rac-(Z)-Methyl 1-benzyl-3-[(3-hy­droxy­quinuclidin-2-yl­idene)meth­yl]-1H-indole-6-carboxyl­ate

Penthala, N.R.; Ponugoti, P.R.; Parkin, S.; Crooks, P.A.

doi:10.1107/S1600536812040731

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 68| Part 11| November 2012| Page o3111

doi:10.1107/S1600536812040731

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rac-(Z)-Methyl 1-benzyl-3-[(3-hydroxyquinuclidin-2-ylidene)methyl]-1H-indole-6-carboxylate

Narsimha Reddy Penthala,^a Purushotham Rao Ponugoti,^a Sean Parkin ^b and Peter A. Crooks ^a ^*

^aDept. of Pharm. Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA, and ^bDept. of Chemistry, University of Kentucky, Lexington KY 40506, USA
^*Correspondence e-mail: pacrooks@uams.edu

(Received 13 August 2012; accepted 26 September 2012; online 13 October 2012)

In the title compound, C₂₅H₂₆N₂O₃, the double bond connecting the aza-bicyclic and indole units has Z geometry. The compound was obtained as a racemate, and since the crystal is centrosymmetric it contains equal amounts of the S and R enantiomers. However, the structure is disordered such that the asymmetric unit contains both enantiomers in unequal amounts [refined occupancies 0.904 (2) and 0.096 (2)]. The dihedral angle between the benzene ring of the benzyl group and the mean plane of the indole ring is 76.07 (3) °. In the crystal, molecules are linked by O—H⋯O_carbonyl hydrogen bonds into chains propagating in [110].

Related literature

For background literature, see: Sekhar et al., (2003 ), Amudhan et al., (2010 ). For the biological activity of N-benzyl indole quinuclidinone, see: Sonar et al. (2007 ). For a similar crystal structure, see: Sonar et al., (2004 ).

Experimental

Crystal data

C₂₅H₂₆N₂O₃
M_r = 402.48
Triclinic, $[P \overline 1]$
a = 6.1619 (1) Å
b = 10.3119 (2) Å
c = 16.5959 (3) Å
α = 75.6705 (7)°
β = 80.0939 (7)°
γ = 85.9410 (7)°
V = 1006.04 (3) Å³
Z = 2
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 90 K
0.28 × 0.22 × 0.12 mm

Data collection

Nonius KappaCCD diffractometer
9126 measured reflections
4597 independent reflections
3831 reflections with I > 2σ(I)
R_int = 0.024

Refinement

R[F² > 2σ(F²)] = 0.039
wR(F²) = 0.102
S = 1.04
4597 reflections
312 parameters
64 restraints
H-atom parameters constrained
Δρ_max = 0.27 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
O1—H1A⋯O2ⁱ	0.84	1.97	2.7989 (13)	169
Symmetry code: (i) x-1, y-1, z.

Data collection: COLLECT (Nonius, 1998 ); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 ); data reduction: DENZO-SMN (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 and local procedures.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536812040731/hg5242sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812040731/hg5242Isup2.hkl

checkCIF report

Comment top

The N-benzyl indole quinuclidin-3-one moiety has been found to possess interesting biological properties which range from NADPH oxidase activity (Sekhar et al., 2003), thermal sensitizing activity to radiation treatment (Sonar et al., 2007), and also exhibit antiangiogenic properties (Amudhan et al., 2010). Previously, we reported the crystal structure of Z-(S)-2-(1- phenylsulfonyl-1H-indol-3-ylmethylene)-1-azabicyclo[2.2.2]octan-3-ol (Sonar et al., 2004) and in continuation of our research work on the N-benzyl indole quinuclidin-3-one scaffold (Sonar et al., 2007) we designed and synthesized a novel series of carboxymethyl N-benzyl indole quinuclidin-3-ones as potent anticancer agents. The title compound was prepared by the reduction of Z-methyl 1-benzyl-3-[(3-oxoquinuclidin-2-ylidene)methyl]-1H-indole-6-carboxylate with NaBH₄ in methanol at room temperature (Sonar et al., 2004). Recrystallization of the title compound from methanol afforded colorless needles that were suitable for X-ray analysis.

The X-ray studies revealed that the title compound is the Z isomer having the C2—C18 bond in a trans position with respect to the C19—C20 bond. The double bond (C18═C19) has a nearly planar atomic arrangement, since the r.m.s. deviation from the best plane passing through atoms N2, C19, C20, C18 and C2 is 0.265 (1) Å. In this molecule, the azabicyclic system presents very small distortions around atoms N2, C24, C21, C22, C23 and C20. The value of the C1—C2—C18—C19 torsion angle [-5.1 (2)°] indicates the deviation of the indole ring from the plane of the double bond connected to the azabicyclic ring. The dihedral angle between the benzene ring of the benzyl group and with the mean plane of the indole ring is 76.07 (3) Å. The crystal of the title compound is a racemic equimolar mixture of R and S configurations. However, the structure is disordered such that the asymmetric unit contains both enantiomers, but in unequal amounts [refined occupancies 0.904 (2) and 0.096 (2)]. The hydrogen atom of the disordered OH group is involved in an intermolecular hydrogen bond with the carbonyl oxygen O2 on an adjacent molecule, thus forming an infinite chain-like structure along the (110) direction.

Related literature top

For background literature, see: Sekhar et al., (2003), Amudhan et al., (2010). For the biological activity of N-benzyl indole quinuclidinone, see: Sonar et al. (2007). For a similar crystal structure, see: Sonar et al., (2004).

Experimental top

The compound Z-methyl 1-benzyl-3-[(3-oxoquinuclidin-2-ylidene)methyl] -1H-indole-6-carboxylate was prepared by the available literature procedure (Sonar et al., 2004). To a stirred solution of Z-methyl 1-benzyl-3-((3-oxoquinuclidin-2-ylidene)methyl)-1H-indole-6-carboxylate (0.40 g, 1 mmol) in methanol (15 ml) at 273 K was added NaBH₄ (0.38 g, 10 mmol) over a period of 15 min and stirring was continued for 2 h at room temperature. Water (50 ml) was added and the mixture was extracted with CHCl₃ (3 times 10 ml). The combined organic layers were dried over Na₂SO₄ and evaporated to give the title compound as a white solid. Recrystallization from methanol afforded colorless needles suitable for X-ray analysis.

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO-SMN (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and local procedures.

Figures top

Fig. 1. A view of the molecule with displacement ellipsoids drawn at the 50% probability level.

rac-(Z)-Methyl 1-benzyl-3-[(3-hydroxyquinuclidin-2-ylidene)methyl]-1H-indole-6- carboxylate top

Crystal data top

C₂₅H₂₆N₂O₃	Z = 2
M_r = 402.48	F(000) = 428
Triclinic, P1	D_x = 1.329 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.1619 (1) Å	Cell parameters from 4571 reflections
b = 10.3119 (2) Å	θ = 1.0–27.5°
c = 16.5959 (3) Å	µ = 0.09 mm⁻¹
α = 75.6705 (7)°	T = 90 K
β = 80.0939 (7)°	Block, yellow
γ = 85.9410 (7)°	0.28 × 0.22 × 0.12 mm
V = 1006.04 (3) Å³

Data collection top

Nonius KappaCCD diffractometer	3831 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.024
Graphite monochromator	θ_max = 27.5°, θ_min = 2.0°
Detector resolution: 9.1 pixels mm^-1	h = −8→8
ω scans at fixed χ = 55°	k = −13→13
9126 measured reflections	l = −21→21
4597 independent reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.039	H-atom parameters constrained
wR(F²) = 0.102	w = 1/[σ²(F_o²) + (0.0442P)² + 0.3522P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max = 0.001
4597 reflections	Δρ_max = 0.27 e Å⁻³
312 parameters	Δρ_min = −0.20 e Å⁻³
64 restraints	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.023 (4)

Crystal data top

C₂₅H₂₆N₂O₃	γ = 85.9410 (7)°
M_r = 402.48	V = 1006.04 (3) Å³
Triclinic, P1	Z = 2
a = 6.1619 (1) Å	Mo Kα radiation
b = 10.3119 (2) Å	µ = 0.09 mm⁻¹
c = 16.5959 (3) Å	T = 90 K
α = 75.6705 (7)°	0.28 × 0.22 × 0.12 mm
β = 80.0939 (7)°

Data collection top

Nonius KappaCCD diffractometer	3831 reflections with I > 2σ(I)
9126 measured reflections	R_int = 0.024
4597 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	64 restraints
wR(F²) = 0.102	H-atom parameters constrained
S = 1.04	Δρ_max = 0.27 e Å⁻³
4597 reflections	Δρ_min = −0.20 e Å⁻³
312 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-value wR and goodness of fit S are based on F². Conventional R-values R are based on F, with F set to zero for negative F². The threshold expression of F² > 2σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-values based on F² are statistically about twice as large as those based on F, and R-values 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	Occ. (<1)
N1	0.31767 (16)	0.66937 (10)	0.24130 (6)	0.0190 (2)
O2	1.05912 (15)	0.90627 (9)	0.09629 (6)	0.0280 (2)
O3	1.17472 (13)	0.78520 (8)	0.00096 (5)	0.0213 (2)
C1	0.1919 (2)	0.56139 (12)	0.24673 (7)	0.0196 (2)
H1	0.0613	0.5379	0.2861	0.024*
C2	0.28163 (19)	0.49219 (11)	0.18719 (7)	0.0181 (2)
C3	0.47803 (19)	0.56153 (11)	0.14234 (7)	0.0172 (2)
C4	0.64453 (19)	0.53937 (11)	0.07749 (7)	0.0180 (2)
H4	0.6356	0.4677	0.0517	0.022*
C5	0.82107 (19)	0.62300 (11)	0.05167 (7)	0.0182 (2)
H5	0.9329	0.6092	0.0072	0.022*
C6	0.83869 (19)	0.72871 (11)	0.08999 (7)	0.0171 (2)
C7	0.67658 (19)	0.75346 (11)	0.15415 (7)	0.0181 (2)
H7	0.6879	0.8245	0.1802	0.022*
C8	0.49701 (19)	0.67018 (11)	0.17875 (7)	0.0171 (2)
C9	1.03202 (19)	0.81587 (11)	0.06408 (7)	0.0184 (2)
C10	1.3663 (2)	0.86728 (12)	−0.02905 (8)	0.0230 (3)
H10A	1.3191	0.9616	−0.0455	0.035*
H10B	1.4539	0.8408	−0.0779	0.035*
H10C	1.4557	0.8552	0.0159	0.035*
C11	0.2901 (2)	0.75327 (12)	0.30102 (8)	0.0212 (3)
H11A	0.1373	0.7463	0.3319	0.025*
H11B	0.3117	0.8477	0.2696	0.025*
C12	0.4496 (2)	0.71600 (12)	0.36448 (7)	0.0196 (3)
C13	0.4619 (2)	0.79843 (13)	0.41841 (8)	0.0248 (3)
H13	0.3700	0.8769	0.4156	0.030*
C14	0.6069 (2)	0.76729 (14)	0.47622 (8)	0.0302 (3)
H14	0.6149	0.8250	0.5122	0.036*
C15	0.7402 (2)	0.65246 (15)	0.48175 (8)	0.0307 (3)
H15	0.8390	0.6309	0.5215	0.037*
C16	0.7282 (2)	0.56959 (14)	0.42883 (8)	0.0300 (3)
H16	0.8186	0.4905	0.4325	0.036*
C17	0.5845 (2)	0.60137 (13)	0.37025 (8)	0.0250 (3)
H17	0.5786	0.5441	0.3338	0.030*
C18	0.2112 (2)	0.36924 (12)	0.17230 (7)	0.0203 (3)
H18	0.2905	0.3426	0.1244	0.024*
C19	0.0490 (3)	0.28894 (14)	0.21750 (9)	0.0190 (3)	0.904 (2)
C20	0.0007 (2)	0.15731 (14)	0.19936 (9)	0.0204 (3)	0.904 (2)
H20	−0.0961	0.1753	0.1550	0.025*	0.904 (2)
O1	0.20291 (17)	0.09447 (10)	0.16992 (7)	0.0268 (3)	0.904 (2)
H1A	0.1766	0.0378	0.1445	0.040*	0.904 (2)
C21	−0.1226 (3)	0.07182 (18)	0.28158 (11)	0.0203 (4)	0.904 (2)
H21	−0.1372	−0.0216	0.2763	0.024*	0.904 (2)
C22	0.0068 (3)	0.07145 (14)	0.35275 (9)	0.0237 (3)	0.904 (2)
H22A	0.1614	0.0414	0.3378	0.028*	0.904 (2)
H22B	−0.0598	0.0092	0.4054	0.028*	0.904 (2)
C23	−0.0005 (3)	0.2159 (2)	0.36551 (10)	0.0232 (3)	0.904 (2)
H23A	−0.0995	0.2201	0.4186	0.028*	0.904 (2)
H23B	0.1488	0.2397	0.3703	0.028*	0.904 (2)
N2	−0.0804 (3)	0.31334 (13)	0.29406 (9)	0.0209 (3)	0.904 (2)
C24	−0.3148 (3)	0.28641 (16)	0.29584 (10)	0.0258 (4)	0.904 (2)
H24A	−0.3657	0.3432	0.2447	0.031*	0.904 (2)
H24B	−0.4054	0.3110	0.3455	0.031*	0.904 (2)
C25	−0.3496 (2)	0.13790 (14)	0.29981 (9)	0.0243 (3)	0.904 (2)
H25A	−0.4259	0.0929	0.3563	0.029*	0.904 (2)
H25B	−0.4408	0.1311	0.2575	0.029*	0.904 (2)
C19'	0.116 (2)	0.2718 (12)	0.2322 (7)	0.013 (3)*	0.096 (2)
C20'	0.080 (3)	0.1336 (14)	0.2189 (9)	0.033 (4)*	0.096 (2)
H20'	0.1935	0.0690	0.2434	0.039*	0.096 (2)
O1'	0.1065 (19)	0.1428 (11)	0.1316 (6)	0.035 (3)*	0.096 (2)
H1'	0.0220	0.0896	0.1222	0.052*	0.096 (2)
C21'	−0.148 (3)	0.0902 (19)	0.2671 (11)	0.039 (5)*	0.096 (2)
H21'	−0.1966	0.0125	0.2494	0.047*	0.096 (2)
C22'	−0.124 (3)	0.0512 (14)	0.3604 (9)	0.036 (4)*	0.096 (2)
H22C	−0.2711	0.0409	0.3964	0.044*	0.096 (2)
H22D	−0.0383	−0.0339	0.3739	0.044*	0.096 (2)
C23'	−0.005 (3)	0.1654 (15)	0.3737 (10)	0.022 (4)*	0.096 (2)
H23C	−0.0666	0.1803	0.4300	0.027*	0.096 (2)
H23D	0.1519	0.1378	0.3743	0.027*	0.096 (2)
N2'	−0.016 (2)	0.2938 (14)	0.3109 (8)	0.021 (3)*	0.096 (2)
C24'	−0.240 (3)	0.3146 (15)	0.2931 (10)	0.022 (4)*	0.096 (2)
H24C	−0.2543	0.4049	0.2558	0.026*	0.096 (2)
H24D	−0.3418	0.3118	0.3465	0.026*	0.096 (2)
C25'	−0.310 (2)	0.2096 (15)	0.2506 (10)	0.036 (4)*	0.096 (2)
H25C	−0.4629	0.1816	0.2752	0.043*	0.096 (2)
H25D	−0.3038	0.2475	0.1893	0.043*	0.096 (2)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0196 (5)	0.0182 (5)	0.0198 (5)	−0.0002 (4)	−0.0017 (4)	−0.0068 (4)
O2	0.0274 (5)	0.0277 (5)	0.0337 (5)	−0.0079 (4)	−0.0019 (4)	−0.0166 (4)
O3	0.0178 (4)	0.0223 (4)	0.0242 (4)	−0.0048 (3)	−0.0004 (3)	−0.0073 (3)
C1	0.0183 (6)	0.0188 (6)	0.0211 (6)	−0.0006 (4)	−0.0034 (5)	−0.0034 (5)
C2	0.0179 (6)	0.0178 (5)	0.0182 (5)	−0.0005 (4)	−0.0045 (4)	−0.0027 (4)
C3	0.0180 (6)	0.0162 (5)	0.0174 (5)	0.0000 (4)	−0.0057 (4)	−0.0023 (4)
C4	0.0208 (6)	0.0173 (5)	0.0177 (5)	−0.0005 (4)	−0.0047 (4)	−0.0061 (4)
C5	0.0176 (6)	0.0194 (6)	0.0182 (5)	0.0007 (4)	−0.0028 (4)	−0.0058 (4)
C6	0.0177 (6)	0.0165 (5)	0.0178 (5)	−0.0008 (4)	−0.0060 (4)	−0.0033 (4)
C7	0.0209 (6)	0.0156 (5)	0.0192 (6)	0.0006 (4)	−0.0063 (5)	−0.0055 (4)
C8	0.0181 (6)	0.0169 (5)	0.0163 (5)	0.0018 (4)	−0.0039 (4)	−0.0038 (4)
C9	0.0186 (6)	0.0181 (6)	0.0194 (6)	0.0008 (4)	−0.0061 (5)	−0.0048 (4)
C10	0.0173 (6)	0.0235 (6)	0.0273 (6)	−0.0051 (5)	−0.0028 (5)	−0.0037 (5)
C11	0.0233 (6)	0.0190 (6)	0.0223 (6)	0.0025 (5)	−0.0014 (5)	−0.0088 (5)
C12	0.0206 (6)	0.0184 (6)	0.0179 (5)	−0.0025 (4)	0.0014 (4)	−0.0034 (4)
C13	0.0289 (7)	0.0210 (6)	0.0245 (6)	−0.0008 (5)	−0.0021 (5)	−0.0070 (5)
C14	0.0375 (8)	0.0316 (7)	0.0244 (7)	−0.0059 (6)	−0.0052 (6)	−0.0106 (5)
C15	0.0287 (7)	0.0395 (8)	0.0236 (6)	−0.0015 (6)	−0.0069 (5)	−0.0052 (6)
C16	0.0288 (7)	0.0320 (7)	0.0263 (7)	0.0078 (6)	−0.0034 (5)	−0.0049 (6)
C17	0.0300 (7)	0.0230 (6)	0.0218 (6)	0.0029 (5)	−0.0030 (5)	−0.0069 (5)
C18	0.0220 (6)	0.0209 (6)	0.0191 (6)	−0.0019 (5)	−0.0033 (5)	−0.0062 (5)
C19	0.0175 (7)	0.0211 (7)	0.0195 (7)	0.0005 (6)	−0.0064 (6)	−0.0048 (5)
C20	0.0179 (7)	0.0246 (7)	0.0207 (7)	−0.0037 (5)	−0.0028 (6)	−0.0082 (5)
O1	0.0232 (5)	0.0290 (6)	0.0325 (6)	−0.0072 (4)	0.0033 (4)	−0.0194 (5)
C21	0.0188 (7)	0.0180 (7)	0.0250 (8)	−0.0030 (5)	−0.0025 (6)	−0.0066 (6)
C22	0.0238 (8)	0.0230 (7)	0.0233 (7)	0.0025 (6)	−0.0058 (6)	−0.0035 (5)
C23	0.0242 (8)	0.0260 (9)	0.0215 (8)	−0.0027 (7)	−0.0035 (5)	−0.0095 (7)
N2	0.0193 (8)	0.0196 (6)	0.0230 (7)	−0.0018 (5)	−0.0001 (6)	−0.0055 (5)
C24	0.0156 (8)	0.0233 (8)	0.0344 (9)	0.0021 (6)	−0.0008 (6)	−0.0025 (6)
C25	0.0174 (7)	0.0251 (7)	0.0302 (8)	−0.0037 (5)	−0.0030 (5)	−0.0059 (6)

Geometric parameters (Å, º) top

N1—C1	1.3772 (15)	C19—C20	1.5204 (18)
N1—C8	1.3787 (15)	C20—O1	1.4296 (18)
N1—C11	1.4510 (15)	C20—C21	1.536 (2)
O2—C9	1.2174 (14)	C20—H20	1.0000
O3—C9	1.3334 (14)	O1—H1A	0.8400
O3—C10	1.4450 (14)	C21—C25	1.528 (2)
C1—C2	1.3771 (17)	C21—C22	1.533 (2)
C1—H1	0.9500	C21—H21	1.0000
C2—C3	1.4419 (16)	C22—C23	1.552 (2)
C2—C18	1.4583 (16)	C22—H22A	0.9900
C3—C4	1.4042 (16)	C22—H22B	0.9900
C3—C8	1.4185 (15)	C23—N2	1.483 (2)
C4—C5	1.3784 (16)	C23—H23A	0.9900
C4—H4	0.9500	C23—H23B	0.9900
C5—C6	1.4100 (15)	N2—C24	1.484 (2)
C5—H5	0.9500	C24—C25	1.545 (2)
C6—C7	1.3890 (16)	C24—H24A	0.9900
C6—C9	1.4819 (16)	C24—H24B	0.9900
C7—C8	1.3907 (16)	C25—H25A	0.9900
C7—H7	0.9500	C25—H25B	0.9900
C10—H10A	0.9800	C19'—N2'	1.473 (13)
C10—H10B	0.9800	C19'—C20'	1.532 (14)
C10—H10C	0.9800	C20'—O1'	1.410 (14)
C11—C12	1.5245 (17)	C20'—C21'	1.525 (16)
C11—H11A	0.9900	C20'—H20'	1.0000
C11—H11B	0.9900	O1'—H1'	0.8400
C12—C17	1.3894 (17)	C21'—C22'	1.530 (16)
C12—C13	1.3924 (17)	C21'—C25'	1.534 (16)
C13—C14	1.3871 (19)	C21'—H21'	1.0000
C13—H13	0.9500	C22'—C23'	1.511 (15)
C14—C15	1.386 (2)	C22'—H22C	0.9900
C14—H14	0.9500	C22'—H22D	0.9900
C15—C16	1.382 (2)	C23'—N2'	1.474 (14)
C15—H15	0.9500	C23'—H23C	0.9900
C16—C17	1.3906 (18)	C23'—H23D	0.9900
C16—H16	0.9500	N2'—C24'	1.449 (14)
C17—H17	0.9500	C24'—C25'	1.552 (15)
C18—C19'	1.317 (11)	C24'—H24C	0.9900
C18—C19	1.3414 (18)	C24'—H24D	0.9900
C18—H18	0.9500	C25'—H25C	0.9900
C19—N2	1.4473 (17)	C25'—H25D	0.9900

C1—N1—C8	108.58 (10)	C25—C21—C20	107.91 (15)
C1—N1—C11	125.67 (10)	C22—C21—C20	108.15 (13)
C8—N1—C11	124.84 (10)	C25—C21—H21	110.5
C9—O3—C10	116.16 (9)	C22—C21—H21	110.5
C2—C1—N1	110.67 (11)	C20—C21—H21	110.5
C2—C1—H1	124.7	C21—C22—C23	108.31 (12)
N1—C1—H1	124.7	C21—C22—H22A	110.0
C1—C2—C3	105.81 (10)	C23—C22—H22A	110.0
C1—C2—C18	129.80 (11)	C21—C22—H22B	110.0
C3—C2—C18	124.28 (11)	C23—C22—H22B	110.0
C4—C3—C8	118.63 (10)	H22A—C22—H22B	108.4
C4—C3—C2	134.05 (11)	N2—C23—C22	110.86 (12)
C8—C3—C2	107.24 (10)	N2—C23—H23A	109.5
C5—C4—C3	119.14 (10)	C22—C23—H23A	109.5
C5—C4—H4	120.4	N2—C23—H23B	109.5
C3—C4—H4	120.4	C22—C23—H23B	109.5
C4—C5—C6	121.22 (11)	H23A—C23—H23B	108.1
C4—C5—H5	119.4	C19—N2—C23	107.06 (13)
C6—C5—H5	119.4	C19—N2—C24	109.12 (13)
C7—C6—C5	121.04 (10)	C23—N2—C24	108.13 (12)
C7—C6—C9	117.76 (10)	N2—C24—C25	112.14 (12)
C5—C6—C9	121.20 (10)	N2—C24—H24A	109.2
C6—C7—C8	117.38 (10)	C25—C24—H24A	109.2
C6—C7—H7	121.3	N2—C24—H24B	109.2
C8—C7—H7	121.3	C25—C24—H24B	109.2
N1—C8—C7	129.70 (10)	H24A—C24—H24B	107.9
N1—C8—C3	107.67 (10)	C21—C25—C24	107.59 (12)
C7—C8—C3	122.56 (11)	C21—C25—H25A	110.2
O2—C9—O3	123.10 (11)	C24—C25—H25A	110.2
O2—C9—C6	124.16 (11)	C21—C25—H25B	110.2
O3—C9—C6	112.74 (9)	C24—C25—H25B	110.2
O3—C10—H10A	109.5	H25A—C25—H25B	108.5
O3—C10—H10B	109.5	C18—C19'—N2'	123.0 (10)
H10A—C10—H10B	109.5	C18—C19'—C20'	123.3 (9)
O3—C10—H10C	109.5	N2'—C19'—C20'	112.0 (9)
H10A—C10—H10C	109.5	O1'—C20'—C21'	114.7 (13)
H10B—C10—H10C	109.5	O1'—C20'—C19'	108.5 (11)
N1—C11—C12	113.36 (10)	C21'—C20'—C19'	107.0 (12)
N1—C11—H11A	108.9	O1'—C20'—H20'	108.8
C12—C11—H11A	108.9	C21'—C20'—H20'	108.8
N1—C11—H11B	108.9	C19'—C20'—H20'	108.8
C12—C11—H11B	108.9	C20'—O1'—H1'	109.5
H11A—C11—H11B	107.7	C20'—C21'—C22'	106.2 (13)
C17—C12—C13	118.55 (11)	C20'—C21'—C25'	108.6 (14)
C17—C12—C11	121.83 (11)	C22'—C21'—C25'	109.8 (14)
C13—C12—C11	119.62 (11)	C20'—C21'—H21'	110.7
C14—C13—C12	120.72 (12)	C22'—C21'—H21'	110.7
C14—C13—H13	119.6	C25'—C21'—H21'	110.7
C12—C13—H13	119.6	C23'—C22'—C21'	104.9 (12)
C15—C14—C13	120.31 (12)	C23'—C22'—H22C	110.8
C15—C14—H14	119.8	C21'—C22'—H22C	110.8
C13—C14—H14	119.8	C23'—C22'—H22D	110.8
C16—C15—C14	119.39 (12)	C21'—C22'—H22D	110.8
C16—C15—H15	120.3	H22C—C22'—H22D	108.8
C14—C15—H15	120.3	N2'—C23'—C22'	116.0 (12)
C15—C16—C17	120.38 (13)	N2'—C23'—H23C	108.3
C15—C16—H16	119.8	C22'—C23'—H23C	108.3
C17—C16—H16	119.8	N2'—C23'—H23D	108.3
C12—C17—C16	120.65 (12)	C22'—C23'—H23D	108.3
C12—C17—H17	119.7	H23C—C23'—H23D	107.4
C16—C17—H17	119.7	C24'—N2'—C23'	107.8 (12)
C19'—C18—C2	123.8 (5)	C24'—N2'—C19'	104.4 (11)
C19—C18—C2	128.40 (12)	C23'—N2'—C19'	105.6 (11)
C19'—C18—H18	115.1	N2'—C24'—C25'	113.8 (11)
C19—C18—H18	115.8	N2'—C24'—H24C	108.8
C2—C18—H18	115.8	C25'—C24'—H24C	108.8
C18—C19—N2	122.23 (12)	N2'—C24'—H24D	108.8
C18—C19—C20	123.71 (12)	C25'—C24'—H24D	108.8
N2—C19—C20	113.72 (11)	H24C—C24'—H24D	107.7
O1—C20—C19	109.43 (11)	C21'—C25'—C24'	106.2 (12)
O1—C20—C21	112.52 (13)	C21'—C25'—H25C	110.5
C19—C20—C21	106.93 (11)	C24'—C25'—H25C	110.5
O1—C20—H20	109.3	C21'—C25'—H25D	110.5
C19—C20—H20	109.3	C24'—C25'—H25D	110.5
C21—C20—H20	109.3	H25C—C25'—H25D	108.7
C25—C21—C22	109.07 (13)

C8—N1—C1—C2	−1.61 (13)	C2—C18—C19—C20	−175.48 (13)
C11—N1—C1—C2	−171.05 (10)	C18—C19—C20—O1	35.0 (2)
N1—C1—C2—C3	0.62 (13)	N2—C19—C20—O1	−138.42 (14)
N1—C1—C2—C18	176.88 (11)	C18—C19—C20—C21	157.16 (17)
C1—C2—C3—C4	177.33 (12)	N2—C19—C20—C21	−16.29 (19)
C18—C2—C3—C4	0.8 (2)	O1—C20—C21—C25	−171.58 (11)
C1—C2—C3—C8	0.56 (12)	C19—C20—C21—C25	68.25 (16)
C18—C2—C3—C8	−175.96 (10)	O1—C20—C21—C22	70.56 (15)
C8—C3—C4—C5	0.38 (16)	C19—C20—C21—C22	−49.60 (17)
C2—C3—C4—C5	−176.11 (12)	C25—C21—C22—C23	−51.32 (16)
C3—C4—C5—C6	0.94 (17)	C20—C21—C22—C23	65.79 (16)
C4—C5—C6—C7	−1.10 (17)	C21—C22—C23—N2	−13.47 (17)
C4—C5—C6—C9	178.01 (11)	C18—C19—N2—C23	−104.06 (18)
C5—C6—C7—C8	−0.11 (16)	C20—C19—N2—C23	69.50 (18)
C9—C6—C7—C8	−179.26 (10)	C18—C19—N2—C24	139.14 (17)
C1—N1—C8—C7	−175.07 (12)	C20—C19—N2—C24	−47.30 (18)
C11—N1—C8—C7	−5.52 (19)	C22—C23—N2—C19	−50.65 (16)
C1—N1—C8—C3	1.92 (12)	C22—C23—N2—C24	66.81 (15)
C11—N1—C8—C3	171.47 (10)	C19—N2—C24—C25	64.01 (16)
C6—C7—C8—N1	178.07 (11)	C23—N2—C24—C25	−52.12 (16)
C6—C7—C8—C3	1.47 (16)	C22—C21—C25—C24	65.38 (16)
C4—C3—C8—N1	−178.88 (10)	C20—C21—C25—C24	−51.89 (16)
C2—C3—C8—N1	−1.52 (12)	N2—C24—C25—C21	−12.01 (18)
C4—C3—C8—C7	−1.63 (17)	C19—C18—C19'—N2'	−82.4 (17)
C2—C3—C8—C7	175.73 (10)	C2—C18—C19'—N2'	27.3 (16)
C10—O3—C9—O2	−0.86 (16)	C19—C18—C19'—C20'	81.5 (17)
C10—O3—C9—C6	178.94 (9)	C2—C18—C19'—C20'	−168.7 (10)
C7—C6—C9—O2	1.15 (17)	C18—C19'—C20'—O1'	−16.1 (19)
C5—C6—C9—O2	−177.99 (11)	N2'—C19'—C20'—O1'	149.4 (13)
C7—C6—C9—O3	−178.65 (10)	C18—C19'—C20'—C21'	−140.4 (14)
C5—C6—C9—O3	2.21 (15)	N2'—C19'—C20'—C21'	25.1 (17)
C1—N1—C11—C12	98.55 (13)	O1'—C20'—C21'—C22'	165.5 (13)
C8—N1—C11—C12	−69.23 (14)	C19'—C20'—C21'—C22'	−74.1 (15)
N1—C11—C12—C17	−8.29 (16)	O1'—C20'—C21'—C25'	−76.4 (17)
N1—C11—C12—C13	171.63 (11)	C19'—C20'—C21'—C25'	44.0 (16)
C17—C12—C13—C14	0.46 (19)	C20'—C21'—C22'—C23'	48.1 (17)
C11—C12—C13—C14	−179.46 (12)	C25'—C21'—C22'—C23'	−69.2 (17)
C12—C13—C14—C15	−0.7 (2)	C21'—C22'—C23'—N2'	21 (2)
C13—C14—C15—C16	0.3 (2)	C22'—C23'—N2'—C24'	42.2 (18)
C14—C15—C16—C17	0.3 (2)	C22'—C23'—N2'—C19'	−68.9 (17)
C13—C12—C17—C16	0.21 (19)	C18—C19'—N2'—C24'	92.0 (15)
C11—C12—C17—C16	−179.87 (12)	C20'—C19'—N2'—C24'	−73.5 (15)
C15—C16—C17—C12	−0.6 (2)	C18—C19'—N2'—C23'	−154.4 (13)
C1—C2—C18—C19'	−32.0 (8)	C20'—C19'—N2'—C23'	40.0 (15)
C3—C2—C18—C19'	143.6 (8)	C23'—N2'—C24'—C25'	−64.7 (16)
C1—C2—C18—C19	−5.1 (2)	C19'—N2'—C24'—C25'	47.2 (16)
C3—C2—C18—C19	170.57 (14)	C20'—C21'—C25'—C24'	−67.2 (16)
C19'—C18—C19—N2	83.7 (14)	C22'—C21'—C25'—C24'	48.5 (17)
C2—C18—C19—N2	−2.6 (2)	N2'—C24'—C25'—C21'	18.4 (18)
C19'—C18—C19—C20	−89.2 (14)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···O2ⁱ	0.84	1.97	2.7989 (13)	169

Symmetry code: (i) x−1, y−1, z.

Experimental details

Crystal data
Chemical formula	C₂₅H₂₆N₂O₃
M_r	402.48
Crystal system, space group	Triclinic, P1
Temperature (K)	90
a, b, c (Å)	6.1619 (1), 10.3119 (2), 16.5959 (3)
α, β, γ (°)	75.6705 (7), 80.0939 (7), 85.9410 (7)
V (Å³)	1006.04 (3)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.28 × 0.22 × 0.12

Data collection
Diffractometer	Nonius KappaCCD diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	9126, 4597, 3831
R_int	0.024
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.102, 1.04
No. of reflections	4597
No. of parameters	312
No. of restraints	64
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.27, −0.20

Computer programs: COLLECT (Nonius, 1998), SCALEPACK (Otwinowski & Minor, 1997), DENZO-SMN (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 2008), XP in SHELXTL (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008) and local procedures.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···O2ⁱ	0.84	1.97	2.7989 (13)	169.4

Symmetry code: (i) x−1, y−1, z.

Acknowledgements

This investigation was supported by NIH/National Cancer Institute grant PO1 CA140409.

References

Amudhan, V., Reddy, Y. T., Sonar, V. N., Venkatraj, M., Crooks, P. A., Michael, L., Freeman, M. L. & Sekhar, K. R. (2010). Bioorg. Med. Chem. Lett. 20, 7323–7326. Web of Science PubMed Google Scholar
Nonius (1998). COLLECT. Nonius, BV, Delft, The Netherlands. Google Scholar
Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr and R. M. Sweet, pp. 307–326. New York: Academic Press. Google Scholar
Sekhar, K. R., Crooks, P. A., Sonar, V. N., Friedman, D. B., Chan, J. Y., Meredith, M. J., Stames, J. H., Kelton, K. R., Summar, S. R., Sasi, S. & Freeman, M. L. (2003). Cancer Res. 63, 5636–5645. Web of Science PubMed CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sonar, V. N., Parkin, S. & Crooks, P. A. (2004). Acta Cryst. C60, o659–o661. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Sonar, V. N., Reddy, Y. T., Sekhar, K. R., Sowmya, S., Freeman, M. L. & Crooks, P. A. (2007). Bioorg. Med. Chem. Lett. 17(24), 6821–6824. Web of Science CrossRef Google Scholar

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

rac-(Z)-Methyl 1-benzyl-3-[(3-hy­dr­oxy­quinuclidin-2-yl­­idene)meth­yl]-1H-indole-6-carboxyl­ate

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Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

rac-(Z)-Methyl 1-benzyl-3-[(3-hydroxyquinuclidin-2-ylidene)methyl]-1H-indole-6-carboxylate