Recent crystal structure determinations by neutron diffraction at Oak Ridge

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Recent crystal structure determinations by neutron diffraction at Oak Ridge

George M. Brown, Henri A. Levy

To cite this version:

George M. Brown, Henri A. Levy. Recent crystal structure determinations by neutron diffraction at Oak Ridge. Journal de Physique, 1964, 25 (5), pp.469-473. �10.1051/jphys:01964002505046900�.

�jpa-00205809�

RECENT CRYSTAL STRUCTURE DETERMINATIONS BY NEUTRON DIFFRACTION AT OAK RIDGE

By ^{GEORGE M. BROWN} and HENRI A. LEVY,

Chemistry ^Division

Oak Ridge ^National Laboratory (1),

Oak Ridge, Tennessee, ^{U. S. A.}

Résumé.

Des structures cristallines ont été déterminées à partir des données tridimensionnelles

aux

neutrons pour ^le difluorure de xénon, ^le tétraflorure de xénon, ^le chlorure de baryum dihydraté l’heptafluoniobate ^de potassium, l’hydrate ^de chloral, ^le

^et l’hydroxyde ^{de strontium} octahydraté. ^{Les valeurs ont été relevées} grace

diffractomètre à neutrons d’Oak Ridge position-

nant automatiquement les trois angles ^{d’Euler. Les} raffinements, par la méthode des moindres

carrés, ^{ont fourni des} paramètres structuraux de haute précision.

Abstract.

Crystal structures have been determined from three-dimensional neutron data for

difluoride,

tetrafluoride, barium chloride dihydrate, potassium heptafluoniobate,

chloral hydrate, sucrose, and strontium hydroxide octahydrate. ^Data

^taken

^{the Oak} Ridge automatic three-circle neutron diffractometer. Refinements, by the method of least squares, ^have yielded structural parameters ^of high precision.

PHYSIQUE 25, 1964,

Introduction.

In the last ^two years, approxi- mately, ^{seven different} crystal structures have been determined from three-dimensional data by

the neutron diffraction group in the Chemistry

Division of the Oak Ridge ^National Laboratory.

Data used in determining ^the structures of XeF2, XeF4, BaC’2.2H20, KNbF, ^chloral hydrate, ^and

sucrose were obtained with the new automatic three-circle neutron diffractometer at the Oak

Ridge ^Research Reactor. The work on these struc- tures has demonstrated very clearly ^{that auto-}

matic collection of neutron data is practical. ^Data

of high quality ^{can be} collected in reasonable time.

The precision ^{of the} structures derived from the data is very satisfactory. ^{It is} the purpose of ^this paper ^to review the six determinations made on

data from the automatic instrument.

For Sr(OH)2.8H20, ^{data were obtained} [1] ^on

the crystal orienter of the automatic diffracto- meter, but before it was in automatic operation.

Refinement of the structure of Sr(OH) . BH O ^has

not yet ^been completed, ^{and this structure will not}

be discussed further here.

The structure d6terminations.

General infor- mation on the diffractometer and its operation ^is presented ^{in an} accompanying ^paper by Busing ^and Levy [2]. Information on procedures followed in data collection and on data processing ^is given ⁱⁿ

another paper by ^{Brown and} Levy [3].

Absorption corrections have been applied ^{to the}

data for all of the structures discussed here, except

the data in the determination of the XeF2, ^which

did not require correction. The corrections were

(1) Operated for the U. S. Atomic Energy ^Commission by Union Carbide Corporation.

computed ^{with the} program of Wehe, Busing, ^and Levy for the IBM 7090 computer [4].

Final refinement was carried out in every ^case

by ^{the method of} least squares, ^with adjustment

of individual anisotropic ^thermal parameters ^for

each atom. The full-matrix Fortran least-squares

program (OR FLS) ^of Busing, Martin, ^and Levy [5],

or a modification of it, ^was always ^{used. The}

observations were the values of F 0 2b,,., ^{the observed}

square of the ^structure factor. Observations were

weighted by ^the reciprocals ^of their variances

(see ^{reference 3 for} calculation of variances). Qua- lity of each refinement is indicated by specifying

the value of the discrepancy factor,

and the value of the standard deviation of an obser- vation of unit weight,

where w is the weight ^{of an} observatiou, ^{It is the}

number of observations, ^and p is the number of

parameters being determined. The expected ^value

of _6i on convergence is unity, ^{if the} errors are truly

random and correctly estimated and if the model is correct.

The Fortran function and error program

(OR FFE) ^of Busing, Martin, ^and Levy [6] ^was

used for calculation of bond lengths, angles, ^mean

vibrational displacements, ^{and so} forth, ^{with the}

attendant errors. Bond lengths ^{were corrected}

for the effects of thermal motion in some instances, according ^{to the method of} Busing ^and Levy, assuming ^{the "} riding " ^model [7].

Article published online by EDP Sciences and available at http://dx.doi.org/10.1051/jphys:01964002505046900

470

TABLE 1

CRYSTALLOGRAPIIIC DATA

Data on unit-cell parameters ^and symmetry ^are presented in Table 1 for all the structures reported,

for convenient reference.

XeF2.

^{The structure was} determined by

H. A. Levy ^{and P. A.} Agron. ^{For a} preliminary

account, ^{see reference} [14]. ^{A more} complete ^des- cription ^{of the} work will appear ^soon [15].

The crystal specimen ^{used was an} irregular ^hexa- gonal platelet, - 1.5 x ^{1.0 x 0.5 mm,} weighing

- 2 _mg, enclosed in a thin-walled capillary ^of

vitreous silica. A total of 334 separate intensity

observations were made, ^{for 91} independent ^reflec-

tions. Absorption ^{was so} slight, ^{less than 1} %,

that no absorption corrections were necessary.

During ^{the 10} days ^{of data} collection, ^the crystal

grew by sublimation at the expense of ^other

crystals ^{in the same tube. The data were correc-}

ted for this growth by ^{f actors} derived from repea- ted measurements of the (020) reflection.

The tetragonal body-centered ^{lattice was indi-}

cated from _x-ray precession photography ^{and trom}

the neutron measurements. Inspection ^{of neutron}

intensities quickly resulted in placement ^{of Xe at}

the origin ^and placement ^{ot the two fluorine atoi-ns}

on the tetrad axis at (0, 0, z) ^and (0, 0,

z), ^with

z

2/7, ^{in the} symmetry ^of space group I 4/minm.

In the least-squares refinement that followed,

the parameters adjusted ^{were the z} coordinate ot

fluorine, ^{the thermal} parameters ^for fluorine and xenon, the neutron scattering factor of xenon, and an overall scale lactor. In the last cycle, ^the

value of the xenon scattering ^{tactor from the}

neutron study ^of XeF4 ^{was used. The value of}

0.55 X cm [18] ^was used for the scattering

factor of fluorine throughout ^the refinement.

RF2

0.090 ; al

1.67.

The uncorrected Xe-F bond length in the sym- metrical linear triatomic molecule is 1.984 A

6 =

0.002 A). Correction of this length ^{for the}

effect of thermal motion, computed ^{on the reaso-}

nable assumption ^{that the} fluorine atom "rides" on

the heavier xenon atom, yielded ^{the value} 2.00 A (s ^{= 0 . 01} A) ^{for the mean} separation ^{of Xe and F.}

Each fluorine atom has one fluorine neighbor ^at

3.02 A and four at 3.09 as. Each xenon atom has eight non-bonded fluorine neighbors ^{at 3.41} A,

a somewhat greater separation ^{than the non-}

bonded xenon-fluorine distances in the XeF4 ^struc-

ture.

XeF4.

This work was carried out by

J. H. Burns, ^{P. A.} Agron, ^{and H. A.} Levy [15, 16].

The crystal specimen, weighing ^{about 25} mg,

was grown inside ^a sealed thin-walled tube of vitreous silica, ^{about 1 mm} in diameter. To the limit sin 0 Jx

0.76, ⁶²³ independent reflections

were recorded. In the period ^{of data} collection,

about one month, ^a nearly ^linear growth ^{of the} specimen ^{was observed to occur,} by transfer from other crystals ^{in the} tube. Corrections for the

growth ^were applied ^{to the} data in the same manner as in the XeF2 ^work. Absorption ^correc- tions, amounting ^{to about 5} %, ^were applied.

By ^{the time} data collection was completed,

results of two independent x-ray determinations had become available [9, 17]. Least-squares ^refi-

nement on the neutron data was started with the

parameters ^of Templeton et ^ale [9]. The para- meters adjusted ^{were :} coordinates of the fluorine atoms (the ^{xenon atoms are in fixed} positions),

individual anisotropic ^thermal parameters, ^the

neutron scattering factor of xenon, and an overall scale factor. The 24 strongest reflections were

eventually ^omitted from the data set, ^because they clearly showed effects of extinction.

The value established for the neutron scattering

factor of xenon is 0.476 X 10-12 cm. The value 0.55 X 10112 cm was used for fluorine [17].

It is a very pleasing result that the structural _pa-

rameters from the neutron analysis ^{and those}

from the two x-ray analyses ^are generally ⁱⁿ good agreement. ^{For reasons} presently unknown, however, the thermal parameters ^{of xenon are si-} gnificantly lower in the x-ray ^case.

The distances between observed atomic posi- tions, Xe-F(1) - ^1.932 A (6

^0.002 A) ^and Xe-F(2) = ^1.939 A (6

^0.002 A), were ^corrected

on the assumption that the fluorine atoms " ride "

the heavier ^xenon atom, yielding ^{the bond} length

1.95 ak (6

^0.01 ai) ^{for each.} Angle F(I)-Xe-F(2)

is 90.0~ (6

0.1~). Clearly the molecule has almost exactly ^the symmetry D4h ; ^{it is} planar by crystal symmetry.

Each fluorine atom has two intramolecular con-

tacts with fluorine atoms at 2 . 74 A and eight ^inter-

molecular contacts with fluorine atoms at 2.99 to 3.26 A. Non-bonded Xe-F contacts are at 3.25 and 3.22 A.

Results of an x-ray analysis ^{of the} crystal ^struc-

ture of the addition compound XeF2. XeF4 ^recen- tly ^{carried out at Oak} Ridge by ^{J. H. Burns} (2),

R. D. Ellison, ^{and H. ~..} Levy [15, 19] ^{are of} great

interest in connection with the neutron work on

XeF2 ^and XeF~. ^The compound ^was originally thought ^{to be a} polymorph ^of XeF4, ^{but the x-ray} analysis showed that it is indeed a molecular addi- tion compound, ^{in which the two molecules} XeF2

and XeF4 retain almost exactly ^{the same mole-}

cular parameters ^{exhibited in their individual} crystal structures.

BaC12 . 2H20. - ^The determination of structure

was carried out by V.. M. Padmanabhan (3),

W. R. Busing, ^{and A. H.} Levy. ^{For an abstract}

of the work, ^which reports the atomic coordinates,

see reference [20].

A total of 1 242 independent reflections were

collected and corrected for absorption. ^Coordi-

nates of the Ba, Cl and 0 atoms were already

available from _x-ray work [101. Hydrogen ^coordi-

nates that had been proposed ^{on the basis of a} proton-magnetic-resonance study [21] ^{were found}

to be inconsistent with the neutron data. Correct

hydrogen positions ^{were obtained from a three-}

dimensional Fourier synthesis, using ^the signs ^of

structure factors calculated from the heavy ^atom

coordinates. After preliminary refinement by

least squares, it ^was recognized that many of the

more intense reflections suffered from extinction

errors. Final refinement was on 961 observations

judged ^to be free of extinction. RF2

0.107 ;

a1

1.65. Standard errors of coordinates vary from 0.00~ to 0.004 A, ^the largest ^errors being, ^of

course, those of the hydrogen coordinates.

For each water molecule, ^{the two} hydrogen

( ~) ^Reactor Chemistry ^Division.

(1) Guest scientist from Atomic Energy Establishment, Bombay, ^India.

atoms and two Ba2+ ions make up ^an approximate

tetrahedral arrangement about the oxygen ^atom.

Three of the four hydrogen ^{atoms make} good hydrogen ^{bonds to chlorine} ions ; ^{the other} hydro-

gen is loosely ^{shared between two chlorine ions.}

Further discussion of the structure is beyond ^the

scope of this paper. It is worth noting, however,

that the structure suggests ^a plausible ^mechanism

for the unusual phenomenon of pressure twinning

that BaCI2. 2H 20 ^shows [22].

K2NbF7’

This refinement has just ^{been com-} pleted by ^{G. M.} Brown, ^{L. A. Walker} (4) ^and

H. A. Levy.

A crystal weighing ^18.5 mg ^was sealed inside a

thin-walled tube of vitreous silica for protection against ^{moisture. A} total of 1 754 observations

were made, ^{of which 1 358 were} independent. ^The

data were corrected for absorption effects, though

the corrections needed were very small, only ^about 3 ~/ .

Least-squares refinement was carried out very

quickly ^and easily, starting ^with the atomic coor-

dinates from the two-dimensional _x-ray analysis

of Hoard [11]. ^{In the} final refinement the 67 reflections of highest intensity ^were omitted from the set of observations, ^because they clearly ^were subject ^to extinction errors. 0.089 ;

61

1.11. Standard errors of coordinates are

about 0 . 001 r ^A for the niobium atom, 0 . 0016- 0 . 0025 ^{A f or the fluorine} atoms, ^and 0.0025 ^{A for}

the potassium ^ions.

The atomic coordinates are quite ^{close to those} given by Hoard, ^but they ^{are now known much}

more

precisely. Hoard remarked that the NbF?

polyhedron ^is conveniently visualized as derived from an Nb Fs group in the form of a trigonal prism by ^{the addition of a seventh fluorine atom} through

the center of one square face, ^followed by the appro-

priate distortion ". The distortion is considerable,

and the structure of the complex ^{ion is} something

of a curiosity. ^{The Nb-F bond} lengths ^{all fall in}

the range 1.91 to 1.96 ak. The intramolecular F-F distances vary ^more widely, ^{from 2.36 to}

2 . 91 A.

Chloral hydrate, CC13CH( OH) 2. - This is the work of G. M. Brown and H. A. Levy [23, 24], ^to

be published ^{in detail soon.}

Three different crystal specimens, weighing 29, 6, ^{and 2} milligrams, ^were used, ^{in an} attempt ^to

minimize extinction errors. The crystals ^were

enclosed in silica tubes to prevent sublimation.

Some 4 100 observations were recorded for selec- tion of data for averaging ^to obtain reliable values for about 2 100 independent reflections.

(4) ^Research participaut, ^Oak Ridge Institute of Nuclear

Studies, summer, 1963.

472

Approximate coordinates for the chlorine

carbon, ^and oxygen ^atoms had become available in November of 1960, ^{from a} redetermination of the chloral hydrate ^structure by ^two dimensional x-ray analysis ^{that was in} progress ^at that time and which later has been published [12]. ^{As soon}

as neutron data had been obtained from the two

larger crystals, ^a three-dimensional Fourier _syn- thesis was computed ^with signs from calculated structure factors including only ^the heavy atoms, from which reasonable locations for all three H atoms of the molecule were immediately ^obtained.

After five cycles ^of least-squares refinement, ^the

last two of which included adjustment ^{of indivi-}

dual anisotropic ^thermal parameters, ^{the value}

of RF2 ^reached 0.066, ^{and the value of} 6i reached 1.28. The largest standard deviation of an atomic coordinate was 0.0011 A for chlorine atoms,

0.0015 A for oxygen, 0.0011 A for carbon, ^and

0 . 0031 A for hydrogen.

Subsequently, ^{in a} further effort to minimize extinction _errors, data were collected using ^the

2 mg crystal ^{for those} reflections showing ^the highest intensities from the 6 mg crystal. ^Even- tually ^it appeared that data for the two smaller

crystals ^{were about} equally ^affected by extinction,

and it seemed advisable ^to omit entirely ^about

50 reflections of highest intensity. ^{After further}

refinement the value of RFI ^{went to} 0.071, ^but

the value of ₆₁ decreased to 1.02. Coordinate

changes ^were negligible, and coordinate errors re-

mained essentially unchanged.

General features of the refined structure are, of course, the ^{same as} those found in the x-ray work, except ^{that the nature of the} hydrogen bonding ^is

revealed unambiguously ^{in the neutron structure.}

All structural parameters ^{are much more} precisely

determined in the neutron work.

The and -CH(OH)2 groups ^are in staggered

conformation about the C-C axis of the molecule.

Differences in length among chemically equivalent

but crystallographically non-equivalent ^{bonds do}

not appear significant. ^Bond lengths ^{are as}

f ollows : C-Cl,1. 76 A ; C-C, ^{2 . 55} A ; C-0,1. 39 Å ;

0-H, ^{0. 98} A ; C-H, 1.10 A (lengths ^{can be} repor- ted to higher precision ^{when more reliable} cell para- meters are obtained). ^{The C-0 bond} lengths ^is significantly ^{lower than} the normal value of ~ . 42 A.

There ^are quite significant differences _{among che-}

mically equivalent ^valence angles, resulting pre-

sumably ^{from the} packing of the molecules.

Each oxygen ^atom is involved in two hydrogen

bonds. Two hydrogen ^{bonds 0-H ... 0 link two}

molecules about each of the symmetry ^{centers at} (0, 0, 0) ^and (0, 1/2, 1/2). ^Each molecule is also linked by ^two other bonds 0-H ... 0 to two neigh-

bor molecules in a helical chain about one of the

screw axes. The easy cleavage parallel ^to (100)

is consistent with the structure.

Sucrose (Cl,H22011)’

^{The sucrose structure}

was determined by ^G. M. Brown and H. A. Levy.

A preliminary report ^{is in} press [25].

Considerable effort was expended ^{to minimize}

extinction errors. Three different crystal spe- cimens were employed, weighing approxima- tely 80, 10, ^and 5 mg. The ^two smaller crystals

were immersed repeatedly ⁱⁿ liquid nitrogen ^before

data were recorded from them. Averaged ^data

for some 2 800 independent reflections were obtai- ned by careful selection and averaging ^{from about}

5 800 individual observations. Absorption ^correc-

tions were applied.

The rough ^structure of Beevers et a2. [13] ^for

sucrose furnished starting coordinates for the 12 carbon and 11 oxygen ^atoms of the molecule.

The 14 hydrogen ^{atoms attached to carbon atoms}

were inserted at calculated positions, and refine- ment was carried out by ^a combination of least- squares and Fourier methods. Eventually ^all

atoms were located precisely. jR~ === 0.046 ;

1.15. The discrepancy ^factor computed

on F instead of F2 is I~F

0.035. The standard

errors in the coordinates are as follows : 0 . 001 Q ^to 0.0015 ^A for the carbon atoms and the ether oxygen atoms ; 0.001.4 ^to 0.002~ ^{A for the} hydro- xyl oxygen atoms ; 0 . 0024 ^to 0 . 004~ ^{A for} hydro-

gen ^atoms attached to carbon atoms ; ^and 0.0023

to 0 . 0054 ^{Å f or} hydrogen ^{atoms of} hydroxyl

groups. ^From beginning ^{to end of} refinement,

the average shift of position ^{of the} 23 oxygen and carbon atoms was 0 . 28 A ; ^minimum shift, ^{0 . 06} A. ;

maximum shift, ^{0 . 91.} A.

All of the 8 hydroxyl groups per molecule parti- cipate ⁱⁿ hydrogen bonding except ^{one. Two of}

the hydrogen ^{bonds are} intramolecular. The observed cleavage parallel ^to (100) ^is neatly explained by ^the pattern ^{of the} hydrogen ^bonds.

No attempt will be made here to discuss the wealth of structural information on the sucrose

molecule made available by this determination.

Conclusion.

The order of presentation ^{of struc-}

tures in this paper ^was deliberately ^{chosen as the}

order of increasing scale of the problems, ^{as mea-}

sured by the volume of data and the number of parameters ^{to be} determined, rather than the chro-

nological ^{order in which the} determinations were

made. Perhaps this may ^{serve to} emphasize ^the greatly ^increased potential ^{of neutron} diffraction

analysis accompanying automation, ^{which makes} possible for the first time the amassing ^{of a} large

volume of good ^{data in a} reasonable period. ^If

one accepts ^at face value the apparent. quality ^of

the sucrose determination, ^for example, ^{than this}

determination must be considered at least as satis-

factory ^as any x-ray determination done for a

crystal ^{of even} approximately ^{the same} complexity.

The results seem to speak for themselves as to

what can be expected ^{f rom neutron} diffraction

analysis ^{in the near future.}

Discussion

Dr IBERS.

Vos corrections d’agitation ^ther- mique ^{ne sont pas des} corrections r6elles mais semblent indiquer les effets possibles ^de l’agitation thermique ^sur les distances interatomiques appa- rentes. 11 est clair _{que 1’on} peut maintenant d6ter- miner ^ces distances avec une precision ^bien trop grande par rapport ^{a notre} capacité ^{de les com-} prendre, c’est-A-dire de les relier aux valeurs d’6qui-

libre. L’hypoth6se qu’un ^atome chevauche l’autre est diflicile a justifier ^{dans la} plupart ^{des cas.}

Dr BROWN. - Je pense que XeF 2 ^et XeF4 ^sont

des cas dans lesquels I’hypoth6se ^{du chevau-}

chement est assez bien justifiee. Cependant, ^{il me}

faut admettre que les corrections ^sont plut6t appro- ch6es. Je _{pense que} K2NbF7 ^{est un cas similaire.}

Dr COPPENS.

Avez-vous fait des calculs d’eflets d’extinction et quel ^{crit6re avez-vous uti-}

lis6 pour d6cider qu’une ^{reflexion est} affect6e par 1’extinction ?

Dr BROWN. - Nous n’avons _pas fait de calculés d’extinction. Au contraire nous avons essay6 ^d’611-

miner toute donn6e sujette ^{a 1’effet} d’extinction.

Ce sujet ^sera trait6 dans ma seconde communi-

cation, ^en collaboration avec le Dr Levy.

BIBLIOGRAPHY [1] ^ZOCCHI (M.), ^BUSING (W. R.) ^{and LEVY} (H. A.),

unpublished.

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

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

[3] ^BROWN (G. M.) ^{and LEVY} (H. A.), ^J. Physique, 1964, 25, 497.

[4] ^WEHE (D. J.), ^BUSING (W. R.) ^{and LEVY} (H. A.),

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

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[11] ^HOARD (J. L.), J. Am. Chem. Soc., 1939, 61, ^1252.

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[13] ^BEEVERS (C. A.), ^McDONALD (T. ^R. R.), ^ROBERTSON (J. H.) ^{and STERN} (F.), ^Acta Cryst., 1952, 5, 689.

[14] ^LEVY (H. A.) ^{and AGRON} (P. A.), ^{J. Am. Chem.} Soc., 1963, 85, ^241.

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