Examination of whewellite kidney stones by scanning electron microscopy and powder neutron diffraction techniques

Kidney stones made of whewellite, i.e. calcium oxalate monohydrate, exhibit various morphological aspects. The crystalline structure of whewellite at the atomic scale was revisited through a single-crystal neutron study at room temperature using a four-circle automated diffractometer. The possible relationships between the various morphological types of whewellite stones and their structural characteristics were examined at the mesoscopic scale by the use of scanning electron microscopy and at the nanometric scale by powder neutron diffraction. All types of whewellite stones displayed a similar structure at the nanometric scale. However, significant differences were found at the mesoscopic scale. In particular, the crystallites in kidney stones resulting from a genetic hyperoxaluria exhibited a peculiar structure. There was a close relationship between stone morphology and crystallite organization at the mesoscopic level and the effectiveness of extracorporeal shockwave lithotripsy.

Computing details

Data collection: DIF4 STOE MODIFIED VERSION; cell refinement: DIF4 STOE MODIFIED VERSION; data reduction: COLL5 LOCAL MODIFIED VERSION; program(s) used to solve structure: Echigo et al. 2005; program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).

Figures

(I)

Crystal data

C4H4Ca2O10	F(000) = 328
Mr = 292.23	Dx = 2.210 Mg m^−3
Monoclinic, P21/c	Neutron radiation, λ = 0.8302 Å
a = 6.316 (5) Å	Cell parameters from 15 reflections
b = 14.541 (3) Å	θ = 32–45°
c = 10.116 (2) Å	µ = 1.35 mm^−1
β = 109.0 (3)°	T = 293 K
V = 878.2 (18) Å^3	Half pyramid, white
Z = 4	6 × 5 × 4 mm

Data collection

Huber circle diffractometer	θmax = 42.6°, θmin = 3.0°
Copper monochromator	h = 0→10
ω scans	k = 0→23
4722 measured reflections	l = −16→14
3933 independent reflections	2 standard reflections every 450min min
1729 reflections with I > 3.0σ(I)	intensity decay: none
Rint = 0.123

Refinement

Refinement on F	Hydrogen site location: difference Fourier map
Least-squares matrix: full	All H-atom parameters refined
R[F^2 > 2σ(F^2)] = 0.074	Method, part 1, Chebychev polynomial, (Watkin, 1994, Prince, 1982) [weight] = 1.0/[A0*T0(x) + A1*T1(x) ··· + An-1]*Tn-1(x)] where Ai are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] * [1-(deltaF/6*sigmaF)^2]^2 Ai are: 16.4 -24.1 18.8 -7.69 2.98
wR(F^2) = 0.079	(Δ/σ)max = 4.249
S = 1.11	Δρmax = 1.21 e Å^−3
1729 reflections	Δρmin = −4.99 e Å^−3
182 parameters	Extinction correction: Larson (1970), Equation 22
0 restraints	Extinction coefficient: 112 (6)

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.9826 (2)	0.32014 (11)	0.24497 (17)	0.0065
C2	1.00111 (19)	0.42754 (12)	0.24937 (15)	0.0074
C3	0.5180 (2)	0.12705 (15)	0.18112 (15)	0.0092
C4	0.4485 (2)	0.11744 (14)	0.31305 (16)	0.0105
Ca1	0.9664 (3)	0.12422 (17)	0.0544 (2)	0.0066
Ca2	0.9951 (3)	0.12347 (16)	0.4356 (2)	0.0060
O1	0.9736 (3)	0.28245 (14)	0.1321 (3)	0.0111
O2	1.0080 (3)	0.46572 (15)	0.1400 (3)	0.0114
O3	0.9782 (3)	0.28165 (14)	0.3546 (3)	0.0117
O4	1.0082 (3)	0.46548 (14)	0.3616 (3)	0.0120
O5	0.3613 (3)	0.1425 (2)	0.0692 (2)	0.0218
O6	0.7226 (2)	0.12210 (18)	0.19753 (18)	0.0113
O7	0.2426 (2)	0.12200 (18)	0.29558 (19)	0.0127
O8	0.6060 (3)	0.1066 (2)	0.4263 (2)	0.0231
O100	0.3920 (4)	0.3464 (3)	0.1022 (3)	0.0269
O200	0.5895 (4)	0.3870 (5)	0.3910 (3)	0.0577
H11	0.4886 (7)	0.3696 (5)	0.0496 (5)	0.0331
H12	0.3956 (12)	0.2819 (8)	0.0941 (10)	0.0563
H21	0.4783 (8)	0.3771 (8)	0.4364 (6)	0.0487
H22	0.5213 (8)	0.3766 (8)	0.2926 (6)	0.0515

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0052 (5)	0.0063 (7)	0.0087 (9)	−0.0003 (3)	0.0030 (4)	−0.0006 (4)
C2	0.0062 (6)	0.0062 (7)	0.0106 (9)	−0.0009 (3)	0.0037 (5)	0.0001 (4)
C3	−0.0002 (4)	0.0169 (7)	0.0109 (6)	0.0010 (4)	0.0020 (4)	0.0007 (6)
C4	0.0000 (4)	0.0199 (8)	0.0112 (6)	0.0003 (4)	0.0014 (4)	0.0010 (6)
Ca1	0.0026 (6)	0.0080 (7)	0.0090 (7)	−0.0001 (5)	0.0015 (5)	0.0008 (8)
Ca2	0.0016 (6)	0.0080 (7)	0.0082 (7)	0.0002 (5)	0.0015 (5)	−0.0013 (7)
O1	0.0150 (7)	0.0086 (8)	0.0111 (8)	−0.0012 (5)	0.0061 (6)	−0.0009 (7)
O2	0.0149 (7)	0.0101 (8)	0.0111 (8)	−0.0015 (5)	0.0068 (6)	0.0008 (7)
O3	0.0178 (7)	0.0075 (8)	0.0108 (9)	−0.0014 (5)	0.0059 (6)	0.0008 (7)
O4	0.0176 (7)	0.0088 (8)	0.0120 (9)	−0.0013 (5)	0.0080 (6)	−0.0013 (7)
O5	0.0023 (6)	0.0497 (18)	0.0127 (8)	0.0047 (6)	0.0016 (5)	0.0054 (8)
O6	0.0000 (5)	0.0222 (8)	0.0114 (6)	−0.0005 (5)	0.0016 (4)	0.0002 (7)
O7	0.0005 (5)	0.0245 (9)	0.0133 (7)	0.0000 (5)	0.0027 (4)	−0.0004 (8)
O8	0.0015 (6)	0.0545 (18)	0.0124 (8)	0.0036 (7)	0.0010 (5)	0.0027 (9)
O100	0.0125 (8)	0.0498 (19)	0.0190 (12)	0.0016 (9)	0.0058 (7)	0.0063 (10)
O200	0.0047 (7)	0.150 (5)	0.0179 (11)	−0.0003 (14)	0.0026 (7)	0.001 (2)
H11	0.0200 (14)	0.055 (3)	0.0280 (19)	−0.0016 (17)	0.0122 (13)	0.001 (2)
H12	0.038 (3)	0.075 (6)	0.053 (4)	0.012 (3)	0.012 (3)	0.020 (4)
H21	0.0192 (16)	0.099 (6)	0.032 (2)	−0.002 (2)	0.0145 (15)	−0.002 (4)
H22	0.0239 (19)	0.108 (6)	0.0218 (19)	0.001 (3)	0.0056 (14)	0.004 (3)

Geometric parameters (Å, º)

C1—C2	1.5657 (19)	Ca1—O200^ii	2.420 (9)
C1—O1	1.251 (3)	Ca1—O1	2.427 (3)
C1—O3	1.251 (3)	Ca1—O6	2.434 (5)
C2—O2	1.251 (3)	Ca2—O100^iv	2.561 (9)
C2—O4	1.250 (3)	Ca2—O1^v	2.453 (3)
C3—C4	1.542 (3)	Ca2—O2^v	2.420 (3)
C3—O5	1.257 (5)	Ca2—O7^i	2.428 (5)
C3—O6	1.250 (2)	Ca2—O2^iii	2.416 (3)
C4—O7	1.255 (2)	Ca2—O3	2.432 (3)
C4—O8	1.259 (5)	Ca2—O6	2.461 (9)
Ca1—O7^i	2.494 (9)	Ca2—O8	2.441 (3)
Ca1—O5^i	2.464 (3)	O100—H11	0.991 (6)
Ca1—O3^ii	2.462 (4)	O100—H12	0.941 (13)
Ca1—O4^iii	2.447 (3)	O200—H21	0.967 (6)
Ca1—O4^ii	2.431 (4)	O200—H22	0.960 (7)
C2—C1—O1	116.34 (16)	O1^v—Ca2—O2^iii	142.10 (15)
C2—C1—O3	116.37 (16)	O2^v—Ca2—O2^iii	75.89 (14)
O1—C1—O3	127.3 (2)	O7^i—Ca2—O2^iii	75.36 (11)
C1—C2—O2	116.19 (17)	O100^iv—Ca2—O3	89.2 (3)
C1—C2—O4	116.50 (16)	O1^v—Ca2—O3	74.79 (13)
O2—C2—O4	127.3 (2)	O2^v—Ca2—O3	141.28 (15)
C4—C3—O5	115.6 (3)	O7^i—Ca2—O3	77.15 (12)
C4—C3—O6	117.0 (2)	O2^iii—Ca2—O3	142.78 (11)
O5—C3—O6	127.3 (2)	O100^iv—Ca2—O6	150.11 (19)
C3—C4—O7	116.6 (2)	O1^v—Ca2—O6	126.26 (19)
C3—C4—O8	115.8 (3)	O2^v—Ca2—O6	130.52 (19)
O7—C4—O8	127.6 (3)	O7^i—Ca2—O6	78.86 (19)
O7^i—Ca1—O5^i	64.58 (14)	O2^iii—Ca2—O6	75.6 (2)
O7^i—Ca1—O3^ii	127.68 (12)	O100^iv—Ca2—O8	143.08 (12)
O5^i—Ca1—O3^ii	71.9 (3)	O1^v—Ca2—O8	76.5 (2)
O7^i—Ca1—O4^iii	72.68 (15)	O2^v—Ca2—O8	74.4 (3)
O5^i—Ca1—O4^iii	97.49 (17)	O7^i—Ca2—O8	143.96 (15)
O3^ii—Ca1—O4^iii	142.50 (15)	O2^iii—Ca2—O8	89.33 (16)
O7^i—Ca1—O4^ii	123.60 (14)	O3—Ca2—O6	74.8 (2)
O5^i—Ca1—O4^ii	74.6 (3)	O3—Ca2—O8	98.58 (15)
O3^ii—Ca1—O4^ii	66.40 (9)	O6—Ca2—O8	65.66 (14)
O4^iii—Ca1—O4^ii	76.13 (13)	Ca2^ii—O1—Ca1	105.44 (14)
O7^i—Ca1—O200^ii	152.30 (19)	Ca2^ii—O1—C1	119.82 (16)
O5^i—Ca1—O200^ii	143.09 (19)	Ca1—O1—C1	134.55 (18)
O3^ii—Ca1—O200^ii	76.3 (4)	Ca2^ii—O2—Ca2^vi	104.11 (14)
O4^iii—Ca1—O200^ii	96.4 (3)	Ca2^ii—O2—C2	121.11 (16)
O4^ii—Ca1—O200^ii	75.9 (4)	Ca2^vi—O2—C2	134.60 (19)
O7^i—Ca1—O1	76.24 (16)	Ca1^v—O3—Ca2	105.02 (13)
O5^i—Ca1—O1	88.06 (14)	Ca1^v—O3—C1	119.64 (16)
O3^ii—Ca1—O1	74.72 (12)	Ca2—O3—C1	135.28 (19)
O4^iii—Ca1—O1	142.15 (11)	Ca1^vi—O4—Ca1^v	103.87 (13)
O4^ii—Ca1—O1	140.64 (14)	Ca1^vi—O4—C2	135.28 (19)
O7^i—Ca1—O6	78.1 (3)	Ca1^v—O4—C2	120.72 (16)
O5^i—Ca1—O6	142.1 (2)	Ca1^vii—O5—C3	121.3 (3)
O3^ii—Ca1—O6	133.63 (19)	Ca2—O6—Ca1	101.9 (3)
O4^iii—Ca1—O6	76.35 (16)	Ca2—O6—C3	119.5 (2)
O4^ii—Ca1—O6	136.54 (18)	Ca1—O6—C3	138.37 (17)
O200^ii—Ca1—O1	101.3 (2)	Ca1^vii—O7—Ca2^vii	101.1 (3)
O200^ii—Ca1—O6	74.5 (3)	Ca1^vii—O7—C4	120.0 (2)
O1—Ca1—O6	76.58 (16)	Ca2^vii—O7—C4	138.83 (17)
O100^iv—Ca2—O1^v	70.88 (11)	Ca2—O8—C4	120.6 (3)
O100^iv—Ca2—O2^v	77.10 (13)	Ca2^viii—O100—H11	103.3 (4)
O1^v—Ca2—O2^v	66.53 (8)	Ca2^viii—O100—H12	99.2 (5)
O100^iv—Ca2—O7^i	73.0 (3)	H11—O100—H12	104.8 (8)
O1^v—Ca2—O7^i	133.95 (18)	Ca1^v—O200—H21	111.8 (5)
O2^v—Ca2—O7^i	130.2 (2)	Ca1^v—O200—H22	135.0 (5)
O100^iv—Ca2—O2^iii	106.03 (16)	H21—O200—H22	108.6 (6)

Symmetry codes: (i) x+1, y, z; (ii) x, −y+1/2, z−1/2; (iii) −x+2, y−1/2, −z+1/2; (iv) x+1, −y+1/2, z+1/2; (v) x, −y+1/2, z+1/2; (vi) −x+2, y+1/2, −z+1/2; (vii) x−1, y, z; (viii) x−1, −y+1/2, z−1/2.