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

Tamazyan, R.; Armen, A.; Ashot, M.; Sahak, G.; Schinazi, R.

doi:10.1107/S1600536807067670

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 64| Part 2| February 2008| Page o368

doi:10.1107/S1600536807067670

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

Rafael Tamazyan,^a ^* Ayvazyan Armen,^a Martirosyan Ashot,^b Gasparyan Sahak ^b and Raymond Schinazi ^c

^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 , 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

Crystal data

C₂₀H₁₇N₃O
M_r = 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)
R_int = 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
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.20 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: CAD-4 Manual; 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.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536807067670/su2039sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536807067670/su2039Isup2.hkl

checkCIF report

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.

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

	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.
	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

C₂₀H₁₇N₃O	Z = 2
M_r = 315.37	F(000) = 332
Triclinic, P1	D_x = 1.286 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.5781 (15) Å	Cell parameters from 22 reflections
b = 9.4521 (19) Å	θ = 14.2–17.5°
c = 12.409 (3) Å	µ = 0.08 mm⁻¹
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	R_int = 0.020
Radiation source: fine-focus sealed tube	θ_max = 30.0°, θ_min = 1.7°
Graphite monochromator	h = −10→10
θ/2θ scans	k = −13→13
9470 measured reflections	l = −17→17
4735 independent reflections	3 standard reflections every 180 min
3450 reflections with I > 2σ(I)	intensity decay: none

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)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.130	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	w = 1/[σ²(F_o²) + (0.0649P)² + 0.0907P] where P = (F_o² + 2F_c²)/3
4735 reflections	(Δ/σ)_max < 0.001
285 parameters	Δρ_max = 0.18 e Å⁻³
0 restraints	Δρ_min = −0.20 e Å⁻³

Crystal data top

C₂₀H₁₇N₃O	γ = 69.68 (3)°
M_r = 315.37	V = 814.2 (3) Å³
Triclinic, P1	Z = 2
a = 7.5781 (15) Å	Mo Kα radiation
b = 9.4521 (19) Å	µ = 0.08 mm⁻¹
c = 12.409 (3) Å	T = 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	R_int = 0.020
9470 measured reflections	3 standard reflections every 180 min
4735 independent reflections	intensity decay: none
3450 reflections with I > 2σ(I)

Refinement top

R[F² > 2σ(F²)] = 0.047	0 restraints
wR(F²) = 0.130	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	Δρ_max = 0.18 e Å⁻³
4735 reflections	Δρ_min = −0.20 e Å⁻³
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

	x	y	z	U_iso*/U_eq
N1	0.22574 (14)	0.71961 (10)	0.23198 (8)	0.0367 (2)
C2	0.20774 (17)	0.64700 (12)	0.14116 (9)	0.0385 (2)
C3	0.3119 (3)	0.72278 (16)	0.04282 (12)	0.0552 (4)
H3A	0.448 (3)	0.655 (2)	0.0402 (14)	0.066 (5)*
H3B	0.258 (2)	0.728 (2)	−0.0253 (16)	0.069 (5)*
C4	0.2913 (3)	0.87637 (17)	0.07212 (14)	0.0642 (4)
H4A	0.182 (3)	0.955 (3)	0.0430 (19)	0.096 (7)*
H4B	0.408 (3)	0.908 (3)	0.049 (2)	0.102 (7)*
C5	0.26566 (17)	0.85107 (13)	0.19576 (12)	0.0453 (3)
O6	0.27772 (15)	0.93414 (11)	0.25649 (10)	0.0628 (3)
C7	0.0051 (2)	0.69595 (15)	0.11645 (11)	0.0503 (3)
N8	−0.1486 (2)	0.73626 (18)	0.09409 (14)	0.0761 (4)
C9	0.28897 (17)	0.47561 (12)	0.16540 (9)	0.0379 (2)
C10	0.2034 (2)	0.37431 (15)	0.15315 (11)	0.0480 (3)
H10	0.076 (2)	0.3968 (19)	0.1273 (14)	0.063 (5)*
H11	0.298 (3)	0.140 (2)	0.1869 (15)	0.073 (5)*
N11	0.32401 (19)	0.22756 (13)	0.18058 (10)	0.0543 (3)
C12	0.48874 (19)	0.23143 (13)	0.21285 (10)	0.0435 (3)
C13	0.6498 (2)	0.11135 (15)	0.24876 (12)	0.0574 (4)
H13	0.655 (2)	0.009 (2)	0.2546 (15)	0.068 (5)*
C14	0.7955 (2)	0.14884 (19)	0.27645 (14)	0.0656 (4)
H14	0.911 (3)	0.066 (2)	0.3034 (16)	0.079 (5)*
C15	0.7826 (2)	0.30164 (19)	0.26931 (15)	0.0641 (4)
H15	0.887 (3)	0.324 (2)	0.2894 (16)	0.078 (5)*
C16	0.62465 (19)	0.42094 (15)	0.23300 (12)	0.0498 (3)
H16	0.620 (2)	0.5269 (19)	0.2264 (14)	0.059 (4)*
C17	0.47300 (17)	0.38670 (12)	0.20376 (9)	0.0379 (2)
C18	0.20486 (17)	0.65739 (14)	0.34923 (10)	0.0395 (2)
H18A	0.258 (2)	0.5459 (17)	0.3571 (12)	0.047 (4)*
H18B	0.280 (2)	0.6986 (17)	0.3851 (13)	0.054 (4)*
C19	0.00691 (16)	0.70242 (13)	0.40041 (9)	0.0376 (2)
C20	−0.1177 (2)	0.63319 (19)	0.38244 (12)	0.0545 (3)
H20	−0.077 (2)	0.557 (2)	0.3324 (15)	0.070 (5)*
C21	−0.2973 (2)	0.6704 (3)	0.43232 (14)	0.0744 (5)
H21	−0.385 (3)	0.624 (2)	0.4196 (19)	0.098 (7)*
C22	−0.3538 (3)	0.7749 (2)	0.50150 (15)	0.0782 (6)
H22	−0.484 (3)	0.800 (2)	0.5378 (19)	0.099 (7)*
C23	−0.2317 (3)	0.8426 (2)	0.52187 (14)	0.0750 (5)
H23	−0.264 (3)	0.914 (3)	0.5704 (19)	0.095 (7)*
C24	−0.0502 (2)	0.80719 (16)	0.47138 (11)	0.0542 (3)
H24	0.038 (2)	0.858 (2)	0.4834 (14)	0.065 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0439 (5)	0.0279 (4)	0.0399 (5)	−0.0152 (4)	0.0056 (4)	−0.0083 (3)
C2	0.0494 (6)	0.0315 (5)	0.0350 (5)	−0.0157 (5)	0.0037 (5)	−0.0062 (4)
C3	0.0742 (10)	0.0429 (7)	0.0425 (7)	−0.0210 (7)	0.0150 (7)	−0.0026 (5)
C4	0.0842 (11)	0.0384 (7)	0.0649 (9)	−0.0266 (7)	0.0159 (8)	0.0017 (6)
C5	0.0426 (6)	0.0272 (5)	0.0655 (8)	−0.0132 (4)	0.0051 (5)	−0.0089 (5)
O6	0.0691 (7)	0.0387 (5)	0.0905 (8)	−0.0253 (5)	0.0011 (6)	−0.0228 (5)
C7	0.0609 (8)	0.0433 (6)	0.0447 (7)	−0.0147 (6)	−0.0096 (6)	−0.0040 (5)
N8	0.0693 (9)	0.0762 (10)	0.0782 (10)	−0.0154 (7)	−0.0267 (8)	−0.0059 (8)
C9	0.0500 (6)	0.0304 (5)	0.0358 (5)	−0.0170 (5)	0.0045 (5)	−0.0089 (4)
C10	0.0624 (8)	0.0415 (6)	0.0490 (7)	−0.0263 (6)	−0.0024 (6)	−0.0121 (5)
N11	0.0788 (8)	0.0341 (5)	0.0594 (7)	−0.0295 (5)	0.0002 (6)	−0.0122 (5)
C12	0.0605 (7)	0.0309 (5)	0.0390 (6)	−0.0180 (5)	0.0111 (5)	−0.0089 (4)
C13	0.0738 (10)	0.0326 (6)	0.0532 (8)	−0.0100 (6)	0.0146 (7)	−0.0041 (5)
C14	0.0545 (9)	0.0536 (8)	0.0666 (10)	−0.0005 (7)	0.0081 (7)	0.0005 (7)
C15	0.0467 (8)	0.0635 (9)	0.0771 (11)	−0.0168 (7)	0.0016 (7)	−0.0070 (8)
C16	0.0471 (7)	0.0418 (6)	0.0622 (8)	−0.0188 (5)	0.0056 (6)	−0.0105 (6)
C17	0.0475 (6)	0.0299 (5)	0.0369 (5)	−0.0156 (4)	0.0097 (5)	−0.0095 (4)
C18	0.0411 (6)	0.0387 (6)	0.0377 (6)	−0.0114 (5)	−0.0004 (5)	−0.0090 (4)
C19	0.0429 (6)	0.0351 (5)	0.0307 (5)	−0.0093 (4)	0.0006 (4)	−0.0049 (4)
C20	0.0553 (8)	0.0719 (9)	0.0436 (7)	−0.0304 (7)	0.0050 (6)	−0.0144 (6)
C21	0.0521 (9)	0.1182 (16)	0.0534 (9)	−0.0380 (10)	0.0035 (7)	−0.0031 (9)
C22	0.0529 (9)	0.0940 (13)	0.0560 (9)	−0.0023 (9)	0.0154 (7)	0.0060 (9)
C23	0.0899 (13)	0.0588 (9)	0.0509 (8)	0.0010 (9)	0.0230 (8)	−0.0149 (7)
C24	0.0726 (9)	0.0435 (7)	0.0429 (7)	−0.0147 (6)	0.0073 (6)	−0.0138 (5)

Geometric parameters (Å, º) top

N1—C5	1.3542 (15)	C13—C14	1.370 (3)
N1—C18	1.4634 (16)	C13—H13	0.944 (18)
N1—C2	1.4775 (15)	C14—C15	1.398 (2)
C2—C7	1.493 (2)	C14—H14	0.99 (2)
C2—C9	1.4979 (16)	C15—C16	1.375 (2)
C2—C3	1.5562 (18)	C15—H15	0.96 (2)
C3—C4	1.521 (2)	C16—C17	1.4018 (18)
C3—H3A	1.009 (18)	C16—H16	0.976 (16)
C3—H3B	0.969 (18)	C18—C19	1.5076 (17)
C4—C5	1.502 (2)	C18—H18A	0.977 (15)
C4—H4A	0.95 (2)	C18—H18B	0.983 (16)
C4—H4B	1.02 (2)	C19—C20	1.3824 (19)
C5—O6	1.2269 (16)	C19—C24	1.3842 (17)
C7—N8	1.142 (2)	C20—C21	1.383 (2)
C9—C10	1.3695 (17)	C20—H20	0.989 (18)
C9—C17	1.4348 (18)	C21—C22	1.366 (3)
C10—N11	1.3689 (19)	C21—H21	0.95 (2)
C10—H10	0.994 (17)	C22—C23	1.365 (3)
N11—C12	1.3707 (19)	C22—H22	1.00 (2)
N11—H11	0.90 (2)	C23—C24	1.399 (2)
C12—C13	1.391 (2)	C23—H23	0.94 (2)
C12—C17	1.4120 (15)	C24—H24	0.986 (17)

C5—N1—C18	122.70 (10)	C14—C13—H13	122.7 (10)
C5—N1—C2	112.91 (10)	C12—C13—H13	120.0 (10)
C18—N1—C2	124.39 (9)	C13—C14—C15	121.35 (15)
N1—C2—C7	109.37 (10)	C13—C14—H14	119.6 (11)
N1—C2—C9	113.04 (10)	C15—C14—H14	119.1 (11)
C7—C2—C9	110.17 (11)	C16—C15—C14	121.65 (16)
N1—C2—C3	101.87 (10)	C16—C15—H15	118.9 (11)
C7—C2—C3	108.24 (12)	C14—C15—H15	119.4 (11)
C9—C2—C3	113.77 (10)	C15—C16—C17	118.50 (13)
C4—C3—C2	104.09 (11)	C15—C16—H16	120.4 (9)
C4—C3—H3A	111.4 (10)	C17—C16—H16	121.1 (9)
C2—C3—H3A	107.7 (10)	C16—C17—C12	118.72 (12)
C4—C3—H3B	115.6 (11)	C16—C17—C9	134.95 (11)
C2—C3—H3B	109.1 (11)	C12—C17—C9	106.31 (11)
H3A—C3—H3B	108.5 (14)	N1—C18—C19	116.05 (10)
C5—C4—C3	104.26 (11)	N1—C18—H18A	106.8 (9)
C5—C4—H4A	108.1 (14)	C19—C18—H18A	109.9 (8)
C3—C4—H4A	112.0 (13)	N1—C18—H18B	103.9 (9)
C5—C4—H4B	109.1 (14)	C19—C18—H18B	108.7 (9)
C3—C4—H4B	112.6 (13)	H18A—C18—H18B	111.5 (12)
H4A—C4—H4B	110.6 (19)	C20—C19—C24	118.62 (13)
O6—C5—N1	124.06 (13)	C20—C19—C18	120.58 (11)
O6—C5—C4	126.73 (12)	C24—C19—C18	120.70 (12)
N1—C5—C4	109.21 (11)	C19—C20—C21	120.72 (15)
N8—C7—C2	177.60 (16)	C19—C20—H20	118.9 (10)
C10—C9—C17	107.09 (11)	C21—C20—H20	120.3 (10)
C10—C9—C2	126.59 (12)	C22—C21—C20	120.49 (18)
C17—C9—C2	126.31 (10)	C22—C21—H21	118.2 (14)
N11—C10—C9	109.47 (13)	C20—C21—H21	121.3 (14)
N11—C10—H10	122.1 (10)	C23—C22—C21	119.72 (16)
C9—C10—H10	128.4 (10)	C23—C22—H22	120.8 (12)
C10—N11—C12	109.29 (11)	C21—C22—H22	119.5 (12)
C10—N11—H11	127.3 (11)	C22—C23—C24	120.51 (16)
C12—N11—H11	122.9 (11)	C22—C23—H23	122.7 (14)
N11—C12—C13	129.75 (12)	C24—C23—H23	116.8 (14)
N11—C12—C17	107.83 (12)	C19—C24—C23	119.93 (17)
C13—C12—C17	122.42 (14)	C19—C24—H24	118.7 (10)
C14—C13—C12	117.34 (13)	C23—C24—H24	121.3 (10)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N11—H11···O6ⁱ	0.90 (2)	2.01 (2)	2.866 (2)	158 (2)

Symmetry code: (i) x, y−1, z.

Experimental details

Crystal data
Chemical formula	C₂₀H₁₇N₃O
M_r	315.37
Crystal system, space group	Triclinic, 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)
V (Å³)	814.2 (3)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.08
Crystal size (mm)	0.4 × 0.3 × 0.2

Data collection
Diffractometer	Enraf–Nonius CAD-4 diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	9470, 4735, 3450
R_int	0.020
(sin θ/λ)_max (Å⁻¹)	0.703

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.047, 0.130, 1.02
No. of reflections	4735
No. of parameters	285
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	D—H···A
N11—H11···O6ⁱ	0.90 (2)	2.01 (2)	2.866 (2)	158 (2)

Symmetry code: (i) x, y−1, z.

Acknowledgements

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

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