organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

1-Benzyl-2-(1H-indol-3-yl)-5-oxo­pyrrolidine-2-carbo­nitrile

aMolecule Structure Research Center, National Academy of Sciences RA, Azatutyan ave. 26, 375014 Yerevan, Republic of Armenia, bInstitute of Fine Organic Chemistry, National Academy of Sciences RA, Azatutyan ave. 26, 375014 Yerevan, Republic of Armenia, and cEmory University School of Medicine, Veterans Affairs Medical Center, 1670 Clairmont Road, 151-H Decatur, Georgia 30033-4004, USA
*Correspondence e-mail: rafael@msrc.am

(Received 10 December 2007; accepted 19 December 2007; online 4 January 2008)

In the title compound, C20H17N3O, a potential anti-human immunodeficiency virus type 1 (HIV-1) non-nucleoside reverse-transcriptase inhibitor, the pyrrolidine ring has an envelope conformation. In the crystal structure, adjacent mol­ecules are connected into infinite chains via an N—H⋯O hydrogen bond.

Related literature

For details of the synthesis, see: Martirosyan et al. (2000[Martirosyan, A. O., Gasparyan, S. P., Oganesyan, V. E., Mndzhoyan, Sh. L., Alexanyan, M. L., Nikishchenko, M. N. & Babayan, G. Sh. (2000). Chem. Heterocycl. Compd. 36, 416-419.], 2004[Martirosyan, A. O., Hovhannesyan, V. E., Gasparyan, S. P., Karapetyan, H. A., Panosyan, G. A. & Martirosyan, V. O. (2004). Chem. Heterocycl. Compd. 40, 1007-1008.]). For details of the pharmacological properties of compounds of this family, see: De Clercq (1996[De Clercq, E. (1996). Rev. Med. Virol. 6, 97-117.]). For the crystal structures of some analogs of the title compound, see: Karapetyan et al. (2002[Karapetyan, H., Tamazyan, R., Martirosyan, A., Hovhannesyan, V. & Gasparyan, S. (2002). Acta Cryst. C58, o399-o401.]); Tamazyan et al. (2002[Tamazyan, R., Karapetyan, H., Martirosyan, A., Hovhannesyan, V. & Gasparyan, S. (2002). Acta Cryst. C58, o386-o388.]).

[Scheme 1]

Experimental

Crystal data
  • C20H17N3O

  • Mr = 315.37

  • Triclinic, [P \overline 1]

  • a = 7.5781 (15) Å

  • b = 9.4521 (19) Å

  • c = 12.409 (3) Å

  • α = 78.02 (3)°

  • β = 83.05 (3)°

  • γ = 69.68 (3)°

  • V = 814.2 (3) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.08 mm−1

  • T = 293 (2) K

  • 0.4 × 0.3 × 0.2 mm

Data collection
  • Enraf–Nonius CAD-4 diffractometer

  • Absorption correction: none

  • 9470 measured reflections

  • 4735 independent reflections

  • 3450 reflections with I > 2σ(I)

  • Rint = 0.020

  • 3 standard reflections frequency: 180 min intensity decay: none

Refinement
  • R[F2 > 2σ(F2)] = 0.047

  • wR(F2) = 0.130

  • S = 1.02

  • 4735 reflections

  • 285 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.20 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N11—H11⋯O6i 0.90 (2) 2.01 (2) 2.866 (2) 158 (2)
Symmetry code: (i) x, y-1, z.

Data collection: CAD-4 Manual (Enraf–Nonius, 1988[Enraf-Nonius (1988). CAD-4 Manual. Version 5.0. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 Manual; data reduction: HELENA (Spek, 1997[Spek, A. L. (1997). HELENA. University of Utrecht, The Netherlands.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.]); molecular graphics: SHELXTL (Bruker 2000[Bruker (2000). SHELXTL-NT. Version 6.10. Bruker AXS Inc., Madison, Wisconsin, USA.]) and ORTEPII (Johnson, 1976[Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

Our interest in the X-ray structural investigation of the title compound was stimulated by its potential HIV-1 RT inhibition properties. Compounds of this type belong to family of non-nucleoside reverse transcriptase inhibitors (NNRTIs).

A view of the molecular structure of the title compound is given in Fig. 1. A l l the bond distances in the molecule are in good agreement with their mean statistical values, except bond C2—C7 which is relatively short, 1.493 (2) Å. We believe that this shortening is caused by the inductive effect of the carbonitryl group C7 N11.

In the crystal structure infinite chains along [010] direction are formed via an intermolecular N—H···O hydrogen bond (see Fig. 2 and Table 1).

Related literature top

For details of the synthesis, see: Martirosyan et al. (2000, 2004). For details of the pharmacological properties of compounds of this family, see: De Clercq (1996). For the crystal structures of some analogs of the title compound, see: Karapetyan et al. (2002); Tamazyan et al. (2002).

Experimental top

The title compound was synthesized by the cycloalkylation of N1-benzyl-N1-cyano(1H-3-indolyl)methyl-3-chloropropanamide in the phase-transfer catalysis condition (Martirosyan et al., 2000, 2004). The compound as synthesized is a racemic mixture. Colorless crystals, suitable for X-ray analysis, were grown from a methanol solution of the compound.

Refinement top

The H-atoms were located from difference Fourier syntheses and freely refined: N—H = 0.90 (2) Å; C—H = 0.94 (2) - 1.02 (2) Å.

Computing details top

Data collection: CAD-4 Manual (Enraf–Nonius, 1988); cell refinement: CAD-4 Manual (Enraf–Nonius, 1988); data reduction: HELENA (Spek, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker 2000) and ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXTL (Bruker, 2000).

Figures top
[Figure 1] Fig. 1. A view of molecular structure of the title compound, showing the atomic numbering scheme and displacement ellipsoids drawn at the 50% probability level. H atoms are omitted for clarity.
[Figure 2] Fig. 2. partial view of the crystal packing showing the formation of the infinite chain of molecules formed via hydrogen bonding [for clarifity only H atoms participating in bonding are depicted]. Symmetry codes: (i) x, 1 + y, z; (ii) x, -1 + y, z.
1-Benzyl-2-(1H-indol-3-yl)-5-oxopyrrolidine-2-carbonitrile top
Crystal data top
C20H17N3OZ = 2
Mr = 315.37F(000) = 332
Triclinic, P1Dx = 1.286 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.5781 (15) ÅCell parameters from 22 reflections
b = 9.4521 (19) Åθ = 14.2–17.5°
c = 12.409 (3) ŵ = 0.08 mm1
α = 78.02 (3)°T = 293 K
β = 83.05 (3)°Prism, colourless
γ = 69.68 (3)°0.4 × 0.3 × 0.2 mm
V = 814.2 (3) Å3
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.020
Radiation source: fine-focus sealed tubeθmax = 30.0°, θmin = 1.7°
Graphite monochromatorh = 1010
θ/2θ scansk = 1313
9470 measured reflectionsl = 1717
4735 independent reflections3 standard reflections every 180 min
3450 reflections with I > 2σ(I) intensity decay: none
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.130H atoms treated by a mixture of independent and constrained refinement
S = 1.02 w = 1/[σ2(Fo2) + (0.0649P)2 + 0.0907P]
where P = (Fo2 + 2Fc2)/3
4735 reflections(Δ/σ)max < 0.001
285 parametersΔρmax = 0.18 e Å3
0 restraintsΔρmin = 0.20 e Å3
Crystal data top
C20H17N3Oγ = 69.68 (3)°
Mr = 315.37V = 814.2 (3) Å3
Triclinic, P1Z = 2
a = 7.5781 (15) ÅMo Kα radiation
b = 9.4521 (19) ŵ = 0.08 mm1
c = 12.409 (3) ÅT = 293 K
α = 78.02 (3)°0.4 × 0.3 × 0.2 mm
β = 83.05 (3)°
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.020
9470 measured reflections3 standard reflections every 180 min
4735 independent reflections intensity decay: none
3450 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0470 restraints
wR(F2) = 0.130H atoms treated by a mixture of independent and constrained refinement
S = 1.02Δρmax = 0.18 e Å3
4735 reflectionsΔρmin = 0.20 e Å3
285 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
xyzUiso*/Ueq
N10.22574 (14)0.71961 (10)0.23198 (8)0.0367 (2)
C20.20774 (17)0.64700 (12)0.14116 (9)0.0385 (2)
C30.3119 (3)0.72278 (16)0.04282 (12)0.0552 (4)
H3A0.448 (3)0.655 (2)0.0402 (14)0.066 (5)*
H3B0.258 (2)0.728 (2)0.0253 (16)0.069 (5)*
C40.2913 (3)0.87637 (17)0.07212 (14)0.0642 (4)
H4A0.182 (3)0.955 (3)0.0430 (19)0.096 (7)*
H4B0.408 (3)0.908 (3)0.049 (2)0.102 (7)*
C50.26566 (17)0.85107 (13)0.19576 (12)0.0453 (3)
O60.27772 (15)0.93414 (11)0.25649 (10)0.0628 (3)
C70.0051 (2)0.69595 (15)0.11645 (11)0.0503 (3)
N80.1486 (2)0.73626 (18)0.09409 (14)0.0761 (4)
C90.28897 (17)0.47561 (12)0.16540 (9)0.0379 (2)
C100.2034 (2)0.37431 (15)0.15315 (11)0.0480 (3)
H100.076 (2)0.3968 (19)0.1273 (14)0.063 (5)*
H110.298 (3)0.140 (2)0.1869 (15)0.073 (5)*
N110.32401 (19)0.22756 (13)0.18058 (10)0.0543 (3)
C120.48874 (19)0.23143 (13)0.21285 (10)0.0435 (3)
C130.6498 (2)0.11135 (15)0.24876 (12)0.0574 (4)
H130.655 (2)0.009 (2)0.2546 (15)0.068 (5)*
C140.7955 (2)0.14884 (19)0.27645 (14)0.0656 (4)
H140.911 (3)0.066 (2)0.3034 (16)0.079 (5)*
C150.7826 (2)0.30164 (19)0.26931 (15)0.0641 (4)
H150.887 (3)0.324 (2)0.2894 (16)0.078 (5)*
C160.62465 (19)0.42094 (15)0.23300 (12)0.0498 (3)
H160.620 (2)0.5269 (19)0.2264 (14)0.059 (4)*
C170.47300 (17)0.38670 (12)0.20376 (9)0.0379 (2)
C180.20486 (17)0.65739 (14)0.34923 (10)0.0395 (2)
H18A0.258 (2)0.5459 (17)0.3571 (12)0.047 (4)*
H18B0.280 (2)0.6986 (17)0.3851 (13)0.054 (4)*
C190.00691 (16)0.70242 (13)0.40041 (9)0.0376 (2)
C200.1177 (2)0.63319 (19)0.38244 (12)0.0545 (3)
H200.077 (2)0.557 (2)0.3324 (15)0.070 (5)*
C210.2973 (2)0.6704 (3)0.43232 (14)0.0744 (5)
H210.385 (3)0.624 (2)0.4196 (19)0.098 (7)*
C220.3538 (3)0.7749 (2)0.50150 (15)0.0782 (6)
H220.484 (3)0.800 (2)0.5378 (19)0.099 (7)*
C230.2317 (3)0.8426 (2)0.52187 (14)0.0750 (5)
H230.264 (3)0.914 (3)0.5704 (19)0.095 (7)*
C240.0502 (2)0.80719 (16)0.47138 (11)0.0542 (3)
H240.038 (2)0.858 (2)0.4834 (14)0.065 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0439 (5)0.0279 (4)0.0399 (5)0.0152 (4)0.0056 (4)0.0083 (3)
C20.0494 (6)0.0315 (5)0.0350 (5)0.0157 (5)0.0037 (5)0.0062 (4)
C30.0742 (10)0.0429 (7)0.0425 (7)0.0210 (7)0.0150 (7)0.0026 (5)
C40.0842 (11)0.0384 (7)0.0649 (9)0.0266 (7)0.0159 (8)0.0017 (6)
C50.0426 (6)0.0272 (5)0.0655 (8)0.0132 (4)0.0051 (5)0.0089 (5)
O60.0691 (7)0.0387 (5)0.0905 (8)0.0253 (5)0.0011 (6)0.0228 (5)
C70.0609 (8)0.0433 (6)0.0447 (7)0.0147 (6)0.0096 (6)0.0040 (5)
N80.0693 (9)0.0762 (10)0.0782 (10)0.0154 (7)0.0267 (8)0.0059 (8)
C90.0500 (6)0.0304 (5)0.0358 (5)0.0170 (5)0.0045 (5)0.0089 (4)
C100.0624 (8)0.0415 (6)0.0490 (7)0.0263 (6)0.0024 (6)0.0121 (5)
N110.0788 (8)0.0341 (5)0.0594 (7)0.0295 (5)0.0002 (6)0.0122 (5)
C120.0605 (7)0.0309 (5)0.0390 (6)0.0180 (5)0.0111 (5)0.0089 (4)
C130.0738 (10)0.0326 (6)0.0532 (8)0.0100 (6)0.0146 (7)0.0041 (5)
C140.0545 (9)0.0536 (8)0.0666 (10)0.0005 (7)0.0081 (7)0.0005 (7)
C150.0467 (8)0.0635 (9)0.0771 (11)0.0168 (7)0.0016 (7)0.0070 (8)
C160.0471 (7)0.0418 (6)0.0622 (8)0.0188 (5)0.0056 (6)0.0105 (6)
C170.0475 (6)0.0299 (5)0.0369 (5)0.0156 (4)0.0097 (5)0.0095 (4)
C180.0411 (6)0.0387 (6)0.0377 (6)0.0114 (5)0.0004 (5)0.0090 (4)
C190.0429 (6)0.0351 (5)0.0307 (5)0.0093 (4)0.0006 (4)0.0049 (4)
C200.0553 (8)0.0719 (9)0.0436 (7)0.0304 (7)0.0050 (6)0.0144 (6)
C210.0521 (9)0.1182 (16)0.0534 (9)0.0380 (10)0.0035 (7)0.0031 (9)
C220.0529 (9)0.0940 (13)0.0560 (9)0.0023 (9)0.0154 (7)0.0060 (9)
C230.0899 (13)0.0588 (9)0.0509 (8)0.0010 (9)0.0230 (8)0.0149 (7)
C240.0726 (9)0.0435 (7)0.0429 (7)0.0147 (6)0.0073 (6)0.0138 (5)
Geometric parameters (Å, º) top
N1—C51.3542 (15)C13—C141.370 (3)
N1—C181.4634 (16)C13—H130.944 (18)
N1—C21.4775 (15)C14—C151.398 (2)
C2—C71.493 (2)C14—H140.99 (2)
C2—C91.4979 (16)C15—C161.375 (2)
C2—C31.5562 (18)C15—H150.96 (2)
C3—C41.521 (2)C16—C171.4018 (18)
C3—H3A1.009 (18)C16—H160.976 (16)
C3—H3B0.969 (18)C18—C191.5076 (17)
C4—C51.502 (2)C18—H18A0.977 (15)
C4—H4A0.95 (2)C18—H18B0.983 (16)
C4—H4B1.02 (2)C19—C201.3824 (19)
C5—O61.2269 (16)C19—C241.3842 (17)
C7—N81.142 (2)C20—C211.383 (2)
C9—C101.3695 (17)C20—H200.989 (18)
C9—C171.4348 (18)C21—C221.366 (3)
C10—N111.3689 (19)C21—H210.95 (2)
C10—H100.994 (17)C22—C231.365 (3)
N11—C121.3707 (19)C22—H221.00 (2)
N11—H110.90 (2)C23—C241.399 (2)
C12—C131.391 (2)C23—H230.94 (2)
C12—C171.4120 (15)C24—H240.986 (17)
C5—N1—C18122.70 (10)C14—C13—H13122.7 (10)
C5—N1—C2112.91 (10)C12—C13—H13120.0 (10)
C18—N1—C2124.39 (9)C13—C14—C15121.35 (15)
N1—C2—C7109.37 (10)C13—C14—H14119.6 (11)
N1—C2—C9113.04 (10)C15—C14—H14119.1 (11)
C7—C2—C9110.17 (11)C16—C15—C14121.65 (16)
N1—C2—C3101.87 (10)C16—C15—H15118.9 (11)
C7—C2—C3108.24 (12)C14—C15—H15119.4 (11)
C9—C2—C3113.77 (10)C15—C16—C17118.50 (13)
C4—C3—C2104.09 (11)C15—C16—H16120.4 (9)
C4—C3—H3A111.4 (10)C17—C16—H16121.1 (9)
C2—C3—H3A107.7 (10)C16—C17—C12118.72 (12)
C4—C3—H3B115.6 (11)C16—C17—C9134.95 (11)
C2—C3—H3B109.1 (11)C12—C17—C9106.31 (11)
H3A—C3—H3B108.5 (14)N1—C18—C19116.05 (10)
C5—C4—C3104.26 (11)N1—C18—H18A106.8 (9)
C5—C4—H4A108.1 (14)C19—C18—H18A109.9 (8)
C3—C4—H4A112.0 (13)N1—C18—H18B103.9 (9)
C5—C4—H4B109.1 (14)C19—C18—H18B108.7 (9)
C3—C4—H4B112.6 (13)H18A—C18—H18B111.5 (12)
H4A—C4—H4B110.6 (19)C20—C19—C24118.62 (13)
O6—C5—N1124.06 (13)C20—C19—C18120.58 (11)
O6—C5—C4126.73 (12)C24—C19—C18120.70 (12)
N1—C5—C4109.21 (11)C19—C20—C21120.72 (15)
N8—C7—C2177.60 (16)C19—C20—H20118.9 (10)
C10—C9—C17107.09 (11)C21—C20—H20120.3 (10)
C10—C9—C2126.59 (12)C22—C21—C20120.49 (18)
C17—C9—C2126.31 (10)C22—C21—H21118.2 (14)
N11—C10—C9109.47 (13)C20—C21—H21121.3 (14)
N11—C10—H10122.1 (10)C23—C22—C21119.72 (16)
C9—C10—H10128.4 (10)C23—C22—H22120.8 (12)
C10—N11—C12109.29 (11)C21—C22—H22119.5 (12)
C10—N11—H11127.3 (11)C22—C23—C24120.51 (16)
C12—N11—H11122.9 (11)C22—C23—H23122.7 (14)
N11—C12—C13129.75 (12)C24—C23—H23116.8 (14)
N11—C12—C17107.83 (12)C19—C24—C23119.93 (17)
C13—C12—C17122.42 (14)C19—C24—H24118.7 (10)
C14—C13—C12117.34 (13)C23—C24—H24121.3 (10)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N11—H11···O6i0.90 (2)2.01 (2)2.866 (2)158 (2)
Symmetry code: (i) x, y1, z.

Experimental details

Crystal data
Chemical formulaC20H17N3O
Mr315.37
Crystal system, space groupTriclinic, P1
Temperature (K)293
a, b, c (Å)7.5781 (15), 9.4521 (19), 12.409 (3)
α, β, γ (°)78.02 (3), 83.05 (3), 69.68 (3)
V3)814.2 (3)
Z2
Radiation typeMo Kα
µ (mm1)0.08
Crystal size (mm)0.4 × 0.3 × 0.2
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
9470, 4735, 3450
Rint0.020
(sin θ/λ)max1)0.703
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.047, 0.130, 1.02
No. of reflections4735
No. of parameters285
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.18, 0.20

Computer programs: CAD-4 Manual (Enraf–Nonius, 1988), HELENA (Spek, 1997), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker 2000) and ORTEPII (Johnson, 1976), SHELXTL (Bruker, 2000).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N11—H11···O6i0.90 (2)2.01 (2)2.866 (2)158 (2)
Symmetry code: (i) x, y1, z.
 

Acknowledgements

We are grateful to the Civilian Research and Development Foundation (CRDF), USA, for financial support (grant No. ARB2–2701-YE-05).

References

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First citationDe Clercq, E. (1996). Rev. Med. Virol. 6, 97–117.  CrossRef PubMed CAS Web of Science Google Scholar
First citationEnraf–Nonius (1988). CAD-4 Manual. Version 5.0. Enraf–Nonius, Delft, The Netherlands.  Google Scholar
First citationJohnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.  Google Scholar
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