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Problems and procedures in collection of

three-dimensional neutron diffraction data for crystal structure determination

George M. Brown, Henri A. Levy

To cite this version:

George M. Brown, Henri A. Levy. Problems and procedures in collection of three-dimensional neutron diffraction data for crystal structure determination. Journal de Physique, 1964, 25 (5), pp.497-502.

�10.1051/jphys:01964002505049700�. �jpa-00205816�

(2)

497.

PROBLEMS AND PROCEDURES IN COLLECTION OF THREE-DIMENSIONAL NEUTRON DIFFRACTION DATA FOR CRYSTAL STRUCTURE DETERMINATION

By GEORGE M. BROWN and HENRI A. LEVY,

Chemistry Division Oak Ridge National Laboratory (1), Oak Ridge, Tennessee, U. S. A.

Résumé.

2014

Les données de diffraction neutronique tridimensionnelles ont été relevées pour des cristaux de 13 composés différents sur le diffractomètre automatique à neutrons d’Oak Ridge.

Problèmes et méthodes dans le relevé des données sont discutés depuis la sélection des cristaux

jusqu’a l’obtention et l’utilisation des données. La précision des mesures

sur

l’appareil est aussi

discutée.

Abstract.

2014

Three-dimensional neutron- diffraction data have been collected for crystals of

thirteen different compounds

on

the Oak Ridge automatic three-circle neutron diffractometer.

Problems and procedures in data collection

are

discussed, from selection of crystals through data processing. Precision of measurements

on

the instruments is also discussed.

LE JOURNAL DE

PHYSIQUE

TOME

25,

MAI

1964,

Introduction.

-

During two years of operation

of the Oak Ridge automatic neutron diffracto- meter, three-dimensional data sets have been re-

corded for crystals of thirteen different substances (see Table 1). A review of the information derived from certain of these data sets is presented in an accompanying paper by G. M. Brown and H. A. Levy [I], and a general description of the

diffractometer and its operation is presented in

another paper by W. R. Busing, Smith (H. G.),

Peterson (S. W.) and H. A. Levy [2]. The present

purpose is to discuss from the aggregate of our group’s experience in automatic collection of neu- tron diffraction data some procedures that have been found useful and some problems that have arisen.

Selection and preparation of crystal specimens.

-

The requirement of obtaining data with good counting statistics in a reasonable period of time

demands that one use rather large crystals speci-

mens. On the other hand, specimens cannot be

too large, if extreme absorption effects are to be

avoided and, especially, if extinction errors are to be minimized. We prefer to use two or more crystals of widely different sizes whenever this is possible. For all reflections likely to be affected

by extinction, only data from the smaller crystals

are chosen for structure refinement. For the other

reflections, data are taken from a large crystal.

First one usually prepares the largest available crystal, up to the limit imposed by consideration of the area of homogeneous intensity of the beam

cross section or by the absorption property of the

substance. From this crystal all independent re-

flections are recorded out to the limiting value of

sin 6/X of the instrument (~ 0.76~, or at least as

far out as is useful to measure. A somewhat (1) Operated for the U. S. Atomic Energy Commission by Union Carbide Corporation.

smaller crystal is then chosen for recording again,

with the monitor count (2) set correspondingly higher, those reflections having intensities from the first crystal so high as to make one fear extinction

errors. Similarly, a still smaller crystal may be chosen for recording the reflections having the very

highest intensities. Analysis of the sets of data

for the various crystals (see discussion of averaging

below under heading Data Processing) allows one

to evaluate the effects of extinction independently

of the structural model and to decide, for example,

the cutoff levels of intensity above which data for the larger crystals should not be used in structure refinement.

This procedure allows collection of a set of data

having reasonably low fractional standard errors

overall, without including data seriously affected by extinction. It seems preferable to the alter-

nate procedure of attempting in the final stages of

structure refinement to apply corrections for

extinction, especially since proper calculation of corrections is difficult because extinction is gene-

rally anisotropic. It is still advisable, however, to

look for residual extinction errors by comparison

of observed and calculated structure factors near the end of refinement. A finding of errors at this stage suggests the need for re-examination of the chosen cutoff levels for data of the different crys-

tals, or even the advisability of omitting a few data altogether.

The[chloral hydrate data were obtained from three crystals, weighing - 29, 10, and 2 mg. Of the - 2 150 independent data from the largest crystal,

~

300 were rejected because of extinction

effects. Near the end of refinement, - 50 reflec-

tions of highest intensity were omitted from the (2) At each point in

a

scan, reflected counts

are

recorded during the time required for

a

monitor counter in the inci- dent beam to register

a

preset count [2].

Article published online by EDP Sciences and available at http://dx.doi.org/10.1051/jphys:01964002505049700

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498

data of the two smaller crystals, for which approxi- mately 500 and 150 independent measurements had been made, respectively.

The sucrose data are from three crystals also.

About 500 of the - 2 800 independent observa-

tions from the largest crystal (~ 80 mg) were rejected. Data from a crystal weighing about

10 mg and from another weighing about 5 mg show little, if any, evidence of extinction. Both of these smaller crystals had been immersed repea-

tedly in liquid nitrogen before they were put on

the diffractometer.

A crystal specimen is selected only after thorough x-ray examination by precession photo- graphy to determine if it is truly a single crystal.

Often a much larger crystal is examined, and the

actual portion used is separated from any miso- riented sections. Sometimes the crystal is shaped

to a simple geometric form, in order to simplify

calculation of the absorption corrections that

usually are applied.

When a small crystal is to be used for the pur- pose of reducing extinction errors, it is preferable

to cut it from a larger one. Otherwise the small crystal may show as much extinction as a larger

one, or even more. Similarly, the familiar proce- dure of repeated immersion of a specimen in liquid nitrogen is usually more effective in reducing

extinction effects for large crystals than for small

ones.

Recording of data.

-

So far all of our data have been recorded by the 0

-

26, stepscan method.

The scan for each reflection is made over a range centered around the computed value of 26 for the

peak. Usually the range of 26 is 5°, counts being

recorded on the output paper tape for 51 points

at 0.1 ° intervals, each for the same preset value of

the monitor count.

Sometimes the 50 range can safely be reduced,

with some saving of time. Usually, however, even though most of the reflections of a series being

recorded are sufficiently narrow in breadth for,

say, a 40 scan, some require 50. The wider range is safer also whenever peaks are likely to f all off

center in the computed range because of the use of

slightly inaccurate cell parameters in the compu- tation of the orienter settings ; and it is necessary at high angles 20, where the peaks broaden because

of the spread of wave lengths in the neutron beam.

Data are usually collected in order of increasing

value of 0. Inspection of the recorder chart reveals when a different range of scan should be chosen.

A problem of resolution appears at high values

of 0 for crystals having one or more cell translations of about 20 A. A portion of neighbor peak may be recorded near the beginning or end of the scan

of a given reflection. The processing of the output

data tape for the reflection being measured cannot

then be done properly by the computer program

routinely used (see below under the heading Data Processing). It appears that 20 A is the approxi-

mate limit on cell translations of crystals to be

studied on the instrument, unless the divergence

of the neutron beam and the wave length spread

are reduced, with an accompanying increase in

recording time per reflection.

In the course of collecting a set of three-dimen- sional data, we often collect replicate data for a large number of reflections. It was especially desi-

rable to do so when the instrument was first put into operation, for the purpose of checking its relia- bility. As a matter of routine, one or two stan-

dard reflections of the crystal under study are

scanned at regular intervals, say every 30 to 50 reflections. Also, the performance of the instru- ment is checked frequently, every week or so, by scanning a standard reflection (400) of a standard crystal of sodium chloride, kept permanently on a goniometer head for this purpose.

Data from these two kinds of standard obser- vations are used to choose the proper scale factor to apply to a given group of intensity data to bring them to absolute scale. When the internal standard reflection remains at constant intensity,

the data are scaled by comparison with the inten- sity of the (400) reflection of sodium chloride. In the w ork on XeF 2 and XeF4 (see review in refe-

rence [1] and other references there) the obser- vations of the internal standard were very impor- tant, because they provided a basis for correction of the data for growth of the crystal specimens during the period of data collection.

Internal standard reflections have in two ins- tances proved, in a rather interesting way,

7

to be rather poor standards. In the work on chloral

hydrate, the intensity of the (200) reflection from the largest crystal used (29 mg) gradually increased

from its original value to

a

value about 10 % higher over a period of two months, during which

the intensity of the (400) reflection from the NaCI standard remained stationary. The (200) reflec-

tion is a strong one, and its measured intensity for

the 29 mg crystal is little more than half of its correct value because of extinction. The increase of intensity is tentatively attributed to an increase of mosaic spread in the crystal resulting from

neutron irradiation. Such increases only appeared

in the data from this crystal for reflections of high intensity, which were subject to severe extinction

errors and which subsequently were deleted from

the data set.

A similar effect, but in the opposite direction,

was observed in the strongest reflections from a

sucrose crystal weighing about 80 mg. Again, no

changes were observed except for those reflections

later shown to be severely affected by extinction.

(4)

An explanation in terms of mosaic spread hardly

seems reasonable in this case.

Data processing.

-

Raw data recorded by the

diffractometer are processed either on the Control

Data Corporation 1 604A computer or on the

IBM 7090, after a preliminary step in which data

are transferred from paper tape to magnetic tape.

Details of the processor program will not be given here ; only the basic process which has been adop-

ted and programmed for deriving the integrated

count for a given reflection will be discussed [4].

The computer first examines the data for a given

reflection to determine if the reflection is " weak "

or " strong ". The peak is taken to be strong only if the difference Cmax.

-

Cmin.avg. is greater

than or equal to 4adif., where Cmax is the highest

count in the scan, is the minimum value of the average of all groups of three adjacent counts

and adif. is the standard error of the difference.

If the peak is found to be strong, its center, pc, above half-height is next determined by the pro- gram. For a weak peak, pc is taken to be the midpoint of the scan.

The n points of an assigned range centered as

closely as possible about the value pc are consi- dered to belong to the peak. An equal number m

of points on each side of the n points are used to

determine background, m being taken as large as possible. The net count under the peak, Cnet, is

obtained by subtracting from the total count under

the peak, Ctotal, a background correction, Cback, computed as the sum of the 2m counts of back- ground multiplied by the factor n /2m, the ratio of the number of points under the peak to those of background. The variance, 6cnet, of Cl,et is given by

The number n used above is an input datum

which is set after examination of the peaks on the

recorder chart. It is fixed at the same value for all reflections processed in a single processing job,

the value appropriate for the widest peaks being processed, unless these peaks are to receive special

treatment later.

Counts. for fewer and fewer points are employed

in determining the background as a peak is more

and more displaced from its proper position at the

center of the scan. In case of extreme displa- cement, the processing for the particular reflection fails, and the program proceeds to the next reflec-

tion.

It will be clear that a fundamental assumption

at the basis of this rather simple processing scheme

is that the background intensity over the range of the scan is a linear function of 26. A more sophis-

ticated processing scheme would be desirable, since

the assumption of linearity is not always a good

approximation ; but no better one has yet been

devised. It is advisable for the user of the instru- ment to inspect daily the recorder chart for evi- dence of malfunctions of the instrument which will not be recognized as such by the processor program and which may otherwise go undetected.

For each reflection processed, an IBM card is automatically punched with values of the following quantities : the indices h, 1~, and 1, the orienter setting angles 20, x, and p ; Cnet, Cbflk, 6net, and pc. The deck so produced is used as input

data for calculation of absorption corrections by

the program of Wehe, Busing, and Levy [5]. The absorption factors are stored on magnetic tape,

to be applied in the next stage of processing, which

also employs the same deck of data cards. In this next stage a so-called data library is set up on

magnetic tape [6]. The data are scaled absolu- tely by application of the proper factors, derived

from the measurements on standard reflections,

and the absorption and Lorentz corrections are

applied. For each reflection the values of F2 and and a number of other functions, are

recorded on the tape, from which they can be read

and punched on cards at any time later. Data cards appropriate for input to the Fortran least- squares program of Busing, Martin, and Levy [7]

may be produced automatically.

If desired, a different set of data cards may be

punched for input to a program that has been written for averaging equivalent data from one or

several crystals [8]. This program accepts a deck

of cards each of which bears the indices of a parti-

cular reflection, an integer identifying the crystal specimen, the intensity (scaled and corrected for

absorption), the statistical standard error of the

intensity, and the Lorentz correction factor. The deck must be sorted so that equivalent reflections

are grouped. Averaging, with proper weighting

and with simple rejection criteria, is carried out

for each independent set of indices, first over the

data for each crystal specimen separately and then,

if desired, over the data for all the specimens. The

function averaged may be either the intensity or

the square of the structure factor. At the user’s

option, input data cards for the least-squares pro- gram may be punched, or a set of average inten-

sity cards may be punched. The latter cards,

when sorted on intensity, are useful in appraising

the magnitude of extinction effects, by comparison

of the data from different crystal specimens.

Some remarks are required concerning compu- tation of the variance the reciprocal of which

is the weight of the observation Fob.. in least-

squares refinement. The variance ought

ideally to be related to G2",t, the calculation of

which has been mentioned earlier, in the same way

that F o 2b,. is related to Cnet. Experience in many

refinements (see, for example, reference [9]) sug-

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500

TABLE 1

NEUTRON

DIFFRACTION DATA COLLECTED

ON THE

OAK RIDGL

AUTOMATIC THREE-CIRCLE NEUTRON

DIFFRACTOMETER,

AS OF

AUGUST, 1963

(*) Work of S. W. Peterson, Washington State University (see reference [3]).

gests, however, that estimates of variance that are more realistic and more appropriate for computing weights are obtained by adding a correction term

(kF2)2 to the variance derived from where k is a constant, usually set at 0 .03. The extra term makes allowance for instability in the instrument (see below under Precision of Measurements), errors

in corrections for absorption, deficiences of the structure model, and so forth. When replicate or equivalent observations are made for a reflection from a given crystal specimen, it is customary to

make the variance correction after averaging the

observations. Later, if data for the same reflec- tion from different crystals are averaged, they are regarded as independent and the variance of the average is computed accordingly.

Precision of measurements.

--

A study of the precision of intensity measurements on the diffrac- tometer was made through statistical analysis of

data recorded from a small crystal of potassium

chloride [10]. Three types of test have been made

on the data : for consistency of replicate measu-

rements on a single reflection, for consistency of the equivalent reflections measured for a given form,

and for the external consistency of all accessible

independent reflections with the crystal structure,

as given by a least-squares fit of scattering factors

and temperature factors.

The KCI crystal was approximately cubical in shape and weighed 2.53 milligrams. Data were

collected at a monitor count settings of 60,000 to

~00,000. An absorption correction factor was

computed and applied for each reflection. The average factor was about 1. 05.

Some statistics (3) of a portion of the KCI data,

relevant to the first and second types of test, are given in Table 2. The different series of measu-

rements, a, b, etc..., for a particular reflection or

form were made at different times with different monitor count settings. For each series of measu-

rements an internal estimate, S, and an external estimate, 6, of the standard error of a single obser-

vation are given. The internal estimate is the unbiased estimate of standard error from the

sample, given by the equation

where F2 is the mean of the n observations Fi2 of

the sample. The external estimate is the mean

of the n standard errors derived from counting sta-

tistics (without application of the variance correc-

tion discussed in the previous section). When F2 is

derived from a large count, its distribution about the true value of F2 approximates the normal dis- tribution with variance a2 ; and the quantity x2 = (n

=

is then distributed in the chi- square distribution, on n - I degrees of free-

dom [11]. The probability that X2 for the sample be found greater than the value actually

found may be taken as a measure of consistency of

the data in the sample, or as a measure of consis- tency of the internal and external estimates of

error. The ideal value of P,. to be expected on

the average is 0 . 5. For a reasonably large sample,

a probability deviating greatly from 0.5, approa- (3) See . general discussion

on

satistics in [11] and other

references there.

(6)

TABLE 2

PRECISION

OF SOME INTENSITY MEASUREMENTS FROM A

KCI

CRYSTAL

TABLE 3

PRECISION

OF INTENSITY MEASUREMENTS ON TWO STANDARD REFLECTIONS OF

K2’bF

ching either zero or unity, indicates inconsistency

in the estimates of error and the presence of syste-

matic errors of some sort.

The data of Table 2, which may be taken to

represent fairly the whole set of KCl data, show

that the consistency is reasonably satisfactory

within a given series of measurements, both for replicate measurements and for measurements of

equivalent reflections. There are no deviations of

probability from the value 0.5 to an extent that

may be regarded as significant by the usual criteria.

It is clear, however, that the consistency of the

values F2 for the various series of observations of

a given reflection or of a given form is not quite so satisfactory. For example, the difference of 0.36 between the values F2 of series a and b of reflec- tion (004) is 3.5 times the standard deviation com-

puted from the values of

6.

Since the probability

of obtaining a ratio greater than this according to

the properties of the normal distribution is only

N

5 X 10-4, there is clearly a significant difference

between the two averages. The same conclusion is reached if one uses the estimates of error S from the two samples and Student’s statistic t. The

probability estimated from this statistic is about

10-3, and the conclusion is essentially the same.

Discrepancies of this sort, which reflect instru-

mental instability, are allowed for by the variance corrections discussed in the previous section.

In the least-squares refinement on the KCI data,

the scale factor for the values of F2, the ratio of

the sodium nuclear scattering amplitude to that

of chlorine (fixed at 0.98 X 10-12 cm), and the

thermal parameters of both ions were adjusted.

The variances of the observations were corrected in the manner described before weights were calcu-

lated. Similar least-squares analyses were carried

out on data from measurements on Nacl and RbCI

crystals. The agreement reached in each case

between observed and calculated values of ~li’2 is

strikingly close. Thus, for NaCI, KCI, and RbCI,

the discrepancy factors (4) for F2 were 0.026, 0.019, and 0.023 ; and the values of the standard deviation of an observation of unit weight (5) were 0.99, 0.86, 0.88, respectively.

The many replicate data of the reflections used

as internal standards in the course of collecting a

data set may also be used to test for consistency.

For example, the 50 observations of reflection (060)

and the 48 observations of (400) recorded in the

(5) For definition

see

reference [1].

(7)

502

work on K2NbF 7 are remarkably consistent (see

Table 3). Clearly, the instrumental stability was quite satisfactory during the period of five weeks

required to record the data for K2NbF7.

Taken altogether, these tests (6) indicate high consistency and precision in the measurements made with the automatic instrument. The indi- cation is borne out by the quality of the refine- (6) The least-squares analyses also provide nuclear scat- tering amplitudes for Na, K, and Rb, relative to the value

0.98 X 10-12

cm

for Cl, whch

are

slightly different from previous values and

more

precisely determined [10].

ments that have been made on neutron data for six substances [1]. The discrepancy factors on F2, ranging from 0.107 to 0.046, and the generally

small standard errors in the structural parameters

attest to the quality of the data. Some confidence that errors in the observations are being estimated nearly correctly is engendered by the fact that the

standard deviation of an observation of unit weight

reached values of 1.02 - ~ .15 in four of these refinements (XeF4, KNbF, chloral hydrate, and sucrose) and values 1.65 and 1.67 for the other two ~XeF2 and BaCl2. 2H 20).

REFERENCES [1] BROWN (G. M.) and LEVY (H. A.), J. Physique, 1964,

25, 469,

"

Recent Crystal Structure Determinations

by Neutron Diffraction at Oak Ridge ".

[2] BUSING (W. R.), SMITH (H. G.), PETERSON (S. W.)

and LEVY (H. A.), J. Physique, 1964, 25, 495,

"

Experience with the Oak Ridge Automatic Three-

Circle Neutron Diffractometer ".

[3] PETERSON (S. W.), Abstracts of the Communications Sixth International Congress and Symposia, Inter-

national Union of Crystallography, Rome, Italy, September 1963, p. 30.

[4] BUSING (W. R.), WEHE (D. J.), MARTIN (K). and

LEVY (H. A.), Unpublished work.

[5] WEHE (D. J.), BUSING (W. R.) and LEVY (H. A.),

"

OR ABS, A Fortran Program for Calculating Single Crystal Absorption Corrections ", Report

No. TM-229, Oak Ridge National Laboratory, 1962.

[6] BUSING (W. R.), Unpublished work.

[7] BUSING (W. R.), MARTIN (K.) and LEVY (H. A.),

"

OR FLS, A Fortran Crystallographic Least- Squares Program ", Report No. TM-305, Oak Ridge

National Laboratory, 1962.

[8] BROWN (G. M.), Unpublished work.

[9] PETERSON (S. W.) and LEVY (H. A.), Acta Cryst., 1957, 10, 70.

[10] LEVY (H. A.), AGRON (P. A.) and BUSING (W. R.),

Annual Progress Report, Chemistry Division, Oak Ridge National Laboratory, ORNL-3320, 1962, p. 108.

[11] CRUICKSHANK (D. W. J.), Statistics, section 2.6, p .84,

I nternational Tables for X-Ray Crystallography,

vol. 2, J. Kasper and K. Lonsdale, Editors,

Kynoch Press, Birmingham, 1959.

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