Literature DB >> 25161594

5-Amino-5'-bromo-6-(4-methyl-benzo-yl)-8-nitro-2,3-di-hydro-1H-spiro-[imidazo[1,2-a]pyridine-7,3'-indolin]-2'-one including an unknown solvate.

R A Nagalakshmi1, J Suresh1, S Sivakumar2, R Ranjith Kumar2, P L Nilantha Lakshman3.   

Abstract

In the title compound, C22H18BrN5O4, the central six-membered ring, derived from n class="Chemical">1,4-di-hydro-pyridine, adopts a distorted boat conformation with a puckering amplitude of 0.197 (3) Å, the imidazole ring adopts a twisted conformation with a puckering amplitude of 0.113 (3) Å, and the oxindole moiety is planar with an r.m.s. deviation of 0.0125 Å. Two intra-molecular N-H⋯O hydrogen bonds are formed, each closing an S(6) loop. In the crystal, strong N-H⋯O hydrogen bonds lead to the formation of zigzag chains along the c axis. These are consolidated in the three-dimensional crystal packing by weak N-H⋯O hydrogen bonding, as well as by C-H⋯O, C-H⋯Br and C-H⋯π inter-actions. A small region of electron density well removed from the main mol-ecule was removed with the SQUEEZE procedure in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148-155] following unsuccessful attempts to model it as a plausible solvent mol-ecule. The unit-cell characteristics do not take into account this feature of the structure.

Entities:  

Keywords:  crystal structure

Year:  2014        PMID: 25161594      PMCID: PMC4120621          DOI: 10.1107/S1600536814014391

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


Related literature

For a similar structure, see: Nagalakshmi et al. (2014 ▶). For additional conformational analysis, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C22H18BrN5O4 M = 496.32 Monoclinic, a = 15.5482 (9) Å b = 14.7033 (7) Å c = 12.1907 (6) Å β = 101.856 (2)° V = 2727.5 (2) Å3 Z = 4 Mo Kα radiation μ = 1.54 mm−1 T = 293 K 0.21 × 0.19 × 0.18 mm

Data collection

Bruker Kappa APEXII diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2004 ▶) T min = 0.967, T max = 0.974 30073 measured reflections 5962 independent reflections 4098 reflections with I > 2σ(I) R int = 0.035

Refinement

R[F 2 > 2σ(F 2)] = 0.040 wR(F 2) = 0.114 S = 1.04 5962 reflections 289 parameters 1 restraint H-atom parameters constrained Δρmax = 0.30 e Å−3 Δρmin = −0.41 e Å−3 Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2009 ▶); software used to prepare material for publication: SHELXL97. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814014391/tk5316sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814014391/tk5316Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S1600536814014391/tk5316Isup3.cml CCDC reference: 1009067 Additional supporting information: crystallographic information; 3D view; checkCIF report
C22H18BrN5O4F(000) = 1008
Mr = 496.32Dx = 1.209 Mg m3
Monoclinic, P21/cMelting point: 530 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 15.5482 (9) ÅCell parameters from 2000 reflections
b = 14.7033 (7) Åθ = 2–31°
c = 12.1907 (6) ŵ = 1.54 mm1
β = 101.856 (2)°T = 293 K
V = 2727.5 (2) Å3Block, brown
Z = 40.21 × 0.19 × 0.18 mm
Bruker Kappa APEXII diffractometer5962 independent reflections
Radiation source: fine-focus sealed tube4098 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.035
Detector resolution: 0 pixels mm-1θmax = 27.0°, θmin = 1.9°
ω and φ scansh = −19→11
Absorption correction: multi-scan (SADABS; Bruker, 2004)k = −18→18
Tmin = 0.967, Tmax = 0.974l = −15→15
30073 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)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.114H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.0653P)2] where P = (Fo2 + 2Fc2)/3
5962 reflections(Δ/σ)max < 0.001
289 parametersΔρmax = 0.30 e Å3
1 restraintΔρmin = −0.41 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
C10.10831 (12)−0.03982 (13)0.29919 (16)0.0302 (4)
C20.16209 (12)0.04483 (12)0.33939 (15)0.0273 (4)
C30.15943 (12)0.06548 (13)0.46280 (15)0.0302 (4)
C40.13013 (12)−0.00186 (13)0.52880 (16)0.0335 (4)
C50.08565 (12)−0.10239 (13)0.37313 (16)0.0315 (4)
C60.04187 (16)−0.22940 (16)0.45722 (19)0.0509 (6)
H6A0.0818−0.28080.46940.061*
H6B−0.0174−0.25080.45550.061*
C70.06850 (15)−0.15800 (14)0.54656 (19)0.0421 (5)
H7A0.0184−0.13740.57590.051*
H7B0.1133−0.18080.60780.051*
C80.12622 (12)0.12869 (13)0.26493 (15)0.0305 (4)
C90.26599 (13)0.10750 (13)0.24292 (16)0.0327 (4)
C100.25462 (12)0.03862 (12)0.31650 (15)0.0291 (4)
C110.32166 (12)−0.02155 (14)0.35672 (16)0.0363 (5)
H110.3146−0.06800.40590.044*
C120.39967 (14)−0.01014 (17)0.32108 (19)0.0461 (5)
C130.41184 (14)0.05743 (17)0.2473 (2)0.0498 (6)
H130.46530.06260.22500.060*
C140.34405 (14)0.11796 (16)0.20630 (18)0.0449 (5)
H140.35090.16370.15620.054*
C310.18598 (14)0.15050 (13)0.51348 (17)0.0376 (5)
C320.23171 (13)0.22376 (13)0.46127 (16)0.0346 (4)
C330.31931 (14)0.21652 (15)0.45811 (19)0.0452 (5)
H330.34890.16210.47810.054*
C340.36363 (16)0.29024 (19)0.4251 (2)0.0608 (6)
H340.42280.28450.42300.073*
C350.3216 (2)0.37187 (19)0.3955 (2)0.0621 (7)
C360.23388 (18)0.37875 (16)0.3996 (2)0.0515 (6)
H360.20430.43320.37980.062*
C370.18933 (14)0.30590 (14)0.43283 (16)0.0381 (5)
H370.13040.31200.43610.046*
C380.3699 (3)0.4543 (3)0.3619 (4)0.1206 (16)
H38A0.32990.50460.34580.181*
H38B0.39260.43990.29650.181*
H38C0.41750.47030.42230.181*
N10.09080 (11)−0.06034 (12)0.18652 (14)0.0389 (4)
N20.12708 (14)0.00993 (13)0.63557 (15)0.0548 (5)
H2A0.1089−0.03330.67250.066*
H2B0.14330.06080.66800.066*
N30.19037 (10)0.16040 (11)0.21672 (13)0.0336 (4)
H30.18540.20780.17460.040*
N40.10306 (11)−0.08480 (10)0.48544 (13)0.0342 (4)
N50.04712 (11)−0.18207 (12)0.35518 (15)0.0412 (4)
H50.0271−0.20380.28940.049*
O10.05241 (12)−0.13281 (11)0.15117 (13)0.0546 (4)
O20.11477 (11)−0.00570 (11)0.12016 (12)0.0494 (4)
O30.05189 (9)0.15950 (10)0.25570 (12)0.0413 (4)
O40.17505 (15)0.17071 (11)0.60983 (14)0.0669 (5)
Br10.493532 (17)−0.09216 (2)0.37527 (3)0.07818 (15)
U11U22U33U12U13U23
C10.0390 (9)0.0255 (10)0.0254 (10)0.0006 (7)0.0052 (8)−0.0020 (8)
C20.0378 (9)0.0216 (10)0.0219 (9)0.0030 (7)0.0048 (7)0.0008 (8)
C30.0428 (10)0.0230 (10)0.0243 (10)0.0030 (8)0.0058 (8)0.0009 (8)
C40.0427 (10)0.0283 (11)0.0290 (11)0.0032 (8)0.0059 (8)0.0012 (9)
C50.0351 (9)0.0254 (10)0.0332 (11)0.0012 (7)0.0052 (8)−0.0028 (8)
C60.0645 (14)0.0402 (14)0.0485 (14)−0.0178 (11)0.0124 (11)0.0030 (11)
C70.0533 (12)0.0334 (12)0.0411 (13)−0.0091 (9)0.0131 (10)0.0072 (10)
C80.0410 (10)0.0241 (10)0.0244 (10)0.0048 (8)0.0018 (8)−0.0007 (8)
C90.0429 (10)0.0282 (11)0.0260 (10)0.0008 (8)0.0050 (8)−0.0006 (8)
C100.0376 (9)0.0250 (10)0.0245 (10)0.0007 (7)0.0057 (8)−0.0035 (8)
C110.0410 (10)0.0352 (12)0.0306 (11)0.0053 (8)0.0021 (8)0.0019 (9)
C120.0408 (11)0.0527 (14)0.0421 (13)0.0134 (10)0.0028 (9)−0.0025 (11)
C130.0406 (11)0.0635 (16)0.0485 (14)−0.0003 (11)0.0164 (10)−0.0020 (12)
C140.0511 (12)0.0486 (14)0.0379 (13)−0.0054 (10)0.0161 (10)0.0047 (11)
C310.0577 (12)0.0270 (11)0.0279 (11)0.0004 (9)0.0080 (9)−0.0012 (9)
C320.0497 (11)0.0251 (11)0.0261 (10)−0.0015 (8)0.0012 (8)−0.0048 (8)
C330.0483 (11)0.0365 (13)0.0472 (13)0.0031 (9)0.0014 (10)−0.0099 (10)
C340.0533 (13)0.0669 (15)0.0663 (17)−0.0117 (11)0.0217 (12)−0.0200 (13)
C350.0841 (18)0.0504 (13)0.0619 (17)−0.0197 (11)0.0385 (14)−0.0100 (12)
C360.0818 (17)0.0306 (12)0.0455 (14)0.0039 (11)0.0211 (12)0.0050 (10)
C370.0485 (11)0.0317 (12)0.0349 (12)0.0026 (9)0.0105 (9)−0.0019 (9)
C380.143 (4)0.081 (3)0.164 (4)−0.046 (2)0.093 (3)0.000 (3)
N10.0517 (10)0.0333 (10)0.0308 (10)−0.0021 (8)0.0061 (8)−0.0050 (8)
N20.1040 (16)0.0329 (11)0.0321 (11)−0.0126 (10)0.0243 (10)−0.0022 (8)
N30.0464 (9)0.0267 (9)0.0267 (9)0.0032 (7)0.0049 (7)0.0074 (7)
N40.0481 (9)0.0259 (9)0.0284 (9)−0.0050 (7)0.0074 (7)0.0020 (7)
N50.0548 (10)0.0327 (10)0.0348 (10)−0.0114 (8)0.0060 (8)−0.0036 (8)
O10.0814 (11)0.0412 (9)0.0393 (9)−0.0214 (8)0.0080 (8)−0.0155 (7)
O20.0767 (11)0.0408 (9)0.0305 (8)−0.0099 (8)0.0104 (7)−0.0016 (7)
O30.0428 (7)0.0396 (9)0.0387 (9)0.0142 (6)0.0021 (6)0.0049 (6)
O40.1371 (17)0.0322 (9)0.0391 (10)−0.0172 (10)0.0359 (10)−0.0120 (7)
Br10.05198 (16)0.0981 (3)0.0821 (3)0.03710 (14)0.00837 (14)0.01124 (17)
C1—N11.378 (3)C12—C131.379 (3)
C1—C51.383 (3)C12—Br11.904 (2)
C1—C21.523 (3)C13—C141.392 (3)
C2—C101.523 (2)C13—H130.9300
C2—C31.544 (3)C14—H140.9300
C2—C81.564 (3)C31—O41.257 (2)
C3—C41.409 (3)C31—C321.502 (3)
C3—C311.418 (3)C32—C331.374 (3)
C4—N21.324 (3)C32—C371.385 (3)
C4—N41.361 (3)C33—C341.388 (3)
C5—N51.314 (2)C33—H330.9300
C5—N41.365 (3)C34—C351.379 (4)
C6—N51.442 (3)C34—H340.9300
C6—C71.508 (3)C35—C361.379 (4)
C6—H6A0.9700C35—C381.525 (4)
C6—H6B0.9700C36—C371.381 (3)
C7—N41.472 (2)C36—H360.9300
C7—H7A0.9700C37—H370.9300
C7—H7B0.9700C38—H38A0.9600
C8—O31.225 (2)C38—H38B0.9600
C8—N31.341 (2)C38—H38C0.9600
C9—C141.385 (3)N1—O21.250 (2)
C9—C101.388 (3)N1—O11.254 (2)
C9—N31.391 (2)N2—H2A0.8600
C10—C111.378 (3)N2—H2B0.8600
C11—C121.380 (3)N3—H30.8600
C11—H110.9300N5—H50.8600
N1—C1—C5118.64 (17)C14—C13—H13120.0
N1—C1—C2118.86 (16)C9—C14—C13117.5 (2)
C5—C1—C2122.03 (16)C9—C14—H14121.2
C1—C2—C10111.65 (14)C13—C14—H14121.2
C1—C2—C3110.57 (14)O4—C31—C3122.18 (18)
C10—C2—C3113.94 (15)O4—C31—C32113.15 (17)
C1—C2—C8110.53 (15)C3—C31—C32124.64 (17)
C10—C2—C8100.28 (14)C33—C32—C37118.93 (19)
C3—C2—C8109.43 (14)C33—C32—C31120.95 (19)
C4—C3—C31118.04 (17)C37—C32—C31119.27 (18)
C4—C3—C2119.66 (16)C32—C33—C34120.1 (2)
C31—C3—C2122.30 (16)C32—C33—H33120.0
N2—C4—N4115.38 (18)C34—C33—H33120.0
N2—C4—C3123.41 (19)C35—C34—C33121.3 (2)
N4—C4—C3121.21 (17)C35—C34—H34119.4
N5—C5—N4109.02 (17)C33—C34—H34119.4
N5—C5—C1130.78 (18)C36—C35—C34118.3 (2)
N4—C5—C1120.20 (17)C36—C35—C38119.8 (3)
N5—C6—C7103.37 (16)C34—C35—C38121.9 (3)
N5—C6—H6A111.1C35—C36—C37120.9 (2)
C7—C6—H6A111.1C35—C36—H36119.6
N5—C6—H6B111.1C37—C36—H36119.6
C7—C6—H6B111.1C36—C37—C32120.5 (2)
H6A—C6—H6B109.1C36—C37—H37119.7
N4—C7—C6102.60 (16)C32—C37—H37119.7
N4—C7—H7A111.2C35—C38—H38A109.5
C6—C7—H7A111.2C35—C38—H38B109.5
N4—C7—H7B111.2H38A—C38—H38B109.5
C6—C7—H7B111.2C35—C38—H38C109.5
H7A—C7—H7B109.2H38A—C38—H38C109.5
O3—C8—N3127.15 (18)H38B—C38—H38C109.5
O3—C8—C2124.20 (17)O2—N1—O1120.52 (17)
N3—C8—C2108.65 (15)O2—N1—C1118.71 (16)
C14—C9—C10121.71 (18)O1—N1—C1120.76 (17)
C14—C9—N3128.25 (18)C4—N2—H2A120.0
C10—C9—N3110.03 (16)C4—N2—H2B120.0
C11—C10—C9120.72 (17)H2A—N2—H2B120.0
C11—C10—C2130.31 (17)C8—N3—C9112.00 (15)
C9—C10—C2108.97 (15)C8—N3—H3124.0
C10—C11—C12117.34 (19)C9—N3—H3124.0
C10—C11—H11121.3C4—N4—C5122.77 (16)
C12—C11—H11121.3C4—N4—C7125.06 (17)
C13—C12—C11122.7 (2)C5—N4—C7110.57 (16)
C13—C12—Br1118.99 (16)C5—N5—C6113.04 (17)
C11—C12—Br1118.32 (17)C5—N5—H5123.5
C12—C13—C14119.99 (19)C6—N5—H5123.5
C12—C13—H13120.0
N1—C1—C2—C10−62.7 (2)C10—C9—C14—C13−0.9 (3)
C5—C1—C2—C10109.30 (19)N3—C9—C14—C13178.1 (2)
N1—C1—C2—C3169.32 (16)C12—C13—C14—C90.4 (3)
C5—C1—C2—C3−18.7 (2)C4—C3—C31—O4−8.1 (3)
N1—C1—C2—C848.0 (2)C2—C3—C31—O4172.2 (2)
C5—C1—C2—C8−139.99 (18)C4—C3—C31—C32169.99 (18)
C1—C2—C3—C415.3 (2)C2—C3—C31—C32−9.7 (3)
C10—C2—C3—C4−111.41 (19)O4—C31—C32—C33102.3 (2)
C8—C2—C3—C4137.27 (17)C3—C31—C32—C33−75.9 (3)
C1—C2—C3—C31−164.99 (17)O4—C31—C32—C37−67.0 (3)
C10—C2—C3—C3168.3 (2)C3—C31—C32—C37114.8 (2)
C8—C2—C3—C31−43.0 (2)C37—C32—C33—C34−1.0 (3)
C31—C3—C4—N2−0.7 (3)C31—C32—C33—C34−170.3 (2)
C2—C3—C4—N2178.98 (19)C32—C33—C34—C350.3 (4)
C31—C3—C4—N4179.52 (18)C33—C34—C35—C360.2 (4)
C2—C3—C4—N4−0.8 (3)C33—C34—C35—C38178.4 (3)
N1—C1—C5—N5−1.1 (3)C34—C35—C36—C370.1 (4)
C2—C1—C5—N5−173.18 (19)C38—C35—C36—C37−178.1 (3)
N1—C1—C5—N4179.15 (16)C35—C36—C37—C32−0.9 (3)
C2—C1—C5—N47.1 (3)C33—C32—C37—C361.3 (3)
N5—C6—C7—N4−11.3 (2)C31—C32—C37—C36170.8 (2)
C1—C2—C8—O361.5 (2)C5—C1—N1—O2−176.85 (18)
C10—C2—C8—O3179.41 (18)C2—C1—N1—O2−4.6 (3)
C3—C2—C8—O3−60.5 (2)C5—C1—N1—O12.4 (3)
C1—C2—C8—N3−119.69 (16)C2—C1—N1—O1174.70 (17)
C10—C2—C8—N3−1.77 (19)O3—C8—N3—C9−178.42 (19)
C3—C2—C8—N3118.31 (16)C2—C8—N3—C92.8 (2)
C14—C9—C10—C110.7 (3)C14—C9—N3—C8178.2 (2)
N3—C9—C10—C11−178.48 (17)C10—C9—N3—C8−2.7 (2)
C14—C9—C10—C2−179.42 (18)N2—C4—N4—C5166.80 (18)
N3—C9—C10—C21.4 (2)C3—C4—N4—C5−13.5 (3)
C1—C2—C10—C11−62.8 (3)N2—C4—N4—C72.6 (3)
C3—C2—C10—C1163.3 (3)C3—C4—N4—C7−177.68 (18)
C8—C2—C10—C11−179.93 (19)N5—C5—N4—C4−169.47 (17)
C1—C2—C10—C9117.27 (17)C1—C5—N4—C410.3 (3)
C3—C2—C10—C9−116.59 (17)N5—C5—N4—C7−3.2 (2)
C8—C2—C10—C90.18 (19)C1—C5—N4—C7176.55 (17)
C9—C10—C11—C120.1 (3)C6—C7—N4—C4175.24 (19)
C2—C10—C11—C12−179.74 (19)C6—C7—N4—C59.4 (2)
C10—C11—C12—C13−0.7 (3)N4—C5—N5—C6−5.0 (2)
C10—C11—C12—Br1179.96 (14)C1—C5—N5—C6175.2 (2)
C11—C12—C13—C140.4 (4)C7—C6—N5—C510.7 (2)
Br1—C12—C13—C14179.77 (17)
D—H···AD—HH···AD···AD—H···A
N5—H5···O10.862.092.608 (2)118
N2—H2B···O40.861.872.518 (2)131
N3—H3···O4i0.861.952.792 (2)168
N5—H5···O3ii0.862.362.961 (2)127
C7—H7A···O3iii0.972.543.342 (3)140
C33—H33···Br1iv0.932.913.675 (2)141
C14—H14···Cg1i0.932.833.553 (2)135
Table 1

Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C32–C37 ring.

D—H⋯A D—HH⋯A DA D—H⋯A
N5—H5⋯O10.862.092.608 (2)118
N2—H2B⋯O40.861.872.518 (2)131
N3—H3⋯O4i 0.861.952.792 (2)168
N5—H5⋯O3ii 0.862.362.961 (2)127
C7—H7A⋯O3iii 0.972.543.342 (3)140
C33—H33⋯Br1iv 0.932.913.675 (2)141
C14—H14⋯Cg1i 0.932.833.553 (2)135

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

  3 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.  5-Amino-6-benzoyl-8-nitro-2,3-di-hydro-1H-spiro-[imidazo[1,2-a]pyridine-7,3'-indolin]-2'-one dimethyl sulfoxide monosolvate.

Authors:  R A Nagalakshmi; J Suresh; S Sivakumar; R Ranjith Kumar; P L Nilantha Lakshman
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2014-04-26

3.  Structure validation in chemical crystallography.

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

1.  Crystal structure and Hirshfeld surface analysis of 5-amino-5'-bromo-2'-oxo-2,3-di-hydro-1H-spiro-[imidazo[1,2-a]pyridine-7,3'-indoline]-6,8-dicarbo-nitrile dimethyl sulfoxide disolvate.

Authors:  Farid N Naghiyev; Victor N Khrustalev; Anton P Novikov; Mehmet Akkurt; Rovnag M Rzayev; Anzurat A Akobirshoeva; Ibrahim G Mamedov
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2022-05-10
  1 in total

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