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Acta Crystallogr Sect E Struct Rep Online. 2010 February 1; 66(Pt 2): o442.
Published online 2010 January 23. doi:  10.1107/S1600536810001960
PMCID: PMC2979779

2-[2-(Methyl­sulfan­yl)benzimidazol-1-yl]ethanol

Abstract

In the title compound, C10H12N2OS, the asymmetric unit consists of two independent mol­ecules. In the crystal structure, mol­ecules form R 4 4(28) centrosymmetric tetra­mers via O—H(...)N hydrogen bonds. These tetra­mers are stacked along the c axis via C—H(...)O hydrogen bonds. C—H(...)π and π–π inter­actions are also present; in the latter, the centroid–centroid distances are 4.075 (1) and 3.719 (1) Å.

Related literature

For the biological activity of compounds having benzimidazole ring systems, and a related structure, see: Akkurt et al. (2006 [triangle]). For other studies of the biological activity of benzimidazoles, see: Küçükbay et al. (2003 [triangle]), (2004 [triangle]); Puratchikody et al. (2008 [triangle]). For hydrogen-bond graph sets, see: Bernstein et al. (1995 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0o442-scheme1.jpg

Experimental

Crystal data

  • C10H12N2OS
  • M r = 208.28
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o442-efi1.jpg
  • a = 9.3235 (2) Å
  • b = 9.7659 (2) Å
  • c = 11.4588 (3) Å
  • α = 78.0849 (9)°
  • β = 88.9066 (8)°
  • γ = 88.1399 (9)°
  • V = 1020.25 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.29 mm−1
  • T = 223 K
  • 0.20 × 0.20 × 0.15 mm

Data collection

  • Nonius KappaCCD diffractometer
  • 13769 measured reflections
  • 5257 independent reflections
  • 3996 reflections with I > 2σ(I)
  • R int = 0.036

Refinement

  • R[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.102
  • S = 0.96
  • 5242 reflections
  • 261 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.51 e Å−3
  • Δρmin = −0.32 e Å−3

Data collection: COLLECT (Nonius, 2001 [triangle]); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994 [triangle]); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]) and PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: CRYSTALS.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810001960/wn2372sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810001960/wn2372Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We thank the Laboratoire de Physique des Inter­actions Ioniques et Spectropôle, Université de Provence, et Université Paul Cézanne, Faculté des Sciences et Techniques de Saint Jérôme, Marseilles, France, for the use of their diffractometer.

supplementary crystallographic information

Comment

Numerous compounds having benzimidazole ring systems possess versatile pharmacological activities such as antiviral, anthelmintic, spasmolytic, antihypertensive and vasodilator (Akkurt et al., 2006). It has also been reported that many benzimidazole derivatives have antimicrobial and antifungal activities (Küçükbay et al., 2003, 2004, Puratchikody et al., 2008). Therefore, the synthesis of new benzimidazole derivatives is of considerable interest. In order to explore new benzimidazole properties, the title compound has been synthesized and its crystal structure determined.

The two independent molecules in the asymmetric unit of the title compound and the atomic labeling scheme are shown in Fig.1. In this structure, the nine-membered benzimidazole ring systems (N1A/C3A/N2A/C6A/C7A/C8A/C9A/C10A/C5A, N1B/C3B/N2B/C6B/C7B/C8B/C9B/C10B/C5B) of both independent molecules are essentially planar, the maximum deviation from planarity being, respectively, 0.016 (2) Å for atom C8A and 0.078 (16) Å for atom C3B. These two ring systems make a dihedral angle of 73.95 (6)°.

In the crystal structure, we observe the formation of R44(28) centrosymmetric tetramers (Bernstein et al., 1995) via O—H···N hydrogen bonds. The tetramers are linked by two symmetric C—H···O hydrogen bonds to form a zigzag infinite chain along the c axis. The supramolecular aggregation is completed by the presence of C—H···π interactions (Table 1) and π–π stacking between two parallel imidazole rings. The centroid···centroid distance of those rings, Cg1···Cg1(1 - x,1 - y,1 - z) and Cg4···Cg4(-x,2 - y,-z) are 4.075 (1) Å and 3.719 (1) Å, respectively (Fig.3).

Experimental

2-Chloroethanol (1.6 ml, 24.4 mmol) and potasium carbonate (1.68 g, 12.2 mmol) were added to 2-methylsulfanyl-1H-benzimidazole (1 g, 6.1 mmol) in dimethyl sulfoxide (DMSO) (5 ml). The reaction mixture was successively agitated for 30 min at room temperature and at 323 K for 24 h. 50 ml of water was then added to the reaction mixture, and the products were extracted with dichloromethane (3 × 50 ml). The combined organic extracts were washed with brine (10 g of sodium chloride in 100 ml of water), dried (Na2SO4) and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (elution: hexane/ethyl acetate (70:30, v/v)) and the title compound resulted as a brown powder (0.77 g, 61%) with a melting point of 409 K. The brown powder was dissolved in ethanol/hexane (3:1, v/v) and, after four days, brown crystals suitable for single-crystal X-ray diffraction analysis were obtained.

Refinement

The H atoms bonded to O1A and O1B were located in a difference Fourier map; their positional parameters and Uiso were refined freely. Other H atoms were placed at calculated positions, with C—H = 0.95 Å and refined using a riding model, with Uiso(H) constrained to be 1.2Ueq(C).

Figures

Fig. 1.
The structure of the asymmetric unit of the title compound, showing the atomic labeling scheme, with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius.
Fig. 2.
Crystal packing, viewed down the a axis, showing the zigzag infinite chain of cyclic tetramers along the c axis. Dashed lines indicate hydrogen bonds. H atoms not involved in hydrogen bonds have been omitted for clarity.
Fig. 3.
Crystal packing, showing the π–π and C—H···π stacking interactions. The yellow dots are the centroids of benzene and imidazole rings. H atoms not involved in C—H···π ...

Crystal data

C10H12N2OSZ = 4
Mr = 208.28F(000) = 440
Triclinic, P1Dx = 1.356 Mg m3
Hall symbol: -P 1Melting point: 409 K
a = 9.3235 (2) ÅMo Kα radiation, λ = 0.71073 Å
b = 9.7659 (2) ÅCell parameters from 13769 reflections
c = 11.4588 (3) Åθ = 2–29°
α = 78.0849 (9)°µ = 0.28 mm1
β = 88.9066 (8)°T = 223 K
γ = 88.1399 (9)°Prism, brown
V = 1020.25 (4) Å30.20 × 0.20 × 0.15 mm

Data collection

Nonius KappaCCD diffractometer3996 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.036
graphiteθmax = 29.1°, θmin = 1.8°
[var phi] and ω scansh = −12→12
13769 measured reflectionsk = −12→12
5257 independent reflectionsl = −15→15

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.102H atoms treated by a mixture of independent and constrained refinement
S = 0.96 Method = Modified Sheldrick w = 1/[σ2(F2) + (0.04P)2 + 0.62P], where P = [max(Fo2,0) + 2Fc2]/3
5242 reflections(Δ/σ)max = 0.001
261 parametersΔρmax = 0.51 e Å3
0 restraintsΔρmin = −0.32 e Å3
88 constraints

Special details

Experimental. 1H NMR (DMSO-d6, 300 MHz, p.p.m.) δ: 2.71 (s, 3H, CH3); 3.68–3.74 (m 2H, CH2O, JCH2—CH2 = 5.7 Hz and JCH2—OH = 5.4 Hz); 4.17 (t, 2H, CH2N, JCH2—CH2 = 5.7 Hz); 5.00 (t, 1H, OH, JCH2—OH = 5.4 Hz); 7.13–7.17 and 7.46–7.55 (m, 4H, C6H4). 13C NMR (DMSO-d6, 300 MHz, p.p.m.) δ: 14.35 (CH3); 46.25 (CH2N); 59.14 (CH2O); 109.75, 117.31, 121.14, 121.21, 136.75, 142.92 (C6H5); 152.48 (C═N).
Refinement. The 15 reflections 1 0 0; -1 1 0; 0 1 0; 1 1 0; -1 - 1 1; 0 - 1 1; 1 - 1 1; -1 0 1; 0 0 1; 1 0 1; -1 1 1; 0 1 1; 1 1 1; 0 0 2; 0 1 2 have been measured with too low intensities. It might be caused by some systematical error, probably by shielding by a beam stop of these diffractions. They were not used in the refinement.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
S1A0.49131 (5)0.82212 (5)0.49825 (4)0.0390
C3A0.42886 (16)0.69994 (15)0.42198 (14)0.0286
N1A0.28691 (13)0.66663 (13)0.43140 (12)0.0286
C5A0.26838 (17)0.57367 (15)0.35708 (15)0.0298
C6A0.40349 (17)0.55494 (15)0.30706 (15)0.0309
N2A0.50366 (14)0.63619 (13)0.34868 (12)0.0309
C7A0.4221 (2)0.46382 (18)0.22858 (18)0.0430
C8A0.3031 (2)0.39422 (19)0.20412 (19)0.0507
C9A0.1686 (2)0.41504 (19)0.25355 (19)0.0481
C10A0.14723 (19)0.50586 (17)0.33090 (17)0.0386
C2A0.17826 (17)0.70834 (17)0.51181 (15)0.0336
C1A0.07853 (17)0.82574 (17)0.45194 (16)0.0354
O1A0.15279 (14)0.95034 (13)0.41601 (12)0.0405
C4A0.67938 (19)0.8087 (2)0.4688 (2)0.0463
S1B0.34070 (5)1.07040 (5)0.04701 (4)0.0402
C3B0.16057 (17)1.10450 (15)0.07442 (14)0.0299
N2B0.09036 (15)1.06622 (14)0.17658 (12)0.0325
C6B−0.04765 (17)1.12427 (16)0.15371 (14)0.0307
C5B−0.05673 (17)1.19801 (16)0.03565 (14)0.0306
N1B0.07856 (14)1.18307 (13)−0.01412 (12)0.0313
C2B0.12112 (19)1.23474 (17)−0.13814 (14)0.0357
C1B0.1892 (2)1.37598 (19)−0.15947 (16)0.0419
O1B0.21179 (14)1.42576 (15)−0.28301 (12)0.0521
C10B−0.18151 (19)1.26805 (18)−0.01093 (16)0.0395
C9B−0.2986 (2)1.2612 (2)0.06571 (18)0.0458
C8B−0.2918 (2)1.1879 (2)0.18335 (18)0.0449
C7B−0.16712 (19)1.11853 (18)0.22973 (16)0.0381
C4B0.3871 (2)0.9554 (2)0.18458 (19)0.0578
H1B0.305 (3)1.398 (3)−0.306 (3)0.091 (9)*
H1A0.136 (3)0.992 (3)0.329 (3)0.094 (9)*
H10A0.05550.52110.36420.0468*
H9A0.08950.36570.23370.0576*
H8A0.31340.33030.15200.0612*
H7A0.51300.45010.19340.0516*
H10B−0.18621.3181−0.09130.0468*
H9B−0.38601.30780.03730.0552*
H8B−0.37481.18550.23310.0540*
H7B−0.16301.06880.31020.0456*
H41A0.72840.87150.50620.0552*
H42A0.69660.83190.38510.0552*
H43A0.71320.71570.49930.0552*
H41B0.48550.92760.18220.0696*
H42B0.37071.00250.24860.0681*
H43B0.32960.87510.19610.0681*
H11A0.00390.83960.50630.0420*
H12A0.03830.80110.38380.0420*
H21A0.22570.73820.57440.0408*
H22A0.12260.62930.54420.0408*
H21B0.03831.2421−0.18630.0432*
H22B0.18811.1693−0.16090.0432*
H11B0.12771.4401−0.12890.0504*
H12B0.27871.3675−0.12000.0504*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S1A0.0358 (2)0.0417 (2)0.0440 (3)−0.00593 (17)−0.00121 (18)−0.01874 (19)
C3A0.0264 (7)0.0263 (7)0.0320 (8)−0.0010 (5)−0.0012 (6)−0.0030 (6)
N1A0.0250 (6)0.0282 (6)0.0324 (7)−0.0025 (5)0.0027 (5)−0.0059 (5)
C5A0.0301 (8)0.0237 (7)0.0345 (8)−0.0019 (6)−0.0017 (6)−0.0030 (6)
C6A0.0304 (8)0.0254 (7)0.0370 (9)0.0010 (6)−0.0024 (6)−0.0067 (6)
N2A0.0258 (6)0.0304 (7)0.0371 (7)0.0003 (5)0.0009 (5)−0.0085 (5)
C7A0.0469 (10)0.0357 (9)0.0496 (11)0.0062 (7)−0.0007 (8)−0.0174 (8)
C8A0.0676 (14)0.0342 (9)0.0557 (12)0.0016 (9)−0.0119 (10)−0.0213 (8)
C9A0.0518 (11)0.0344 (9)0.0596 (12)−0.0108 (8)−0.0156 (10)−0.0107 (8)
C10A0.0331 (8)0.0319 (8)0.0487 (10)−0.0086 (6)−0.0055 (7)−0.0017 (7)
C2A0.0312 (8)0.0368 (8)0.0311 (8)−0.0020 (6)0.0077 (7)−0.0034 (6)
C1A0.0288 (8)0.0419 (9)0.0362 (9)0.0013 (6)0.0049 (7)−0.0107 (7)
O1A0.0449 (7)0.0375 (6)0.0389 (7)−0.0012 (5)−0.0030 (6)−0.0068 (5)
C4A0.0330 (9)0.0471 (10)0.0608 (13)−0.0082 (7)−0.0080 (8)−0.0140 (9)
S1B0.0384 (2)0.0427 (2)0.0365 (2)0.00559 (17)0.00863 (18)−0.00300 (17)
C3B0.0355 (8)0.0259 (7)0.0286 (8)−0.0031 (6)0.0039 (6)−0.0065 (6)
N2B0.0381 (7)0.0304 (7)0.0284 (7)−0.0011 (5)0.0044 (6)−0.0051 (5)
C6B0.0365 (8)0.0270 (7)0.0296 (8)−0.0048 (6)0.0043 (6)−0.0079 (6)
C5B0.0341 (8)0.0292 (7)0.0292 (8)−0.0060 (6)0.0040 (6)−0.0072 (6)
N1B0.0349 (7)0.0315 (7)0.0263 (7)−0.0031 (5)0.0037 (5)−0.0036 (5)
C2B0.0414 (9)0.0400 (9)0.0245 (8)−0.0014 (7)0.0047 (7)−0.0041 (6)
C1B0.0409 (10)0.0404 (9)0.0397 (10)−0.0038 (7)0.0071 (8)0.0021 (7)
O1B0.0349 (7)0.0628 (9)0.0443 (8)0.0089 (6)0.0116 (6)0.0195 (6)
C10B0.0398 (9)0.0407 (9)0.0367 (9)−0.0002 (7)−0.0023 (7)−0.0052 (7)
C9B0.0358 (9)0.0508 (11)0.0519 (12)0.0036 (8)0.0000 (8)−0.0137 (9)
C8B0.0390 (10)0.0491 (10)0.0491 (11)−0.0024 (8)0.0116 (8)−0.0170 (8)
C7B0.0433 (10)0.0378 (9)0.0336 (9)−0.0055 (7)0.0104 (7)−0.0088 (7)
C4B0.0442 (11)0.0745 (14)0.0448 (12)0.0157 (10)0.0037 (9)0.0072 (10)

Geometric parameters (Å, °)

S1A—C3A1.7383 (16)S1B—C3B1.7369 (16)
S1A—C4A1.7851 (19)S1B—C4B1.788 (2)
C3A—N1A1.3700 (19)C3B—N2B1.321 (2)
C3A—N2A1.321 (2)C3B—N1B1.368 (2)
N1A—C5A1.384 (2)N2B—C6B1.396 (2)
N1A—C2A1.461 (2)C6B—C5B1.398 (2)
C5A—C6A1.396 (2)C6B—C7B1.396 (2)
C5A—C10A1.396 (2)C5B—N1B1.390 (2)
C6A—N2A1.397 (2)C5B—C10B1.388 (2)
C6A—C7A1.395 (2)N1B—C2B1.458 (2)
C7A—C8A1.382 (3)C2B—C1B1.509 (2)
C7A—H7A0.950C2B—H21B0.950
C8A—C9A1.392 (3)C2B—H22B0.950
C8A—H8A0.950C1B—O1B1.413 (2)
C9A—C10A1.385 (3)C1B—H11B0.950
C9A—H9A0.950C1B—H12B0.950
C10A—H10A0.950O1B—H1B0.95 (3)
C2A—C1A1.510 (2)C10B—C9B1.382 (3)
C2A—H21A0.950C10B—H10B0.950
C2A—H22A0.950C9B—C8B1.391 (3)
C1A—O1A1.402 (2)C9B—H9B0.950
C1A—H11A0.950C8B—C7B1.385 (3)
C1A—H12A0.950C8B—H8B0.950
O1A—H1A1.01 (3)C7B—H7B0.950
C4A—H41A0.950C4B—H41B0.950
C4A—H42A0.950C4B—H42B0.950
C4A—H43A0.950C4B—H43B0.950
C3A—S1A—C4A100.28 (8)C3B—S1B—C4B100.22 (9)
S1A—C3A—N1A119.56 (12)S1B—C3B—N2B126.69 (13)
S1A—C3A—N2A126.71 (12)S1B—C3B—N1B119.73 (12)
N1A—C3A—N2A113.67 (14)N2B—C3B—N1B113.53 (14)
C3A—N1A—C5A106.27 (13)C3B—N2B—C6B104.41 (13)
C3A—N1A—C2A127.66 (14)N2B—C6B—C5B110.28 (14)
C5A—N1A—C2A125.82 (13)N2B—C6B—C7B129.65 (15)
N1A—C5A—C6A105.66 (13)C5B—C6B—C7B120.07 (16)
N1A—C5A—C10A131.55 (15)C6B—C5B—N1B105.33 (14)
C6A—C5A—C10A122.79 (15)C6B—C5B—C10B122.56 (15)
C5A—C6A—N2A110.23 (13)N1B—C5B—C10B132.10 (15)
C5A—C6A—C7A120.05 (15)C5B—N1B—C3B106.45 (13)
N2A—C6A—C7A129.72 (15)C5B—N1B—C2B126.32 (14)
C6A—N2A—C3A104.17 (13)C3B—N1B—C2B127.15 (14)
C6A—C7A—C8A117.44 (17)N1B—C2B—C1B113.41 (14)
C6A—C7A—H7A120.6N1B—C2B—H21B108.5
C8A—C7A—H7A122.0C1B—C2B—H21B108.4
C7A—C8A—C9A121.94 (17)N1B—C2B—H22B108.5
C7A—C8A—H8A119.0C1B—C2B—H22B108.5
C9A—C8A—H8A119.0H21B—C2B—H22B109.5
C8A—C9A—C10A121.66 (17)C2B—C1B—O1B109.85 (15)
C8A—C9A—H9A119.2C2B—C1B—H11B109.4
C10A—C9A—H9A119.2O1B—C1B—H11B109.5
C5A—C10A—C9A116.10 (17)C2B—C1B—H12B109.4
C5A—C10A—H10A122.0O1B—C1B—H12B109.3
C9A—C10A—H10A121.9H11B—C1B—H12B109.5
N1A—C2A—C1A113.63 (13)C1B—O1B—H1B110.3 (18)
N1A—C2A—H21A108.4C5B—C10B—C9B116.51 (17)
C1A—C2A—H21A108.3C5B—C10B—H10B121.8
N1A—C2A—H22A108.5C9B—C10B—H10B121.7
C1A—C2A—H22A108.5C10B—C9B—C8B121.79 (18)
H21A—C2A—H22A109.5C10B—C9B—H9B119.1
C2A—C1A—O1A110.78 (13)C8B—C9B—H9B119.1
C2A—C1A—H11A109.2C9B—C8B—C7B121.60 (17)
O1A—C1A—H11A109.2C9B—C8B—H8B119.2
C2A—C1A—H12A109.1C7B—C8B—H8B119.2
O1A—C1A—H12A109.0C6B—C7B—C8B117.47 (17)
H11A—C1A—H12A109.5C6B—C7B—H7B121.3
C1A—O1A—H1A110.8 (16)C8B—C7B—H7B121.3
S1A—C4A—H41A109.5S1B—C4B—H41B109.5
S1A—C4A—H42A109.5S1B—C4B—H42B109.5
H41A—C4A—H42A109.5H41B—C4B—H42B109.5
S1A—C4A—H43A109.5S1B—C4B—H43B109.4
H41A—C4A—H43A109.5H41B—C4B—H43B109.5
H42A—C4A—H43A109.5H42B—C4B—H43B109.5

Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the N1A-C3A-N2A-C6A-C5A and C5A—C10A rings, respectively.
D—H···AD—HH···AD···AD—H···A
O1B—H1B···N2Ai0.95 (3)1.88 (3)2.825 (3)174 (3)
O1A—H1A···N2B1.01 (3)1.80 (3)2.808 (3)175 (3)
C4A—H41A···O1Aii0.952.423.366 (3)174
C4A—H43A···Cg2iii0.952.863.627 (2)139
C4B—H43B···Cg10.952.863.486 (2)125
C10B—H10B···Cg2iv0.952.743.631 (2)157

Symmetry codes: (i) −x+1, −y+2, −z; (ii) −x+1, −y+2, −z+1; (iii) −x+1, −y+1, −z+1; (iv) −x, −y+2, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: WN2372).

References

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