dibromohexane: 1,6-dichlorohexane UIC.

Characterisation of the urea adducts was carried out by ‘H NMR,

therm al analysis, XRD and solid state 13C NMR for the identification of

possible solid solution formation in the UIC.

The ]H NMR results in table 8.2 shows that the ratios of guest

species in the starting solution was present in alm ost exact ratios in the

UIC w hen the two solutions were cocrystallised. This result was

reproducible on selection of different pow der samples from the same

prepared UIC and also from different batches.

181

Starting ratios of 1,6-

dibromohexane:

1,6-dichlorohexane

Percentage of 1,6-

dibromohexane present in

the UIC

Percentage of 1,6-

dichlorohexane

present in the UIC

0:100 0 100

25:75 28 (3) 72(3)

50:50 58 (4) 42 (4)

75:25 73(2) 27 (2)

100:0 100 0

Table 8.2: Ratio of guest species in the starting and final solutions for 1,6- dibromohexane:l,6-dichlorohexane UIC.

The DSC results are shown in figure 8.4. on page 189. The mW /

m g vs tem perature decomposition graph of the 25 % 1,6-dibromohexane:

75 % 1,6-dichlorohexane UIC showed that in two batches of the UIC the

decomposition of the UIC were at the same tem perature. This technique

gave evidence for solid solution formation as is show n in figure 8.5 on

page 189 where a systematic shift in the decom position tem perature was

observed w hen proceeding from 100 % 1,6-dibromohexane UIC to 100 %

dichlorohexane UIC. The DSC plots for 100 % 1,6-dibromohexane UIC

and 100 % 1,6-dichlorohexane UIC and 25:75 of 1,6-dibromohexane: 1,6-

dichlorohexane UIC are superimposed. This clearly shows that the

decomposition tem perature for the 25 % 1,6-dibromohexane UIC is

between the two extreme pure phases at 0 = 74 °C, how ever it is closer to

the decomposition tem perature of pure 1,6-dichlorohexane guest species

due to it being richer in this UIC. This contrasts w ith a heterogeneous

mixture, where one expects to see two peaks in the mW / m g vs

tem perature DSC curve.

182

Figure 8.6 on page 190 shows an X-ray diffractogram of the

different ratios of 1,6-dibromohexane and 1,6-dichlorohexane UIC. The

evidence for solid solution formation is the systematic shift in the

reflections in the diffraction pattern when going from a pure phase UIC to

one that contains two guest species. In this case the lattice constants are

altered which results in the shifts. For example for w ith the (4 1 1) Bragg

reflection, the shift proceeds from 100 % 1,6-dibromohexane UIC w here

the reflection occurs at 20 = 27.33° (± 0.02), to the pure 1,6-dichlorohexane

UIC, where the same reflection occurs at 20 ~ 29.44° (± 0.02).

The 13C NMR spectrum of a 25:75 m ixture of 1,6-dibromohexane

and 1,6-dichlorohexane UIC show two characteristic peaks of the

halogenoalkanes (-CH2-Br and -C H 2C1) in the spectra at 5 = 34.5 and 5 =

30.07. The relative ratios of 27 % :73 % of 1,6-dibromohexane: 1,6-

dichlorohexane respectively in the UIC show that after cocrystallisation of

the UIC there is almost exact quantities to that present in their individual

starting mixture.

To summarise the above results, one can confidently conclude that

a full range of solid solutions can be form ed betw een 1,6-

dibromohexane : 1,6-dichlor ohexane UIC.

8.3 Expt 2 :1,8-Dibromooctane: Decane UIC.

The individual UICs were prepared as described in chapter 3 and

the same m ethod for the preparation of the solid solution was used as that

described in section 8.2. The solid solutions w ere prepared three times in

the ratios listed in table 8.3.

183

1,8-dibromooctane UIC ( % ) decane UIC (% )

0 100

25 75

50 50

75 25

100 0

Table 8.3 : Relative ratios of 1, 8-dibromooctane and decane guest species present in the UIC.

The UICs again were characterised by solid state 13C NMR,

NMR and therm al analysis.

The characterisation by ’H NMR of the UIC show ed in some cases

the presence of 1,8-dibromooctane UIC and in other cases almost pure

decane UIC. For example in the attem pt to prepare a solid solution of

25:75 1,8-dibromooctane: decane almost pure 1,8-dibromooctane was

present in the UIC, (see figure 8.7 on page 191 ). Furtherm ore, the UIC

that crystallised was not found to be reproducible and hence these results

are not considered in detail.

The DSC plots (mW / m g vs tem perature) gave results that were

impossible to reproduce. For example for a m ixture of 25 % 1,8-

dibromooctane UIC and 75 % decane UIC three unsuccessful attem pts

were m ade to reproduce the m easurements.

The results obtained from the Solid state 13C NMR data showed the

decane and the 1,8-dibromooctane guest species which w ere prepared in

a ratio of 75:25 did not form a solid solution. The spectrum showed the

presence of almost pure decane UIC.

W hen the X-ray diffraction patterns of the individual ratios of the

1,8-dibromooctane and decane guest species in the UIC were

184

superim posed onto one X-ray diffractogram there show ed no apparent

shift in peak position as a function of exchange. It was also attem pted to

form solid solutions w ith 1,8-dibromooctane and longer chain alkane

nam ely undecane, tetradecane and pentadecane. The results showed

there to be no solid solution formation.

8.4 Expt 3: Valeric A nhydride U IG U ndecane UIC

The m ethod for the preparation of the anhydride UIC49 is described

in the experimental section and McAdie m ethod was used for the

undecane UIC. The NMR spectrum show ed the presence of a

carboxylic acid group and an ester functional group in the UIC which was

due to the hydrolysis of the anhydride.

8.5 Sum m ary and D iscussion

In this study solid solution formation in the commensurate UIC has

been shown to occur. The properties of 1,6-dibromohexane have been

studied previously by Elizabe et alni, Smart57 and Hollingsworth et a/113'114

w ho suggested that the external m orphology of the UIC w as truncated

instead of the conventional hexagonal needles. The reason for this

uncharacteristic m orphology is unclear, although Smart57 suggested that

the relatively short length of the guest molecule is insufficient to stabilise

the formation of the conventional hexagonal urea host structure. Otto38

used photographic X-ray m ethods to solve the host structure of 1,6-

dibromohexane UIC and 1,6-dichlorohexane UIC and they were

identified as comm ensurate channel type UIC w ith 6:1 urea: guest

stoichiometries. The fact that the structure is com m ensurate suggests that

some energetically favourable docking in' of the guest structure into the

host occurs. Both structures have space group P 2 j/n and contain guest

185

molecules in unstaggered conformation w ith a = 8.22 A, b = 14.24 A, c =

11.01 A. The similarities in crystal structure for the 1,6-dichlorohexane

UIC and 1,6-dibromohexane UIC appear from this w ork to allow solid

solution formation. In particular the shifts in the relative decomposition

tem peratures of the different ratio of guest in the UIC is an indication of

solid solution formation. As the UIC becomes progressively richer in one

particular guest species the transition tem perature progressively shifts to

that of the pure guest species. Furtherm ore the pow der X-ray diffraction

pattern of the different ratio of guest species provide strong evidence for

solid solution formation in that a systematic shift in the reflection

positions as a function of the ratio of guest species in each UIC was

observed. Thus, the com m ensurate 1,6-dibromohexane: 1,6-

dichlorohexane UIC system forms a complete series of well defined solid

solutions which could be prepared w ith perfect reproducibility.

The results obtained from the experim ents carried out on

incommensurate UICs showed that it was impossible to form a solid

solution. This was confirmed by lH NMR, therm al analysis, solid state 13C

NMR and pow der X-ray diffraction. A plausible explanation for why

there was no solid solution formation w ith the incom m ensurate UIC

systems of the alkane guest species and the 1,8-dibromooctane was that

the repeat distances of the guest structure w ere too different. As

explained in section 1.2.5 the offset for alkanes are A g = 048 and for the

halogenoalkane, A g = Cg / 349; it therefore seems unlikely that the guest

species can be accommodated in the same UIC. The diagram in figure 8.8

and 8.9 shows the arrangem ent of the alkane and the halogenoalkane

guest species in a UIC respectively.

186

g = 0

Figure. 8.8

9=Cg/3

Figure. 8.9

Thus the packing of the guest species in the UIC has been show n to be an

im portant factor that controls solid solution formation. Alternative guest

molecules were chosen, namely undecane Cg = 16.33 A ±0.1436, Ag = 0,

and valeric anhydride Cg =16.14 A ±0.14,49 Ag = 0 both of which had the

same packing arrangem ents in the UIC. However the attem pt to form a

solid solution w ith the alkane and the anhydride w as once again

unsuccessful. The *H NMR data showed the presence of an ester and a

carboxylic acid group which was a consequence of the hydrolysis of the

anhydride. This m ay have interfered w ith the experiment.

187

Figure 8.3: Single crystal X-ray diffraction rotation photograph of pure 1,6 dibromohexane UIC. The crystal was rotated about its c-axis

188

DSCmW

0 . 00 -

■20 . 00 -

- 30 . 00 -

- 40 . 00 - 1 1- 100.00 0.00 100.00 200.00

Temp[C]

Figure 8.4: mW / mg versus temperature DSC curve for 25:75 1,6-dibromohexane UIC, (reproduced twice).

DSC mW/mg

0.00

- 1.00

- 2.00

- 3.00

L [

-4-00- ...................... i i , i i i i i i i i , i i i- 200.00 - 100.00 0.00 100.00 200.00

Temp[C]

Figure 8.5: mW / mg versus temperature DSC curve for 100:0 1,6-dibromohexane (red): 1,6-dichlorohexane (UIC), 25: 75 1,6-dibromohexane: 1,6-dichlorohexane (UIC) (blue), and 0:100 1,6 dibromohexane: 1,6-dichlorohexane (green) (UIC)

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CHAPTER 9

SUMMARY AND CONCLUSIONS

The initial aim of the project was to prepare solid solutions of a

series of incommensurate alkane UIC w ith 1,8-dibromooctane UIC and 1,8-

dichlorooctane UIC by cocrystallisation and then to further investigate

their low tem perature phase transitions (which are associated with

rotation of the guest molecules). This study how ever d id not progress

beyond attem pts to prepare a solid solution due to the fact that it proved

to be impossible to form compounds of this nature (see chapter 8). The

commensurate 1,6 dibromohexane : 1,6 dichlorohexane UIC solid solution

was however successfully prepared, as this was evident from the pow der

X-ray diffraction, therm al studies and 13C NMR, bu t such commensurate

compounds do not show low tem perature phase transitions. In light of

these results an alternative area in the field of inclusion chemistry was

chosen.

The first evidence for the migration of a second guest species into

polycrystalline UIC was reported by M ahydafar and H arris115, who

investigated the migration of decane into 1,8-dichlorooctane UIC by 13C

NMR. This report inspired the present w ork in which the properties of the

exchange reactions of the alkane and the halogenoalkane UICs have been

determ ined in detail. The relative stabilities of alkane UIC and factors that

determine whether two guest species in one UIC are compatible w ith

regards to their periodicities, A g for an alkane = 0, Ag for a

halogenoalkane = Cg / 3 has been understood. ]H NMR analysis w ith a

series of poly crystalline alkane UIC exchanging w ith 1,8-dibromooctane

192

and 1,10-dichIorodecane (see chapter 4) show ed that the exchange

proceeds w ith preferences for systems where the incoming guest species

is of a longer chain length to that already present in the UIC. The

exchange reactions have thus shown to be selective to particular guest

species. This result is supported by Pem berton et al54 w ho show ed by

specific heat m easurem ents that longer chain UICs are

therm odynamically m ore stable than the shorter chain ones and for every

CH2 group there is a 1.6 kcal mol’1 increment in the stabilisation energy of

the UIC21. Further experiments that confirmed the exchange process was

pow der X-ray diffraction where pentadecane w as observed to be

incorporated into the 1,8-dibromooctane UIC. Mass change experiments

were carried out w ith a series of alkanes and 1,8-dibromooctane UIC and

the change in the masses after the exchange w ere consistent w ith the loss

of the 1,8-dibromooctane from the UIC.

The results obtained from this study of the exchange reactions with

the polycrystalline UIC and the earlier reports in the literature provides

an understanding of fundam ental requirem ents in selecting guest species

for an exchange reaction. To investigate the mechanism of the reaction,

single crystal X-ray m easurements were perform ed (see chapters 5 and 6).

The exchange reactions were carried out on a num ber of systems and

showed to occur w ith only a small loss in integrity of the UIC crystal

except for one system, the 'self exchange' reaction of the decane UIC,

where there was severe damage to the structure upon exchange w ith the

development of a polycrystalline structure. This experim ent confirms that

even when the guest species in the liquid phase and in the UIC are the

same, the guest enters the UIC as opposed to travelling up the sides of the

crystal into the capillary tube. The single crystal X-ray diffraction pattern

of the pentadecane exchanging w ith the 1,8-dibromooctane, on the other

193

hand clearly showed that the exchange occurs w ithout significant

disruption to the host urea framework. The discrete Bragg reflections and

diffuse bands due to both the guest species w ere present in the UIC as

large macroscopic domains rather than as a solid solution of the two guest

species (which w ould result in layer lines in an average position). This is

again consistent w ith the fact that incom m ensurate UICs w ould not form

a solid solution. With small dom ains one w ould expect a large num ber of

defects, m ainly as a consequence of the different periodicities of the guest

species which in effect would result in severe dam age to the host

framework. This is not observed in the diffraction pattern. To our

knowledge this is the first preparation of a UIC containing two different

guest species segregated in ordered domains.

The potential for selective exchange of chiral species w as also

studied. The results from the experiments suggests that it m ay be possible

to selectively include one enantiomeric form of the racemic m ixture into

the tunnels of urea depending on the chirality of the helices. This result is

consistent w ith the early work of Schlenk and w ith further studies it could

develop into a m ethod of separation of chiral com pounds on a molecular

level. From recent results obtained by Yeo et a f4 it m ay be possible to

identify the crystals as P6522 or P6222 depending on the specific rotation of

the included guest species obtained from this work.

In conclusion, the property of urea inclusion com pounds as

incom m ensurate 'intergrow th' com pounds has been well exploited in the

exchange reactions65,66 67 investigated in this work. One can argue that the

'sliding m ode' phenom enon67,68,69 in the UIC allows for the exchange of

guest species to occur inside the channels by translation of an incoming

guest along the incommensurate axis w ith the out going guest m ost likely

to leave from the other end of the crystal. A ttem pts to form a solid

194

solution UIC using the m ethod of co-crystallisation and by the m ethod of

exchange of guest molecules w ithin a UIC was show n to be impossible. It

was how ever shown that w ith the m ethod of exchange by translation

along the incom m ensurate axis, two guest molecules can be included in a

UIC as a heterogeneous mixture. The type of exchange reaction described

here has the potential to separate mixtures of molecules based on their

size and shape characteristics and on their chirality.

Future studies related to this science include the study of the

m echanism of the 'partly im m ersed' exchange reactions m ore deeply in

order to understand the significance of capillarity in the exchange

process. The selectivity should be studied further w ith m ixtures of

potential guest species and to observe w hether the crystal selectively

takes up both or only one of the guest molecules. Phase transitions of the

UIC crystal before and after exchange and possibly at interm ediate stages

can be investigated using low tem perature X-ray diffraction or specific

heat m easurements. In chiral systems the m ain area of future study is to

obtain the pure enantiom er from the UIC crystal. In this w ork chiral shift

reagents in XH NMR were used in order to m easure the percentage optical

purity of the liquid phase enantiomer. This m ethod how ever failed to

w ork and further investigations to find alternative m eans are required.

This w ork w ould provide a trem endous future as a potential for using the

uptake and transport of guest molecules through the single crystal UIC as

a practical means of separating enantiomers of chiral guest species.

195

APPENDIX: Details of Calculations and Experimental Data

CHAPTER 3

Section 3.2:

Data for the bond lengths and Van der Waals radii required for calculations of the lengths of the guest molecules

Bond lengths (nm)

C - C 0.154

C - H 0.109

C - B r 0.194

C - C l 0.177

van Der Waals radius for hydrogen 0.12

van der W aals radius for brom ine 0.195

van der Waals radius for chlorine 0.180

As an example, the calculation of the length of a pentadecane molecule

using the bond length data is shown below:

Using the bond length data and assum ing the bond angle 0 is 109.5°, x can

be calculated using geometry:

sin (0/2) = r / x

x = sin 54.75° x 0.154 x 10'9 m = 2.5 A

therefore the length of a pentadecane molecule is:

196

7 (2x) + 2(C-H) + (Van der W aals radius ) - 0.5 A = (7.0 x 2.5) + 2.18 + 2.4 - 0.5 = 21.58 A(An alternative m ethod is to use (C-H) sin (0 / 2), and neglect the

correction of 0.5 A; however this m ethod was not used in this work).

The length of one unit cell is 11 A which contains six urea molecules in it.

Therefore one urea molecule occupies 11 / 6 = 1.833 A of space in the unit

cell.

Hence in a pentadecane molecule the num ber of urea molecules required

is:

21.58 / 1.833 = 11.77 urea molecules required

Calculation of required am ounts of h o s t : guest

Mass of pentadecane used in this experiment = 1.5 g

Therefore the am ount of pentadecane = 1.5 / 212.42 = 7.062 xl0"3moles

Therefor the ratio of urea : pentadecane is 1:11.77

Hence the mass of urea required = x = 7.062 x 10'3x 11.77 x 60.06 = 4.99 g

CHAPTER 4

Section 4.2:

Method for calculating the amounts and volumes of alkane (1) guest for

experiment 1.

In all the exchange reactions w ith the different alkane guest species

0.2595 g of 1,8-dibromooctane UIC or 0.2074 g of 1,10-dichlorodecane UIC

was used. The m ethod used to calculate the am ount of CnH2n+2 required

w ith respect to the C8H 16Br2(UIC) exchange reactions is as follows:

uA A(l) + o B B(UIC) <=> i)B B(l) + uA A(UIC)

197

d a A(l) = the am ount of guest A in the liquid phase.

uB B(UIC) = the am ount of guest B in the UIC.

uB B(l) = the am ount of guest B in the liquid phase.

uA A(UIC) = the am ount of guest A in the UIC.

Mx = relative molecular mass of species X.

nx = the am ount of species X.

As calculated from chapter 3 the am ount of urea required per mole

of 1,8-dibromooctane guest (B) was calculated to be 8.75:1

Therefore uB = 1 uUIC =8.75

A = C10H22(1), B = C8H 16Br2

Example r^uic)— (uicj I ( \uici (^(uiq) )

= 3.25 x lO -4 mol

In this example C10H 22(1) (A) was the guest that exchanged w ith the

C8H 16Br2 (B) guest and therefore the am ount of urea required per mole of

C10H 22 guest w ould be different from that of a C8H 16Br2 guest.

From previous calculations uA = 1 then u(ulC) = 8.36

Therefore nA(UIC) = nB(UIC)x (uA / u B) = 3.40 x 1 O'4 mol

m A = nA x Ma = 0.0484 g

The volume of decane required: mA/ p A = 0.066 ml, 100 time excess = 6.6

ml.

The volumes required for each exchange reaction are tabulated below.

198

Relative amounts and volume of n guest species required for the exchange process with C8H16Br2(UIC) (series 1) and C10H20C12(UIC) (series 2) in experiment 1

C n H ^ l) Amount of

C„Hat2(l)

for series 1

(x 1 0 *4)

Amount of

Q H ^ O )

for series 2

(x 10")

Volume of

c „h ^ 2(1)used for

series 1

Volume of

C„H^2(1)

used for

series 2

10 3.40 3.04 6.6 (2) 5.9 (2)

11 3.14 2.81 6.6 (2) 5.9 (2)

12 2.92 2.61 6.7 (2) 5.9 (2)

13 2.73 2.44 6.7 (2) 5.9 (2)

14 2.56 2.29 6.7 (2) 5.9 (2)

15 2.42 2.16 6.7(2) 5.9 (2)

The calculation for the percentage exchange for each alkane guest species

is show n below through the example of undecane exchanging w ith 1,8-

dibromooctane UIC.

Figure 1 on page 208 is a NMR spectrum of 1,8-dibromooctane

and undecane present in the UIC in the ratio of (79:21) after an exchange

reaction. The m ethod for the calculation of these ratios is described below.

The percentage exchange is the am ount of guest species (expressed

as a percentage incorporation) that exchanges w ith the guest species that

was already present in the UIC before the exchange process. The

percentage exchange of the guest molecules in the UIC is expressed in

terms of a mole fraction w here the mole fraction of A = xA. If the mole

fraction of xA = nA / (nA + nB), where A is undecane and B = 1,8-

dibromooctane, then the percentage = xA x 100.

From the JH NMR spectrum the ratio of guest present in the UIC after the

exchange process was calculated.

199

c</ ©£,

The a protons attached to the a carbon atoms for both the guest molecules

are considered. For the undecane guest molecule there are six equivalent

hydrogen atoms. The signal for these protons occur as a triplet at a

chemical shift value of 8 = 0.892. For the 1,8-dibromooctane there are in

this case four equivalent protons and the signal occurs further dow n field

at 8 = 3.541 again as a triplet. This can be observed from the *14 NMR

spectrum show n in figure 1. From the integrated signals the percentage

exchange of undecane into the UIC was calculated as 21 % (error ± 5 %).

Section 4.3:

The calculations for the am ounts and volum es required for each

exchange reaction are the same as that described in section 4.2. The

experimental data is tabulated below. In each of the series of experiments

0.2 g of Q H ^ ^ U IC ) w as used.

200

The no of moles and volumes required for C8H16Br2(l) and C10H20C12(1) in the exchange process described in experiment 2

CnH ^(U IC ) Amount of

C8H 16Br2(l)

(io-4)

Amount of

C10H20C12(1)

( 10-4)

Volume of

C8H 16Br2(l)

(ml)

Volume of

c 10h 20c i2(1)

(ml)

10 2.965 2.66 5.46 (2) 7.49 (2)

11 2.955 2.65 5.44 (2) 7.47 (2)

12 2.947 2.64 5.43 (2) 7.45 (2)

13 2.939 2.63 5.41 (2) 7.43 (2)

14 2.932 2.63 5.40 (2) 7.41 (2)

15 2.926 2.62 5.39 (2) 7.41 (2)

Section 4.4:

Calculation of the expected mass changes described for experiment 3.

For each exchange experiment 0.2595 g of 1,8-dibromooctane

(series 1) and 0.2074 g of 1,10-dichlorodecane (series 2) were used. The

example used to explain the calculation is the exchange betw een the

C8H 16Br2(UIC) and C10H22(1). (A = decane B = 1,8-dibromooctane)

5 % incorporation of C10H22(1) into the C8H 16Br2UIC occurred as shown

from experim ent 1 in section 4.2. This implied that the m ass of C10H22(1)

that entered the UIC = (5 / 100) x m A = (5 / 100) x n Ax MA = (5 / 100) x m A

= 2.42 x 10'3 g.

The exact quantities of the C10H 22(1) guest molecule were calculated.

The am ount of C10H22(1) guest that entered the UIC equalled the am ount of

C8H 16Br2 guest molecule that leaves the channels, w hen corrected by the

factor uB / oA. This implied that the am ount of C8H 16Br2 that was expelled

from the UIC was 5 % of its original mass that w as present in the UIC.

m B(uic) — 0.2595 g

n B(UIC) ~ ■ ^ b(u i c ) I • ^ b(u i c ) 3.25 x 10 mol

201

m B= V ) x m b= 00884 8therefore the mass of C8H 16Br2 that left the UIC :

m B = (5 / 100) x m B= 4.42 x 10'3 g.

therefore the expected change in mass = (4.5 x 10’3 - 2.5 x 10"3) = 2 x 10"3 g.

The initial, final and change in masses for both the series of experiments

are tabulated below.

Data recorded for the initial, final and the change in masses for each exchange process with the CnH2n+2(l) and C8H16Br2(UIC) guest species in section 4.4.

Q H ^ O ) Initial mass of

C8H 16Br2(UIC) (g)

Final mass of

C8H 16Br2UIC (g)

Change in mass

of C8H 16Br2UIC

(g)10 0.2595 (1) 0.2592 (2) 0.0003 (2)

11 0.2595 (2) 0.2503 (2) 0.0092 (3)

12 0.2595 (1) 0.2347 (1) 0.0248 (1)

13 0.2595 (2) 0.2289 (1) 0.0306 (2)

14 0.2595 (1) 0.2264 (3) 0.0331 (3)

15 0.2595 (1) 0.2225 (2) 0.0370 (2)

202

Data recorded for the initial, final and expected masses for exchange process with C^H^O) and C10H20C12(UIC) guest species in section 4.4.

Q H ^ d ) Initial mass

of the

C TT ClV-'l(r120V-'i 2

UIC(g)

Final mass of UIC ( g ) Experimental change

in mass (g)

10 0.2074 0.2072 (3) 0.0002 (3)

11 0.2074 0.2068 (3) 0.0006 (3)

12 0.2074 0.2044 (4) 0.0030 (4)

13 0.2074 0.2037 (1) 0.0037 (2)

14 0.2074 0.2014 (1) 0.006 (2)

15 0.2074 0.2009 (1) 0.0065 (2)

Section 4.5:

Calculation of the volume ratios of 1,8-dibromooctane to pentadecane

in the exchange reactions of experiment 4

In this experiment for all the exchange processes 0.05 g of 1,8-

dibromooctane UIC was used.

A = pentadecane and B = 1,8-dibromooctane.

^ ^ b(uic)- ^ b(uic) / Mb(uic) — 6.269 x 10 moles

uA/ i ) B = (8.75 / 11.77).

The am ount of C15H 32 (UIC) = nA(UIC) = n B(UIC)x (oA / oB) = 4.66 xlO"5 moles.

Hence a 7.5 % solution of C15H32(1) required: nB = 7.5 /100 x 4.66xl0‘6 =

3.494 x 10’6 moles

m A — Va(uiq x Ma = 7.425 x 10 g

volum e of C15H32(1) = 7.425 x 10'4 / 0.769 = 0.000966 ml.

100 fold excess of C15H32(1) was used therefore the volum e = 0.0966 ml

203

The volumes required to form a 92.5 % mixture of C8H 16Br2 (1)

n B(urea)= (92‘5 / 100) X n B (urea) = 5'7988 X 10'5 moleS.

^B — B(UIC) X ^-B- 0.0158 g

The volume of C8H 16Br2 (1) guest = mB / pB. = 0.0107 ml.

100 % excess of the C8H 16Br2 (1) = 1.07 ml.

The volumes for the different ratio of guest used in the experim ent are

tabulated on page 205.

CHAPTER 5

Section 5.2:

Relative amounts and volumes of alkane guest species required for the exchange process (fully immersed single crystals)

The calculations for the num ber of moles and volum es are the same

as those described in chapter 4.

C H J 1 ) No of moles of Number of moles Volume of

C8H 16Br2 ofC nH ,+2(l) Q H ^ d )

(x 10'6) (x 10‘6) (ml)

10 6.78 7.09 1.38 (2)

11 6.41 6.20 1.31 (2)

12 4.48 4.03 0.92 (2)

13 4.47 3.76 0.92 (2)

14 3.74 2.95 0.77 (2)

15 5.52 4.11 1.08 (2)

204

Ratios of volumes of C15H32(1) and C8H14Br2(l) required for experiment 4 in section

4.5

no of moles c 15h 32(1) C.H.BM1)4.66 x 105 6.269 x 10'5

0 % C 15H 32(1) V = 1.155 ml

7.5 % C 15H 32(1) 3.495 x 106 mol 5.7988 x 105 molV = 0.0966 ( 2) ml V = 1.07 (2) ml

15.5 % C 15H 32(1) 7.223 x 106 mol 5.297 x 10'5 molV = 0.1995 (2) ml V = 0.98 (2) ml

23.8 % C 15H 32(1) 1.109 x 10'5mol 4.777 x 105 molV = 0.306 (2) ml V = 0.879 (2) ml

32.7 % C 15H 32(1) 1.524 x 10'5 mol 4.213 x 105 molV = 0.421 (2) ml V = 0.78 (2) ml

42.3 % C 15H 32(1) 1.971 x 105 mol 3.62 x 105 molV = 0.544 (2) ml V = 0.666 (2) ml

52.3 % C 1SH 32(1) 2.44 x 105 mol 2.99 x 105 molV = 0.673 (2) ml V = 0.551ml

63.1 % C 15H 32(1) 2.94 x 105 mol 2.313 x 10'5V = 0.8122 (2) ml V = 0.426 (2) ml

74.5 % C 15H 32(1) 3.47 x 105 1.599 x 10'5 molV = 0.959 (2) ml V = 0.294 (2) ml

86.8 % C 15H 32(1) 4.036 x 10’5 mol 8.275 x 10‘6 molV = 1.11 (2) ml V = 0.152 (2) ml

100 % C 15H 32(1) 4.66 x 10'5 mol V = 1.29 (2) ml

205

Section 5.3:

Calculation for the volume of pentadecane (1) required for the 'five day'

single crystal X-ray diffraction exchange experiment

m B(UIC) = 0 -2 1 2 X 10'3 g

^b(uic)- ^b(uic) ! ^b(uic) — 2.65 x 10 moles

therefore n A(UIC) = n B(UIC) x (oB / oA) = 1.97 xlO'7 moles,

w here A and B = pentadecane and 1,8-dibromooctane respectively.

Hence m A = nA x MA = 4.198 x 10’5 g,

and the volume of pentadecane = m A / pA = 5.46 xlO’5 ml; (0.55 ml; 10000

times excess).

CHAPTER 7

Section 7.2

Calculations for optical rotation measurements.

The m ass of 2-dodecanol guest present in the UIC is required in order to

obtain a value for the specific optical rotation. The m ethod used for this

calculation is described using the example below,

moles of urea: 2-dodecanol UIC for 5 x lO^g crystal:

V o / ua = 9.73 : 1

= 5X10"4 /(9.73(60.06) + 186.34) = 5 x 10'4 / 770.7 = 6.48 x 10'7 mol. Mass of

2-dodecanol in the UIC = 6.48 x 10'7 x 186.34 = 1.21 x 10 4 g = 0.121 mg

Optical Rotation measurements:

[a]d= a / c l ( eqn.l)

W here [oc]d= specific rotation

a = observed rotation (degrees)

c = concentration (g / ml)

1 = length of cell (dm)

206

Using eqn.l the specific rotation of the inclusion complex can be obtained.

For example polarim eter reading = -0.014

The specific rotation is the num ber of degrees of rotation observed if 1 dm

(10 cm) tube is used. The am ount of rotation depends upon how m any

molecules the light encounters in passing through the tube. For a given

tube length, light will encounter twice as m any molecules in a solution of

2 g per 100 m l of solvent as in a solution containing 1 g per 100 m l of

solvent and the rotation will be twice as large.

The concentration of 2-dodecanol in the complex can be calculated:

w here c = 1 w hen there is 10 mg / ml therefore

mass of dodecanol = 0.121 x 10'3g

c = 0.0121 / 2

c = 6.05 x 10‘3g / ml

substituting into eqn.l:

[cc]d = - 0.014 / (6.05 x 10'3 x 0.01) = [<x]d = -231.4°

CHAPTER 8

Section 8.2:

Calculation of the required amounts of starting mixtures for 1,6-

dibromohexane and 1,6-dichlorohexane UICs (solid solution formation)

Mass of 1,6-dibromohexane = 1.5 g.

A m ount of 1,6-dibromohexane = 6.15 x 10'3 mol.

25 % of 1,6-dibromohexane = 1.5375 x 10’3 mol.

Mass of 25 % 1,6-dibromohexane required = 0.375 g.

No of urea molecules required per 1,6-dibromohexane molecule = 7.4.

Mass of urea = 0.554 g.

207

o

CO

208

Figu

re

1:

NMR

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the

exch

ange

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s wi

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IC

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l).

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exchange reactions of urea inclusion compounds

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