X-ray Powder (Polycrystalline) Diffraction on the BRUKER

SMART 1000 CCD

Joseph H. ReibenspiesX-Ray Diffraction Laboratory

Texas A & M UniversityCollege Station, Texas

XDL

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The Problem• The problem with single-crystal

X-ray diffraction is the single-crystal!

• The structure that is determined is actually the structure seen in that single-crystal!

• ¿ Is the structure of the single-crystal the structure of the bulk sample ?

The Conformational Isomer Problem CYCLEN

• CYCLEN (C8H16N4 Hx) – 12 member ring with over 18 “allowed” conformational isomersa.

[3333]-B [3333]-A [2424]-B[2334]-B

4 known molecular structures of CYCLEN

Highest Lowest Energy

aDale, J. Acta Chem. Scand. (1973) 27, 115-1129. : Meyer, M. et.al Coord. Chem. Rev. (1998) 178-180, 1313-1405.

The Powder Preparation Problem

Not all compounds are accommodating to powder work.

Grinding, packing and sieving can effect the powder’s structure

Some samples show preferred-orientation (texture)

We need non-obtrusive, non-destructive and convenient procedure to prepare the powder, that is closest to the

conditions of the single-crystal experiment.

Sample Preparation in Apiezon® Grease

Stainless Steel Spatula

Grind crystals in the greasebetween spatula and slide

Crystals in Apiezon® Greaseon a microscope slide

Dip mounting pin in powder/grease and spin Mount pin and center

Powder in grease ~0.3 mm diameter

1. Place crystals in grease on slide

2. Grind Crystals to fine powder.

3. Mount powder/grease on glass fiber

The Powder Data Collection on the SMART 1000.

Molybdenum Radiation (=0.7109Å) (1024 resolution)

The detector is set to a reproducible position (e.g. the first stop in the dove tail ~14.55cm)

Mount a standard and calibrate swing angle, specimen to detector distance and beam/detector intersection. (Silicon powder 12.989o, Mo)

Mount specimen and optically align. Specimen should be ~0.3 mm in diameter or in a 0.3mm capillary (0.5mm beam)

Collect rotation frame with swing angle at the zero position. (good Debye rings should be visible, if not re-grind)

Drive swing angle to 10o (or -10o) on 2 and acquire rotation photo (uncheck Zero option). Take long exposure (1200 sec) against appropriate dark current.

Save un-warped frame (interpolated data).

Mo = 0.7109Å K1

Calibration with SiliconSample – Detector = 3.0cm

Calibration with SiliconSample – Detector = 14.55cmSwing Angle = 10.0o (2)Pixel center 507x , 504yFirst ring at 12.989o (2)

Silicon Standard

Data Processing in GADDS.

Load standard frame and calibrate.

Confirm known 2 positions of the standard.

Load data frame. If more than one frame is to be added use the LOAD command.

Integrate (chi option) frame cone and save as a PLOTSO file. Adjust cone to include as much of the frame as possible

In the PEAKS option, manually select peaks.

Run XPOW for simulation with known data set or molecular structure (XFOG).

Calculatea

aJenkins & Synder “Introduction to X-ray Powder Diffractometery” pp 315.

predicted

observedn N

NF

|2|

1

Fn > 20 is a good match

The CYCLEN Powder Pattern

GADDS peak outputa

0

5000

10000

15000

20000

25000

0.0 4.0 8.0 12.0 16.0 20.0

Background Subtractionb

XPOW simulation for CYCLENc

a) GADDS, Bruker AXS, Madison, WIb)POWDERX, Cheng Dong, Institute of Physics, Chinese Academy of Sciences, P. O. Box 603, Beijing 100080, e-mail: chengdon@aphy01.iphy.ac.cnc) SHELXTL 5.0 Bruker AXS, Madison, WI

Frame Data 1200 sec at 10o 2

Predicted Experimental h k l 2 Relative

Intensity 2 Relative

Intensity 2

A. 1 1 2 9.811 100.00 9.878 100.0 -0.067 B. 4 2 0 10.890 39.14 10.884 54.1 0.006 C. 2 0 0 4.871 25.90 4.849 29.8 0.022 D. 3 3 2 13.830 23.90 13.869 23.2 -0.039 E. 2 4 2 14.257 21.28 14.372 25.0 -0.115 F. 4 4 2 16.580 17.39 16.685 17.8 -0.105 0 0 2 9.169 16.16

G. 3 1 1 8.970 16.08 8.973 24.3 -0.003 0 2 2 10.393 10.73

H. 3 1 3 15.825 9.07 15.880 9.9 -0.055 I. 2 2 0 6.885 8.27 6.894 8.9 -0.009 J. 5 5 1 13.322 6.87 13.299 7.2 0.023 K. 0 2 4 19.060 5.28 19.301 9.2 -0.241 L. 1 3 2 11.979 4.84 11.991 4.1 -0.012 M. 4 6 1 18.163 3.54 18.194 5.1 -0.031

Powder Pattern Peaks for CYCLEN

0.0 4.0 8.0 12.0 16.0 20.0

A

B

CD E

FG

HJ KL MI

Experimental Powder PatternSimulated Pattern

2

Np=15; N=13; |2| = 0.055o ; Fn = 15.7Simulate and experimental patterns match.

Sample Preparationa

Grinding

Hard Materials

                                

Soft Materials

Sieving

Paint Pigment Sieve

                                         

325mesh (~30m)

Mounting

Capillaries

Stands

QuartzBoron GlassGlass

Metal/plastic Single-crystal

aSmith, D.K. & Barrett, C.S. Adv. X-ray Anal. (1979) 22, 1-18.

Poor Grinding Better Grinding

Good Grinding Textured Sample

Grindinga

aBish D.L. & Reynolds, R.C. “Modern Powder Diffraction” Bish & Post Eds. pp73-78.

Dry Powder Preparation

Capillary Hair Spray

LoopsRubber Cement

The Binder and The Background

a0.3mm thickness all materials

two-theta

0 10 20 30 40 500

1000

2000

3000

4000

5000

6000

7000

Inte

nsit

y

Background Scattering/ Protectants

Legend

air

spray

capillary

vasaline

cement

grease

paratone

a

Transmission vs Reflection

Transmission Modea Reflection Modeb

Capillary, Loops, Grease etc.Samples with low

PlatformSamples with high

Single-crystalZero backgroundMicro-samples

aDecker, B.F., Asp, E.T. & Harker, D. J. Appl. Phys. (1948) 19, 388-392.bSchultz, L.G. J. Appl. Phys. (1949) 20, 1030-1033.

Dark Currents are Important

Turn smoothing routines off before collecting the dark current.Long exposures are effected the most by “hot” specs.

Fly specs! The “hot pixel” problem!

Air scattering with smoothed andun-smoothed dark currents

Legend

smooth

nosmooth

two-theta

22 24 24 26 26 28 28 30

Dark current smoothing 1200 sec exposure

400

500

600

700

800

900

1000

1100

1200

Inte

nsit

y

Smoothed dark current

Un-smoothed dark current

two-theta

0.0 5.0 10.0 15.0 20.0 25.0 30.0 35.0 40.0 45.0

Data frame - Background frame

Single Data Frame

Fe(NH4)2(SO4)2 6H2O

Sample

Background

Final = Sample - Background

Chem-wipe

capillary

Background Subtraction in GADDSa

aJenkins & Synder “Introduction to X-ray Powder Diffractometery” pp 297.

Micro-Samplesa

Fe(NH4)2(SO4)2 6H2O A single crystal of the sample was placed on the NaCl and ground. (~100 g)

NaCl crystal

aBish D.L. & Reynolds, R.C. “Modern Powder Diffraction” Bish & Post Eds. pp93-97.

0.3mm capillary

Single-crystal (NaCl) holder

D8 High resolution (Cu)

5.0 10.0 15.0 20.0

Two-Theta (Mo)

5 6 8 9 11 12 13 15 16 18 19 20 22 23 25 26 27 29 30 32 33 34 36 37 39 40 41 43 44 46 47 48 50

0.0 deg

2.0 deg

4.0 deg

6.0 deg

8.0 deg

10.0 deg

Two-Theta

90-tilt angle

Gold Plating on Brass Pina

Metal Two-theta (=0.7109)……………………....Au 17.46 20.02CuSn 19.57 22.25 31.66 37.57

Brass

Au

aBunge, H. “Defect and microstructure Analysis by Diffraction” Synder, Fiala, Bunge eds. pp411-519. Iyengar, S.S. et.al. Adv. Xray Anal. (1986) 30, 457-464.

“Information Depth”

Tilt Angle

two-theta

0.0 5.0 10.0 15.0 20.0 25.0 30.0 35.0 40.0

Inte

nsi

ty

0

5000

10000

15000

20000

Back (side) Diffraction

5mm

Direction of the X-ray Beam

Comparison of Fe(NH4)2(SO4)2 6H2O powder patterns

10.0 15.0 20.0 25.0 30.0 35.0 45.0 50.040.0

2-theta

D-8 Discover Sol-X

D-8 Discover Hi-Star

SMART1000 Mo

It’s all Relative

10 20 30 40 50 60 70 80

2-Theta

10 20 30 40 50 60 70 80

2-theta

AcknowledgementsBruker AXS -Uwe Preckwinkel

- Brian Litteer- Arnt Kern- K. Smith

TAMU - X. Ouyang- A. Clearfield- R. Motekaitis XDL

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