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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

for use within the Government,

and review. For this reason, th

whole or in part, is not authoi

Bureau of Standards, Washingti

the Report has been specifically

Approved for public release by the

Director of the National Institute ofStandards and Technology (NIST)

on October 9, 2015.

!SS accounting documents intended

subjected to additional evaluation

: listing of this Report, either in

e Office of the Director, National

by the Government agency for which

copies for its own use.

U.S. DEPARTMENT OF COMMERCE

NATIONAL BUREAU OF STANDARDS

The Crystal Structureof the Aragonite Phase of CaCOs

Research

the Nati

B. Dickens and J. S. Bowen*

Institute for Materials ResearchNational Bureau of Standards

Washington, D. C. 20234

associate of the American Dental Association at

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; COMPUTAT ION : setting programs.

-4-

those of reference [6] as adapted by Picker Nuclear

AXCorporation; scan range: 1.4° + 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 programStewart, 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)

J

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 Univacin 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 (^UFo 1”

1^* minimized; refine-

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 1h® +

B§2 k^ + c*® B 33 J,® + 2a*b*B, „hk + 2a* c*B^ 3 M + 2b*c*B, .,k .

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/errorfor 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 1 , and ^33 temperature factors of Ca.

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.

The coordination contains three CO 3 edges, 0(1,2), 0(1^, 2^)

IV V II II IIIand 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 consistentwith the 0 ( 2 , 2 ^) edgeof 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,

ACKNOWLEDGEMENT

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

Table

1

Atomic

Parameters

in

Aragonite

(CaCOg)

iH IT) roC*D

1

>—' '—• '—

'

I iH m CTi

PQ 1O o o O

•

1

• • •

1

were

ent

.

eno (U

ca1

O o o ro c c1

o o o —ro -H

PQ 1o o o CM vw

o o o O - <u

• • • • no s-i

I 0)

4-> to

0 CD

Q> UTO

1O o o ro cr to

r~i o o o 3PQ o o o CM 0) C

o o o ro U CO

• • • •

1

3 1

tri -P•iH tovp fO

0)+J iH

<Ti ,—. cTO in ro ro X TO

TO 1

'—

'

W' U -H 0(<33

PQ o VO CM •H }-l

\D o O VW 4J G• • • • •H rO •H

<—

I

r—

1

C 61 (U

•H tH uto rH ro

3^ 1

in ro 4J 4-1 to

TO 1 (T>—

'

'—

^

to PPQ 1

a^ in ro ro vw Q)

in 00 uo O i-H 0 -p• • • • 0)

rH C <D e•H f—

1

ro

O pto >1 3

*,

(T> ,

—

P 0 Drft

1in in ro 0— — H rH «H

PQ 1v£) in o pH H ro fO

VO in «s 0) C g• • • • •H p

i-H ^3 VH 0)

H x;ro (1) EHno Xi

VD ,—, ,—, C -Pro CM CM 3 *•w' P c00 CO rH to -H

N| cr> roin rH o rH OJ n3CN U 0)

• • • • ro 4J

3m aQ) e

in , to 0'

—

CM CM rH (U o— ^

—

o VO o VO -pm 00 <Ti C00 ro pH 0)

in CM o ro u• • • • ro

CU

C•H

CM CO

o o o 0)

o o o r-- H>i\ o o o CO 3

If) in in tnCM CM CM H

• • • • &4

to

g iH CM0 ro+J

<U u O O

[

[

f

J 0

)U 1 «UI? 2<>^ 2S4

7 »t* l>t

•« >?• -2B•* IfiA -luV

111 iM no1

1

#.» -66ini) VU

2 *« 7 <: •464

iU \ii -124t I jJ -5912 1 -W -134

? 6 1A6 -1A47 I5fl 157

/O 64 7 %is 3J9 1.K.H A IS6 -iA7J47 -iSO A 4A 53 9 65 -6927* -16 9 47 -45 0 lAl -|A7 lO 146 14A46 -44 15 42 40 1 117 lln II 46 4?57 -52 11 ISO -157 2 47 -20 12 160 15627* 0 1? 25* 3 3 143 146 13 39 V.

151 li. IM lUH

13 Vi 72

464 -506HO -h399* -l3

to». -113

7 192 -1979 68 -929 21* 13

9 29* 37

inn -1042S « 2 UUo -157

12 96

2 32

W »«2

0 471 4541 4U7 -4042 16* -73 476 -4714 16* -in5 214 -2176 153 -1567 191 185B 44 -429 241 ?42

10 24* -4

237 -23943 -3939 -31

A 25* -159 152 152

in 3A 3511 27» 5

10494

1 145 145

5 126 -129A 23* 179 222 -226M 42 -44It 104 -10712 25* 713 101 97

KKtS

257 24Q 2 6325

2 n *20*

5 >IA -2166 22* -517 15A -162A «;3» 49 25» 6

10 45 -34I! 153 15212 47 45

3 llA -119

-466I5l 146 V 24*615 635

9 2|a 410 7l -7112 205 -20114 119 -117

2 * 5 f 1

1 264 2542 653 6593 253 -2474 270 2725 117 1196 51 507 90 -85A 256 -2539 49 -5510 227 -2301 1 47 S412 2A« 2A13 2A* 14}4 146 144

2 * Kt 2

0 515 5131 123 1202 141 1423 61 -584 234 -2575 199 -194

4 129 -i355 116 -11A6 27* -2A7 274 -27

to 149 147

6 126 1297 21* -24M 177 1A09 22* 12

10 64 62n 26* 2112 39 -A13 29* 12

116 -117176 1A2167 -16A

5 53 52

1 50 -5n2 56 52

in 127 -12911 54 5612 135 -130

2.V»5

1 201 -2022 290 2923 123 1224 165 1645 22* 106 23* 177 132 i29A 1A2 -1A09 46 37in 150 -15011 a9 -9612 4A 27

155 157105 10972 -6975 63

343 -34655 -5524* -1

62 -71

5 » K »2

0 120 -1221 206 2042 74 -733 360 3604 194 -255 200 2046 1A9 19a7 194 -196A 234 -219 19A -19A10 234 911 90 -AT12 47 -47

13 105 A3

5 221 -2246 21* 37 268 -266A 45 -429 24* -A10 47 -3AIt 179 194

2A* -2

9 225 »2911 .39 2413 101 -102

256 -259206 -20151 -46

11 144 -|4612 27* 1313 101 -AA

6 47 45

1 107 114

0 3A 331 16A -1692 20* lA3 305 -3030 74 -775 191 -1916 59 567 179 179A 60 -599 1A9 1A6

3 21* -194 71 -725 220 213

154 146 6 35A 26* 239 24* -20

10 25* -411 120 -123

^ 2u3 -2023 <.9 -52

Ibl ISV7 244 -lA 5 2l4

in luu -lui11 264 -3612 IcU -117

5 150 -150

9 294 26

0 129 122

3 1 36 -1364 29 -125 94 -A26 151 -153

1 143 -1472 A9 -90

0 669 6752 39 394 152 -1456 268 -2759 196 -171

to 116 11612 225 217

4.K*

2 2A6 -26A3 106 -1114 335 -340

1 44 -34/ 2o6 2723 4 I 4 10

1 176 176

6 IW -192

1/5 -1773 u5 69

2u3 -2075 130 -1316 ^64 217 v2 -91ri IvV 1659 ^'** 40

10 lil> 94

4 * 5 *n

10 12A 129 j115} 56 412 304 23 5 h7

2 42 -433 59 -724 46 -485 259 2636 234 -I7 224 213

54 39294 -11 9 73 -673.1* 34 10 274 25

152 -152 11 77 -83

5 101 102b 264 397 64 -889 2b4 -14V 178 -ITS

lU <94 -2A

I 177 177b2 67

50 -57113 119164 -Ibl234 -3

131 -134At -7642 -10

•I 221 2251 2oh -2lu2 *9 -543 235 -2324 214 -115 112 -109

7 104 101

3 39 -294 43 -305 149 -1406 254 -47 118 -1216 284 159 27* -5

3 190 -1694 274 -275 53 -54b 51 -49

1 120 -122

9 129 -127

1 294 32

I 7h -1702A4 -9

159 -136

3 254 7

4 126 -1235 7S -626 141 -1397 b6 60A 59 -929 47 -4310 tOu 101

7 264 -17

ITO -173254 -31HO -77

3 175 -1654 54 -515 113 -U6

47 43 5 294 37243 241 6 201 -203

1 49 302 152 -151

5 27# 207 294 -119 171 167

5 I7l 1756 55 -417 97 lOS

5 116 1166 130 1227 I2A -127A 47 -42

2 147 -1433 274 -in4 142 -1425 264 13

5 2A4 17

5 97 -9«

0 so 52

26 1 63

3 304 15

1 IA7 189

Table 3

The Ca environment in aragonite (CaCOg)

Atoms Distance,

Ca, O(lII) 2.414(1)

Ca

,

0(2^1, 2III) 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 andangles, the figures in parentheses are standarddeviations in the last digit and were cal-culated from the standard deviations in theatomic positional parameters and the unit

cell parameters.

Table 4

The CO3 group and its environment in aragonite (CaCOg)

Atoms Distance, A, or angle,

C, 0(1) 1.288(2) AC, 0(2) 1.283(1)

0 ( 1 ) , 0 ( 2 ) 2.229(1)0 ( 2 ) , 0 ( 2 l) 2.219(1)

0 ( 1 ) , C, 0(2) 120.13(8) °

0 ( 2 ) , C, 0(2l) 119.62(4)

0 ( 1 ) , 2.414(1) A0 ( 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

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