Chiral molecules of the title compound, C
22H
24N
4·H
2O, have approximate twofold symmetry, essentially planar benzimidazole fragments, and a ladder-like appearance in profile, with the benzimidazole planes exhibiting a dihedral angle of 68.75 (4)°. Geometric parameters are consistent with those of comparable species containing benzimidazole or cyclohexyl fragments. Adventitious water molecules of solvation form strong O—H
N(imine) hydrogen bonds to yield infinite 2
1 columns along the
c-axis direction. The columns are related by glide-plane symmetry operations and are linked by C—H
π interactions to yield racemic crystals.
Supporting information
CCDC reference: 296719
Key indicators
- Single-crystal X-ray study
- T = 100 K
- Mean (C-C) = 0.003 Å
- R factor = 0.041
- wR factor = 0.106
- Data-to-parameter ratio = 11.9
checkCIF/PLATON results
No syntax errors found
Alert level C
ABSTM02_ALERT_3_C The ratio of expected to reported Tmax/Tmin(RR') is < 0.90
Tmin and Tmax reported: 0.831 1.000
Tmin(prime) and Tmax expected: 0.977 0.998
RR(prime) = 0.849
Please check that your absorption correction is appropriate.
PLAT061_ALERT_3_C Tmax/Tmin Range Test RR' too Large ............. 0.85
Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
correct. If it is not, please give the correct count in the
_publ_section_exptl_refinement section of the submitted CIF.
From the CIF: _diffrn_reflns_theta_max 30.55
From the CIF: _reflns_number_total 3030
Count of symmetry unique reflns 3029
Completeness (_total/calc) 100.03%
TEST3: Check Friedels for noncentro structure
Estimate of Friedel pairs measured 1
Fraction of Friedel pairs measured 0.000
Are heavy atom types Z>Si present no
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
2 ALERT level C = Check and explain
1 ALERT level G = General alerts; check
0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
0 ALERT type 2 Indicator that the structure model may be wrong or deficient
2 ALERT type 3 Indicator that the structure quality may be low
1 ALERT type 4 Improvement, methodology, query or suggestion
Trans-1,2-bis(1-methylbenzimidazol-2-yl)cyclohexane hydrate was prepared in two steps. Firstly, trans(1,2-bis(1-H-benzimidazol-2-yl) was prepared by the Phillips condensation method (Phillips, 1931) from trans-1,2-cyclohexane dicarboxylic acid and two equivalents of 1,2-phenylenediamine. Secondly, using the procedure described previously by Stibrany et al. (2004), methylation of the amine N atoms, effected using methyl iodide, yielded the non-hydrated product. Crystals of the title compound, (II), were obtained by slow evaporation in air of an acetone solution of the product. Incorporation of adventitious water resulted in the monohydrate [m.p. 479 K (soften), 491 K (melt)]. Spectroscopic analysis: IR (KBr pellet, cm−1): 3384 (m), 3051 (w), 2929 (s), 2853 (m), 1614 (w), 1468 (s), 1443 (s), 1329 (m), 1008 (w), 745 (s).
The water H atoms, which are involved in hydrogen bonding, were refined isotropically. C-bound H atoms were positioned geometrically and treated as riding, with Csp2—H and Csp3—H distances set to 0.93 and 0.96 Å, respectively, and with Uiso(H) = 1.2Ueq(C) and 1.5Ueq(C), respectively. A final difference Fourier map revealed 37 peaks larger than the absolute value of the largest negative peak. Of these, 33 of the first 35 peaks were located approximately midway along the C—C or C—N vectors, of which there are a total of 30 in the molecular framework. The 33 peaks are consistent with residual bond density, with three of the bonds exhibiting split peaks.
Data collection: SMART (Bruker, 2000); cell refinement: SAINT-Plus (Bruker, 2000); data reduction: SAINT-Plus (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and ORTEP-32 (Farrugia, 1997); software used to prepare material for publication: SHELXTL (Bruker, 2000).
trans-1,2-Bis(1-methylbenzimidazol-2-yl)cyclohexane monohydrate
top
Crystal data top
C22H24N4·H2O | Dx = 1.264 Mg m−3 |
Mr = 362.47 | Melting point: 479 K (soften), 491 K (melt) K |
Orthorhombic, Pna21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2c -2n | Cell parameters from 6763 reflections |
a = 9.6596 (7) Å | θ = 2.5–30.6° |
b = 14.5552 (11) Å | µ = 0.08 mm−1 |
c = 13.547 (1) Å | T = 100 K |
V = 1904.7 (2) Å3 | Lath, colourless |
Z = 4 | 0.29 × 0.14 × 0.03 mm |
F(000) = 776 | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 3030 independent reflections |
Radiation source: fine-focus sealed tube | 2785 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.038 |
ϕ and ω scans | θmax = 30.6°, θmin = 2.1° |
Absorption correction: multi-scan (SADABS; Blessing, 1995) | h = −12→13 |
Tmin = 0.831, Tmax = 1.00 | k = −10→20 |
14429 measured reflections | l = −19→14 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.106 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | w = 1/[σ2(Fo2) + (0.071P)2 + 0.2238P] where P = (Fo2 + 2Fc2)/3 |
3030 reflections | (Δ/σ)max = 0.001 |
254 parameters | Δρmax = 0.37 e Å−3 |
1 restraint | Δρmin = −0.16 e Å−3 |
Crystal data top
C22H24N4·H2O | V = 1904.7 (2) Å3 |
Mr = 362.47 | Z = 4 |
Orthorhombic, Pna21 | Mo Kα radiation |
a = 9.6596 (7) Å | µ = 0.08 mm−1 |
b = 14.5552 (11) Å | T = 100 K |
c = 13.547 (1) Å | 0.29 × 0.14 × 0.03 mm |
Data collection top
Bruker SMART CCD area-detector diffractometer | 3030 independent reflections |
Absorption correction: multi-scan (SADABS; Blessing, 1995) | 2785 reflections with I > 2σ(I) |
Tmin = 0.831, Tmax = 1.00 | Rint = 0.038 |
14429 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.041 | 1 restraint |
wR(F2) = 0.106 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | Δρmax = 0.37 e Å−3 |
3030 reflections | Δρmin = −0.16 e Å−3 |
254 parameters | |
Special details top
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N11 | 0.81216 (16) | 1.00399 (11) | 0.92421 (12) | 0.0190 (3) | |
N13 | 0.64846 (16) | 0.93479 (11) | 1.01498 (13) | 0.0183 (3) | |
N21 | 0.41947 (15) | 0.81453 (10) | 0.82663 (12) | 0.0163 (3) | |
N23 | 0.58166 (16) | 0.89532 (11) | 0.74536 (12) | 0.0179 (3) | |
C11 | 0.88160 (19) | 0.94786 (12) | 0.99015 (14) | 0.0192 (3) | |
C12 | 0.67326 (17) | 0.99353 (12) | 0.94277 (14) | 0.0176 (3) | |
C13 | 0.77785 (18) | 0.90483 (13) | 1.04589 (14) | 0.0182 (3) | |
C14 | 0.8138 (2) | 0.84054 (14) | 1.11798 (14) | 0.0217 (4) | |
H14 | 0.7462 | 0.8109 | 1.1550 | 0.026* | |
C15 | 0.9528 (2) | 0.82222 (16) | 1.13281 (17) | 0.0268 (4) | |
H15 | 0.9785 | 0.7787 | 1.1797 | 0.032* | |
C16 | 1.0559 (2) | 0.86786 (15) | 1.07863 (17) | 0.0272 (4) | |
H16 | 1.1486 | 0.8557 | 1.0920 | 0.033* | |
C17 | 1.02215 (19) | 0.93073 (14) | 1.00551 (17) | 0.0244 (4) | |
H17 | 1.0900 | 0.9601 | 0.9684 | 0.029* | |
C18 | 0.8761 (2) | 1.06134 (14) | 0.84882 (19) | 0.0301 (5) | |
H18A | 0.8291 | 1.0525 | 0.7871 | 0.045* | |
H18B | 0.9717 | 1.0447 | 0.8417 | 0.045* | |
H18C | 0.8695 | 1.1247 | 0.8679 | 0.045* | |
C21 | 0.48462 (18) | 0.75291 (12) | 0.76407 (13) | 0.0165 (3) | |
C22 | 0.48202 (17) | 0.89762 (12) | 0.81235 (13) | 0.0158 (3) | |
C23 | 0.58566 (18) | 0.80432 (12) | 0.71422 (14) | 0.0169 (3) | |
C24 | 0.67272 (19) | 0.76034 (13) | 0.64641 (13) | 0.0200 (4) | |
H24 | 0.7401 | 0.7930 | 0.6122 | 0.024* | |
C25 | 0.6559 (2) | 0.66706 (13) | 0.63174 (16) | 0.0222 (4) | |
H25 | 0.7143 | 0.6367 | 0.5880 | 0.027* | |
C26 | 0.5529 (2) | 0.61712 (13) | 0.68122 (15) | 0.0214 (4) | |
H26 | 0.5434 | 0.5546 | 0.6688 | 0.026* | |
C27 | 0.46464 (19) | 0.65946 (12) | 0.74862 (14) | 0.0194 (3) | |
H27 | 0.3959 | 0.6269 | 0.7816 | 0.023* | |
C28 | 0.3083 (2) | 0.79329 (13) | 0.89543 (15) | 0.0213 (4) | |
H28A | 0.3353 | 0.8111 | 0.9609 | 0.032* | |
H28B | 0.2898 | 0.7285 | 0.8941 | 0.032* | |
H28C | 0.2263 | 0.8263 | 0.8767 | 0.032* | |
C31 | 0.56325 (19) | 1.04464 (12) | 0.88790 (14) | 0.0173 (3) | |
H31 | 0.6009 | 1.0642 | 0.8241 | 0.021* | |
C32 | 0.43844 (18) | 0.98159 (12) | 0.86918 (13) | 0.0161 (3) | |
H32 | 0.4028 | 0.9614 | 0.9333 | 0.019* | |
C33 | 0.32200 (19) | 1.03345 (12) | 0.81575 (15) | 0.0193 (3) | |
H33A | 0.3537 | 1.0524 | 0.7509 | 0.023* | |
H33B | 0.2431 | 0.9931 | 0.8071 | 0.023* | |
C34 | 0.2784 (2) | 1.11799 (13) | 0.87522 (16) | 0.0227 (4) | |
H34A | 0.2073 | 1.1512 | 0.8394 | 0.027* | |
H34B | 0.2397 | 1.0986 | 0.9379 | 0.027* | |
C35 | 0.4018 (2) | 1.18153 (13) | 0.89374 (15) | 0.0231 (4) | |
H35A | 0.4353 | 1.2053 | 0.8313 | 0.028* | |
H35B | 0.3724 | 1.2332 | 0.9338 | 0.028* | |
C36 | 0.5189 (2) | 1.13053 (13) | 0.94622 (15) | 0.0215 (4) | |
H36A | 0.4884 | 1.1124 | 1.0116 | 0.026* | |
H36B | 0.5976 | 1.1713 | 0.9537 | 0.026* | |
O1 | 0.38699 (16) | 0.93244 (12) | 0.12819 (13) | 0.0280 (3) | |
H1O | 0.464 (3) | 0.927 (2) | 0.099 (2) | 0.030 (7)* | |
H2O | 0.386 (3) | 0.984 (2) | 0.158 (3) | 0.046 (9)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N11 | 0.0208 (7) | 0.0175 (7) | 0.0188 (8) | −0.0020 (5) | 0.0032 (6) | −0.0036 (6) |
N13 | 0.0198 (7) | 0.0214 (7) | 0.0137 (7) | −0.0001 (5) | −0.0005 (5) | 0.0003 (6) |
N21 | 0.0194 (6) | 0.0153 (7) | 0.0142 (7) | 0.0012 (5) | 0.0004 (5) | 0.0003 (6) |
N23 | 0.0206 (6) | 0.0175 (7) | 0.0157 (7) | −0.0003 (5) | −0.0001 (6) | 0.0001 (6) |
C11 | 0.0206 (8) | 0.0184 (8) | 0.0185 (8) | −0.0004 (6) | 0.0013 (6) | −0.0065 (7) |
C12 | 0.0192 (8) | 0.0173 (8) | 0.0163 (9) | −0.0011 (6) | 0.0014 (6) | −0.0041 (7) |
C13 | 0.0190 (7) | 0.0212 (8) | 0.0144 (8) | 0.0008 (6) | −0.0004 (6) | −0.0033 (6) |
C14 | 0.0229 (8) | 0.0271 (9) | 0.0151 (9) | 0.0039 (7) | 0.0001 (7) | −0.0015 (7) |
C15 | 0.0284 (9) | 0.0332 (11) | 0.0188 (9) | 0.0090 (8) | −0.0033 (8) | −0.0027 (8) |
C16 | 0.0205 (8) | 0.0339 (10) | 0.0272 (10) | 0.0069 (8) | −0.0023 (7) | −0.0094 (9) |
C17 | 0.0194 (8) | 0.0266 (9) | 0.0272 (10) | −0.0005 (7) | 0.0029 (7) | −0.0068 (8) |
C18 | 0.0337 (10) | 0.0210 (9) | 0.0355 (12) | −0.0024 (8) | 0.0151 (9) | 0.0030 (8) |
C21 | 0.0188 (7) | 0.0173 (7) | 0.0134 (7) | 0.0022 (6) | −0.0009 (6) | 0.0003 (6) |
C22 | 0.0181 (7) | 0.0158 (7) | 0.0135 (8) | 0.0007 (6) | −0.0021 (6) | 0.0012 (6) |
C23 | 0.0198 (7) | 0.0165 (8) | 0.0143 (8) | 0.0012 (6) | −0.0026 (6) | −0.0003 (6) |
C24 | 0.0218 (8) | 0.0237 (8) | 0.0145 (8) | 0.0011 (6) | 0.0012 (6) | 0.0001 (7) |
C25 | 0.0277 (9) | 0.0222 (8) | 0.0168 (8) | 0.0056 (7) | 0.0019 (7) | −0.0031 (7) |
C26 | 0.0291 (9) | 0.0153 (8) | 0.0198 (9) | 0.0031 (7) | −0.0015 (7) | −0.0021 (7) |
C27 | 0.0235 (8) | 0.0164 (8) | 0.0184 (9) | −0.0001 (6) | 0.0001 (6) | −0.0003 (7) |
C28 | 0.0251 (8) | 0.0187 (8) | 0.0201 (9) | −0.0029 (6) | 0.0051 (7) | −0.0006 (7) |
C31 | 0.0223 (8) | 0.0141 (7) | 0.0155 (8) | −0.0006 (6) | −0.0004 (6) | 0.0005 (6) |
C32 | 0.0208 (7) | 0.0142 (7) | 0.0133 (8) | 0.0008 (6) | −0.0012 (6) | −0.0002 (6) |
C33 | 0.0226 (8) | 0.0187 (8) | 0.0167 (8) | 0.0036 (6) | −0.0028 (7) | −0.0005 (7) |
C34 | 0.0277 (9) | 0.0217 (8) | 0.0187 (9) | 0.0070 (7) | 0.0015 (7) | 0.0014 (7) |
C35 | 0.0340 (10) | 0.0171 (8) | 0.0182 (9) | 0.0027 (7) | 0.0018 (7) | 0.0013 (7) |
C36 | 0.0306 (9) | 0.0148 (7) | 0.0192 (9) | 0.0007 (7) | −0.0001 (7) | −0.0017 (7) |
O1 | 0.0273 (7) | 0.0333 (8) | 0.0233 (7) | −0.0082 (6) | 0.0041 (6) | −0.0066 (7) |
Geometric parameters (Å, º) top
N11—C12 | 1.374 (2) | C23—C24 | 1.400 (3) |
N21—C22 | 1.366 (2) | C24—C25 | 1.382 (3) |
N13—C12 | 1.321 (3) | C24—H24 | 0.9300 |
N23—C22 | 1.323 (2) | C25—C26 | 1.403 (3) |
N11—C11 | 1.384 (3) | C25—H25 | 0.9300 |
N21—C21 | 1.385 (2) | C26—C27 | 1.393 (3) |
N13—C13 | 1.388 (2) | C26—H26 | 0.9300 |
N23—C23 | 1.391 (2) | C27—H27 | 0.9300 |
C11—C13 | 1.402 (3) | C28—H28A | 0.9600 |
C21—C23 | 1.403 (3) | C28—H28B | 0.9600 |
C12—C31 | 1.495 (2) | C28—H28C | 0.9600 |
C22—C32 | 1.505 (2) | C31—C36 | 1.540 (3) |
C31—C32 | 1.536 (2) | C31—H31 | 0.9800 |
N11—C18 | 1.456 (3) | C32—C33 | 1.536 (2) |
N21—C28 | 1.455 (2) | C32—H32 | 0.9800 |
C11—C17 | 1.396 (3) | C33—C34 | 1.530 (3) |
C13—C14 | 1.396 (3) | C33—H33A | 0.9700 |
C14—C15 | 1.384 (3) | C33—H33B | 0.9700 |
C14—H14 | 0.9300 | C34—C35 | 1.529 (3) |
C15—C16 | 1.404 (3) | C34—H34A | 0.9700 |
C15—H15 | 0.9300 | C34—H34B | 0.9700 |
C16—C17 | 1.387 (3) | C35—C36 | 1.528 (3) |
C16—H16 | 0.9300 | C35—H35A | 0.9700 |
C17—H17 | 0.9300 | C35—H35B | 0.9700 |
C18—H18A | 0.9600 | C36—H36A | 0.9700 |
C18—H18B | 0.9600 | C36—H36B | 0.9700 |
C18—H18C | 0.9600 | O1—H1O | 0.85 (3) |
C21—C27 | 1.390 (3) | O1—H2O | 0.85 (3) |
| | | |
N13—C12—N11 | 112.60 (16) | C27—C26—C25 | 121.20 (18) |
N23—C22—N21 | 113.36 (16) | C27—C26—H26 | 119.4 |
C12—N11—C11 | 106.85 (15) | C25—C26—H26 | 119.4 |
C22—N21—C21 | 106.60 (15) | C21—C27—C26 | 116.54 (18) |
C12—N13—C13 | 105.27 (15) | C21—C27—H27 | 121.7 |
C22—N23—C23 | 104.61 (15) | C26—C27—H27 | 121.7 |
N11—C11—C13 | 105.36 (16) | N21—C28—H28A | 109.5 |
N21—C21—C23 | 105.38 (15) | N21—C28—H28B | 109.5 |
N13—C13—C11 | 109.91 (16) | H28A—C28—H28B | 109.5 |
N23—C23—C21 | 110.04 (16) | N21—C28—H28C | 109.5 |
C12—N11—C18 | 127.30 (17) | H28A—C28—H28C | 109.5 |
C11—N11—C18 | 125.84 (17) | H28B—C28—H28C | 109.5 |
C22—N21—C28 | 127.25 (15) | C12—C31—C32 | 110.03 (14) |
C21—N21—C28 | 126.14 (15) | C12—C31—C36 | 110.29 (15) |
N11—C11—C17 | 132.30 (18) | C32—C31—C36 | 110.57 (15) |
C17—C11—C13 | 122.34 (19) | C12—C31—H31 | 108.6 |
N13—C12—C31 | 124.15 (15) | C32—C31—H31 | 108.6 |
N11—C12—C31 | 123.24 (16) | C36—C31—H31 | 108.6 |
N13—C13—C14 | 130.19 (17) | C22—C32—C33 | 111.28 (15) |
C14—C13—C11 | 119.87 (17) | C22—C32—C31 | 110.50 (14) |
C15—C14—C13 | 118.17 (19) | C33—C32—C31 | 111.04 (15) |
C15—C14—H14 | 120.9 | C22—C32—H32 | 108.0 |
C13—C14—H14 | 120.9 | C33—C32—H32 | 108.0 |
C14—C15—C16 | 121.4 (2) | C31—C32—H32 | 108.0 |
C14—C15—H15 | 119.3 | C34—C33—C32 | 110.40 (16) |
C16—C15—H15 | 119.3 | C34—C33—H33A | 109.6 |
C17—C16—C15 | 121.22 (18) | C32—C33—H33A | 109.6 |
C17—C16—H16 | 119.4 | C34—C33—H33B | 109.6 |
C15—C16—H16 | 119.4 | C32—C33—H33B | 109.6 |
C16—C17—C11 | 116.93 (19) | H33A—C33—H33B | 108.1 |
C16—C17—H17 | 121.5 | C35—C34—C33 | 111.00 (16) |
C11—C17—H17 | 121.5 | C35—C34—H34A | 109.4 |
N11—C18—H18A | 109.5 | C33—C34—H34A | 109.4 |
N11—C18—H18B | 109.5 | C35—C34—H34B | 109.4 |
H18A—C18—H18B | 109.5 | C33—C34—H34B | 109.4 |
N11—C18—H18C | 109.5 | H34A—C34—H34B | 108.0 |
H18A—C18—H18C | 109.5 | C36—C35—C34 | 111.06 (16) |
H18B—C18—H18C | 109.5 | C36—C35—H35A | 109.4 |
N21—C21—C27 | 131.51 (17) | C34—C35—H35A | 109.4 |
C27—C21—C23 | 123.10 (17) | C36—C35—H35B | 109.4 |
N23—C22—C32 | 125.09 (16) | C34—C35—H35B | 109.4 |
N21—C22—C32 | 121.54 (16) | H35A—C35—H35B | 108.0 |
N23—C23—C24 | 130.62 (17) | C35—C36—C31 | 111.20 (16) |
C24—C23—C21 | 119.32 (16) | C35—C36—H36A | 109.4 |
C25—C24—C23 | 118.23 (17) | C31—C36—H36A | 109.4 |
C25—C24—H24 | 120.9 | C35—C36—H36B | 109.4 |
C23—C24—H24 | 120.9 | C31—C36—H36B | 109.4 |
C24—C25—C26 | 121.59 (18) | H36A—C36—H36B | 108.0 |
C24—C25—H25 | 119.2 | H1O—O1—H2O | 108 (3) |
C26—C25—H25 | 119.2 | | |
| | | |
C12—N11—C11—C17 | −179.9 (2) | C22—N23—C23—C24 | −177.98 (19) |
C18—N11—C11—C17 | 1.1 (3) | C22—N23—C23—C21 | 0.53 (19) |
C12—N11—C11—C13 | 0.49 (19) | N21—C21—C23—N23 | −0.3 (2) |
C18—N11—C11—C13 | −178.46 (18) | C27—C21—C23—N23 | −179.62 (17) |
C13—N13—C12—N11 | 0.0 (2) | N21—C21—C23—C24 | 178.41 (15) |
C13—N13—C12—C31 | −178.96 (16) | C27—C21—C23—C24 | −0.9 (3) |
C11—N11—C12—N13 | −0.3 (2) | N23—C23—C24—C25 | 177.99 (19) |
C18—N11—C12—N13 | 178.58 (18) | C21—C23—C24—C25 | −0.4 (3) |
C11—N11—C12—C31 | 178.67 (16) | C23—C24—C25—C26 | 1.4 (3) |
C18—N11—C12—C31 | −2.4 (3) | C24—C25—C26—C27 | −1.1 (3) |
C12—N13—C13—C14 | −177.9 (2) | N21—C21—C27—C26 | −177.93 (18) |
C12—N13—C13—C11 | 0.3 (2) | C23—C21—C27—C26 | 1.2 (3) |
N11—C11—C13—N13 | −0.49 (19) | C25—C26—C27—C21 | −0.2 (3) |
C17—C11—C13—N13 | 179.87 (17) | N13—C12—C31—C32 | −39.6 (2) |
N11—C11—C13—C14 | 177.93 (17) | N11—C12—C31—C32 | 141.48 (17) |
C17—C11—C13—C14 | −1.7 (3) | N13—C12—C31—C36 | 82.6 (2) |
N13—C13—C14—C15 | 178.84 (19) | N11—C12—C31—C36 | −96.3 (2) |
C11—C13—C14—C15 | 0.8 (3) | N23—C22—C32—C33 | 91.0 (2) |
C13—C14—C15—C16 | 1.2 (3) | N21—C22—C32—C33 | −89.1 (2) |
C14—C15—C16—C17 | −2.4 (3) | N23—C22—C32—C31 | −32.9 (2) |
C15—C16—C17—C11 | 1.5 (3) | N21—C22—C32—C31 | 147.01 (16) |
N11—C11—C17—C16 | −178.97 (19) | C12—C31—C32—C22 | −57.82 (19) |
C13—C11—C17—C16 | 0.6 (3) | C36—C31—C32—C22 | −179.89 (15) |
C22—N21—C21—C27 | 179.19 (19) | C12—C31—C32—C33 | 178.20 (16) |
C28—N21—C21—C27 | 0.5 (3) | C36—C31—C32—C33 | 56.12 (19) |
C22—N21—C21—C23 | −0.05 (19) | C22—C32—C33—C34 | 179.48 (15) |
C28—N21—C21—C23 | −178.78 (16) | C31—C32—C33—C34 | −57.0 (2) |
C23—N23—C22—N21 | −0.6 (2) | C32—C33—C34—C35 | 57.1 (2) |
C23—N23—C22—C32 | 179.29 (16) | C33—C34—C35—C36 | −56.7 (2) |
C21—N21—C22—N23 | 0.4 (2) | C34—C35—C36—C31 | 55.9 (2) |
C28—N21—C22—N23 | 179.12 (16) | C12—C31—C36—C35 | −177.43 (15) |
C21—N21—C22—C32 | −179.47 (15) | C32—C31—C36—C35 | −55.5 (2) |
C28—N21—C22—C32 | −0.8 (3) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1O···N13i | 0.85 (3) | 2.12 (3) | 2.955 (2) | 171 (2) |
O1—H2O···N23ii | 0.85 (3) | 2.14 (3) | 2.983 (2) | 170 (2) |
Symmetry codes: (i) x, y, z−1; (ii) −x+1, −y+2, z−1/2. |
Experimental details
Crystal data |
Chemical formula | C22H24N4·H2O |
Mr | 362.47 |
Crystal system, space group | Orthorhombic, Pna21 |
Temperature (K) | 100 |
a, b, c (Å) | 9.6596 (7), 14.5552 (11), 13.547 (1) |
V (Å3) | 1904.7 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.29 × 0.14 × 0.03 |
|
Data collection |
Diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Blessing, 1995) |
Tmin, Tmax | 0.831, 1.00 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 14429, 3030, 2785 |
Rint | 0.038 |
(sin θ/λ)max (Å−1) | 0.715 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.041, 0.106, 1.00 |
No. of reflections | 3030 |
No. of parameters | 254 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.37, −0.16 |
Selected geometric parameters (Å, º) topN11—C12 | 1.374 (2) | N23—C23 | 1.391 (2) |
N21—C22 | 1.366 (2) | C11—C13 | 1.402 (3) |
N13—C12 | 1.321 (3) | C21—C23 | 1.403 (3) |
N23—C22 | 1.323 (2) | C12—C31 | 1.495 (2) |
N11—C11 | 1.384 (3) | C22—C32 | 1.505 (2) |
N21—C21 | 1.385 (2) | C31—C32 | 1.536 (2) |
N13—C13 | 1.388 (2) | | |
| | | |
N13—C12—N11 | 112.60 (16) | C22—N23—C23 | 104.61 (15) |
N23—C22—N21 | 113.36 (16) | N11—C11—C13 | 105.36 (16) |
C12—N11—C11 | 106.85 (15) | N21—C21—C23 | 105.38 (15) |
C22—N21—C21 | 106.60 (15) | N13—C13—C11 | 109.91 (16) |
C12—N13—C13 | 105.27 (15) | N23—C23—C21 | 110.04 (16) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1O···N13i | 0.85 (3) | 2.12 (3) | 2.955 (2) | 171 (2) |
O1—H2O···N23ii | 0.85 (3) | 2.14 (3) | 2.983 (2) | 170 (2) |
Symmetry codes: (i) x, y, z−1; (ii) −x+1, −y+2, z−1/2. |
Intermolecular C—H···Cgn interactions in (II) (Å, °) with H···Cgn distances less than 3.0 Å. The ring centroid designations n correspond to the numbers given in the scheme. topC—H···Cgn | H···Cgn | C—H···Cgn | C···Cgn |
C25—H25···Cg1i | 2.98 | 141 | 3.749 |
C26—H26···Cg3i | 2.88 | 156 | 3.748 |
C28—H28B···Cg1ii | 2.98 | 154 | 3.864 |
C28—H28C···Cg4ii | 2.91 | 124 | 3.534 |
Symmetry codes: (i) −x + 1/2, y + 1/2; z + 1/2; (ii) x + 1/2, −y + 1/2, z. |
Bis(2-benzimidazol-2-yl)species, (I), bridged by a variety of alkyl or aryl spacers, X, are remarkably versatile. They have, for example, been tested as anti-tumoor and antimicrobial agents (Baraldi et al., 2004), and as topoisomerase inhibitors (Walker & Saravia, 2004). Furthermore, they have been used as polymerization catalysts (Stibrany, 2001), as agents to study electron self-exchange (Knapp et al., 1990; Xie et al., 1999), in selective ion-exchange resins (van Berkel et al., 1995), as proton sponges (Stibrany et al., 2002), and as geometrically constraining ligands (Stibrany et al., 2004). Here, we report the structure of the title compound, (II), a bis(benzimidazole) ligand with a rigid two-carbon bridge and two torsional degrees of freedom.
Molecules of (II) (Fig. 1) exhibit approximate diad axes, which pass through the midpoints of the C31—C32 and C34—C35 bonds of the cyclohexyl fragments. Both benzimidazole fragments are essentially planar, as expected, and they are oriented in such a way as to give the molecule a ladder-like appearance in profile (Fig. 2). The dihedral angle between the benzimidazole planes [68.75 (4)°] is approximately 5° larger than that reported for bis(benzimidazole-2-yl)methane [63.53 (2)°; Duan et al., 2005], a molecule related to (II) but with R = H and with a one-carbon atom bridge X = CH2. Geometric parameters for (II) (Table 1) agree well with those reported for other structures of bis(benzimidazole)s with rigid two-carbon bridges (Stibrany et al., 2005). In particular, in the N—C—N fragments, the C—N(imine) distances are approximately 0.05 Å shorter than the C—N(amine) distances, consonant with the partial double-bond character of the former bonds.
In the crystal structure of (II), water molecules of solvation form strong O—H···N(imine) hydrogen bonds (Table 2) with the organic molecules to yield infinite chains or columns parallel to the c axis direction, in which successive molecules of a given type are related by the 21 symmetry operations of the space group (Fig. 3). The organic molecules of (II) are chiral and, as a result, individual `21' columns contain one enantiomer exclusively. The glide-plane symmetry operations produce parallel columns containing the other enantiomer exclusively and, as a result, crystals of (II) are racemic. To complete the structure, the columns are linked by C—H···π interactions, some of which are shown in Table 3. There is little, if any, evidence for π–π stacking.