Literature DB >> 22347115

(E)-5-(2-Chloro-phen-yl)-7-ethyl-2-oxo-2,3-dihydro-1H-thieno[2,3-e][1,4]diazepin-4-ium 2,4,6-trinitro-phenolate.

Richard Betz, Thomas Gerber, Eric Hosten, Alaloor S Dayananda, Hemmige S Yathirajan, A R Ramesha.   

Abstract

In the title molecular salt, C(15)H(14)ClN(2)OS(+)·C(6)H(2)N(3)O(7) (-), protonation occurred on the double-bonded N atom. One of the nitro groups shows slight disorder over two orientations, with an occupancy ratio of 0.91:0.09. In the crystal, classical N-H⋯O hydrogen bonds, as well as C-H⋯O contacts connect the components into a three-dimensional network. The seven-membered ring adopts a boat-like conformation. The least-squares plane defined by its non-H atoms encloses an angle of 38.99 (6)° with the benzene ring bonded to it.

Entities:  

Year:  2012        PMID: 22347115      PMCID: PMC3275259          DOI: 10.1107/S1600536812002607

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


Related literature

For pharmaceutical background to benzodiazepines, see: Robol et al. (1996 ▶); Evans et al. (2001 ▶). For related structures, see: Scammells et al. (2001 ▶); Jasinski et al. (2010 ▶). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶). For puckering analysis, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C15H14ClN2OS+·C6H2N3O7 − M = 533.90 Monoclinic, a = 10.5704 (2) Å b = 20.0667 (5) Å c = 11.3741 (2) Å β = 110.666 (1)° V = 2257.35 (8) Å3 Z = 4 Mo Kα radiation μ = 0.32 mm−1 T = 200 K 0.59 × 0.49 × 0.36 mm

Data collection

Bruker APEXII CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶). T min = 0.807, T max = 0.892 21254 measured reflections 5607 independent reflections 5073 reflections with I > 2σ(I) R int = 0.013

Refinement

R[F 2 > 2σ(F 2)] = 0.031 wR(F 2) = 0.081 S = 1.05 5607 reflections 343 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.38 e Å−3 Δρmin = −0.24 e Å−3 Data collection: APEX2 (Bruker, 2010 ▶); cell refinement: SAINT (Bruker, 2010 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ▶) and Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812002607/pk2384sup1.cif Supplementary material file. DOI: 10.1107/S1600536812002607/pk2384Isup2.cdx Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812002607/pk2384Isup3.hkl Supplementary material file. DOI: 10.1107/S1600536812002607/pk2384Isup4.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C15H14ClN2OS+·C6H2N3O7F(000) = 1096
Mr = 533.90Dx = 1.571 Mg m3
Monoclinic, P21/cMelting point: 518 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 10.5704 (2) ÅCell parameters from 9909 reflections
b = 20.0667 (5) Åθ = 2.9–28.3°
c = 11.3741 (2) ŵ = 0.32 mm1
β = 110.666 (1)°T = 200 K
V = 2257.35 (8) Å3Block, brown
Z = 40.59 × 0.49 × 0.36 mm
Bruker APEXII CCD diffractometer5607 independent reflections
Radiation source: fine-focus sealed tube5073 reflections with I > 2σ(I)
graphiteRint = 0.013
φ and ω scansθmax = 28.3°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2008).h = −13→14
Tmin = 0.807, Tmax = 0.892k = −26→26
21254 measured reflectionsl = −15→15
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.031Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.081H atoms treated by a mixture of independent and constrained refinement
S = 1.05w = 1/[σ2(Fo2) + (0.0349P)2 + 1.1718P] where P = (Fo2 + 2Fc2)/3
5607 reflections(Δ/σ)max < 0.001
343 parametersΔρmax = 0.38 e Å3
0 restraintsΔρmin = −0.24 e Å3
xyzUiso*/UeqOcc. (<1)
Cl10.57956 (3)0.230591 (16)0.27567 (3)0.03062 (8)
S10.08122 (3)0.038903 (15)−0.15866 (3)0.02327 (8)
O10.53537 (10)0.04170 (5)−0.16774 (10)0.0361 (2)
O310.75141 (9)0.09665 (4)0.21426 (8)0.02763 (19)
O3210.75835 (10)0.21026 (6)0.09075 (9)0.0377 (2)
O3220.96274 (13)0.23796 (7)0.11380 (11)0.0495 (3)
O3411.27262 (12)0.24856 (6)0.54001 (12)0.0505 (3)
O3421.25204 (13)0.17919 (7)0.67751 (12)0.0607 (4)
N360.84539 (12)0.04459 (6)0.46335 (11)0.0328 (3)
O3610.8483 (2)0.04566 (12)0.57264 (12)0.0591 (7)0.913 (5)
O3620.79227 (19)−0.00036 (7)0.39045 (12)0.0432 (5)0.913 (5)
O3630.8925 (12)0.0218 (6)0.5586 (12)0.023 (3)*0.087 (5)
O3640.7289 (16)0.0258 (8)0.3784 (12)0.037 (4)*0.087 (5)
N10.49406 (10)0.12534 (5)0.07439 (9)0.01965 (19)
H710.5767 (19)0.1274 (9)0.1273 (17)0.040 (5)*
N20.34466 (10)0.03182 (5)−0.12197 (9)0.0216 (2)
H720.3224 (17)−0.0023 (9)−0.1669 (16)0.033 (4)*
N320.87981 (11)0.21070 (6)0.15093 (10)0.0277 (2)
N341.21470 (12)0.20290 (6)0.57125 (12)0.0375 (3)
C10.45809 (12)0.06515 (6)−0.12171 (11)0.0229 (2)
C20.47774 (12)0.13264 (6)−0.05765 (11)0.0228 (2)
H2A0.55880.1545−0.06450.027*
H2B0.39850.1613−0.10020.027*
C30.39456 (11)0.11469 (5)0.11481 (10)0.0186 (2)
C4−0.11953 (12)0.08838 (7)−0.07592 (13)0.0272 (3)
H4A−0.13300.10150.00280.033*
H4B−0.16270.0444−0.10170.033*
C5−0.18803 (14)0.13922 (8)−0.17752 (15)0.0399 (3)
H5A−0.15020.1835−0.14980.060*
H5B−0.28540.1397−0.19330.060*
H5C−0.17270.1273−0.25490.060*
C110.24806 (11)0.05778 (6)−0.07911 (10)0.0194 (2)
C120.26416 (11)0.09611 (6)0.02726 (10)0.0198 (2)
C130.13619 (12)0.10916 (6)0.04104 (11)0.0230 (2)
H130.12770.13420.10880.028*
C140.02920 (12)0.08249 (6)−0.05130 (11)0.0232 (2)
C210.42065 (11)0.11893 (6)0.25106 (11)0.0210 (2)
C220.50465 (12)0.16687 (6)0.33080 (11)0.0243 (2)
C230.52897 (15)0.16634 (8)0.45900 (13)0.0368 (3)
H230.58590.19920.51190.044*
C240.47029 (17)0.11802 (9)0.50923 (13)0.0428 (4)
H240.48780.11740.59710.051*
C250.38611 (16)0.07037 (8)0.43273 (14)0.0377 (3)
H250.34560.03730.46780.045*
C260.36134 (13)0.07120 (7)0.30489 (12)0.0283 (3)
H260.30280.03870.25260.034*
C310.85448 (11)0.12197 (6)0.29523 (11)0.0208 (2)
C320.92952 (12)0.17741 (6)0.27217 (11)0.0225 (2)
C331.04736 (12)0.20209 (6)0.35838 (12)0.0256 (2)
H331.09530.23710.33630.031*
C341.09452 (12)0.17498 (6)0.47757 (12)0.0267 (3)
C351.02603 (13)0.12448 (6)0.51186 (12)0.0280 (3)
H351.05690.10800.59550.034*
C360.91220 (12)0.09847 (6)0.42255 (11)0.0244 (2)
U11U22U33U12U13U23
Cl10.03397 (16)0.02676 (15)0.03248 (16)−0.01114 (12)0.01341 (13)−0.00916 (11)
S10.01661 (13)0.02786 (15)0.02118 (14)−0.00278 (10)0.00153 (10)−0.00509 (10)
O10.0307 (5)0.0438 (6)0.0402 (5)−0.0040 (4)0.0204 (4)−0.0127 (4)
O310.0212 (4)0.0225 (4)0.0289 (4)−0.0008 (3)−0.0038 (3)−0.0028 (3)
O3210.0293 (5)0.0464 (6)0.0305 (5)0.0064 (4)0.0020 (4)0.0102 (4)
O3220.0465 (6)0.0593 (7)0.0426 (6)−0.0143 (6)0.0155 (5)0.0147 (5)
O3410.0336 (6)0.0361 (6)0.0629 (8)−0.0136 (5)−0.0065 (5)−0.0026 (5)
O3420.0493 (7)0.0693 (9)0.0367 (6)−0.0165 (6)−0.0183 (5)0.0039 (6)
N360.0317 (6)0.0376 (6)0.0242 (5)−0.0089 (5)0.0037 (4)0.0028 (5)
O3610.0699 (12)0.0805 (14)0.0235 (6)−0.0390 (11)0.0124 (6)−0.0028 (7)
O3620.0621 (11)0.0307 (7)0.0354 (6)−0.0185 (7)0.0154 (6)−0.0032 (5)
N10.0162 (4)0.0225 (5)0.0180 (4)−0.0010 (4)0.0032 (4)−0.0027 (3)
N20.0201 (5)0.0224 (5)0.0212 (5)−0.0016 (4)0.0061 (4)−0.0056 (4)
N320.0303 (5)0.0265 (5)0.0250 (5)0.0003 (4)0.0082 (4)0.0009 (4)
N340.0264 (6)0.0322 (6)0.0397 (7)−0.0035 (5)−0.0060 (5)−0.0066 (5)
C10.0205 (5)0.0290 (6)0.0179 (5)−0.0004 (4)0.0052 (4)−0.0012 (4)
C20.0228 (5)0.0253 (5)0.0201 (5)−0.0040 (4)0.0074 (4)−0.0002 (4)
C30.0166 (5)0.0174 (5)0.0194 (5)0.0000 (4)0.0035 (4)−0.0028 (4)
C40.0158 (5)0.0295 (6)0.0344 (6)−0.0011 (4)0.0065 (5)−0.0028 (5)
C50.0244 (6)0.0466 (8)0.0456 (8)0.0098 (6)0.0083 (6)0.0099 (7)
C110.0168 (5)0.0203 (5)0.0185 (5)−0.0011 (4)0.0030 (4)−0.0006 (4)
C120.0163 (5)0.0213 (5)0.0199 (5)−0.0009 (4)0.0041 (4)−0.0025 (4)
C130.0186 (5)0.0248 (5)0.0247 (5)0.0001 (4)0.0066 (4)−0.0043 (4)
C140.0177 (5)0.0242 (5)0.0263 (6)0.0001 (4)0.0059 (4)−0.0011 (4)
C210.0184 (5)0.0240 (5)0.0195 (5)−0.0013 (4)0.0052 (4)−0.0040 (4)
C220.0218 (5)0.0271 (6)0.0237 (6)−0.0050 (4)0.0077 (4)−0.0051 (4)
C230.0376 (7)0.0466 (8)0.0237 (6)−0.0133 (6)0.0077 (5)−0.0128 (6)
C240.0486 (9)0.0593 (10)0.0206 (6)−0.0123 (8)0.0125 (6)−0.0044 (6)
C250.0406 (8)0.0459 (8)0.0302 (7)−0.0110 (6)0.0168 (6)0.0014 (6)
C260.0278 (6)0.0305 (6)0.0267 (6)−0.0073 (5)0.0099 (5)−0.0036 (5)
C310.0171 (5)0.0210 (5)0.0218 (5)0.0022 (4)0.0037 (4)−0.0029 (4)
C320.0212 (5)0.0226 (5)0.0215 (5)0.0022 (4)0.0049 (4)−0.0002 (4)
C330.0204 (5)0.0226 (5)0.0317 (6)−0.0009 (4)0.0065 (5)−0.0029 (5)
C340.0185 (5)0.0257 (6)0.0283 (6)−0.0011 (4)−0.0014 (5)−0.0056 (5)
C350.0260 (6)0.0291 (6)0.0223 (5)−0.0002 (5)0.0005 (5)−0.0009 (5)
C360.0227 (5)0.0246 (6)0.0231 (5)−0.0023 (4)0.0044 (5)−0.0004 (4)
Cl1—C221.7337 (13)C4—C51.5199 (19)
S1—C111.7164 (11)C4—H4A0.9900
S1—C141.7415 (12)C4—H4B0.9900
O1—C11.2102 (15)C5—H5A0.9800
O31—C311.2590 (14)C5—H5B0.9800
O321—N321.2234 (15)C5—H5C0.9800
O322—N321.2277 (15)C11—C121.3925 (15)
O341—N341.2222 (18)C12—C131.4396 (15)
O342—N341.2273 (18)C13—C141.3528 (16)
N36—O3631.118 (12)C13—H130.9500
N36—O3621.2196 (16)C21—C261.3985 (17)
N36—O3611.2330 (19)C21—C221.4029 (16)
N36—O3641.323 (14)C22—C231.3885 (18)
N36—C361.4542 (16)C23—C241.379 (2)
N1—C31.3056 (15)C23—H230.9500
N1—C21.4574 (15)C24—C251.384 (2)
N1—H710.870 (19)C24—H240.9500
N2—C11.3720 (15)C25—C261.3836 (18)
N2—C111.3795 (15)C25—H250.9500
N2—H720.836 (18)C26—H260.9500
N32—C321.4534 (15)C31—C361.4380 (16)
N34—C341.4519 (15)C31—C321.4431 (16)
C1—C21.5170 (17)C32—C331.3771 (16)
C2—H2A0.9900C33—C341.3803 (18)
C2—H2B0.9900C33—H330.9500
C3—C121.4358 (15)C34—C351.3793 (18)
C3—C211.4776 (15)C35—C361.3745 (17)
C4—C141.5011 (16)C35—H350.9500
C11—S1—C1492.26 (5)C12—C11—S1111.57 (8)
O363—N36—O362107.3 (6)C11—C12—C3122.62 (10)
O362—N36—O361122.68 (13)C11—C12—C13111.32 (10)
O363—N36—O364124.9 (9)C3—C12—C13125.89 (10)
O361—N36—O364115.2 (6)C14—C13—C12113.81 (10)
O363—N36—C36120.9 (6)C14—C13—H13123.1
O362—N36—C36119.46 (11)C12—C13—H13123.1
O361—N36—C36117.83 (12)C13—C14—C4130.33 (11)
O364—N36—C36114.2 (6)C13—C14—S1111.02 (9)
C3—N1—C2124.21 (10)C4—C14—S1118.55 (9)
C3—N1—H71120.1 (12)C26—C21—C22117.76 (11)
C2—N1—H71115.7 (12)C26—C21—C3118.24 (10)
C1—N2—C11124.78 (10)C22—C21—C3123.97 (11)
C1—N2—H72117.2 (11)C23—C22—C21120.93 (12)
C11—N2—H72116.2 (11)C23—C22—Cl1116.52 (10)
O321—N32—O322123.13 (12)C21—C22—Cl1122.52 (9)
O321—N32—C32118.95 (11)C24—C23—C22119.79 (13)
O322—N32—C32117.92 (11)C24—C23—H23120.1
O341—N34—O342123.85 (12)C22—C23—H23120.1
O341—N34—C34118.31 (12)C23—C24—C25120.57 (13)
O342—N34—C34117.84 (13)C23—C24—H24119.7
O1—C1—N2122.16 (12)C25—C24—H24119.7
O1—C1—C2123.78 (11)C26—C25—C24119.56 (13)
N2—C1—C2114.05 (10)C26—C25—H25120.2
N1—C2—C1110.59 (10)C24—C25—H25120.2
N1—C2—H2A109.5C25—C26—C21121.37 (12)
C1—C2—H2A109.5C25—C26—H26119.3
N1—C2—H2B109.5C21—C26—H26119.3
C1—C2—H2B109.5O31—C31—C36123.67 (11)
H2A—C2—H2B108.1O31—C31—C32124.57 (11)
N1—C3—C12119.59 (10)C36—C31—C32111.76 (10)
N1—C3—C21118.98 (10)C33—C32—C31124.39 (11)
C12—C3—C21121.36 (10)C33—C32—N32116.33 (11)
C14—C4—C5112.41 (11)C31—C32—N32119.27 (10)
C14—C4—H4A109.1C32—C33—C34118.69 (12)
C5—C4—H4A109.1C32—C33—H33120.7
C14—C4—H4B109.1C34—C33—H33120.7
C5—C4—H4B109.1C35—C34—C33121.57 (11)
H4A—C4—H4B107.9C35—C34—N34119.12 (12)
C4—C5—H5A109.5C33—C34—N34119.21 (12)
C4—C5—H5B109.5C36—C35—C34118.68 (12)
H5A—C5—H5B109.5C36—C35—H35120.7
C4—C5—H5C109.5C34—C35—H35120.7
H5A—C5—H5C109.5C35—C36—C31124.71 (11)
H5B—C5—H5C109.5C35—C36—N36116.33 (11)
N2—C11—C12129.56 (10)C31—C36—N36118.94 (10)
N2—C11—S1118.77 (8)
C11—N2—C1—O1−175.18 (12)C22—C23—C24—C25−0.7 (3)
C11—N2—C1—C25.61 (16)C23—C24—C25—C260.3 (3)
C3—N1—C2—C1−77.66 (14)C24—C25—C26—C210.6 (2)
O1—C1—C2—N1−117.45 (13)C22—C21—C26—C25−1.1 (2)
N2—C1—C2—N161.75 (13)C3—C21—C26—C25177.14 (13)
C2—N1—C3—C1212.62 (17)O31—C31—C32—C33−175.40 (12)
C2—N1—C3—C21−170.29 (10)C36—C31—C32—C334.22 (17)
C1—N2—C11—C12−41.65 (19)O31—C31—C32—N324.86 (18)
C1—N2—C11—S1142.17 (10)C36—C31—C32—N32−175.52 (10)
C14—S1—C11—N2177.15 (10)O321—N32—C32—C33−152.12 (12)
C14—S1—C11—C120.32 (9)O322—N32—C32—C3328.00 (17)
N2—C11—C12—C3−0.8 (2)O321—N32—C32—C3127.64 (17)
S1—C11—C12—C3175.59 (9)O322—N32—C32—C31−152.24 (12)
N2—C11—C12—C13−176.29 (12)C31—C32—C33—C34−3.70 (19)
S1—C11—C12—C130.10 (13)N32—C32—C33—C34176.05 (11)
N1—C3—C12—C1132.88 (17)C32—C33—C34—C35−0.45 (19)
C21—C3—C12—C11−144.13 (12)C32—C33—C34—N34−176.78 (12)
N1—C3—C12—C13−152.30 (12)O341—N34—C34—C35−178.51 (13)
C21—C3—C12—C1330.68 (18)O342—N34—C34—C351.4 (2)
C11—C12—C13—C14−0.65 (15)O341—N34—C34—C33−2.1 (2)
C3—C12—C13—C14−175.96 (11)O342—N34—C34—C33177.82 (14)
C12—C13—C14—C4−175.42 (12)C33—C34—C35—C363.5 (2)
C12—C13—C14—S10.88 (14)N34—C34—C35—C36179.86 (12)
C5—C4—C14—C1399.93 (17)C34—C35—C36—C31−2.8 (2)
C5—C4—C14—S1−76.14 (14)C34—C35—C36—N36178.98 (12)
C11—S1—C14—C13−0.69 (10)O31—C31—C36—C35178.71 (12)
C11—S1—C14—C4176.10 (10)C32—C31—C36—C35−0.92 (17)
N1—C3—C21—C26−138.62 (12)O31—C31—C36—N36−3.08 (18)
C12—C3—C21—C2638.41 (16)C32—C31—C36—N36177.29 (11)
N1—C3—C21—C2239.47 (17)O363—N36—C36—C35−7.5 (9)
C12—C3—C21—C22−143.50 (12)O362—N36—C36—C35−144.83 (16)
C26—C21—C22—C230.68 (19)O361—N36—C36—C3533.3 (2)
C3—C21—C22—C23−177.42 (12)O364—N36—C36—C35173.3 (8)
C26—C21—C22—Cl1−177.61 (10)O363—N36—C36—C31174.1 (8)
C3—C21—C22—Cl14.29 (17)O362—N36—C36—C3136.8 (2)
C21—C22—C23—C240.2 (2)O361—N36—C36—C31−145.06 (19)
Cl1—C22—C23—C24178.56 (13)O364—N36—C36—C31−5.1 (9)
D—H···AD—HH···AD···AD—H···A
N1—H71···O310.870 (19)1.865 (19)2.6847 (13)156.3 (17)
N2—H72···O31i0.836 (18)2.047 (18)2.8331 (13)156.4 (16)
N2—H72···O362i0.836 (18)2.400 (17)2.9495 (16)123.9 (14)
C2—H2A···O3210.992.493.2465 (16)133
C2—H2B···O342ii0.992.483.2505 (17)134
C23—H23···O321iii0.952.513.4193 (18)161
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H71⋯O310.870 (19)1.865 (19)2.6847 (13)156.3 (17)
N2—H72⋯O31i0.836 (18)2.047 (18)2.8331 (13)156.4 (16)
N2—H72⋯O362i0.836 (18)2.400 (17)2.9495 (16)123.9 (14)
C2—H2A⋯O3210.992.493.2465 (16)133
C2—H2B⋯O342ii0.992.483.2505 (17)134
C23—H23⋯O321iii0.952.513.4193 (18)161

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

  6 in total

1.  A short history of SHELX.

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

2.  Graph-set analysis of hydrogen-bond patterns in organic crystals.

Authors:  M C Etter; J C MacDonald; J Bernstein
Journal:  Acta Crystallogr B       Date:  1990-04-01

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Authors:  B Evans; A Pipe; L Clark; M Banks
Journal:  Bioorg Med Chem Lett       Date:  2001-05-21       Impact factor: 2.823

4.  5,7-Dimethyl-2,3-dihydro-1H-1,4-diazepin-4-ium picrate.

Authors:  Jerry P Jasinski; Ray J Butcher; H S Yathirajan; B Narayana; K Prakash Kamath
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-04-28

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Journal:  J Med Chem       Date:  1996-01-19       Impact factor: 7.446

6.  Structure validation in chemical crystallography.

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

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