Literature DB >> 22064770

2-Amino-4,6-dimeth-oxy-pyrimidin-1-ium p-toluene-sulfonate.

Sundaramoorthy Gomathi1, Packianathan Thomas Muthiah.   

Abstract

In the title salt, C(6)H(10)N(3)O(2) (+)·C(7)H(7)O(3)S(-), the 2-amino-4,6-dimeth-oxy-pyrimidinium cation inter-acts with the sulfonate group of the p-toluene-sulfonate anion via a pair of N-H⋯O hydrogen bonds, forming a cyclic hydrogen-bonded R(2) (2)(8) motif, which in the crystal is linked by further intemolecular N-H⋯O hydrogen bonds, forming supra-molecular chains along the c axis. Furthermore, neighboring chains are inter-linked via weak C-H⋯O hydrogen bonds and C-H⋯π inter-actions, forming layers.

Entities:  

Year:  2011        PMID: 22064770      PMCID: PMC3201388          DOI: 10.1107/S160053681103755X

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For background to crystal engineering and supra­molecular chemistry, see: Desiraju (1989 ▶). For the role of amino­pyrimidine–carboxyl­ate inter­actions in protein-nuleic acid recognition and protein-drug binding, see: Hunt et al. (1980 ▶); Baker & Santi (1965 ▶). For the role of sulfate–protein inter­actions, see: Pflugrath & Quiocho (1985 ▶); Jacobson & Quiocho (1988 ▶). For information on carb­oxy­lic acid inter­actions with a 2-amino heterocyclic ring system, see: Etter & Adsmond (1990 ▶); Lynch & Jones (2004 ▶); Allen et al. (1998 ▶). For a survey of hydrogen-bonding patterns involving sulfonate salts, see: Haynes et al. (2004 ▶). For hydrogen-bonding patterns involving sulfonate groups in biological systems and metal complexes, see: Russell et al. (1994 ▶); Cai et al. (2001 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶); Etter (1990 ▶). For related structures, see: Low et al. (2002 ▶); Arora & Sundaralingam (1971 ▶); Balasubramani et al. (2007 ▶); Hemamalini et al. (2005 ▶); Thanigaimani et al. (2007 ▶, 2008 ▶); Ebenezer & Muthiah (2010 ▶).

Experimental

Crystal data

C6H10N3O2 +·C7H7O3S M = 327.37 Orthorhombic, a = 15.2116 (2) Å b = 12.1422 (2) Å c = 8.3497 (1) Å V = 1542.21 (4) Å3 Z = 4 Mo Kα radiation μ = 0.24 mm−1 T = 296 K 0.20 × 0.18 × 0.15 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T min = 0.954, T max = 0.965 35029 measured reflections 5264 independent reflections 4257 reflections with I > 2σ(I) R int = 0.032

Refinement

R[F 2 > 2σ(F 2)] = 0.035 wR(F 2) = 0.098 S = 1.04 5264 reflections 202 parameters 1 restraint H-atom parameters constrained Δρmax = 0.21 e Å−3 Δρmin = −0.23 e Å−3 Absolute structure: Flack (1983 ▶) 2449, Friedel pairs Flack parameter: −0.01 (6) Data collection: APEX2 (Bruker, 2008 ▶); cell refinement: SAINT (Bruker, 2008 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2009 ▶) and POV-RAY (Cason, 2004) ▶; software used to prepare material for publication: PLATON. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S160053681103755X/lh5333sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681103755X/lh5333Isup2.hkl Supplementary material file. DOI: 10.1107/S160053681103755X/lh5333Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C6H10N3O2+·C7H7O3SF(000) = 688
Mr = 327.37Dx = 1.410 Mg m3
Orthorhombic, Pca21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2acCell parameters from 5264 reflections
a = 15.2116 (2) Åθ = 1.7–31.9°
b = 12.1422 (2) ŵ = 0.24 mm1
c = 8.3497 (1) ÅT = 296 K
V = 1542.21 (4) Å3Prism, colourless
Z = 40.20 × 0.18 × 0.15 mm
Bruker SMART APEXII CCD area-detector diffractometer5264 independent reflections
Radiation source: fine-focus sealed tube4257 reflections with I > 2σ(I)
graphiteRint = 0.032
φ and ω scansθmax = 31.9°, θmin = 1.7°
Absorption correction: multi-scan (SADABS; Bruker, 2008)h = −21→22
Tmin = 0.954, Tmax = 0.965k = −17→18
35029 measured reflectionsl = −12→12
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.098w = 1/[σ2(Fo2) + (0.0621P)2 + 0.0019P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max = 0.001
5264 reflectionsΔρmax = 0.21 e Å3
202 parametersΔρmin = −0.23 e Å3
1 restraintAbsolute structure: Flack (1983) 2449, Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: −0.01 (6)
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
Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.
xyzUiso*/Ueq
O10.19507 (6)0.22303 (9)0.38465 (14)0.0511 (3)
O20.11421 (6)−0.06832 (9)0.04130 (13)0.0501 (3)
N10.29344 (7)0.11712 (9)0.26107 (13)0.0402 (3)
N20.40346 (7)0.01635 (11)0.14147 (18)0.0496 (4)
N30.25982 (7)−0.03173 (10)0.08987 (14)0.0404 (3)
C20.31858 (9)0.03320 (10)0.16420 (17)0.0390 (3)
C40.17567 (9)−0.00833 (12)0.11384 (17)0.0403 (4)
C50.14437 (8)0.07733 (12)0.21022 (17)0.0428 (3)
C60.20693 (8)0.13947 (11)0.28454 (15)0.0400 (4)
C70.14081 (10)−0.16405 (13)−0.0479 (2)0.0540 (4)
C80.10582 (10)0.25880 (15)0.4142 (2)0.0563 (5)
S10.50030 (2)0.23323 (3)0.42863 (6)0.0428 (1)
O30.52077 (8)0.12267 (9)0.37468 (16)0.0570 (4)
O40.41176 (7)0.26565 (10)0.3831 (2)0.0647 (5)
O50.51823 (10)0.24747 (13)0.59809 (18)0.0739 (5)
C90.57224 (9)0.32344 (11)0.32795 (17)0.0422 (3)
C100.66162 (10)0.30482 (15)0.3425 (2)0.0591 (5)
C110.72049 (13)0.37635 (17)0.2707 (3)0.0705 (6)
C120.69171 (15)0.46724 (14)0.1854 (2)0.0648 (6)
C130.60373 (15)0.48291 (15)0.1698 (3)0.0698 (6)
C140.54237 (12)0.41230 (13)0.2414 (2)0.0601 (5)
C150.7578 (2)0.54823 (18)0.1173 (3)0.0919 (9)
H10.332700.156600.308100.0480*
H2A0.42080−0.035900.079500.0600*
H2B0.441400.057600.188700.0600*
H50.084600.091100.222800.0510*
H7A0.16740−0.216500.023300.0810*
H7B0.18250−0.14290−0.128600.0810*
H7C0.09030−0.19660−0.098000.0810*
H8A0.073100.199800.462100.0840*
H8B0.078800.279500.314800.0840*
H8C0.106400.320900.485400.0840*
H100.682000.244500.400200.0710*
H110.780500.363100.279800.0850*
H130.583600.542300.109700.0840*
H140.482400.425300.230600.0720*
H15A0.729300.595000.040600.1380*
H15B0.804500.508600.065700.1380*
H15C0.781600.592300.202300.1380*
U11U22U33U12U13U23
O10.0369 (5)0.0605 (6)0.0559 (6)0.0002 (4)−0.0028 (4)−0.0136 (5)
O20.0340 (4)0.0573 (6)0.0589 (6)−0.0034 (4)−0.0075 (4)−0.0086 (5)
N10.0323 (5)0.0477 (6)0.0407 (5)−0.0051 (4)−0.0035 (4)0.0014 (4)
N20.0311 (5)0.0558 (7)0.0619 (8)−0.0011 (5)−0.0030 (5)−0.0073 (6)
N30.0325 (5)0.0456 (5)0.0431 (5)−0.0023 (4)−0.0030 (4)0.0026 (4)
C20.0337 (5)0.0427 (6)0.0405 (6)−0.0006 (4)−0.0012 (5)0.0067 (5)
C40.0327 (6)0.0474 (7)0.0409 (6)−0.0038 (5)−0.0056 (5)0.0060 (5)
C50.0299 (5)0.0512 (7)0.0473 (6)−0.0002 (5)−0.0042 (5)0.0005 (6)
C60.0363 (6)0.0466 (7)0.0370 (6)−0.0005 (5)−0.0020 (5)0.0043 (5)
C70.0480 (7)0.0532 (7)0.0609 (9)−0.0052 (6)−0.0075 (7)−0.0063 (7)
C80.0427 (7)0.0624 (9)0.0638 (9)0.0085 (6)−0.0062 (7)−0.0131 (8)
S10.0333 (1)0.0475 (2)0.0477 (2)−0.0056 (1)−0.0002 (1)−0.0003 (2)
O30.0512 (5)0.0429 (5)0.0770 (8)−0.0034 (4)−0.0008 (5)0.0019 (5)
O40.0348 (5)0.0570 (7)0.1024 (11)−0.0026 (4)−0.0073 (6)−0.0052 (6)
O50.0665 (8)0.1106 (12)0.0446 (6)−0.0298 (7)0.0061 (6)0.0007 (6)
C90.0424 (6)0.0414 (6)0.0427 (6)−0.0060 (5)−0.0025 (5)−0.0021 (5)
C100.0417 (7)0.0613 (9)0.0742 (11)−0.0056 (6)0.0011 (7)0.0173 (9)
C110.0507 (9)0.0794 (12)0.0814 (12)−0.0191 (8)0.0087 (9)0.0105 (10)
C120.0847 (13)0.0603 (9)0.0493 (8)−0.0265 (8)0.0092 (8)0.0011 (8)
C130.0933 (14)0.0511 (9)0.0649 (10)−0.0095 (8)−0.0067 (10)0.0150 (8)
C140.0591 (10)0.0530 (8)0.0682 (10)0.0010 (7)−0.0086 (8)0.0096 (8)
C150.123 (2)0.0774 (13)0.0754 (13)−0.0454 (14)0.0247 (14)0.0022 (11)
S1—O41.4538 (12)C7—H7B0.9600
S1—O51.4513 (16)C7—H7C0.9600
S1—C91.7618 (14)C8—H8B0.9600
S1—O31.4498 (12)C8—H8C0.9600
O1—C61.3269 (17)C8—H8A0.9600
O1—C81.4466 (18)C9—C101.384 (2)
O2—C71.4386 (19)C9—C141.376 (2)
O2—C41.3310 (17)C10—C111.384 (3)
N1—C21.3560 (17)C11—C121.385 (3)
N1—C61.3579 (16)C12—C131.358 (3)
N2—C21.3210 (17)C12—C151.517 (3)
N3—C41.3264 (17)C13—C141.401 (3)
N3—C21.3438 (18)C10—H100.9300
N1—H10.8600C11—H110.9300
N2—H2B0.8600C13—H130.9300
N2—H2A0.8600C14—H140.9300
C4—C51.399 (2)C15—H15A0.9600
C5—C61.3638 (18)C15—H15B0.9600
C5—H50.9300C15—H15C0.9600
C7—H7A0.9600
S1···H2B3.0600C10···H7Aiv2.8700
S1···H2Ai2.9600C10···H7Bi3.0900
S1···H12.8900C11···H7Aiv2.9500
O1···C2ii3.2870 (17)C11···H15Bix2.9600
O2···O3iii3.1944 (17)C15···H8Cx2.8300
O3···C5iv3.3642 (18)H1···O41.9000
O3···N22.9398 (18)H1···S12.8900
O3···N2i3.0233 (19)H1···H2B2.2700
O3···O2iv3.1944 (17)H2A···O5vii2.7400
O4···N12.7441 (16)H2A···O3vii2.2000
O5···C5ii3.356 (2)H2A···S1vii2.9600
O5···C8ii3.248 (2)H2B···O2iv2.9100
O1···H15Av2.8100H2B···O32.1200
O2···H2Biii2.9100H2B···H12.2700
O3···H102.8700H2B···S13.0600
O3···H2B2.1200H2B···H8Aviii2.5700
O3···H2Ai2.2000H5···C82.6100
O4···H142.5600H5···H8A2.4000
O4···H11.9000H5···H8B2.4100
O5···H5ii2.6700H5···O5viii2.6700
O5···H8Bii2.3700H7A···N32.7100
O5···H2Ai2.7400H7A···C11iii2.9500
O5···H7Cvi2.8300H7A···C10iii2.8700
N1···O42.7441 (16)H7A···H10vii2.5300
N1···C4ii3.3492 (18)H7B···C10vii3.0900
N2···O3vii3.0233 (19)H7B···N32.5600
N2···O32.9398 (18)H7B···H10vii2.4100
N3···C6viii3.3281 (17)H7B···N3viii2.8500
N2···H8Aviii2.7100H7B···C2viii2.7500
N3···H7B2.5600H7C···H8Axiii2.5400
N3···H7A2.7100H7C···O5xiv2.8300
N3···H7Bii2.8500H7C···C8xiii3.0800
C2···O1viii3.2870 (17)H8A···C52.7900
C2···C7ii3.449 (2)H8A···H52.4000
C2···C6viii3.4445 (19)H8A···H7Cxii2.5400
C4···N1viii3.3492 (18)H8A···N2ii2.7100
C5···O5viii3.356 (2)H8A···H2Bii2.5700
C5···O3iii3.3642 (18)H8B···H52.4100
C6···C2ii3.4445 (19)H8B···O5viii2.3700
C6···N3ii3.3281 (17)H8B···C52.7900
C7···C2viii3.449 (2)H8C···H15Bv2.5600
C7···C10vii3.577 (2)H8C···C15v2.8300
C8···C15v3.559 (3)H10···O32.8700
C8···O5viii3.248 (2)H10···C7i2.9000
C10···C7i3.577 (2)H10···H7Ai2.5300
C11···C15ix3.583 (3)H10···H7Bi2.4100
C15···C8x3.559 (3)H11···H15B2.5400
C15···C11xi3.583 (3)H11···C7i3.0600
C2···H7Bii2.7500H13···H15A2.3800
C5···H8A2.7900H14···O42.5600
C5···H8B2.7900H15A···H132.3800
C7···H11vii3.0600H15A···O1x2.8100
C7···H10vii2.9000H15B···H112.5400
C8···H7Cxii3.0800H15B···H8Cx2.5600
C8···H52.6100H15B···C11xi2.9600
O5—S1—C9105.93 (8)H7B—C7—H7C109.00
O3—S1—C9107.10 (7)H8B—C8—H8C109.00
O3—S1—O4111.62 (8)O1—C8—H8A109.00
O3—S1—O5111.89 (9)O1—C8—H8B109.00
O4—S1—O5113.38 (9)O1—C8—H8C109.00
O4—S1—C9106.40 (7)H8A—C8—H8B110.00
C6—O1—C8117.69 (11)H8A—C8—H8C109.00
C4—O2—C7118.70 (11)S1—C9—C10117.83 (11)
C2—N1—C6120.64 (11)S1—C9—C14122.21 (12)
C2—N3—C4116.52 (12)C10—C9—C14119.92 (14)
C6—N1—H1120.00C9—C10—C11119.68 (16)
C2—N1—H1120.00C10—C11—C12121.23 (18)
C2—N2—H2B120.00C11—C12—C13118.21 (18)
C2—N2—H2A120.00C11—C12—C15120.0 (2)
H2A—N2—H2B120.00C13—C12—C15121.76 (18)
N2—C2—N3119.53 (12)C12—C13—C14121.99 (18)
N1—C2—N2118.54 (12)C9—C14—C13118.94 (17)
N1—C2—N3121.92 (12)C9—C10—H10120.00
O2—C4—N3119.47 (13)C11—C10—H10120.00
N3—C4—C5125.08 (13)C10—C11—H11119.00
O2—C4—C5115.45 (12)C12—C11—H11119.00
C4—C5—C6115.83 (12)C12—C13—H13119.00
O1—C6—N1112.06 (11)C14—C13—H13119.00
N1—C6—C5120.00 (12)C9—C14—H14121.00
O1—C6—C5127.94 (12)C13—C14—H14121.00
C4—C5—H5122.00C12—C15—H15A110.00
C6—C5—H5122.00C12—C15—H15B109.00
H7A—C7—H7B109.00C12—C15—H15C110.00
H7A—C7—H7C109.00H15A—C15—H15B109.00
O2—C7—H7A109.00H15A—C15—H15C110.00
O2—C7—H7B109.00H15B—C15—H15C109.00
O2—C7—H7C109.00
O4—S1—C9—C10−175.52 (13)C4—N3—C2—N2−177.98 (13)
O3—S1—C9—C10−56.03 (14)C2—N3—C4—O2178.80 (12)
O3—S1—C9—C14126.16 (13)O2—C4—C5—C6−179.77 (12)
O5—S1—C9—C14−114.27 (14)N3—C4—C5—C6−0.5 (2)
O4—S1—C9—C146.66 (15)C4—C5—C6—N10.8 (2)
O5—S1—C9—C1063.54 (14)C4—C5—C6—O1−178.16 (13)
C8—O1—C6—N1177.13 (12)S1—C9—C10—C11−177.39 (15)
C8—O1—C6—C5−3.9 (2)C14—C9—C10—C110.5 (3)
C7—O2—C4—N36.4 (2)S1—C9—C14—C13177.50 (14)
C7—O2—C4—C5−174.33 (13)C10—C9—C14—C13−0.3 (2)
C2—N1—C6—C5−0.07 (18)C9—C10—C11—C120.6 (3)
C2—N1—C6—O1179.01 (12)C10—C11—C12—C13−1.9 (3)
C6—N1—C2—N2178.19 (13)C10—C11—C12—C15175.99 (19)
C6—N1—C2—N3−1.0 (2)C11—C12—C13—C142.1 (3)
C4—N3—C2—N11.2 (2)C15—C12—C13—C14−175.73 (19)
C2—N3—C4—C5−0.4 (2)C12—C13—C14—C9−1.1 (3)
Cg is the centroid of the C9–C14 ring.
D—H···AD—HH···AD···AD—H···A
N1—H1···O40.861.902.7441 (16)169
N2—H2A···O3vii0.862.203.0233 (19)161
N2—H2B···O30.862.122.9398 (18)159
C8—H8B···O5viii0.962.373.248 (2)152
C7—H7A···Cgiii0.962.963.7815 (18)145
Table 1

Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C9–C14 ring.

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1⋯O40.861.902.7441 (16)169
N2—H2A⋯O3i0.862.203.0233 (19)161
N2—H2B⋯O30.862.122.9398 (18)159
C8—H8B⋯O5ii0.962.373.248 (2)152
C7—H7ACgiii0.962.963.7815 (18)145

Symmetry codes: (i) ; (ii) ; (iii) .

  13 in total

1.  Hydrogen bonding in 2-amino-4,6-dimethoxypyrimidine, 2-benzylamino-4,6-bis(benzyloxy)pyrimidine and 2-amino-4,6-bis(N-pyrrolidino)pyrimidine: chains of fused rings and a centrosymmetric dimer.

Authors:  John N Low; Antonio Quesada; Antonio Marchal; Manuel Melguizo; Manuel Nogueras; Christopher Glidewell
Journal:  Acta Crystallogr C       Date:  2002-04-30       Impact factor: 1.172

2.  Hydrogen-bonding patterns in 2-amino-4,6-dimethylpyrimidinium hydrogen sulfate.

Authors:  Madhukar Hemamalini; Packianathan Thomas Muthiah; Urszula Rychlewska; Agnieszka Plutecka
Journal:  Acta Crystallogr C       Date:  2005-01-22       Impact factor: 1.172

3.  Hydrogen-bonded supramolecular motifs in 2-amino-4,6-dimethoxypyrimidinium 4-hydroxybenzoate monohydrate, 2-amino-4,6-dimethoxypyrimidinium 6-carboxypyridine-2-carboxylate monohydrate and 2-amino-4,6-dimethoxypyrimidinium hydrogen (2R,3R)-tartrate 2-amino-4,6-dimethoxypyrimidine.

Authors:  Kaliyaperumal Thanigaimani; Packianathan Thomas Muthiah; Daniel E Lynch
Journal:  Acta Crystallogr C       Date:  2007-04-21       Impact factor: 1.172

4.  4,6-Dimeth-oxy-pyrimidin-2-amine-2-(1H-indol-3-yl)acetic acid (1/1).

Authors:  Samuel Ebenezer; Packianathan Thomas Muthiah
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-09-25

5.  Hydrogen-bonding patterns in the cocrystal 2-amino-4,6-dimethoxy-pyrimidine-anthranilic acid (1/1).

Authors:  Kaliyaperumal Thanigaimani; Packianathan Thomas Muthiah; Daniel E Lynch
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2007-12-06

6.  Sulfate-binding protein dislikes protonated oxyacids. A molecular explanation.

Authors:  B L Jacobson; F A Quiocho
Journal:  J Mol Biol       Date:  1988-12-05       Impact factor: 5.469

7.  Analogs of tetrahydrofolic acid XXIV. Further observations on the mode of pyrimidyl binding to dihydrofolic reductase and thymidylate synthetase by the 2-amino-5-(3-anilinopropyl)-6-methyl-4-pyrimidinol type of inhibitor.

Authors:  B R Baker; D V Santi
Journal:  J Pharm Sci       Date:  1965-09       Impact factor: 3.534

8.  Crystallographic and molecular-orbital studies on the geometry of antifolate drugs.

Authors:  W E Hunt; C H Schwalbe; K Bird; P D Mallinson
Journal:  Biochem J       Date:  1980-05-01       Impact factor: 3.857

9.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20

10.  R2(2)(8) motifs in Aminopyrimidine sulfonate/carboxylate interactions: crystal structures of pyrimethaminium benzenesulfonate monohydrate (2:2:1) and 2-amino-4,6-dimethylpyrimidinium sulfosalicylate dihydrate (4:2:2).

Authors:  Kasthuri Balasubramani; Packianathan Thomas Muthiah; Daniel E Lynch
Journal:  Chem Cent J       Date:  2007-11-13       Impact factor: 4.215

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1.  Crystal structure of 2,4-di-amino-6-oxo-3,6-di-hydro-pyrimidin-1-ium p-toluene-sulfonate.

Authors:  Krishnasamy Mamallan; Sadasivam Sharmila Tagore; Sundaramoorthy Gomathi; Velusamy Sethuraman
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2015-04-11
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