The sample submitted for analysis consisted of many small pieces passed
spontaneously by a young boy. Because of its peculiar composition, as revealed
by the structure determination, we conclude that the sample probably did not
come from the urinary tract and may correspond to a spurious stone. No
pathology is yet known which would lead to such lithiasis (Daudon et
al., 1993; Bazin et al., 2012). Indeed, calcium
glycinate is a
common compound in a variety of manufactured cosmetic products or is proposed
as a complementary food. The chemical phase commonly reported is the
monohydrate. However, we cannot exclude changes in the hydration related to
special storage of the product, or even the possibility that the pure
trihydrate is sold as such with the `calcium glycinate' name. Factitious
stones are not exceptional findings and the literature contains many clinical
cases reporting the history of patients with psychatric disorders who
simulated a false nephrolithiasis disease (Gault et al., 1988;
Sabot
et al., 1999). Urolithiasis is only one aspect of Munchausen
syndrome,
which may be observed as a variety of clinical symptoms. In the present case,
the father of the child experienced a history of recurrent nephrolithiasis,
thus probably explaining why the boy may have chosen to simulate urolithiasis
rather than another type of disease.
The cell parameters are those obtained from powder data indexing. The reduced
cell [a = 5.7627 (3), b = 9.6572 (5) and c = 9.6878 (5) Å,
and α = 82.533 (2), β = 89.412 (3) and γ = 76.997 (3)°] is obtained by the
transformation matrix (001/100/010). Rietveld refinement was carried out
with restraints on the glycine [C—C = 1.527 (5) Å, N—C = 1.453 (5) Å,
O—C = 1.255 (5) Å, O—O = 2.230 (5) Å, C—H = 1.00 (1) Å and N—H =
0.92 (1) Å] and water [O—H = 0.90 (1) Å and H···H = 1.49 (1) Å]
molecules, as taken from the Ca(gly)2.H2O crystal structure (Fox et
al., 2007).
Data collection: HIGHSCORE (PANalytical, 2003); cell refinement: McMaille (Le Bail, 2004); data reduction: HIGHSCORE (PANalytical, 2003); program(s) used to solve structure: ESPOIR (Le Bail, 2001); program(s) used to refine structure: FULLPROF (Rodriguez-Carvajal, 1993); molecular graphics: DIAMOND (Brandenburg, 1999); software used to prepare material for publication: PLATON (Spek, 2009).
poly[[di-µ-aqua-bis(glycinato-
κ2N,
O)calcium(II)]
monohydrate]
top
Crystal data top
[Ca(C2H4NO2)2(H2O)2]·H2O | V = 520.76 (5) Å3 |
Mr = 242.25 | Z = 2 |
Triclinic, P1 | F(000) = 256 |
Hall symbol: -P 1 | The cell parameters are those obtained from powder data indexing.
The reduced cell a = 5.763, b = 9.657, c = 9.688, alpha = 82.53,
beta = 89.41, gamma = 77.00 is obtained by the transformation
matrix (0 0 -1, -1 0 0, 0 1 0) |
a = 9.6572 (5) Å | Dx = 1.545 Mg m−3 |
b = 9.6878 (5) Å | Cu Kα radiation, λ = 1.540560 Å |
c = 5.7627 (3) Å | T = 293 K |
α = 90.588 (3)° | Particle morphology: fine powder |
β = 76.997 (3)° | white |
γ = 97.467 (2)° | flat sheet, 8 × 8 mm |
Data collection top
PANalytical X'Pert PRO diffractometer | Data collection mode: reflection |
Radiation source: X-ray tube | Scan method: step |
None monochromator | 2θmin = 4.943°, 2θmax = 69.943°, 2θstep = 0.017° |
Specimen mounting: dusted through a sieve | |
Refinement top
Rp = 2.044 | 126 parameters |
Rwp = 2.710 | 67 restraints |
Rexp = 1.323 | Hydrogen site location: inferred from neighbouring sites |
RBragg = 2.63 | H atoms treated by a mixture of independent and constrained refinement |
R(F) = 6.82 | (Δ/σ)max = 0.03 |
χ2 = 4.202 | Background function: interpolated |
3825 data points | Preferred orientation correction: none |
Profile function: pseudo-Voigt | |
Crystal data top
[Ca(C2H4NO2)2(H2O)2]·H2O | β = 76.997 (3)° |
Mr = 242.25 | γ = 97.467 (2)° |
Triclinic, P1 | V = 520.76 (5) Å3 |
a = 9.6572 (5) Å | Z = 2 |
b = 9.6878 (5) Å | Cu Kα radiation, λ = 1.540560 Å |
c = 5.7627 (3) Å | T = 293 K |
α = 90.588 (3)° | flat sheet, 8 × 8 mm |
Data collection top
PANalytical X'Pert PRO diffractometer | Scan method: step |
Specimen mounting: dusted through a sieve | 2θmin = 4.943°, 2θmax = 69.943°, 2θstep = 0.017° |
Data collection mode: reflection | |
Refinement top
Rp = 2.044 | χ2 = 4.202 |
Rwp = 2.710 | 3825 data points |
Rexp = 1.323 | 126 parameters |
RBragg = 2.63 | 67 restraints |
R(F) = 6.82 | H atoms treated by a mixture of independent and constrained refinement |
Special details top
Geometry. Bond distances, angles etc. have been calculated using the rounded
fractional coordinates. All su's are estimated from the variances of the
(full) variance-covariance matrix. The cell e.s.d.'s are taken into account in
the estimation of distances, angles and torsion angles |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
Ca1 | 0.8757 (3) | 0.8959 (3) | 0.2978 (5) | 0.0873 (19)* | |
OW1 | 0.8683 (8) | 1.0369 (7) | 0.6539 (14) | 0.126 (3)* | |
H11 | 0.8490 (12) | 1.1169 (8) | 0.624 (2) | 0.126 (3)* | |
H12 | 0.8356 (12) | 0.9849 (11) | 0.7746 (14) | 0.126 (3)* | |
OW2 | 0.9626 (7) | 1.1346 (8) | 0.0889 (14) | 0.126 (3)* | |
H21 | 0.8726 (12) | 1.1566 (13) | 0.097 (4) | 0.126 (3)* | |
H22 | 0.995 (2) | 1.1748 (12) | 0.213 (3) | 0.126 (3)* | |
OW3 | 0.7748 (9) | 0.2564 (7) | 0.897 (2) | 0.139 (5)* | |
H31 | 0.815 (7) | 0.340 (4) | 0.83 (2) | 0.139 (5)* | |
H32 | 0.687 (4) | 0.262 (3) | 0.990 (12) | 0.139 (5)* | |
N1 | 0.8325 (6) | 0.6569 (5) | 0.1838 (6) | 0.095 (2)* | |
H41 | 0.7505 (9) | 0.6331 (10) | 0.1160 (15) | 0.095 (2)* | |
H42 | 0.9065 (10) | 0.6256 (9) | 0.0636 (15) | 0.095 (2)* | |
N2 | 0.6257 (5) | 0.8512 (6) | 0.5114 (6) | 0.095 (2)* | |
H51 | 0.6062 (11) | 0.7795 (9) | 0.6308 (14) | 0.095 (2)* | |
H52 | 0.5886 (9) | 0.9274 (9) | 0.5966 (19) | 0.095 (2)* | |
O1 | 0.9089 (8) | 0.7462 (3) | 0.5953 (8) | 0.094 (2)* | |
O2 | 0.8296 (8) | 0.5377 (5) | 0.7711 (11) | 0.094 (2)* | |
O3 | 0.5112 (5) | 0.8158 (8) | −0.0467 (11) | 0.094 (2)* | |
O4 | 0.7221 (4) | 0.9006 (8) | 0.0328 (8) | 0.094 (2)* | |
C1 | 0.8120 (6) | 0.5621 (5) | 0.3836 (7) | 0.095 (2)* | |
H61 | 0.7063 (7) | 0.5364 (13) | 0.4468 (15) | 0.095 (2)* | |
H62 | 0.8496 (12) | 0.4733 (7) | 0.3278 (15) | 0.095 (2)* | |
C2 | 0.8787 (9) | 0.6159 (4) | 0.5866 (8) | 0.095 (2)* | |
C3 | 0.5337 (6) | 0.8088 (6) | 0.3513 (7) | 0.095 (2)* | |
H71 | 0.5141 (13) | 0.7046 (6) | 0.3559 (17) | 0.095 (2)* | |
H72 | 0.4393 (7) | 0.8419 (12) | 0.4124 (18) | 0.095 (2)* | |
C4 | 0.5918 (5) | 0.8560 (11) | 0.0928 (6) | 0.095 (2)* | |
Geometric parameters (Å, º) top
Ca1—O1 | 2.359 (5) | OW2—H21 | 0.913 (15) |
Ca1—OW1 | 2.446 (8) | OW3—H31 | 0.90 (6) |
Ca1—OW2 | 2.569 (8) | OW3—H32 | 0.90 (5) |
Ca1—O4 | 2.361 (5) | N1—C1 | 1.442 (6) |
Ca1—N1 | 2.410 (6) | N2—C3 | 1.441 (7) |
Ca1—N2 | 2.436 (5) | N1—H41 | 0.961 (10) |
Ca1—OW2i | 2.456 (8) | N1—H42 | 0.955 (10) |
Ca1—OW1ii | 2.550 (8) | N2—H51 | 0.953 (10) |
O1—C2 | 1.261 (5) | N2—H52 | 0.947 (11) |
O2—C2 | 1.275 (7) | C1—C2 | 1.515 (8) |
O3—C4 | 1.265 (8) | C3—C4 | 1.521 (6) |
O4—C4 | 1.247 (8) | C1—H61 | 1.003 (10) |
OW1—H11 | 0.848 (11) | C1—H62 | 0.999 (9) |
OW1—H12 | 0.839 (12) | C3—H72 | 0.994 (10) |
OW2—H22 | 0.908 (18) | C3—H71 | 1.002 (8) |
| | | |
O1···OW1 | 2.900 (8) | N2···O3iii | 2.545 (7) |
O1···O4iii | 3.229 (7) | N2···O4 | 2.731 (6) |
O1···N1 | 2.738 (7) | N2···OW1 | 3.023 (9) |
O1···N2 | 3.174 (9) | N2···C4iii | 3.293 (5) |
O1···OW1ii | 2.933 (9) | N2···O1 | 3.174 (9) |
O1···OW2ii | 2.605 (9) | N2···N1 | 3.210 (7) |
OW1···OW2ii | 3.077 (11) | N1···H22i | 2.884 (16) |
OW1···OW2iii | 2.960 (11) | C2···N1iii | 3.395 (6) |
OW1···OW3iv | 2.677 (11) | C2···C2x | 3.435 (10) |
OW1···O1 | 2.900 (8) | C4···N2vi | 3.293 (5) |
OW1···N2 | 3.023 (9) | C2···H41iii | 3.035 (10) |
OW1···O1ii | 2.933 (9) | C2···H31 | 2.96 (6) |
OW1···O4iii | 2.587 (9) | C2···H22ii | 2.622 (16) |
OW1···OW1ii | 2.923 (11) | C2···H62x | 3.009 (14) |
O2···N1iii | 2.637 (7) | C2···H42iii | 2.821 (10) |
O2···OW3 | 2.780 (9) | C3···H41 | 2.953 (11) |
OW2···OW1ii | 3.077 (11) | C3···H52xi | 2.937 (11) |
OW2···O1ii | 2.605 (9) | C4···H51vi | 2.734 (9) |
OW2···O4 | 3.097 (10) | C4···H12vi | 2.794 (12) |
OW2···N1i | 2.845 (9) | C4···H41 | 2.826 (13) |
OW2···OW3v | 2.719 (12) | C4···H52vi | 2.957 (11) |
OW2···O4i | 3.031 (8) | C4···H32vii | 2.92 (4) |
OW2···OW2i | 2.911 (11) | H11···OW3iv | 2.125 (14) |
OW2···OW1vi | 2.960 (11) | H11···H22 | 2.50 (2) |
O3···N2vi | 2.545 (7) | H11···H31iv | 2.48 (7) |
O3···OW3vii | 2.702 (11) | H12···OW2iii | 2.715 (12) |
OW3···OW1viii | 2.677 (11) | H12···OW3iv | 2.817 (13) |
OW3···O2 | 2.780 (9) | H12···C4iii | 2.794 (12) |
OW3···O3vii | 2.702 (11) | H12···H21iii | 2.54 (2) |
OW3···OW2ix | 2.719 (12) | H12···O4iii | 1.772 (10) |
O4···N2 | 2.731 (6) | H12···H22ii | 2.41 (2) |
O4···OW2i | 3.031 (8) | H21···H31v | 2.56 (8) |
O4···N1 | 2.930 (8) | H21···H32v | 2.37 (4) |
O4···OW2 | 3.097 (10) | H21···OW1vi | 2.80 (2) |
O4···O1vi | 3.229 (7) | H21···OW3v | 1.976 (19) |
O4···OW1vi | 2.587 (9) | H21···H12vi | 2.54 (2) |
O1···H12 | 2.639 (11) | H22···H11 | 2.50 (2) |
O1···H22ii | 1.711 (18) | H22···O1ii | 1.711 (18) |
O1···H11ii | 2.593 (13) | H22···C2ii | 2.622 (16) |
OW1···H22 | 2.826 (18) | H22···H12ii | 2.41 (2) |
OW1···H52 | 2.860 (12) | H22···H42i | 2.467 (16) |
OW1···H21iii | 2.80 (2) | H31···C2 | 2.96 (6) |
OW1···H22ii | 2.780 (17) | H31···H11viii | 2.48 (7) |
O2···H31 | 1.93 (4) | H31···O2 | 1.93 (4) |
O2···H42iii | 2.118 (11) | H31···H21ix | 2.56 (8) |
O2···H41iii | 2.202 (11) | H32···C4vii | 2.92 (4) |
OW2···H42i | 2.559 (12) | H32···O3vii | 1.92 (4) |
OW2···H12ii | 2.656 (13) | H32···H21ix | 2.37 (4) |
OW2···H12vi | 2.715 (12) | H41···C2vi | 3.035 (10) |
O3···H51vi | 1.929 (10) | H41···O2vi | 2.202 (11) |
O3···H32vii | 1.92 (4) | H41···H71 | 2.564 (15) |
O3···H52vi | 2.258 (12) | H41···C3 | 2.953 (11) |
OW3···H12viii | 2.817 (13) | H41···C4 | 2.826 (13) |
OW3···H21ix | 1.976 (19) | H42···H22i | 2.467 (16) |
OW3···H11viii | 2.125 (14) | H42···O2vi | 2.118 (11) |
O4···H21 | 2.772 (15) | H42···C2vi | 2.821 (10) |
O4···H41 | 2.700 (12) | H51···O3iii | 1.929 (10) |
O4···H12vi | 1.772 (10) | H51···C4iii | 2.734 (9) |
N1···O1 | 2.738 (7) | H52···C4iii | 2.957 (11) |
N1···O2vi | 2.637 (7) | H52···O3iii | 2.258 (12) |
N1···O4 | 2.930 (8) | H52···C3xi | 2.937 (11) |
N1···OW2i | 2.845 (9) | H52···H72xi | 2.288 (14) |
N1···C2vi | 3.395 (6) | H62···C2x | 3.009 (14) |
N1···C3 | 3.353 (8) | H71···H41 | 2.564 (15) |
N1···N2 | 3.210 (7) | H72···H52xi | 2.288 (14) |
N1···C4 | 3.337 (9) | | |
| | | |
O1—Ca1—OW1 | 74.2 (2) | Ca1—OW2—H22 | 95.0 (10) |
O1—Ca1—OW2 | 144.1 (3) | H21—OW2—H22 | 108.2 (19) |
O1—Ca1—O4 | 138.1 (3) | Ca1—OW2—H21 | 94.7 (11) |
O1—Ca1—N1 | 70.06 (16) | Ca1i—OW2—H22 | 122.0 (13) |
O1—Ca1—N2 | 82.9 (2) | Ca1i—OW2—H21 | 120.7 (15) |
O1—Ca1—OW2i | 112.0 (3) | H31—OW3—H32 | 111 (6) |
O1—Ca1—OW1ii | 73.3 (3) | Ca1—N1—C1 | 111.7 (3) |
OW1—Ca1—OW2 | 82.0 (3) | Ca1—N2—C3 | 111.1 (3) |
OW1—Ca1—O4 | 125.4 (3) | Ca1—N1—H41 | 116.0 (7) |
OW1—Ca1—N1 | 140.6 (2) | C1—N1—H41 | 105.5 (7) |
OW1—Ca1—N2 | 76.5 (2) | C1—N1—H42 | 105.6 (7) |
OW1—Ca1—OW2i | 139.6 (3) | Ca1—N1—H42 | 115.7 (7) |
OW1—Ca1—OW1ii | 71.6 (3) | H41—N1—H42 | 101.2 (8) |
OW2—Ca1—O4 | 77.7 (3) | Ca1—N2—H51 | 114.4 (7) |
OW2—Ca1—N1 | 137.4 (2) | Ca1—N2—H52 | 115.4 (7) |
OW2—Ca1—N2 | 117.5 (2) | C3—N2—H51 | 105.8 (8) |
OW2—Ca1—OW2i | 70.8 (3) | C3—N2—H52 | 106.5 (7) |
OW1ii—Ca1—OW2 | 73.9 (2) | H51—N2—H52 | 102.8 (9) |
O4—Ca1—N1 | 75.8 (2) | N1—C1—C2 | 115.8 (4) |
O4—Ca1—N2 | 69.39 (16) | O1—C2—C1 | 116.3 (5) |
OW2i—Ca1—O4 | 78.0 (2) | O1—C2—O2 | 123.3 (5) |
OW1ii—Ca1—O4 | 144.2 (2) | O2—C2—C1 | 110.4 (5) |
N1—Ca1—N2 | 83.0 (2) | N2—C3—C4 | 115.7 (5) |
OW2i—Ca1—N1 | 71.5 (2) | O3—C4—C3 | 115.0 (6) |
OW1ii—Ca1—N1 | 112.2 (2) | O3—C4—O4 | 126.0 (4) |
OW2i—Ca1—N2 | 142.6 (2) | O4—C4—C3 | 116.8 (4) |
OW1ii—Ca1—N2 | 144.2 (2) | N1—C1—H62 | 109.7 (6) |
OW1ii—Ca1—OW2i | 72.5 (3) | C2—C1—H61 | 108.7 (7) |
Ca1—O1—C2 | 121.5 (4) | N1—C1—H61 | 108.0 (7) |
Ca1—OW1—Ca1ii | 108.4 (3) | H61—C1—H62 | 105.6 (10) |
Ca1—OW2—Ca1i | 109.2 (3) | C2—C1—H62 | 108.6 (8) |
Ca1—O4—C4 | 121.8 (4) | N2—C3—H71 | 108.4 (8) |
Ca1ii—OW1—H12 | 99.8 (10) | N2—C3—H72 | 109.0 (7) |
Ca1—OW1—H12 | 108.7 (9) | C4—C3—H72 | 109.5 (8) |
H11—OW1—H12 | 129.7 (14) | H71—C3—H72 | 105.8 (11) |
Ca1—OW1—H11 | 108.6 (10) | C4—C3—H71 | 108.0 (8) |
Ca1ii—OW1—H11 | 99.2 (10) | | |
| | | |
OW1—Ca1—O1—C2 | 156.0 (7) | N2—Ca1—N1—C1 | −68.8 (4) |
OW2—Ca1—O1—C2 | −153.7 (6) | OW2i—Ca1—N1—C1 | 138.9 (5) |
O4—Ca1—O1—C2 | 30.1 (8) | OW1ii—Ca1—N1—C1 | 77.5 (5) |
N1—Ca1—O1—C2 | −7.1 (6) | O1—Ca1—N2—C3 | −129.2 (4) |
N2—Ca1—O1—C2 | 78.0 (7) | OW1—Ca1—N2—C3 | 155.4 (4) |
OW2i—Ca1—O1—C2 | −66.4 (7) | OW2—Ca1—N2—C3 | 82.0 (5) |
OW1ii—Ca1—O1—C2 | −129.0 (7) | O4—Ca1—N2—C3 | 18.9 (4) |
O1—Ca1—OW1—Ca1ii | 77.2 (3) | N1—Ca1—N2—C3 | −58.5 (4) |
OW2—Ca1—OW1—Ca1ii | −75.6 (3) | OW2i—Ca1—N2—C3 | −11.9 (6) |
O4—Ca1—OW1—Ca1ii | −144.3 (3) | OW1ii—Ca1—N2—C3 | −177.2 (4) |
N1—Ca1—OW1—Ca1ii | 102.9 (4) | O1—Ca1—OW2i—Ca1i | −141.7 (3) |
N2—Ca1—OW1—Ca1ii | 163.5 (3) | OW1—Ca1—OW2i—Ca1i | −50.4 (5) |
OW2i—Ca1—OW1—Ca1ii | −28.3 (5) | OW2—Ca1—OW2i—Ca1i | 0.0 (3) |
OW1ii—Ca1—OW1—Ca1ii | 0.0 (3) | O4—Ca1—OW2i—Ca1i | 81.0 (3) |
O1—Ca1—OW2—Ca1i | 101.2 (4) | N1—Ca1—OW2i—Ca1i | 159.9 (3) |
OW1—Ca1—OW2—Ca1i | 149.7 (3) | N2—Ca1—OW2i—Ca1i | 110.3 (4) |
O4—Ca1—OW2—Ca1i | −81.4 (3) | O1—Ca1—OW1ii—Ca1ii | −78.5 (3) |
N1—Ca1—OW2—Ca1i | −28.9 (5) | OW1—Ca1—OW1ii—Ca1ii | 0.0 (3) |
N2—Ca1—OW2—Ca1i | −140.1 (2) | OW2—Ca1—OW1ii—Ca1ii | 86.7 (3) |
OW2i—Ca1—OW2—Ca1i | 0.0 (3) | O4—Ca1—OW1ii—Ca1ii | 125.5 (4) |
OW1ii—Ca1—OW2—Ca1i | 76.6 (3) | N1—Ca1—OW1ii—Ca1ii | −138.0 (2) |
O1—Ca1—O4—C4 | 38.5 (9) | N2—Ca1—OW1ii—Ca1ii | −28.1 (5) |
OW1—Ca1—O4—C4 | −68.4 (8) | Ca1—O1—C2—O2 | −145.8 (7) |
OW2—Ca1—O4—C4 | −139.2 (8) | Ca1—O1—C2—C1 | −3.5 (9) |
N1—Ca1—O4—C4 | 74.4 (7) | Ca1—O4—C4—O3 | −157.7 (8) |
N2—Ca1—O4—C4 | −13.3 (7) | Ca1—O4—C4—C3 | 4.7 (11) |
OW2i—Ca1—O4—C4 | 148.2 (8) | Ca1—N1—C1—C2 | −24.3 (6) |
OW1ii—Ca1—O4—C4 | −177.2 (7) | Ca1—N2—C3—C4 | −24.3 (7) |
O1—Ca1—N1—C1 | 16.2 (4) | N1—C1—C2—O1 | 19.4 (9) |
OW1—Ca1—N1—C1 | −10.1 (6) | N1—C1—C2—O2 | 166.3 (6) |
OW2—Ca1—N1—C1 | 167.7 (4) | N2—C3—C4—O3 | 178.7 (7) |
O4—Ca1—N1—C1 | −139.3 (4) | N2—C3—C4—O4 | 14.4 (11) |
Symmetry codes: (i) −x+2, −y+2, −z; (ii) −x+2, −y+2, −z+1; (iii) x, y, z+1; (iv) x, y+1, z; (v) x, y+1, z−1; (vi) x, y, z−1; (vii) −x+1, −y+1, −z+1; (viii) x, y−1, z; (ix) x, y−1, z+1; (x) −x+2, −y+1, −z+1; (xi) −x+1, −y+2, −z+1. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
OW1—H11···OW3iv | 0.848 (11) | 2.125 (14) | 2.677 (11) | 122.4 (11) |
OW1—H12···O4iii | 0.839 (12) | 1.772 (10) | 2.587 (9) | 163.2 (13) |
OW2—H21···OW3v | 0.913 (15) | 1.976 (19) | 2.719 (12) | 137.3 (19) |
OW2—H22···O1ii | 0.908 (18) | 1.711 (18) | 2.605 (9) | 167.7 (18) |
OW3—H31···O2 | 0.90 (6) | 1.93 (4) | 2.780 (9) | 156 (7) |
OW3—H32···O3vii | 0.90 (5) | 1.92 (4) | 2.702 (11) | 144 (4) |
N1—H41···O2vi | 0.961 (10) | 2.202 (11) | 2.637 (7) | 106.2 (7) |
N1—H42···O2vi | 0.955 (10) | 2.118 (11) | 2.637 (7) | 112.6 (8) |
N2—H51···O3iii | 0.953 (10) | 1.929 (10) | 2.545 (7) | 120.1 (8) |
N2—H52···O3iii | 0.947 (11) | 2.258 (12) | 2.545 (7) | 96.5 (6) |
Symmetry codes: (ii) −x+2, −y+2, −z+1; (iii) x, y, z+1; (iv) x, y+1, z; (v) x, y+1, z−1; (vi) x, y, z−1; (vii) −x+1, −y+1, −z+1. |
Experimental details
Crystal data |
Chemical formula | [Ca(C2H4NO2)2(H2O)2]·H2O |
Mr | 242.25 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 293 |
a, b, c (Å) | 9.6572 (5), 9.6878 (5), 5.7627 (3) |
α, β, γ (°) | 90.588 (3), 76.997 (3), 97.467 (2) |
V (Å3) | 520.76 (5) |
Z | 2 |
Radiation type | Cu Kα, λ = 1.540560 Å |
Specimen shape, size (mm) | Flat sheet, 8 × 8 |
|
Data collection |
Diffractometer | PANalytical X'Pert PRO diffractometer |
Specimen mounting | Dusted through a sieve |
Data collection mode | Reflection |
Scan method | Step |
2θ values (°) | 2θmin = 4.943 2θmax = 69.943 2θstep = 0.017 |
|
Refinement |
R factors and goodness of fit | Rp = 2.044, Rwp = 2.710, Rexp = 1.323, RBragg = 2.63, R(F) = 6.82, χ2 = 4.202 |
No. of data points | 3825 |
No. of parameters | 126 |
No. of restraints | 67 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Selected geometric parameters (Å, º) topCa1—O1 | 2.359 (5) | Ca1—OW1ii | 2.550 (8) |
Ca1—OW1 | 2.446 (8) | O1—C2 | 1.261 (5) |
Ca1—OW2 | 2.569 (8) | O2—C2 | 1.275 (7) |
Ca1—O4 | 2.361 (5) | O3—C4 | 1.265 (8) |
Ca1—N1 | 2.410 (6) | O4—C4 | 1.247 (8) |
Ca1—N2 | 2.436 (5) | N1—C1 | 1.442 (6) |
Ca1—OW2i | 2.456 (8) | N2—C3 | 1.441 (7) |
| | | |
O1—Ca1—OW1 | 74.2 (2) | OW1ii—Ca1—O4 | 144.2 (2) |
O1—Ca1—OW2 | 144.1 (3) | N1—Ca1—N2 | 83.0 (2) |
O1—Ca1—O4 | 138.1 (3) | OW2i—Ca1—N1 | 71.5 (2) |
O1—Ca1—N1 | 70.06 (16) | OW1ii—Ca1—N1 | 112.2 (2) |
O1—Ca1—N2 | 82.9 (2) | OW2i—Ca1—N2 | 142.6 (2) |
O1—Ca1—OW2i | 112.0 (3) | OW1ii—Ca1—N2 | 144.2 (2) |
O1—Ca1—OW1ii | 73.3 (3) | OW1ii—Ca1—OW2i | 72.5 (3) |
OW1—Ca1—OW2 | 82.0 (3) | Ca1—O1—C2 | 121.5 (4) |
OW1—Ca1—O4 | 125.4 (3) | Ca1—OW1—Ca1ii | 108.4 (3) |
OW1—Ca1—N1 | 140.6 (2) | Ca1—OW2—Ca1i | 109.2 (3) |
OW1—Ca1—N2 | 76.5 (2) | Ca1—O4—C4 | 121.8 (4) |
OW1—Ca1—OW2i | 139.6 (3) | Ca1—N1—C1 | 111.7 (3) |
OW1—Ca1—OW1ii | 71.6 (3) | Ca1—N2—C3 | 111.1 (3) |
OW2—Ca1—O4 | 77.7 (3) | N1—C1—C2 | 115.8 (4) |
OW2—Ca1—N1 | 137.4 (2) | O1—C2—C1 | 116.3 (5) |
OW2—Ca1—N2 | 117.5 (2) | O1—C2—O2 | 123.3 (5) |
OW2—Ca1—OW2i | 70.8 (3) | O2—C2—C1 | 110.4 (5) |
OW1ii—Ca1—OW2 | 73.9 (2) | N2—C3—C4 | 115.7 (5) |
O4—Ca1—N1 | 75.8 (2) | O3—C4—C3 | 115.0 (6) |
O4—Ca1—N2 | 69.39 (16) | O3—C4—O4 | 126.0 (4) |
OW2i—Ca1—O4 | 78.0 (2) | O4—C4—C3 | 116.8 (4) |
Symmetry codes: (i) −x+2, −y+2, −z; (ii) −x+2, −y+2, −z+1. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
OW1—H11···OW3iii | 0.848 (11) | 2.125 (14) | 2.677 (11) | 122.4 (11) |
OW1—H12···O4iv | 0.839 (12) | 1.772 (10) | 2.587 (9) | 163.2 (13) |
OW2—H21···OW3v | 0.913 (15) | 1.976 (19) | 2.719 (12) | 137.3 (19) |
OW2—H22···O1ii | 0.908 (18) | 1.711 (18) | 2.605 (9) | 167.7 (18) |
OW3—H31···O2 | 0.90 (6) | 1.93 (4) | 2.780 (9) | 156 (7) |
OW3—H32···O3vi | 0.90 (5) | 1.92 (4) | 2.702 (11) | 144 (4) |
N1—H41···O2vii | 0.961 (10) | 2.202 (11) | 2.637 (7) | 106.2 (7) |
N1—H42···O2vii | 0.955 (10) | 2.118 (11) | 2.637 (7) | 112.6 (8) |
N2—H51···O3iv | 0.953 (10) | 1.929 (10) | 2.545 (7) | 120.1 (8) |
N2—H52···O3iv | 0.947 (11) | 2.258 (12) | 2.545 (7) | 96.5 (6) |
Symmetry codes: (ii) −x+2, −y+2, −z+1; (iii) x, y+1, z; (iv) x, y, z+1; (v) x, y+1, z−1; (vi) −x+1, −y+1, −z+1; (vii) x, y, z−1. |
The chemical formulae of compounds found in pathological calcifications are quite diverse, and stones occur in many tissues and organs (Daudon et al., 1993; Bazin et al., 2012). Although many of them were first characterized as minerals or were synthesized, it sometimes happens that they are encountered for the very first time in living bodies. One such recent new crystal structure is calcium tartrate tetrahydrate form II from rat urinary stones (Le Bail, Bazin et al., 2009). This paper deals with the structure determination of a new calcium glycinate hydrate, namely poly[[di-µ-aqua-bis(glycinato-κ2N,O)calcium(II)] monohydrate], (I) (informally known as calcium glycinate trihydrate), possibly coming from the kidney of a young boy, although this remains to be verified since the sample was not surgically removed but given hand-to-hand from the patient to the physician as passed spontaneously (see Experimental).
When a sample of (I) was received for X-ray diffraction analysis, no complete chemical characterization had yet been made. FT–IR, the usual identification method (which failed) for such kidney stones, indicated the presence of carbonyl groups in the form of carboxylate and the very probable purity (Fig. 1) of the sample, and X-ray fluorescence demonstrated the presence of calcium. In the absence of any suitable single crystal, the structure determination by powder diffractometry was undertaken following the most modern approaches, as detailed in recent blind tests (Le Bail, Cranswick et al., 2009). Indexing using the McMaille software (Le Bail, 2004) led to a triclinic cell with figures of merit (FoM) M20 = 70 (de Wolff, 1968) and F20 = 137 (0.004, 38) (Smith & Snyder, 1979). The intensities were extracted from the powder pattern by the Le Bail (2005) method, confirming the cell by an excellent profile fitting using the FULLPROF software (Rodriguez-Carvajal, 1993) and allowing an attempt at structure solution. Meanwhile, DSC–TGA (differential scanning calorimetry–thermogravimetric analysis), followed by X-ray powder analysis, showed that the residue at 873 K was CaCO3 calcite. The initial model allowing for further Rietveld refinements was obtained from the ESPOIR direct-space software (Le Bail, 2001) working in `scratch mode', inserting one Ca atom and testing various hypothetical compositions (all atoms moved randomly under a Monte Carlo process to obtain agreement between the extracted structure factors and the calculated ones). A model corresponding to the best agreement obtained by this direct-space approach allowed us to recognize infinite zigzag chains of Ca atoms in an eightfold coordination, with square antiprisms sharing edges. The two identical very simple molecules involved in the structure could only be glycine, according to their characteristic three-dimensional shape and given the context of the sample origin and the structural relationship with synthetic calcium glycinate monohydrate, (II), pre-existing in the literature (Fox et al., 2007). The H-atom positions were inferred from neighbouring sites. The final Rietveld plot is shown in Fig. 2 and an ellipsoid plot of (I) is shown in Fig. 3.
The crystal structure of (I) is built up from [CaOW4O2N2] square antiprisms (OW is a water O atom) sharing two OW–OW edges to form infinite zigzag Ca···Ca···Ca chains along the c axis. These chains are interconnected in a three-dimensional manner by hydrogen bonding through the uncoordinated OW3 water molecule (Fig. 4), which connects to three chains, one via the two coordinated water molecules OW1 and OW2 through OW1—H11···OW3iii and OW2—H21···OW3iv hydrogen bonds [symmetry codes: x, y + 1, z; (v) x, y + 1, z - 1] and the other two via the uncoordinated O atoms (involved in the C═O bond) of the two independent glycinate ligands through OW3—H31···O2 and OW3—H32···O3vi hydrogen bonds [symmetry code: (vi) -x + 1, -y + 1, -z + 1]. The remaining hydrogen bonds are within chains. The two NH2 groups also point towards uncoordinated atoms O2 and O3, while atoms H12 and H22 of the two coordinated water molecules are directed towards atoms O1 and O4.
In the monohydrate, (II), the water molecule enters only one corner of the [CaOWO5N2] square antiprisms, which share two O–O edges forming similar zigzag chains. In both structures, there is N,O-chelation, i.e. each glycinate ligand coordinates via both the carboxylate and the amino groups. No O,O-chelation occurs. The trihydrate adds the basic motif of the terminal N,O-chelating form to the list of binding modes of Hgly or gly- in calcium glycine compounds (Natarajan et al., 2012), while the monohydrate is characterized by the µ3-bridging O,O,O',N-tetradendate and µ2-bridging O,O,N-tridentate modes. The chains corresponding to both hydrates are compared in Figs. 5 and 6. A topotactic dehydration from the trihydrate to the monohydrate looks possible, in spite of the need for some reorientation of the glycine molecules. However, the first endothermic peak on the DSC graph at 400 K corresponds to 19% mass loss, which is probably associated with the departure of 2.5 water molecules, so it may exist as a hemihydrate, but this was not checked by thermodiffractometry. The next events on the DSC–TGA curve correspond to the departure of the remaining water (in the 473–573 K range), followed by a strong endothermic peak at 593 K and two small exothermic peaks at 683 and 723 K, CaCO3 calcite being present in the 773–873 K range.