Literature DB >> 23284448

5-Bromo-2-(thio-phen-2-yl)-1-(thio-phen-2-ylmeth-yl)-1H-benzimidazole.

David K Geiger1, Matthew R Destefano.   

Abstract

There are two independent mol-ecules in the asymmetric unit of the title compound, C(16)H(11)BrN(2)S(2). In the crystal, weak C-H⋯N hydrogen bonds and C-H⋯thio-phene ring inter-actions link the mol-ecules into chains along [100]. The structure exhibits disorder of the 2-thio-phen-2-yl substituent of one of the symmetry-unique mol-ecules with a major:minor component ratio of 0.914 (3):0.086 (3).

Entities:  

Year:  2012        PMID: 23284448      PMCID: PMC3515228          DOI: 10.1107/S1600536812042146

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


Related literature

For the characterization of 2-(thio­phen-2-yl)-1-(thio­phen-2-ylmeth­yl)-1H-benzimidazole, see: Geiger et al. (2012 ▶). For examples of pharmacological uses of benzimidazoles, see: López-Rodríguez et al. (1999 ▶); Varala et al. (2007 ▶); Horton et al. (2003 ▶). For the synthesis of substituted benzimidazoles, see: Grimmett (1997 ▶).

Experimental

Crystal data

C16H11BrN2S2 M = 375.30 Monoclinic, a = 12.6753 (17) Å b = 10.5413 (11) Å c = 23.581 (3) Å β = 100.878 (4)° V = 3094.1 (6) Å3 Z = 8 Mo Kα radiation μ = 2.92 mm−1 T = 200 K 0.60 × 0.20 × 0.10 mm

Data collection

Bruker SMART X2S benchtop diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 2008a ▶) T min = 0.46, T max = 0.76 19813 measured reflections 5581 independent reflections 4191 reflections with I > 2σ(I) R int = 0.059

Refinement

R[F 2 > 2σ(F 2)] = 0.038 wR(F 2) = 0.091 S = 1.02 5581 reflections 392 parameters 91 restraints H-atom parameters constrained Δρmax = 0.65 e Å−3 Δρmin = −0.80 e Å−3 Data collection: APEX2 (Bruker, 2010 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008b ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008b ▶); molecular graphics: XSHELL (Bruker, 2004 ▶) and Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶). Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812042146/lr2085sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812042146/lr2085Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536812042146/lr2085Isup3.mol Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536812042146/lr2085Isup4.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C16H11BrN2S2F(000) = 1504
Mr = 375.30Dx = 1.611 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 12.6753 (17) ÅCell parameters from 6104 reflections
b = 10.5413 (11) Åθ = 2.5–24.4°
c = 23.581 (3) ŵ = 2.92 mm1
β = 100.878 (4)°T = 200 K
V = 3094.1 (6) Å3Plate, colourless
Z = 80.60 × 0.20 × 0.10 mm
Bruker SMART X2S benchtop diffractometer5581 independent reflections
Radiation source: XOS X-beam microfocus source4191 reflections with I > 2σ(I)
Doubly curved silicon crystal monochromatorRint = 0.059
Detector resolution: 8.3330 pixels mm-1θmax = 25.4°, θmin = 2.1°
ω scansh = −15→15
Absorption correction: multi-scan (SADABS; Sheldrick, 2008a)k = −12→12
Tmin = 0.46, Tmax = 0.76l = −28→24
19813 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.091H-atom parameters constrained
S = 1.02w = 1/[σ2(Fo2) + (0.036P)2 + 0.884P] where P = (Fo2 + 2Fc2)/3
5581 reflections(Δ/σ)max = 0.001
392 parametersΔρmax = 0.65 e Å3
91 restraintsΔρmin = −0.80 e Å3
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) 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*/UeqOcc. (<1)
Br10.75134 (3)1.11709 (4)0.458735 (16)0.05101 (14)
Br20.11272 (3)1.13960 (3)0.03496 (14)0.03685 (12)
S10.41783 (7)0.73442 (9)0.17228 (4)0.0370 (2)
S20.81366 (8)1.15655 (8)0.16253 (4)0.0354 (2)
S3−0.03440 (10)0.73244 (14)0.31444 (5)0.0301 (3)0.914 (3)
C240.0711 (5)0.8382 (6)0.32690 (16)0.0225 (9)0.914 (3)
C250.1030 (6)0.8601 (8)0.3841 (3)0.0350 (16)0.914 (3)
H250.15970.91640.39940.042*0.914 (3)
C260.0435 (4)0.7907 (4)0.41889 (18)0.0348 (12)0.914 (3)
H260.05580.7950.45980.042*0.914 (3)
C27−0.0325 (4)0.7179 (4)0.38673 (17)0.0331 (11)0.914 (3)
H27−0.07980.66430.40260.04*0.914 (3)
S3000.118 (2)0.872 (3)0.3950 (10)0.0301 (3)0.086 (3)
C2400.062 (5)0.846 (7)0.3243 (10)0.0225 (9)0.086 (3)
C250−0.013 (4)0.753 (6)0.3166 (15)0.0350 (16)0.086 (3)
H250−0.05040.72530.28010.042*0.086 (3)
C260−0.028 (4)0.702 (5)0.3704 (17)0.0348 (12)0.086 (3)
H260−0.080.63980.37410.042*0.086 (3)
C2700.041 (5)0.753 (5)0.4156 (15)0.0331 (11)0.086 (3)
H2700.04540.72550.45440.04*0.086 (3)
S40.36606 (8)1.15559 (8)0.33291 (4)0.0359 (2)
C290.3469 (2)1.0042 (3)0.35642 (13)0.0243 (7)
C300.37895 (19)0.9943 (2)0.41524 (11)0.0290 (8)
H300.37590.91790.43630.035*
C310.41740 (19)1.1124 (2)0.44115 (11)0.0372 (9)
H310.44221.12380.48140.045*
C320.4144 (3)1.2058 (3)0.40164 (15)0.0383 (9)
H320.43671.29050.41110.046*
N10.6914 (2)0.9247 (2)0.21670 (11)0.0237 (6)
N20.5457 (2)0.9232 (3)0.25919 (11)0.0259 (6)
N30.2090 (2)0.9262 (2)0.27375 (11)0.0232 (6)
N40.0354 (2)0.9291 (2)0.22968 (11)0.0233 (6)
C10.7240 (2)0.9759 (3)0.27135 (13)0.0222 (7)
C20.6323 (2)0.9745 (3)0.29708 (13)0.0225 (7)
C30.6388 (3)1.0186 (3)0.35289 (14)0.0272 (8)
H30.57771.02080.37080.033*
C40.7381 (3)1.0590 (3)0.38108 (13)0.0279 (8)
C50.8299 (3)1.0590 (3)0.35640 (14)0.0275 (8)
H50.89671.08640.37830.033*
C60.8232 (2)1.0189 (3)0.30016 (14)0.0252 (7)
H60.88391.02080.28190.03*
C70.5840 (3)0.8946 (3)0.21240 (14)0.0241 (7)
C80.5183 (2)0.8366 (3)0.16143 (14)0.0266 (7)
C90.5175 (3)0.8543 (3)0.10299 (15)0.0317 (8)
H90.56640.90710.0880.038*
C100.4344 (3)0.7835 (4)0.06878 (16)0.0420 (10)
H100.42130.78380.02780.05*
C110.3754 (3)0.7156 (3)0.09998 (16)0.0399 (9)
H110.31680.66310.08340.048*
C120.7635 (3)0.8988 (3)0.17647 (13)0.0252 (7)
H12A0.73610.8240.15280.03*
H12B0.83520.87660.1990.03*
C130.7760 (2)1.0068 (3)0.13666 (14)0.0260 (8)
C140.7663 (3)1.0014 (3)0.07791 (14)0.0310 (8)
H140.74660.92710.05570.037*
C150.7891 (3)1.1198 (3)0.05394 (16)0.0369 (9)
H150.78661.13290.01390.044*
C160.8147 (3)1.2113 (4)0.09412 (17)0.0408 (10)
H160.83141.29620.08550.049*
C170.2065 (2)0.9796 (3)0.21996 (13)0.0228 (7)
C180.0977 (2)0.9815 (3)0.19334 (13)0.0230 (7)
C190.0678 (3)1.0299 (3)0.13786 (14)0.0251 (7)
H19−0.00531.03410.11910.03*
C200.1492 (3)1.0714 (3)0.11131 (13)0.0262 (7)
C210.2576 (3)1.0675 (3)0.13697 (14)0.0283 (8)
H210.31041.09560.11610.034*
C220.2882 (3)1.0226 (3)0.19272 (14)0.0273 (8)
H220.36141.02110.21150.033*
C230.1038 (2)0.8981 (3)0.27693 (14)0.0226 (7)
C280.3078 (2)0.8977 (3)0.31505 (13)0.0244 (7)
H28A0.3650.87630.29330.029*
H28B0.29520.82180.33760.029*
U11U22U33U12U13U23
Br10.0473 (3)0.0758 (3)0.0317 (2)−0.0111 (2)0.01178 (18)−0.0179 (2)
Br20.0475 (2)0.0365 (2)0.02852 (19)0.00007 (17)0.01243 (17)0.00434 (16)
S10.0262 (5)0.0372 (6)0.0474 (6)−0.0087 (4)0.0061 (4)−0.0036 (4)
S20.0361 (5)0.0294 (5)0.0426 (5)−0.0005 (4)0.0121 (4)−0.0066 (4)
S30.0251 (7)0.0301 (8)0.0354 (6)−0.0096 (4)0.0067 (4)0.0013 (4)
C240.016 (2)0.021 (2)0.0304 (17)−0.0001 (16)0.0044 (14)0.0012 (14)
C250.027 (4)0.044 (4)0.035 (3)−0.012 (2)0.008 (3)0.000 (3)
C260.035 (2)0.040 (3)0.030 (2)−0.009 (2)0.0067 (17)0.0000 (19)
C270.027 (2)0.039 (3)0.035 (2)−0.0082 (19)0.011 (2)0.007 (2)
S3000.0251 (7)0.0301 (8)0.0354 (6)−0.0096 (4)0.0067 (4)0.0013 (4)
C2400.016 (2)0.021 (2)0.0304 (17)−0.0001 (16)0.0044 (14)0.0012 (14)
C2500.027 (4)0.044 (4)0.035 (3)−0.012 (2)0.008 (3)0.000 (3)
C2600.035 (2)0.040 (3)0.030 (2)−0.009 (2)0.0067 (17)0.0000 (19)
C2700.027 (2)0.039 (3)0.035 (2)−0.0082 (19)0.011 (2)0.007 (2)
S40.0356 (5)0.0281 (5)0.0425 (5)−0.0021 (4)0.0030 (4)0.0085 (4)
C290.0116 (16)0.0272 (19)0.0346 (18)0.0006 (13)0.0053 (14)0.0074 (15)
C300.0213 (18)0.027 (2)0.039 (2)−0.0034 (15)0.0060 (15)0.0092 (16)
C310.031 (2)0.039 (2)0.038 (2)0.0003 (17)−0.0014 (17)−0.0018 (18)
C320.036 (2)0.030 (2)0.046 (2)−0.0029 (17)0.0019 (18)−0.0006 (18)
N10.0152 (14)0.0286 (15)0.0279 (14)−0.0007 (12)0.0058 (11)−0.0034 (12)
N20.0166 (15)0.0289 (16)0.0322 (15)0.0000 (12)0.0050 (12)−0.0014 (12)
N30.0155 (14)0.0252 (15)0.0297 (14)−0.0007 (11)0.0061 (11)0.0038 (12)
N40.0148 (14)0.0265 (15)0.0292 (14)0.0007 (11)0.0061 (12)0.0019 (12)
C10.0171 (16)0.0238 (18)0.0266 (17)0.0030 (14)0.0067 (14)−0.0006 (14)
C20.0165 (17)0.0208 (18)0.0302 (17)0.0008 (14)0.0045 (14)0.0024 (14)
C30.0212 (18)0.0292 (19)0.0333 (18)0.0021 (14)0.0107 (15)0.0007 (15)
C40.030 (2)0.029 (2)0.0252 (17)0.0014 (15)0.0072 (15)−0.0043 (15)
C50.0208 (18)0.0253 (19)0.0352 (19)−0.0024 (14)0.0020 (15)−0.0021 (15)
C60.0151 (16)0.0267 (19)0.0348 (18)−0.0023 (14)0.0074 (14)−0.0028 (15)
C70.0183 (17)0.0214 (18)0.0325 (18)0.0005 (14)0.0044 (14)0.0006 (14)
C80.0178 (17)0.0275 (19)0.0335 (18)0.0000 (14)0.0026 (14)−0.0014 (15)
C90.0187 (18)0.034 (2)0.040 (2)−0.0031 (15)−0.0003 (15)−0.0033 (16)
C100.034 (2)0.053 (3)0.037 (2)0.0028 (19)−0.0003 (18)−0.0079 (19)
C110.025 (2)0.042 (2)0.050 (2)−0.0056 (17)−0.0014 (17)−0.0116 (19)
C120.0171 (17)0.0298 (19)0.0306 (18)0.0018 (14)0.0093 (14)−0.0056 (15)
C130.0165 (17)0.0286 (19)0.0343 (19)0.0028 (14)0.0085 (15)−0.0044 (15)
C140.0251 (19)0.033 (2)0.0362 (19)−0.0008 (15)0.0101 (15)−0.0055 (16)
C150.034 (2)0.044 (2)0.034 (2)0.0089 (17)0.0108 (17)0.0057 (18)
C160.039 (2)0.032 (2)0.056 (2)0.0057 (18)0.0203 (19)0.007 (2)
C170.0191 (17)0.0190 (17)0.0311 (17)−0.0001 (13)0.0067 (14)−0.0001 (14)
C180.0173 (17)0.0217 (18)0.0314 (18)0.0012 (14)0.0081 (14)−0.0014 (14)
C190.0192 (17)0.0238 (18)0.0338 (18)0.0019 (14)0.0090 (14)−0.0020 (15)
C200.032 (2)0.0222 (18)0.0269 (17)0.0025 (15)0.0111 (15)−0.0013 (14)
C210.0270 (19)0.0242 (19)0.0378 (19)−0.0022 (15)0.0167 (16)0.0000 (16)
C220.0184 (17)0.0248 (19)0.0404 (19)−0.0018 (14)0.0099 (15)0.0005 (16)
C230.0169 (16)0.0198 (18)0.0325 (18)−0.0020 (13)0.0085 (14)−0.0005 (14)
C280.0171 (17)0.0234 (18)0.0327 (18)0.0005 (14)0.0047 (14)0.0066 (14)
Br1—C41.908 (3)N3—C281.465 (4)
Br2—C201.912 (3)N4—C231.317 (4)
S1—C111.700 (4)N4—C181.384 (4)
S1—C81.723 (3)C1—C61.387 (4)
S2—C161.716 (4)C1—C21.409 (4)
S2—C131.727 (3)C2—C31.384 (4)
S3—C271.707 (4)C3—C41.376 (4)
S3—C241.723 (4)C3—H30.95
C24—C251.352 (6)C4—C51.396 (4)
C24—C231.464 (4)C5—C61.379 (4)
C25—C261.417 (7)C5—H50.95
C25—H250.95C6—H60.95
C26—C271.348 (5)C7—C81.461 (4)
C26—H260.95C8—C91.389 (5)
C27—H270.95C9—C101.412 (5)
S300—C2401.707 (17)C9—H90.95
S300—C2701.721 (17)C10—C111.349 (5)
C240—C2501.353 (17)C10—H100.95
C240—C231.430 (17)C11—H110.95
C250—C2601.422 (17)C12—C131.503 (4)
C250—H2500.95C12—H12A0.99
C260—C2701.349 (16)C12—H12B0.99
C260—H2600.95C13—C141.369 (4)
C270—H2700.95C14—C151.422 (5)
S4—C321.705 (4)C14—H140.95
S4—C291.722 (3)C15—C161.348 (5)
C29—C301.374 (4)C15—H150.95
C29—C281.509 (4)C16—H160.95
C30—C311.4313C17—C221.393 (4)
C30—H300.95C17—C181.404 (4)
C31—C321.351 (4)C18—C191.388 (4)
C31—H310.95C19—C201.375 (4)
C32—H320.95C19—H190.95
N1—C71.383 (4)C20—C211.393 (4)
N1—C11.386 (4)C21—C221.382 (4)
N1—C121.461 (4)C21—H210.95
N2—C71.321 (4)C22—H220.95
N2—C21.387 (4)C28—H28A0.99
N3—C231.383 (4)C28—H28B0.99
N3—C171.383 (4)
C11—S1—C891.52 (17)C5—C6—H6121.4
C16—S2—C1391.50 (17)C1—C6—H6121.4
C27—S3—C2491.35 (18)N2—C7—N1113.4 (3)
C25—C24—C23130.8 (5)N2—C7—C8122.7 (3)
C25—C24—S3110.9 (4)N1—C7—C8123.8 (3)
C23—C24—S3118.0 (3)C9—C8—C7131.0 (3)
C24—C25—C26113.5 (5)C9—C8—S1111.3 (2)
C24—C25—H25123.3C7—C8—S1117.5 (2)
C26—C25—H25123.3C8—C9—C10111.2 (3)
C27—C26—C25111.7 (4)C8—C9—H9124.4
C27—C26—H26124.2C10—C9—H9124.4
C25—C26—H26124.2C11—C10—C9113.5 (3)
C26—C27—S3112.6 (3)C11—C10—H10123.2
C26—C27—H27123.7C9—C10—H10123.2
S3—C27—H27123.7C10—C11—S1112.5 (3)
C240—S300—C27090.3 (11)C10—C11—H11123.8
C250—C240—C23122 (3)S1—C11—H11123.8
C250—C240—S300113.4 (14)N1—C12—C13114.7 (3)
C23—C240—S300124 (2)N1—C12—H12A108.6
C240—C250—C260111.3 (17)C13—C12—H12A108.6
C240—C250—H250124.3N1—C12—H12B108.6
C260—C250—H250124.3C13—C12—H12B108.6
C270—C260—C250112.5 (18)H12A—C12—H12B107.6
C270—C260—H260123.8C14—C13—C12127.0 (3)
C250—C260—H260123.8C14—C13—S2111.2 (3)
C260—C270—S300112.3 (16)C12—C13—S2121.8 (2)
C260—C270—H270123.8C13—C14—C15112.3 (3)
S300—C270—H270123.8C13—C14—H14123.8
C32—S4—C2991.66 (16)C15—C14—H14123.8
C30—C29—C28126.5 (3)C16—C15—C14112.9 (3)
C30—C29—S4111.3 (2)C16—C15—H15123.6
C28—C29—S4122.1 (2)C14—C15—H15123.6
C29—C30—C31112.13 (16)C15—C16—S2112.1 (3)
C29—C30—H30123.9C15—C16—H16123.9
C31—C30—H30123.9S2—C16—H16123.9
C32—C31—C30112.13 (19)N3—C17—C22131.7 (3)
C32—C31—H31123.9N3—C17—C18105.5 (3)
C30—C31—H31123.9C22—C17—C18122.9 (3)
C31—C32—S4112.8 (3)N4—C18—C19130.1 (3)
C31—C32—H32123.6N4—C18—C17110.1 (3)
S4—C32—H32123.6C19—C18—C17119.7 (3)
C7—N1—C1105.9 (2)C20—C19—C18116.9 (3)
C7—N1—C12129.5 (3)C20—C19—H19121.6
C1—N1—C12124.3 (3)C18—C19—H19121.6
C7—N2—C2104.9 (3)C19—C20—C21123.7 (3)
C23—N3—C17106.4 (2)C19—C20—Br2118.7 (3)
C23—N3—C28129.2 (3)C21—C20—Br2117.6 (2)
C17—N3—C28124.2 (3)C22—C21—C20120.0 (3)
C23—N4—C18105.2 (3)C22—C21—H21120.0
N1—C1—C6131.8 (3)C20—C21—H21120.0
N1—C1—C2105.7 (3)C21—C22—C17116.7 (3)
C6—C1—C2122.5 (3)C21—C22—H22121.6
C3—C2—N2129.9 (3)C17—C22—H22121.6
C3—C2—C1120.0 (3)N4—C23—N3112.8 (3)
N2—C2—C1110.1 (3)N4—C23—C240118 (2)
C4—C3—C2116.6 (3)N3—C23—C240129 (2)
C4—C3—H3121.7N4—C23—C24123.2 (3)
C2—C3—H3121.7N3—C23—C24124.0 (3)
C3—C4—C5123.9 (3)C240—C23—C246 (3)
C3—C4—Br1118.0 (2)N3—C28—C29114.4 (3)
C5—C4—Br1118.1 (2)N3—C28—H28A108.7
C6—C5—C4119.8 (3)C29—C28—H28A108.7
C6—C5—H5120.1N3—C28—H28B108.7
C4—C5—H5120.1C29—C28—H28B108.7
C5—C6—C1117.2 (3)H28A—C28—H28B107.6
D—H···AD—HH···AD···AD—H···A
C12i—H12Bi···N40.992.573.454 (4)149
C22—H22···N20.952.613.504 (4)158
C28—H28A···N20.992.613.522 (4)152
C6i—H6i···N40.952.653.547 (4)157
C3—H3···Cg40.952.683.578 (4)158
C19—H19···Cg2i0.952.623.512 (4)157
Table 1

Hydrogen-bond geometry (Å, °)

Cg2 and Cg4 are the centroids of the S2,C13–C16 and S4,C29–C32 rings, respectively.

D—H⋯A D—HH⋯A DA D—H⋯A
C12i—H12B i⋯N40.992.573.454 (4)149
C22—H22⋯N20.952.613.504 (4)158
C28—H28A⋯N20.992.613.522 (4)152
C6i—H6i⋯N40.952.653.547 (4)157
C3—H3⋯Cg40.952.683.578 (4)158
C19—H19⋯Cg2i 0.952.623.512 (4)157

Symmetry code: (i) .

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2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

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3.  4-Bromo-2-(5-bromo-thio-phen-2-yl)-1-[(5-bromo-thio-phen-2-yl)meth-yl]-5,6-dimethyl-1H-benzimidazole.

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4.  5,6-Dimethyl-2-(5-methyl-thio-phen-2-yl)-1-[(5-methyl-thio-phen-2-yl)meth-yl]-1H-benzimidazole.

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