Literature DB >> 23125815

3-[1-(3-Hy-droxy-benz-yl)-1H-benzimid-azol-2-yl]phenol dimethyl sulfoxide monosolvate.

Magdalena Quezada-Miriel1, Alcives Avila-Sorrosa, Juan Manuel German-Acacio, Reyna Reyes-Martínez, David Morales-Morales.   

Abstract

Crystals of the title compound were obtained as a 1:1 dimethyl sulfoxide solvate, C(20)H(16)N(2)O(2)·C(2)H(6)O. The mol-ecular conformation of the organic mol-ecule is similar to that in the previously reported unsolvated structure [Eltayeb et al. (2009 ▶). Acta Cryst. E65, o1374-o1375]. Thus, the dihedral angles formed by the benzimidazole moiety with the two benzene rings are 57.54 (4) and 76.22 (5)°, and the dihedral angle between the benzene rings is 89.23 (5)°. In the crystal, a three-dimensional network features O-H⋯O, O-H⋯N and O-H⋯S hydrogen bonds, as well as C-H⋯O and C-H⋯π inter-actions.

Entities:  

Year:  2012        PMID: 23125815      PMCID: PMC3470402          DOI: 10.1107/S1600536812040275

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


Related literature

For potential applications of benzimidazoles in medicine, see: Narasimhan et al. (2012 ▶); Alper et al. (2003 ▶); Sharma et al. (2011 ▶). For coordination compounds of benzimidazole deriv­atives, see: Tellez et al. (2008 ▶). For the crystal structure of 3-[1-(3-hy­droxy­benz­yl)-1H-benzimidazol-2-yl]phenol, see: Eltayeb et al. (2009 ▶).

Experimental

Crystal data

C20H16N2O2·C2H6OS M = 394.48 Triclinic, a = 8.892 (1) Å b = 9.1951 (10) Å c = 13.1515 (14) Å α = 85.399 (2)° β = 71.947 (2)° γ = 77.442 (2)° V = 997.81 (19) Å3 Z = 2 Mo Kα radiation μ = 0.19 mm−1 T = 298 K 0.36 × 0.24 × 0.20 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer Absorption correction: analytical (SHELXTL; Sheldrick, 2008 ▶) T min = 0.618, T max = 0.752 8327 measured reflections 3656 independent reflections 2912 reflections with I > 2σ(I) R int = 0.046

Refinement

R[F 2 > 2σ(F 2)] = 0.042 wR(F 2) = 0.113 S = 1.00 3656 reflections 261 parameters 2 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.23 e Å−3 Δρmin = −0.32 e Å−3 Data collection: SMART (Bruker, 2007 ▶); cell refinement: SAINT (Bruker, 2007 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL. Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812040275/tk5153sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812040275/tk5153Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536812040275/tk5153Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C20H16N2O2·C2H6OSZ = 2
Mr = 394.48F(000) = 416
Triclinic, P1Dx = 1.313 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.892 (1) ÅCell parameters from 4929 reflections
b = 9.1951 (10) Åθ = 2.5–25.4°
c = 13.1515 (14) ŵ = 0.19 mm1
α = 85.399 (2)°T = 298 K
β = 71.947 (2)°Prism, colourless
γ = 77.442 (2)°0.36 × 0.24 × 0.20 mm
V = 997.81 (19) Å3
Bruker SMART APEX CCD area-detector diffractometer3656 independent reflections
Radiation source: fine-focus sealed tube2912 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.046
Detector resolution: 0.83 pixels mm-1θmax = 25.4°, θmin = 1.6°
ω scansh = −10→10
Absorption correction: analytical (SHELXTL; Sheldrick, 2008)k = −11→11
Tmin = 0.618, Tmax = 0.752l = −15→15
8327 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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.113H atoms treated by a mixture of independent and constrained refinement
S = 1.00w = 1/[σ2(Fo2) + (0.0674P)2] where P = (Fo2 + 2Fc2)/3
3656 reflections(Δ/σ)max < 0.001
261 parametersΔρmax = 0.23 e Å3
2 restraintsΔρmin = −0.32 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*/Ueq
S10.19023 (5)0.03592 (5)0.01994 (4)0.05482 (17)
O10.06161 (15)0.77881 (14)0.21845 (10)0.0553 (3)
H1−0.002 (2)0.8399 (19)0.2668 (13)0.066*
O20.15779 (16)0.67344 (14)0.95005 (9)0.0580 (3)
H20.201 (2)0.7438 (18)0.9583 (16)0.070*
O30.29883 (16)−0.10268 (15)−0.03524 (10)0.0635 (4)
N10.31522 (15)0.88121 (14)0.49775 (10)0.0394 (3)
C20.21131 (18)0.90591 (18)0.59903 (12)0.0393 (4)
N30.15587 (16)1.04883 (15)0.61919 (10)0.0431 (3)
C40.2058 (2)1.27426 (19)0.50197 (15)0.0524 (4)
H40.13741.34420.55190.063*
C50.2900 (2)1.3174 (2)0.40181 (16)0.0585 (5)
H50.27781.41820.38370.070*
C60.3932 (2)1.2133 (2)0.32689 (15)0.0590 (5)
H60.44921.24630.26000.071*
C70.4145 (2)1.0629 (2)0.34927 (14)0.0526 (4)
H70.48400.99340.29940.063*
C80.32694 (19)1.01973 (18)0.45009 (13)0.0417 (4)
C90.22605 (19)1.12258 (18)0.52616 (13)0.0428 (4)
C100.4119 (2)0.74040 (19)0.45014 (13)0.0455 (4)
H10A0.39160.66100.50260.055*
H10B0.52540.74420.43240.055*
C110.37785 (18)0.70334 (17)0.35053 (12)0.0389 (4)
C120.23086 (19)0.75994 (17)0.33238 (12)0.0400 (4)
H120.15090.82360.38180.048*
C130.2017 (2)0.72253 (17)0.24104 (12)0.0421 (4)
C140.3202 (2)0.62518 (19)0.16856 (13)0.0506 (4)
H140.30130.59810.10770.061*
C150.4652 (2)0.5692 (2)0.18709 (14)0.0537 (5)
H150.54440.50390.13830.064*
C160.4962 (2)0.60800 (19)0.27712 (13)0.0482 (4)
H160.59590.57020.28810.058*
C170.16366 (18)0.78669 (18)0.67598 (12)0.0404 (4)
C180.18420 (18)0.78701 (17)0.77632 (12)0.0410 (4)
H180.23030.86010.79270.049*
C190.13664 (19)0.67954 (18)0.85205 (12)0.0429 (4)
C200.0629 (2)0.57380 (19)0.82858 (14)0.0498 (4)
H200.02780.50280.87980.060*
C210.0419 (2)0.5743 (2)0.72924 (15)0.0554 (5)
H21−0.00720.50290.71360.066*
C220.0925 (2)0.6792 (2)0.65240 (14)0.0524 (4)
H220.07880.67770.58520.063*
C230.2768 (3)0.0778 (2)0.11599 (16)0.0656 (5)
H23A0.2826−0.00430.16550.098*
H23B0.21120.16560.15400.098*
H23C0.38350.09490.08040.098*
C240.2345 (3)0.1831 (3)−0.07215 (18)0.0875 (7)
H24A0.34930.1756−0.09840.131*
H24B0.18440.2768−0.03720.131*
H24C0.19360.1767−0.13090.131*
U11U22U33U12U13U23
S10.0502 (3)0.0617 (3)0.0535 (3)−0.0095 (2)−0.0182 (2)−0.0014 (2)
O10.0558 (8)0.0622 (8)0.0513 (7)−0.0008 (6)−0.0261 (6)−0.0111 (6)
O20.0754 (9)0.0598 (8)0.0412 (7)−0.0147 (7)−0.0218 (6)0.0059 (6)
O30.0678 (8)0.0618 (8)0.0617 (8)−0.0089 (7)−0.0206 (7)−0.0126 (6)
N10.0410 (7)0.0417 (8)0.0385 (7)−0.0093 (6)−0.0155 (6)−0.0009 (6)
C20.0398 (8)0.0451 (9)0.0378 (8)−0.0094 (7)−0.0176 (7)−0.0025 (7)
N30.0457 (8)0.0430 (8)0.0430 (7)−0.0095 (6)−0.0160 (6)−0.0011 (6)
C40.0572 (11)0.0447 (10)0.0618 (11)−0.0121 (8)−0.0259 (9)−0.0007 (8)
C50.0646 (12)0.0502 (11)0.0734 (13)−0.0230 (10)−0.0350 (11)0.0155 (10)
C60.0592 (11)0.0679 (13)0.0573 (11)−0.0285 (10)−0.0220 (10)0.0174 (10)
C70.0501 (10)0.0625 (12)0.0474 (10)−0.0175 (9)−0.0145 (8)0.0022 (9)
C80.0422 (9)0.0468 (9)0.0429 (9)−0.0135 (7)−0.0198 (7)0.0019 (7)
C90.0442 (9)0.0454 (9)0.0465 (9)−0.0134 (7)−0.0218 (8)0.0006 (7)
C100.0413 (9)0.0474 (9)0.0479 (9)−0.0035 (7)−0.0168 (8)−0.0021 (8)
C110.0409 (8)0.0348 (8)0.0392 (8)−0.0087 (7)−0.0098 (7)0.0028 (7)
C120.0398 (8)0.0372 (8)0.0406 (9)−0.0054 (7)−0.0093 (7)−0.0046 (7)
C130.0478 (9)0.0380 (9)0.0420 (9)−0.0103 (7)−0.0154 (7)0.0023 (7)
C140.0649 (12)0.0473 (10)0.0381 (9)−0.0087 (9)−0.0138 (8)−0.0057 (8)
C150.0560 (11)0.0495 (10)0.0446 (10)0.0003 (9)−0.0052 (8)−0.0069 (8)
C160.0414 (9)0.0478 (10)0.0490 (10)−0.0033 (8)−0.0086 (8)0.0003 (8)
C170.0382 (8)0.0424 (9)0.0413 (9)−0.0068 (7)−0.0136 (7)−0.0012 (7)
C180.0394 (8)0.0409 (9)0.0427 (9)−0.0065 (7)−0.0126 (7)−0.0035 (7)
C190.0416 (9)0.0419 (9)0.0412 (9)−0.0003 (7)−0.0120 (7)−0.0013 (7)
C200.0529 (10)0.0400 (9)0.0506 (10)−0.0088 (8)−0.0085 (8)0.0042 (8)
C210.0616 (11)0.0486 (10)0.0621 (11)−0.0227 (9)−0.0190 (9)−0.0030 (9)
C220.0604 (11)0.0569 (11)0.0483 (10)−0.0207 (9)−0.0222 (9)−0.0011 (8)
C230.0727 (13)0.0642 (13)0.0660 (13)−0.0122 (10)−0.0292 (11)−0.0068 (10)
C240.0954 (18)0.0770 (16)0.0777 (16)−0.0072 (14)−0.0207 (14)0.0205 (13)
S1—O31.5040 (14)C11—C121.383 (2)
S1—C241.768 (2)C11—C161.383 (2)
S1—C231.7739 (18)C12—C131.388 (2)
O1—C131.353 (2)C12—H120.9300
O1—H10.857 (9)C13—C141.387 (2)
O2—C191.3541 (19)C14—C151.368 (3)
O2—H20.848 (9)C14—H140.9300
N1—C21.3689 (19)C15—C161.385 (2)
N1—C81.384 (2)C15—H150.9300
N1—C101.456 (2)C16—H160.9300
C2—N31.317 (2)C17—C221.385 (2)
C2—C171.471 (2)C17—C181.388 (2)
N3—C91.387 (2)C18—C191.382 (2)
C4—C51.374 (3)C18—H180.9300
C4—C91.391 (2)C19—C201.386 (2)
C4—H40.9300C20—C211.375 (2)
C5—C61.392 (3)C20—H200.9300
C5—H50.9300C21—C221.380 (2)
C6—C71.375 (3)C21—H210.9300
C6—H60.9300C22—H220.9300
C7—C81.390 (2)C23—H23A0.9600
C7—H70.9300C23—H23B0.9600
C8—C91.388 (2)C23—H23C0.9600
C10—C111.512 (2)C24—H24A0.9600
C10—H10A0.9700C24—H24B0.9600
C10—H10B0.9700C24—H24C0.9600
O3—S1—C24105.19 (10)O1—C13—C14117.93 (14)
O3—S1—C23106.18 (9)O1—C13—C12122.59 (14)
C24—S1—C2398.83 (11)C14—C13—C12119.47 (15)
C13—O1—H1110.5 (14)C15—C14—C13119.66 (15)
C19—O2—H2111.5 (14)C15—C14—H14120.2
C2—N1—C8106.73 (13)C13—C14—H14120.2
C2—N1—C10128.31 (13)C14—C15—C16121.20 (16)
C8—N1—C10124.60 (13)C14—C15—H15119.4
N3—C2—N1112.33 (14)C16—C15—H15119.4
N3—C2—C17123.64 (14)C11—C16—C15119.50 (16)
N1—C2—C17124.01 (14)C11—C16—H16120.3
C2—N3—C9105.51 (13)C15—C16—H16120.3
C5—C4—C9117.81 (18)C22—C17—C18119.58 (15)
C5—C4—H4121.1C22—C17—C2121.67 (14)
C9—C4—H4121.1C18—C17—C2118.67 (14)
C4—C5—C6121.35 (17)C19—C18—C17120.52 (15)
C4—C5—H5119.3C19—C18—H18119.7
C6—C5—H5119.3C17—C18—H18119.7
C7—C6—C5121.67 (17)O2—C19—C18122.55 (15)
C7—C6—H6119.2O2—C19—C20117.87 (15)
C5—C6—H6119.2C18—C19—C20119.58 (15)
C6—C7—C8116.73 (18)C21—C20—C19119.72 (16)
C6—C7—H7121.6C21—C20—H20120.1
C8—C7—H7121.6C19—C20—H20120.1
N1—C8—C9105.65 (14)C20—C21—C22120.98 (16)
N1—C8—C7132.22 (16)C20—C21—H21119.5
C9—C8—C7122.13 (16)C22—C21—H21119.5
N3—C9—C8109.77 (14)C21—C22—C17119.58 (16)
N3—C9—C4129.92 (16)C21—C22—H22120.2
C8—C9—C4120.29 (16)C17—C22—H22120.2
N1—C10—C11113.71 (13)S1—C23—H23A109.5
N1—C10—H10A108.8S1—C23—H23B109.5
C11—C10—H10A108.8H23A—C23—H23B109.5
N1—C10—H10B108.8S1—C23—H23C109.5
C11—C10—H10B108.8H23A—C23—H23C109.5
H10A—C10—H10B107.7H23B—C23—H23C109.5
C12—C11—C16119.56 (15)S1—C24—H24A109.5
C12—C11—C10121.69 (14)S1—C24—H24B109.5
C16—C11—C10118.74 (14)H24A—C24—H24B109.5
C11—C12—C13120.60 (15)S1—C24—H24C109.5
C11—C12—H12119.7H24A—C24—H24C109.5
C13—C12—H12119.7H24B—C24—H24C109.5
C8—N1—C2—N30.23 (17)N1—C10—C11—C16156.07 (14)
C10—N1—C2—N3173.56 (13)C16—C11—C12—C13−0.3 (2)
C8—N1—C2—C17178.88 (13)C10—C11—C12—C13−179.05 (14)
C10—N1—C2—C17−7.8 (2)C11—C12—C13—O1−177.93 (14)
N1—C2—N3—C90.35 (17)C11—C12—C13—C141.2 (2)
C17—C2—N3—C9−178.30 (13)O1—C13—C14—C15178.17 (16)
C9—C4—C5—C6−0.4 (3)C12—C13—C14—C15−1.0 (2)
C4—C5—C6—C70.6 (3)C13—C14—C15—C160.0 (3)
C5—C6—C7—C80.5 (3)C12—C11—C16—C15−0.7 (2)
C2—N1—C8—C9−0.70 (16)C10—C11—C16—C15178.00 (15)
C10—N1—C8—C9−174.35 (12)C14—C15—C16—C111.0 (3)
C2—N1—C8—C7179.60 (16)N3—C2—C17—C22121.37 (18)
C10—N1—C8—C76.0 (3)N1—C2—C17—C22−57.1 (2)
C6—C7—C8—N1177.93 (16)N3—C2—C17—C18−55.6 (2)
C6—C7—C8—C9−1.7 (2)N1—C2—C17—C18125.91 (16)
C2—N3—C9—C8−0.81 (17)C22—C17—C18—C191.1 (2)
C2—N3—C9—C4177.74 (16)C2—C17—C18—C19178.10 (14)
N1—C8—C9—N30.94 (16)C17—C18—C19—O2178.41 (14)
C7—C8—C9—N3−179.32 (14)C17—C18—C19—C20−2.2 (2)
N1—C8—C9—C4−177.77 (14)O2—C19—C20—C21−178.78 (15)
C7—C8—C9—C42.0 (2)C18—C19—C20—C211.8 (2)
C5—C4—C9—N3−179.26 (16)C19—C20—C21—C22−0.3 (3)
C5—C4—C9—C8−0.8 (2)C20—C21—C22—C17−0.8 (3)
C2—N1—C10—C11121.77 (16)C18—C17—C22—C210.4 (2)
C8—N1—C10—C11−66.00 (19)C2—C17—C22—C21−176.51 (16)
N1—C10—C11—C12−25.2 (2)
D—H···AD—HH···AD···AD—H···A
O2—H2···O3i0.85 (1)1.83 (1)2.6804 (19)176 (2)
O2—H2···S1i0.85 (1)2.84 (1)3.6209 (14)154 (2)
O1—H1···N3ii0.86 (1)1.88 (2)2.7316 (19)172 (2)
C18—H18···O3i0.932.583.260 (2)130
C23—H23C···O3iii0.962.723.643 (3)162
C10—H10B···Cg1iv0.972.953.622 (2)127
C5—H5···Cg2v0.932.763.624 (2)156
C23—H23B···Cg3vi0.962.863.679 (2)144
Table 1

Hydrogen-bond geometry (Å, °)

Cg1, Cg2 and Cg3 are the centroids of the C4–C9, C11–C16 and C17–C22 rings, respectively.

D—H⋯A D—HH⋯A DA D—H⋯A
O2—H2⋯O3i 0.85 (1)1.83 (1)2.6804 (19)176 (2)
O2—H2⋯S1i 0.85 (1)2.84 (1)3.6209 (14)154 (2)
O1—H1⋯N3ii 0.86 (1)1.88 (2)2.7316 (19)172 (2)
C18—H18⋯O3i 0.932.583.260 (2)130
C23—H23C⋯O3iii 0.962.723.643 (3)162
C10—H10BCg1iv 0.972.953.622 (2)127
C5—H5⋯Cg2v 0.932.763.624 (2)156
C23—H23BCg3vi 0.962.863.679 (2)144

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) ; (vi) .

  4 in total

1.  A short history of SHELX.

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

Review 2.  A review on various heterocyclic moieties and their antitubercular activity.

Authors:  S Sharma; P K Sharma; N Kumar; R Dudhe
Journal:  Biomed Pharmacother       Date:  2011-05-30       Impact factor: 6.529

3.  3-[1-(3-Hydroxy-benz-yl)-1H-benz-imid-azol-2-yl]phenol.

Authors:  Naser Eltaher Eltayeb; Siang Guan Teoh; Hoong-Kun Fun; Samuel Robinson Jebas; Rohana Adnan
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-05-23

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