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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 of

Standards 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 Structure

of the Aragonite Phase of CaCOs

Research

the Nati

B. Dickens and J. S. Bowen*

Institute for Materials Research

National 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 reference 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 UTATI ON : setting programs.
-4-

those of reference [6] as adapted by Picker Nuclear

AX

Corporation; 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 lookup 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 magnitude 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 Xof crystal

ray beam, misalignment/etc. Scattering factors j those f o j-
- 6 -

the neutral atoms in reference IO 7 least-squares refinements; full-matrix, with (^UFo 1 ” 1 ^ * minimized; refinements 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® +

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/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 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 pseudohexagonal 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 CO3 edges, 0(1,2), 0(1^, 2^)

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 CO3 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 distance 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 CO3 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 CO3 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 supported 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 conducted 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. American 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 Computercontrolled 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, University 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) ro

C*D 1 >—' '—• '—

I iH m CTi PQ 1 O o o O •1 • • •1

were ent. e

no (U

ca 1 O o o ro c c 1 o o o — ro -H

PQ 1 o o o CM vw o o o O - <u • • • • no s-i I 0)

4-> to 0 CD

Q>U

TO 1 O o o ro cr to

r~i o o o 3

PQ o o o CM 0)

C o o o ro U CO • • • •1 3 1 tri -P

•iH to vp fO0) +J iH

<Ti ,—. c

TO 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 u

to rH ro 3 ^ 1 in ro 4J 4-1 to

TO 1 (T>

—'—

to P

PQ 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

p

to >1 3 * , (T> ,

P 0 Dr

ft 1 in in ro 0 — — H rH «H

PQ 1 v£) in o pH

H ro fO VO in «s 0) C g • • • • •H p

i-H ^3 VH 0) H x;

ro (1) EH no Xi VD ,—, ,—, C -P ro CM CM 3 *

•w' P c

00 CO rH to -H N| cr> ro

in rH o rH OJ n3

CN

U 0) • • • • ro 4J3 m a

Q) e

in , to 0 '

CM CM rH (U o — ^

o VO o VO -p m 00 <Ti C

00 ro pH 0) in CM o ro u • • • • roCUC

•H

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

tog iH CM 0 ro +J< U u O O
[

[

f

J 0

)U 1 «U

I? 2<>^ 2 S4

7 »t* l>t

•« >?• -2B

•* IfiA -luV

111 iM no

1

#.» -66

ini) VU

2 *« 7 <: •464

iU \ii -124

t I jJ -59

12 1 -W -134

? 6 1A6 -1A4

7 I5fl 157

/O 64 7 %is 3J9 1.K.H A IS6 -iA7

J47 -iSO A 4A 53 9 65 -69

27* -16 9 47 -45 0 lAl -|A7 lO 146 14A

46 -44 15 42 40 1 117 lln II 46 4?

57 -52 11 ISO -157 2 47 -20 12 160 156

27* 0 1? 25* 3 3 143 146 13 39 V.

151 li. IM lUH

13 Vi 72 464 -506

HO -h3

99* -l3

to». -113

7 192 -197

9 68 -92

9 21* 13

9 29* 37

inn -104

2S « 2 U Uo -157

12 96

2 32

W»«2

0 471 454

1 4U7 -404

2 16* -7

3 476 -471

4 16* -in

5 214 -217

6 153 -156

7 191 185

B 44 -42

9 241 ?42

10 24* -4

237 -239

43 -39

39 -31

A 25* -15

9 152 152

in 3A 35

11 27» 5

104

94

1 145 145

5 126 -129

A 23* 17

9 222 -226 M 42 -44

It 104 -107

12 25* 7 13 101 97 KKtS

257 24Q 2 63

25

2 n * 20*

5 >IA -216

6 22* -51

7 15A -162

A «;3» 4 9 25» 6

10 45 -34

I! 153 152

12 47 45

3 llA -119

-466

I5l 146 V 24* 615 635

9 2|a 4

10 7l -71

12 205 -201

14 119 -117

2 * 5 f 1

1 264 254

2 653 659

3 253 -247

4 270 272

5 117 119

6 51 50

7 90 -85

A 256 -253

9 49 -55

10 227 -230

1 1 47 S4

12 2A« 2A

13 2A* 14

}4 146 144

2 * Kt 2

0 515 513

1 123 120

2 141 142

3 61 -58

4 234 -257

5 199 -194

4 129 -i35

5 116 -11A

6 27* -2A

7 274 -27

to 149 147

6 126 129

7 21* -24

M 177 1A0

9 22* 12

10 64 62 n 26* 21 12 39 -A

13 29* 12

116 -117

176 1A2

167 -16A

5 53 52

1 50 -5n

2 56 52

in 127 -129

11 54 56

12 135 -130 2.V»5

1 201 -202

2 290 292

3 123 122

4 165 164

5 22* 10 6 23* 17

7 132 i29

A 1A2 -1A0

9 46 37

in 150 -150

11 a9 -96

12 4A 27

155 157

105 109

72 -69

75 63

343 -346

55 -55

24* -1 62 -71

5 » K »2

0 120 -122

1 206 204

2 74 -73

3 360 360

4 194 -25

5 200 204

6 1A9 19a

7 194 -196

A 234 -21

9 19A -19A

10 234 9

11 90 -AT

12 47 -47

13 105 A3

5 221 -224

6 21* 3

7 268 -266

A 45 -42

9 24* -A

10 47 -3A

It 179 194 2A* -2

9 225 »29

11 .39 24 13 101 -102

256 -259 206 -201

51 -46

11 144 -|46

12 27* 13

13 101 -AA

6 47 45

1 107 114

0 3A 33

1 16A -169

2 20* lA

3 305 -303

0 74 -77

5 191 -191

6 59 56

7 179 179

A 60 -59

9 1A9 1A6

3 21* -19

4 71 -72

5 220 213

154 146 6 35

A 26* 23

9 24* -20

10 25* -4

11 120 -123

^ 2u3 -202

3 <.9 -52

Ibl ISV

7 244 -lA 5 2l4

in luu -lui

11 264 -36

12 IcU -117

5 150 -150

9 294 26

0 129 122

3 1 36 -136

4 29 -12

5 94 -A2

6 151 -153

1 143 -147

2 A9 -90

0 669 675

2 39 39

4 152 -145

6 268 -275

9 196 -171

to 116 116

12 225 217

4.K*

2 2A6 -26A

3 106 -111

4 335 -340

1 44 -34

/ 2o6 272

3 4 I 4 10

1 176 176

6 IW -192

1/5 -177

3 u5 69

2u3 -207

5 130 -131

6 ^64 21

7 v2 -91

ri IvV 165

9 ^'** 40

10 lil> 94

4 * 5 *n

10 12A 129 j 115} 56 4 12 304 23 5 h7

2 42 -43

3 59 -72

4 46 -48

5 259 263

6 234 -I

7 224 213

54 39

294 -11 9 73 -67

3.1* 34 10 274 25

152 -152 11 77 -83

5 101 102 b 264 39

7 64 -88

9 2b4 -14

V 178 -ITS

lU <94 -2A

I 177 177

b2 67

50 -57

113 119

164 -Ibl

234 -3

131 -134

At -76

42 -10

•I 221 225

1 2oh -2lu

2 *9 -54

3 235 -232

4 214 -11

5 112 -109

7 104 101

3 39 -29

4 43 -30

5 149 -140

6 254 -4

7 118 -121

6 284 15

9 27* -5

3 190 -169

4 274 -27

5 53 -54

b 51 -49

1 120 -122

9 129 -127

1 294 32

I 7h -170

2A4 -9

159 -136

3 254 7

4 126 -123

5 7S -62

6 141 -139

7 b6 60

A 59 -92

9 47 -43

10 tOu 101

7 264 -17

ITO -173

254 -31

HO -77

3 175 -165

4 54 -51

5 113 -U6

47 43 5 294 37 243 241 6 201 -203

1 49 30

2 152 -151

5 27# 20

7 294 -11

9 171 167

5 I7l 175

6 55 -41

7 97 lOS

5 116 116

6 130 122

7 I2A -127

A 47 -42

2 147 -143

3 274 -in

4 142 -142

5 264 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, 2 III) 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 calculated from the standard deviations in the

atomic 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) A

C, 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) 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.
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