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» » NATIONAL BUREAU OF STANDARDS REPORT
NBS PROJECT NBS REPORT
31 1.05-11-3110561 June 30, 1970 10 276
Progress Report
on THE CRYSTAL STRUCTURE OF THE ARAGONITE PHASE OF CaC03
B. Dickens* and j. S. BowenT
* Research Chemist, Dental Research Section, National Bureau of Standards, Washington, D. C. 20234.
+ Research Associate from the American Dental Association in the Dental Research Section, National Bureau of Standards, Washington, D. C. 20234.
This investigation is part of the dental research program conducted
by the National Bureau of Standards in cooperation with the Council on Dental Research of the American Dental Association; the National Insti-
tute for Dental Research; the Dental Research Division of the U. S. Army Medical Research and Development Command; the Dental Sciences Division of the School of Aerospace Medicine, USAF; and the Veterans Admin istration.
IMPORTANT NOTICE
NATIONAL BUREAU OF ST !SS accounting documents intended additional evaluation for use within the Government, Approved for public release by the subjected to in and review. For this reason, th : listing of this Report, either Director of the National Institute of whole or in part, is not authoi e Office of the Director, National Bureau of Standards, Washingti Standards and Technology (NIST) by the Government agency for which the Report has been specifically copies for its own use. on October 9, 2015.
U.S. DEPARTMENT OF COMMERCE
NATIONAL BUREAU OF STANDARDS
The Crystal Structure of the Aragonite Phase of CaCOs
B. Dickens and J. S. Bowen*
Institute for Materials Research National Bureau of Standards Washington, D. C. 20234
Research associate of the American Dental Association at the Nati nal Bureau of Standards, Washington, D. C. 20234.
Abstract
Aragonite (CaCOg) crystallizes in the unit cell ^ =
4.9598(5) I, h = 7.9641(9) A, and c = 5.7379(6) i at 25°C with
four formula weights in space-group Pmcn. The structure has
been refined to = 0.024, R = 0.040 using 765 X-ray reflections
from a single crystal. The Ca ion is coordinated to nine
oxygens with Ca...O distances in the range 2.414(1) A to
2,653(1) A. The two unique C-0 distances in the COg group
are 1.288(2) A (on the mirror plane) and 1.283(1) A. The
two unique O-C-0 angles are 119.62(4)® (across the mirror plane) and 120.,13(8)®. - 2 -
1. INTRODUCTION
Aragonite (CaCOg) is found in nature as a mineral and is an important biomineral because of its presence in coral, clam shells, gallstones and otoliths. It is isomorphous with the carbonates of large divalent cations such as Ba, Sr and
Pb.
Aragonite is less stable than the calcite phase of CaCOg at room temperature, but is denser than calcite. This suggests that aragonite is more stable than calcite at low temperatures and/or high pressures. More details are available in ref- erence 1. Because of the importance of aragonite, and because of the possibility of performing calculations on the lattice energies of selected carbonates along the lines suggested by
Busing [2], we have collected new X-ray data from a single crystal of aragonite and have refined the structure from the positions given in 1924 by Bragg [3].
2. STRUCTURE DETERMINATION
FORMULA (ideal) : CaCOg (aragonite phase) ; UNIT CELL ; orthorhombic with a = 4.9598(5) A, b = 7.9641(9) A, _c =
5.7379(6) 1 at 25®C (calculated by least squares from 12 20 values observed on a diffractometer); volume; 226.65 A®; radiation, Mo(Kqj^), \ = 0.70926 A; monochromator; highly -3- oriented graphite crystal; space-group; Pmcn; contents
4 (CaC03 ); reciprocal lattice extinctions, hkO: h + k = 2n f 1,
— 3 hOi,: = 2n + 1; observed density, 2.947(2) g*cm [4];
® calculated density, 2.944 g*cm ; CRYSTAL : material available heavily twinned; small wedge largest single crystal fragment found; this wedge was attached to thin borate glass fiber with clear household cement; fiber attached to insert in goniometer head with epoxy cement; origin of crystal, mineral sample
#75538 from National Museum of Natural History, Smithsonian
Institution, Washington, D. C. Supplied by J. S. White, Jr.; linear absorption corrections made by 8x8x8 Gaussion quadrature using subroutines written by C. W. Burnham [5] and adapted by B. Dickens; maximum and minimum corrections for absorption = 0.963 and 0.880 (transmission factors).
INTENSITY DATA : number of reflections, 2356 collected from 2 octants and merged into a unique set of 765, of which 619 are "observed" and 146 are "unobserved"; unobserved reflections are those less than 2a above background; maximum sin0/X for data 0.907 A method used to estimate data; 6/20 scan, scintillation counter; diffractometer; Picker 4-circle single-crystal diffractometer automated by PDP 8/l computer through FACS-1 interface and adapted to include least
significant digit of counts; COMP UTAT I ON : setting programs. J
-4- those of reference [6] as adapted by Picker Nuclear AX 1.4° = Corporation; scan range: + 114.6 "Y" / AX 0.692,
X = 0.70926 1 ; scan parameters: backgrounds counted at higher and lower 20 for 100 sec. each; 0/20 scan at 0.25°/min for
20 from one background position to the other; attenuators?
0.025 mm thick layers of Nb, 1 layer for first attenuator,
2 for second, 3 for third; scan range correction; table look- up method to obtain values recommended in reference [7]; paper tape processing program written by B. Dickens for Univac
1108 computer, contains adaptions of similar program by
F. A. Mauer (NBS) , standard reflection plotting routine and extince reflection editing routine from programs by J. M. this program Stewart, University of Maryland; /uses an intense standard reflection at low angle to correct for change in intensity
of the primary X-ray beam. Counts in peak = I = P-(T/2T ) 13
+ B^) , a (I) = (P + (Bj^ + Bjj) (T/(2Tg))2)2^ p = ( (AF) (LP) - t (I))®, a(F) = (a ( (I) /2) (LP/l) where P = counts at the peak position, Bj^ and B^^ = background counts at lower and higher
20 respectively, T = time spent counting peak, T = time spent counting background, AF = attenuator factor, LP =
Lorentz-polar ization correction. Data merging program for equivalent reflections, written by B. Dickens for Univac in this program is
1108 computer ; /each set of equivalent reflections/treated as -5-
follows: Reflections which were all unobserved were averaged
and given the largest individual standard deviation in the
set. Unobserved reflections in the presence of at least one
observed reflection were discarded. Observed reflections which^ subsequent to this step^ occurred only once in the list were copied unchanged but their standard deviations were
increased by a factor of three. Observed reflections with magnitudes which agreed within the counting statistics and
reflections with magnitudes whose ratios fell within the
range 0.95 to 1.06 were averaged and given as standard
deviation the maximum of the standard deviation from
counting statistics and the standard deviation from the
range estimate [8,9]. Under these circumstances, reflections whose magnitudes did not pass the criteria were discarded.
If no reflections passed the criteria, the highest magni-
tude was taken and the associated standard deviation multiplied by five. The justification for these arbitrary increases of standard deviations is that without some corroboration, every reflection is suspect because of the possibilities of multiple reflection, including the "tail" of nearby intense
ref lections in its measurement, change in intensity of X- of crystal ray beam, misalignment/etc. Scattering factors j those f o j- - 6 -
the neutral atoms in reference IO 7 least-squares refine-
* ments; full-matrix, with ” ^ minimized; refine- (^UFo 1 1 ments include unobserved reflections which calculate higher than 2 a above background; least-squares weights; 1 /a®;
5,= (2(w11f„1-|f^I1))VE(w|Fo|) = )^, R = XllFol-lF^ll/llF^I;
thermal parameters have the form exp (-1/4 1 h® +
k^ c*® B 2a*b*B, c*B .,k . B §2 + 33 J,® + „hk + 2a* ^ 3 M + 2b*c*B, Least squares and electron density synthesis calculations carried out with X-ray 67 system [11] of computing programs.
FINAL REFINEMENT ; Rw = 0.024; R = 0.040, average shift/error for last cycle = 0.^17; standard deviation of an observation 1 of unit weight = (S(w(Fq-F^) ) ®/(765-28) ) ® = 0.775.
The highest peak in an electron density difference synthesis calculated after the final anisotropic refinement to R^ = 0.024 corresponded to about 1/3 of an electron and was about 0.95 A from C towards 0(1). The largest correlation coefficients are 0.34-0.44 between the scale factor and the and temperature factors of Ca. 1 , ^33
The atomic parameters are given in table 1. The observed
and calculated structure factors are given in table 2 .
3. DESCRIPTION OF THE STRUCTURE
The structure of aragonite, the main points of which are well known, is shown in figure 1. The Ca ions lie in pseudo-
hexagonal layers parallel to ( 001 ) and the layer sequence is . .
-7-
ABAB . The Ca layers are separated by COg groups which lie
in two layers parallel to ( 001 ) , and form columns parallel
to [ 001 ].
3,1. The Ca ion environments
The Ca ion lies on the mirror plane at x = 1/4. Its
environment is shown in figure 2 and summarized in table 3.
2^) The coordination contains three CO 3 edges, 0(1,2), 0(1^, IV V II II III and 0(2 ,2 ) and three apexes, 0(1 ,2 ,2 ). The
apparent thermal motion of Ca is almost isotropic, (table
1, Fig. 2)
3.2, The CO 3 group
The dimensions of the COg group are given in table 4.
All C-0 distances in the COg group are essentially equal with
an average of 1.286 A, This agrees well with the C-0 dis-
tance of 1.283(2) reported [12] for calcite. There appears
to be some significant deviation from trigonality in the
angles; the reported angle of 119.62® for 0(2) -C-0 (2^) is consistent with the 0 ( 2 , 2 ^) edge
of the CO 3 group being coordinated slightly more strongly to
Ca as judged from the Ca...O distances. If the apparent
thermal motions of the atoms in the COg group are attributed
to thermal motion rather than to slight positional disorder,
there seems to be oscillation within the CO 3 layer, i ,e , more or less perpendicular to the edge coordination to Ca.
Similarly, 0(1) may be undergoing some additional wagging
out of the CO 3 layer,
A CKNOWLEDGEMENT
We thank P. B. Kingsbury for technical help. The ORTEP program of C, K. Johnson, Oak Ridge National Laboratory, was used to draw the figures. This investigation was sup- ported in part by research grant DE-00572 to the American
Dental Association from the National Institute of Dental
Research and is part of the dental research program con- ducted by the National Bureau of Standards, in cooperation with the Council on Dental Research of the American Dental
Association; the United States Army Medical Research and
Development Command; the Dental Sciences Division of the
School of Aerospace Medicine, USAF; the National Institute of
Dental Research and the Veterans Administration. ,
- 9 -
References
[1] C. Palache, H, Berman and C. Frondel. Dana's system
of mineralogy, vol II, 7th ed., J. Wiley and Sons, N, Y.
1963, 182-193.
[2] W. R, Busing. An aid to the analysis of interionic and
intermolecular forces in crystals. Abstract Ml. Amer-
ican Crystallographic Association winter meeting, Tucson
Arizona (1968)
[3] W. L. Bragg, The structure of aragonite. Proc. Roy Soc
London, 105, 16-39 (1924).
[4] Reference [1], page 184.
[5] C. W. Burnham. Computation of absorption corrections
and the significance of end effect. Am. Min., _51 159-
167 (1966).
[6] W. R. Busing, R. D. Ellison, H. A. Levy, S. P. King and
R. T, Roseberry. The Oak Ridge Laboratory Computer-
controlled X-ray Diffractometer. Oak Ridge National
Laboratory Report ORNL 4143, January 1968. -]£)-
[7] L. E. Alexander and G. S, Smith. Single crystal
intensity measurements with the three circle counter
diffractometer. Acta Cryst., 983-1004 (1962).
[8] J. A. Ibers. Estimates of the standard deviations of
the observed structure factors and of the electron
density from intensity data. Acta Cryst., 9^ 652-654
(1956) .
[9] L. H. C. Tippett. On the extreme individuals and
the range of samples taken from a normal population.
Biometrika, 17 364-387 (1925).
[10] International Tables for X-ray Crystallography, _3
p. 202. The Kynoch Press, Birmingham, England 1962.
[11] J, M. Stewart, Editor. X-ray 67 program system for
X-ray crystallography. Technical report 67-58, Univ-
ersity of Maryland, College Park, Maryland, 20742,
December, 1967.
[12] H. Chessin, W. C. Hamilton and B. Post. Position and
thermal parameters of oxygen atoms in calcite. Acta
Cryst., IB 689-693 (1965).
USCOMM-NBS-DC — ' —^I' 1 .1
iH IT) ro >—' '—• '— C*D 1 I iH m CTi O o o O PQ 1 • • • •
1 1
were ent e no (U ca O o o ro c c 1 — o o o ro -H 1 o o o CM vw PQ 1 o o o O -
I 0) 4-> to 0 CD Q> U TO O o o ro cr to 1 r~i o o o 3 PQ o o o CM 0) C o o o ro U CO • • • • 3 1
1 tri -P •iH to vp fO 0) +J iH Aragonite to rH ro 3 in ro 4J 4-1 to ^ 1 — '— TO 1 (T> to P in ro ro vw Q) PQ 1 a^ in 00 uo O i-H 0 -p • • • • 0) in rH C CM CO o o o 0) o o o r-- H >i\ o o o CO 3 If) in in tn CM CM CM H • • • • &4 to g iH CM 0 ro +J U u O O < 1 [ [ f J 0 ? 6 1A6 -1A4 5 » K »2 ^ 2u3 -202 2 42 -43 3 175 -165 7 I5fl 157 3 <.9 -52 3 59 -72 4 54 -51 7 »t* l>t /O 64 7 %is 3J9 1.K.H A IS6 -iA7 0 120 -122 6 47 45 Ibl ISV 4 46 -48 9 129 -127 5 113 -U6 •« >?• -2B J47 -iSO A 4A 53 9 65 -69 1 206 204 7 244 -lA 5 2l4 5 259 263 •* IfiA -luV 27* -16 9 47 -45 0 lAl -|A7 lO 146 14A 2 74 -73 6 234 -I 111 iM no 46 -44 15 42 40 1 117 lln II 46 4? 3 360 360 7 224 213 )U 1 «U 1 #.» -66 57 -52 11 ISO -157 2 47 -20 12 160 156 4 194 -25 54 39 I? 2 <>^ 2 S 4 ini) VU 27* 0 1? 25* 3 3 143 146 13 39 V. 5 200 204 294 -11 9 73 -67 1 294 32 4 129 -i35 6 1A9 19a in luu -lui 3.1* 34 10 274 25 5 116 -11A 7 194 -196 11 264 -36 152 -152 11 77 -83 6 27* -2A A 234 -21 1 107 114 12 IcU -117 7 274 -27 9 19A -19A 47 43 5 294 37 10 234 9 243 241 6 201 -203 2 *« 7 <: •464 11 90 -AT 147 47 -47 5 150 -150 to 149 12 1 44 -34 13 105 A3 / 2o6 272 6 126 129 3 4 I 4 10 1 49 30 1 145 145 7 21* -24 2 152 -151 M 177 1A0 9 294 26 5 101 102 I 7h -170 9 22* 12 b 264 39 2A4 -9 A 23* 17 10 64 62 7 64 -88 159 -136 151 li. IM lUH 9 222 -226 5 126 -129 n 26* 21 9 2b4 -14 M 42 -44 12 39 -A 0 129 122 V 178 -ITS It 104 -107 13 29* 12 5 53 52 5 221 -224 lU <94 -2A 12 25* 7 6 21* 3 13 Vi 72 13 101 97 7 268 -266 3 1 36 -136 5 27# 20 A 45 -42 4 29 -12 7 294 -11 464 -506 KKtS 9 24* -A 5 94 -A2 I 177 177 3 254 7 9 171 167 HO -h3 10 47 -3A 6 151 -153 b2 67 4 126 -123 99* -l3 257 24Q 2 63 It 179 194 3 39 -29 5 7S -62 to». -113 2 32 25 3 llA -119 116 -117 1 50 -5n 2A* -2 1 176 176 4 43 -30 6 141 -139 2 n * 176 1A2 2 56 52 5 149 -140 7 b6 60 2 147 -143 20* 167 -16A 6 254 -4 A 59 -92 3 274 -in 5 >IA -216 1 143 -147 7 118 -121 9 47 -43 4 142 -142 6 22* -51 0 3A 33 2 A9 -90 6 284 15 10 tOu 101 5 264 13 7 192 -197 7 15A -162 -466 1 16A -169 6 IW -192 9 27* -5 5 I7l 175 9 68 -92 A «;3» 4 I5l 146 V 24* 2 20* lA 6 55 -41 9 21* 13 9 25» 6 615 635 in 127 -129 3 305 -303 7 97 lOS 10 45 -34 9 2|a 4 11 54 56 0 74 -77 iU \ii -124 I! 153 152 10 7l -71 12 135 -130 5 191 -191 t I jJ -59 12 47 45 12 205 -201 6 59 56 50 -57 12 1 -W -134 14 119 -117 2.V»5 7 179 179 0 669 675 113 119 A 60 -59 2 39 39 164 -Ibl 3 190 -169 2 * 5 f 1 1 201 -202 9 1A9 1A6 4 152 -145 234 -3 4 274 -27 W »«2 2 290 292 6 268 -275 131 -134 5 53 -54 7 264 -17 1 264 254 3 123 122 9 196 -171 1/5 -177 At -76 b 51 -49 0 471 454 2 653 659 4 165 164 to 116 116 3 u5 69 42 -10 1 4U7 -404 237 -239 3 253 -247 5 22 * 10 12 225 217 2u3 -207 5 116 116 2 16* -7 43 -39 4 270 272 6 23* 17 5 130 -131 6 130 122 3 476 -471 39 -31 5 117 119 7 132 i29 9 225 »29 4.K* 6 ^64 21 7 I2A -127 9 29* 37 4 16* -in 6 51 50 A 1A2 -1A0 11 .39 24 7 v2 -91 ITO -173 A 47 -42 -85 46 37 5 214 -217 7 90 9 13 101 -102 ri IvV 165 1 120 -122 254 -31 25* -15 A -253 in -150 3 21* -19 2 2A6 -26A 6 153 -156 A 256 150 9 ^'** 40 •I 221 225 HO -77 5 2A4 17 7 9 9 49 -55 11 a9 -96 4 71 -72 3 106 -111 191 185 152 152 10 lil> 94 1 2oh -2lu B 44 -42 in 3A 35 10 227 -230 12 4A 27 5 220 213 4 335 -340 2 *9 -54 9 241 ?42 11 27» 5 1 1 47 S4 256 -259 4 * 5 *n 3 235 -232 10 24* -4 12 2A« 2A 206 -201 154 146 6 35 4 214 -11 104 13 2A* 14 51 -46 A 26* 23 5 112 -109 26 1 63 12 96 94 }4 146 144 9 24* -20 5 97 -9« inn -104 10 25* -4 7 104 101 3 304 15 2 S « 2 U 2 * Kt 2 155 157 11 120 -123 10 12A 129 j Uo -157 105 109 115} 56 4 0 515 513 72 -69 12 304 23 5 h7 1 123 120 75 63 2 141 142 343 -346 3 61 -58 55 -55 11 144 -|46 0 so 52 4 234 -257 24* -1 12 27* 13 5 199 -194 62 -71 13 101 -AA 1 IA7 189 , Table 3 The Ca environment in aragonite (CaCOg) Atoms Distance, Ca, O(lII) 2.414(1) III) Ca 0(2^1, 2 2.445(1) Ca, 0(2, 2^) 2.520(1) Ca, 0(2lV, 2.544(1) Ca, 0(1, 2.653(1) In all tables of interatomic distances and angles, the figures in parentheses are standard deviations in the last digit and were cal- culated from the standard deviations in the atomic positional parameters and the unit cell parameters. Table 4 The CO 3 group and its environment in aragonite (CaCOg) Atoms Distance, A, or angle, C, 0(1) 1.288(2) A C, 0(2) 1.283(1) 0 ( 1 ) , 0 ( 2 ) 2.229(1) l) 0 ( 2 ) , 0 ( 2 2.219(1) ° 0 ( 1 ) , C, 0(2) 120.13(8) 0(2l) 0 ( 2 ) , C, 119.62(4) 0 ( 1 ) , 2.414(1) A 0 ( 1 ) , (Ca^^, Ca^^^) 2.653(1) 0 ( 2 ) , Ca 2.445(1) 0 ( 2 ) , Ca^^ 2.520(1) 0 ( 2 ), Ca^^ 2.544(1) . Figure legends 1. A stereoscopic illustration of the crystal structure of aragonite (CaCOg) . A unique set of atoms is labelled. The origin of the crystallographic coordinate system is marked by *, 2. The Ca environment in aragonite (CaCOg). The labels refer to atoms in table 3. 3. The COg group environment in aragonite (CaCOg) The labels refer to atoms in table 4. r t r r i t t t i [ [ i I I I i [ [ I I ! I 1 I I \ Id' I t t r