Vibrational Assignmets for 4-AminopyrazoIo[3,4-dlpyrimidine

from FTlR and FTR spectra

Introduction :

The molecule 4-Aminopyrazolo [3,4-dlpyrimidine (C5HSN5) resembles adenine

and purine. 4-Aminopyrazolo[3,4-dlpyrimidine (4APP) is also known as "Adenine

antimetabolite". It is biologically important and present in many biological systems. A

representative structure of the molecule is shown in the fig [I]. It consists of one pyrazole

and one aminopyrimidine ring fused together and exists in solid state at room temperature

and has a nlelting point around 300 "C. The nlolecules 4APP, purine and adenine have

same molecular fonnula and similar in structure but differ in the arrangement of nitrogen

atom in the pyrazole ring.

Perz-Ruiz, et a1 [1] reported the molecular structure of the protonated form of

tisopurine, 4-thioxo-2,5H, 7H'-purazola [3,4-dl pyrimidinium chloride by X-ray

diffraction method. They investigated the recorded Raman and Infrared spectra of the

compounds in the range 4600 to 20 cm-' and discussed briefly the fundamental vibrations

involved in the intermolecular H-bonds.

Raman and IR spe'ctra of polycrystalline adenine and of its deuterium substituted

analogous were examined by Mojoube [2]. The twenty-seven A' inplane and twelve A'

out-of-plane modes for adenine are observed and assigned by assuming C, symmetry.

The stnlctural paranleters e~llployed were taken froni 9-methyladenine and from other

adcni~le dcrivatives. Thesc assignments were n~ade on the basis of experimental data and

on a normal coordinate analysis using Urey - Bradly force 'field. He had also compared the

results with ab initio molecular orbital calculation and normal CO-ordinate calculations

reported by Tsuboi etal and Nishimura etal [3,4] . Mojoube [5] anaIysed vibrational

spectra of purine bases and compared the results with that of adenine and guanine

Majoube [6,7] reported vibrational frequencies for inplane and out of plane normal

nlodcs ror pyrazolc and scvc11 dcutcrium substituted a~lulogues. IIe recorded the FT-IR

spectra for pyrazole at room temperature in vapour phase, in diluted CC14 solution and in

polycrystalline solids and FT-Raman spectra in aqueous solutions. He analysed the N-H

stretching inplane mode and its coupling with the N-H rocking out of plane modes

Fig 1. SWclure of 4-amin~lo(3,4-d]pyrimidine

together with the band contour. To confirm the results, a normal coordi~late analysis was

carried out based on Urey-bradly and general valence force field by assuming payrazole as

planar with C, symnlet~y.

The Raman and IR spectra of adinine and of its derivative viz., adinine

hydrochloride, 1-methyl adenine and 1-methyl adenine hydrochloride have been studied in

relation to the 11lutagenic and carcinogenic activity by Bwetoluzza eta1 [8J. The spectra

gave evidence for a shift of tautonleric stability from the aminic form, which was favoured

in adenine, toward the iminic or iminic-derived form. The different biological activities of

this series of compounds, in particular the mutagenic and carcinogenic effects, can be

interpreted intern~s of different reactivities associated with rc-electronic systenls and of

hydrogen bond interaction between the bases in nucleic acids which was different from the

canonical interactions.

Due to con~plex nature of 4APP molecule a complete vibrational assignment is not

available in literature. Hence an attempt has been made in this chapter to give a complete

vibrational assignments for 4APP molecule using FTIR, FT-Raman spectra and normal

coordinate calculations.

Experimental :

The sample of 4APP obtained commercially from Fluka Chemical Switzerland

with a stated purity of greater than 98% and it was used as such without further

purification. The Raman spectrum in the range between [3500 - 50 cm-'1 of 4APP was

recorded on a Brucker Model IFS 66 interferometer equiped with a model FRA 106 FT-

Raman module accessory. The data were recorded coaddition of 32 scans at i 2 cm-I

resolution wit11 200 I ~ W of power at the sample. The IR spectrum of the sample was

recorded in solid phase on tile same instrunlent in tlle range 4000 - 400 cm-I. The data

were recorded by the coaddition of 32 scans at f 2 cm'l resolution. Fig [2-31 shows the

FTIR and FT-Raman spectra of 4APP molecule.

Fig. 3. FTR Spectrum of 4 - A m l n 0 ~ l o [ 3 ~ 4 d ] ~ r n l d l n e

RSIC. ILT. NAJJWS BRUKER IFS 66v FT-IR SPECTROMETER . TECHMgUE : PMOER

Normal coordinate analysis :

F-G matrix method was used to attempt normal coordinate analysis [g].

The nlo1ecule under investigation has planar structure and belongs to C, point group

symmetry by assuming the amino group as point mass. For a C, symmetry, the 39

fundamental vibrations fall into 28 inplane vibrations of the atspecies and 11 out of

vibrations of a" species. All the vibrations are both infrared and Raman active. In the

present work, both inplane and out of plane vibrations are treated completely. The structural parameters employed in the present work are taken from sutton's table [lo].

The nonnal coordinate calculations were performed using the program developed by

Fuhrer et al [I I], after suitable modification in our laboratory. Internal coordinates for the

out-of-pl~unc vibrations arc defined as recommended by IUPAC. The simple valcnce force

field is adopted for both inplnnc and out-of-plane vibrations. Tablc -1 shows the observed

alld colculntcd \vavcnumbcrs, n a t u ~ c of absorption bands ~~l tc r fns of mixing of v~brntional

nlodes, types of mode and vibrational assignments along* with the potential energy

distribution.

Results and Discussion :

Region between 3000 - 3600 em-'

Thc 1110st interesting spectral region is that located between 3000-3600 cm-' where

the stretching mode of the N-Id, NH2 bonds involved in hydrogen bonding appear together

with the medium intensity C-H stretching modes. In this region, the FT-IR spectra of

4APP shows an intense multi-component absorption, in which two sharp bands at 3318

and 3 180 cm-I dominate. The two bands can be ascribed to the N-H antisymmetric and

symmetric stretching modes of the amino group respectively. Bertoluzza eta1 [8] assigned

this mode in adenine at 3294 and 3 120 cm-I respectively. Another very strong structured

band obsc.l.vc.d at about 3136 cm" is attl-ibutcd to thc K-11 stretching modes of the NII

group involved in hydrogen bonding. In pyrazole vapour the free N-H stretching modes

is observed at 3523 cm-'. In CCI4 solution and in polycrystalline soIid the N-H stretch in

pyrazole is observed at 3480 cm-I and 2800 cm" respectively [6]. This shift in

wavenumber is due the presence of hydrogen bonding in the molecule [4]. In

heterocyclic compounds due to resonance effect the C-H stretching absorption bands are

usually weak [8]. In the present case it is observed at 2788 and 2886 cm-I. There are

some bands around 3000 cm-I which may be due to overtones or combinations bands.

R e g h betw-een 1700 - 700 cm-'

The FTiR and FT-Raman spectrum of 4APP in this region are mainly due to

vibrations of atoms forming the pyrimidine and pyrazole ring. There are some characteristic modes participate in this region due to N-H and amino groups. The proper

assignment of observed frequencies in this region is based on the comparison of the

spectral data with the values obtained from normal coordinate analysis. In the present case

the most intense absorption band appearing in IR at 1606 cm'l is assigned to the scissoring

vibration of'tlle amino group. Tlle very strong absorption band in IR at 1677 cm" appears

as weak band in Rarnan at 1675 cm-'. This mode is assigned to the N-H in plane bending.

We /lave assigned a strong absorption band at 962 cm-' to C-NH2 stretching vibrations.

The anotha characteristic vibration of amino group found at 1067 cm-' in IR is assigned

to t l lc twistiug ~nodc of N112 group. 'l'llesc prcscnt conclusion is well agrce with the

literature values [12, 131

Fro111 the structure of the n~olecule one can expect nine stretching vibrational

modes from the ring. Out of nine stretching vibrations, we have assigned four stretching

modes to C-N bonds and two stretching modes to C-C bonds. These modes are observed

at 693, 725, 785 and 800 cm-' and 1466 and 1478 cm-' respectively. The absorption band

seen at 1677 cm" is already assigned to N-H in plane bending mode is once again

assigned to C=C stretching modes. The remaining three bands predicted to occur at 13 15,

1402 and 1398 cm-' are observed at 1306, 1339 and 1398 cm-I. They are attributed to the

N-N and two N=C bonds. Further, two bands at 1215 and 1265 cm-' are assigned to the

C-H deformation modes. This assignments consistent with literature values 12,161. The

purity of the modes and their relative intensity is presented in the Table -1.

Uclow this region, the f?eiluency assigrlme~lts bcconle more co~uplex sirlce the

bands no longer correspond to pure motions, but instead they are complex mixture of

different internal coordinates. The observed r-nodes will depend on the skeleton of the ring

and the functional groups attached to the skeleton. In the present case the characteristic

vibration of amino group observed at 636 cm" in IR is assigned to the waging mode of

amino group. The other vibrational modes such as deformation, C ~ N H ~ out of plane and

inplane bending modes are observed at 337, 201 and 526 cm-I respectively.

For complex molecule in the low wavenumber region, overlapping of absorption

bands are expected. \Ve assigned the later three wavenumbers once again to CNN inplane

bending, CCN out of plane bending and NNC inplane bending modes respectively. Two

C-H and one N-H out of plane bending absorption modes are also observed in this region.

Their relative intensities and the purity of the modes are presented in the Table -1.

Norn~al coordinate analysis was helpful to us to predict some of the wavenumbers

at 163, 241 and 347,389 cm-'. These are assigned to CNC, CNN out of plane bending and

CNC and CCN inplane bending lnodes respectively. We have also seen a very strong

band in Raman at 129 cm-I, which corresponds to CNN out of plane bending mode. The

above assignments agrees with the earlier values [14-161 Below this, one weak band at

1 12 cm-' in Raman can be due to lattice vibrations of the 111olecule.

potential energy distribution :

To check whether chosen set of assignments contribute ~llaxinlulll to the potential

energy associated with normal coordinates of the .molecules, the potential energy

distribution [PED] has been calculated using the relation

Fii L k 2

PED =

hk

Where F,, are the force constants defined by damped least square technique, L,k the

nonnalised amplitude of the associated element [i,k] and hk the eigen value corresponding

to the vibr-ational frequency of the elenlent k. The higher PED contribution corresponding

to each of the observed frequencies are listed in the present work.

Conclusion A conlplete vibrational spectra and analysis is available in the present work for 4-

Aminopyrazolo[3,4-dlpyri~nidine n~olecule. The close agreement between the observed

and calculated frequencies confirms the validity of the present assignment.

Table -1 Observed and calculated wavenumbers and Potential energy distribution

(PED) for 4-Aminopyrazolo [3,4-dlpyrimidine

G ."

m

a"

a'(

3,'

a''

a''

a'

a'

a'

a'

a'

a'

a'

a"

;I11

a''

i f

alI

a'

a'

FTIR

526w

540vw

600s

630w

693m

725m

785s

800vw

870m

Cal. wave-

number

120

163*

221

241 *

324

347'

3S9*

5 15

527

540

602

625

GS 1

728

792

801

Observed wavenumberAnt

FTR

112w

1 2 % ~

201vw

337vw

527w

537vw

6 15w

725s

Assignments

Lattice vibration

ChW out of plane bending

CNC out of pla~ic bending

C-Nil, out of plane be~ld~ngi

CCN out of plane bend111g

CNN out of planc bend~ng

KH2 deformation/

C h 3 inplane bending

CNC inplane bending

CCN inplane bending

C-NI-I, inplane bcndingi

NNC inplarie bending

CCC inplane bending1

NCN inplane bending

CII out of plane bending '

C1-I out of plane bcndingl

N H out of plane bending

N l I? waggillg

CN strctcliing/

CCC out of plane bending

CN stretching

CN stretching

CN stretching

1398 - 526

PED

="YCNN + 1 8 ~ ~ 4 ~ 2

407 ,.,,,? - 42*1ccN

3 9 6 ~ ~ t ~ ~ P C N S

~ ~ P c - N H : +3 1 PNNC +

1 OP,,,

~ ~ P C C C + 35Pxcx +

IjPcNc

61 y,, t 12yc.,H2

6%,, + 2 6 ~ ~

~ S ( J + ~ H ?

~ O V C N

64~ccc

~ ~ V C N

8 % ~

79vc, + lop,,

1478 - 537

C-NH, stretching

3102-2078

NH, twisting

1675 - 527

2942 - 1738

1066 + 129

CH inplane bending

CI-I inplane bcnding

N-N stetching

I N=C stetching

K=C stetching

C-C stetching

C-C stetching

2 x 785

2866- 1306 .

NH, rocking

C=C stetching1

NH inplane bending

1215 + 526

2 x 903

2 x 938

1265 + 693

1306 + 693

1339 + 725

2 x 1200 - 337

1675 + 537

2 x 526 + 1265

1677 + 725

*calculated from Normal co-ordinate analysis; vs-very strong, s-strong, m-medium,

w-weak, vw-very weak, v - stretching, y - out-of-plane bending, P - inplane bending,

w - wagging, 6 - defonnation, T - twisting

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