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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 69| Part 7| July 2013| Pages o1013-o1014
https://doi.org/10.1107/S1600536813014177

Ethyl 2-[5-(4-fluoro­phen­yl)pyridin-3-yl]-1-[3-(2-oxopyrrolidin-1-yl)prop­yl]-1H-benzimidazole-5-carboxyl­ate

Keng Yoon Yeong,a Mohamed Ashraf Ali,a Tan Soo Choon,a Mohd Mustaqim Roslib and Ibrahim Abdul Razakb*‡

aInstitute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: arazaki@usm.my

(Received 20 May 2013; accepted 22 May 2013; online 8 June 2013)

In the title compound, C28H27FN4O3·H2O, the benzimidazole ring system is essentially planar with a maximum deviation of 0.028 (1) Å. It makes dihedral angles of 47.59 (5) and 60.31 (5)°, respectively, with the pyridine and benzene rings, which make a dihedral angle of 22.58 (6)° with each other. The pyrrolidine ring shows an envelope conformation with one of the methyl­ene C atoms as the flap. In the crystal, the components are connected into a tape along the b-axis direction through O—H⋯O and O—H⋯N hydrogen bonds and a π–π inter­action between the pyridine and benzene rings [centroid–centroid distance of 3.685 (8) Å]. The tapes are further linked into layers parallel to the ab plane by C—H⋯O and C—H⋯F inter­actions.

Related literature

For biological applications of benzimidazole derivatives, see: Tanious et al. (2004[Tanious, F. A., Hamelberg, D., Bailly, C., Czarny, A., Boykin, D. W. & Wilson, W. D. (2004). J. Am. Chem. Soc. 126, 143-153.]); Coburn et al. (1987[Coburn, R. A., Clark, M. T., Evans, R. T. & Genco, R. J. (1987). J. Med. Chem. 30, 205-208.]); Rao et al. (2002[Rao, A., Chimirri, A., Clercq, E. D., Monforte, A. M., Monforte, P., Pannecouque, C. & Zappala, M. (2002). Il Farmaco. 57, 819-823.]). For a related structure, see: Yoon et al. (2012[Yoon, Y. K., Ali, M. A., Choon, T. S., Asik, S. I. J. & Razak, I. A. (2012). Acta Cryst. E68, o59.]).

[Scheme 1]

Experimental

Crystal data

  • C28H27FN4O3·H2O

  • Mr = 504.55

  • Monoclinic, P 21 /c

  • a = 16.0640 (15) Å

  • b = 7.6562 (7) Å

  • c = 20.1991 (19) Å

  • β = 98.163 (2)°

  • V = 2459.1 (4) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 100 K

  • 0.35 × 0.33 × 0.21 mm
Data collection

  • Bruker APEX Duo CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.967, Tmax = 0.980

  • 24841 measured reflections

  • 6502 independent reflections

  • 5002 reflections with I > 2σ(I)

  • Rint = 0.037
Refinement

  • R[F2 > 2σ(F2)] = 0.042

  • wR(F2) = 0.113

  • S = 1.03

  • 6502 reflections

  • 343 parameters

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

  • Δρmax = 0.31 e Å−3

  • Δρmin = −0.25 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O1W—H1W1⋯O3 0.90 (2) 1.89 (2) 2.7881 (16) 174.3 (19)
O1W—H2W1⋯N2i 0.89 (2) 2.04 (2) 2.9309 (16) 175 (2)
C14—H14A⋯O1Wii 0.95 2.49 3.4368 (17) 173
C17—H17A⋯O2iii 0.95 2.45 3.1768 (17) 133
C27—H27A⋯O2iv 0.99 2.45 3.2749 (18) 141
C28—H28B⋯F1i 0.98 2.43 3.2851 (18) 145
Symmetry codes: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) x, y+1, z; (iii) x-1, y, z; (iv) [-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: https://doi.org/10.1107/S1600536813014177/is5275sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536813014177/is5275Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536813014177/is5275Isup3.cml

checkCIF report


Comment top

The benzimidazole core is a key building block for many biologically active compounds that play crucial roles in the function of a number of pharmacologically important molecules (Tanious et al., 2004). Substituted benzimidazoles with a wide range of activities such as antibacterial (Coburn et al., 1987) and anti-HIV (Rao et al., 2002) have been reported. As part of our ongoing structural studies of benzimidazole derivatives (Yoon et al., 2012), we now report the structure of the title compound.

In the title compound (Fig. 1), the benzimidazole ring (N1/N2/C1–C7) is planar with a maximum deviation of 0.028 (1) Å for atom N1. It makes dihedral angles of 47.69 (5) and 60.31 (5)°, respectively, with the pyridine (N3/C8–C12) and the benzene (C13–C18) rings. These two rings make a dihedral angle of 22.58 (6)° with each other. The pyrrolidine ring show a sign of envelope conformation with atom C23 at the flap, and with puckering parameters Q = 0.2695 (16) Å and φ = 81.9 (3)°.

In the crystal, the main molecule is connected to the water through O1W—H1W1···O3 and O1W—H2W1···N2i hydrogen bonds (Table 1). The molecules are further linked into a two-dimensional layer parallel to the ab plane by C14—H14A···O1Wii, C17—H17A···O2iii, C27—H27A···O2iv and C28—H28B···F1v interactions (Table 1). A π–π interaction observed between the pyridine (N3/C8–C12) and the benzene (C1–C6) rings with a centroid-centroid distance of 3.685 (8) Å (1 - x, 1/2 + y, 1/2 - z) further stabilizes the crystal structure.

Related literature top

For biological applications of benzimidazole derivatives, see: Tanious et al. (2004); Coburn et al. (1987); Rao et al. (2002). For a related structure, see: Yoon et al. (2012).

Experimental top

Ethyl 3-amino-4-(3-(2-oxopyrrolidin-1-yl)propylamino)benzoate (0.84 mmol) and sodium metabisulfite adduct of 5-(4-fluorophenyl)nicotinaldehyde (1.68 mmol) were dissolved in DMF. The reaction mixture was reflux at 130 °C for 2 hrs. After completion, the reaction mixture was diluted in Ethyl acetate (20 ml) and washed with water (20 ml). The organic layer was collected, dried over Na2SO4 and the evaporated in vacuo to yield the product. The product was recrystallized from ethyl acetate.

Refinement top

H atom in water molecules were located from difference Fourier maps and freely refined. The remaining H atoms were positioned geometrically and refined using a riding model with with C—H = 0.95–0.99 Å and Uiso(H) = 1.2Ueq(C) or 1.5Ueq(C) for methyl H atoms. A rotating group model was applied to the methyl group.

Structure description top

The benzimidazole core is a key building block for many biologically active compounds that play crucial roles in the function of a number of pharmacologically important molecules (Tanious et al., 2004). Substituted benzimidazoles with a wide range of activities such as antibacterial (Coburn et al., 1987) and anti-HIV (Rao et al., 2002) have been reported. As part of our ongoing structural studies of benzimidazole derivatives (Yoon et al., 2012), we now report the structure of the title compound.

In the title compound (Fig. 1), the benzimidazole ring (N1/N2/C1–C7) is planar with a maximum deviation of 0.028 (1) Å for atom N1. It makes dihedral angles of 47.69 (5) and 60.31 (5)°, respectively, with the pyridine (N3/C8–C12) and the benzene (C13–C18) rings. These two rings make a dihedral angle of 22.58 (6)° with each other. The pyrrolidine ring show a sign of envelope conformation with atom C23 at the flap, and with puckering parameters Q = 0.2695 (16) Å and φ = 81.9 (3)°.

In the crystal, the main molecule is connected to the water through O1W—H1W1···O3 and O1W—H2W1···N2i hydrogen bonds (Table 1). The molecules are further linked into a two-dimensional layer parallel to the ab plane by C14—H14A···O1Wii, C17—H17A···O2iii, C27—H27A···O2iv and C28—H28B···F1v interactions (Table 1). A π–π interaction observed between the pyridine (N3/C8–C12) and the benzene (C1–C6) rings with a centroid-centroid distance of 3.685 (8) Å (1 - x, 1/2 + y, 1/2 - z) further stabilizes the crystal structure.

For biological applications of benzimidazole derivatives, see: Tanious et al. (2004); Coburn et al. (1987); Rao et al. (2002). For a related structure, see: Yoon et al. (2012).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The asymmetric unit of the title compound, showing 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. A crystal packing view of the title compound. Dashed lines indicate hydrogen bonds. H atoms not involved in the hydrogen bond interactions have been omitted for clarity.
Ethyl 2-[5-(4-fluorophenyl)pyridine-3-yl]-1-[3-(2-oxopyrrolidin-1-yl)propyl] -1H-benzo[d]imidazole-5-carboxylate top
Crystal data top
C28H27FN4O3·H2OF(000) = 1064
Mr = 504.55Dx = 1.363 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 7659 reflections
a = 16.0640 (15) Åθ = 3.0–30.3°
b = 7.6562 (7) ŵ = 0.10 mm−1
c = 20.1991 (19) ÅT = 100 K
β = 98.163 (2)°Block, brown
V = 2459.1 (4) Å30.35 × 0.33 × 0.21 mm
Z = 4
Data collection top
Bruker APEX Duo CCD area-detector
diffractometer		6502 independent reflections
Radiation source: fine-focus sealed tube5002 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.037
φ and ω scansθmax = 29.0°, θmin = 1.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		h = −21→21
Tmin = 0.967, Tmax = 0.980k = −8→10
24841 measured reflectionsl = −25→27
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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.113H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.0504P)2 + 0.8415P]
where P = (Fo2 + 2Fc2)/3
6502 reflections(Δ/σ)max < 0.001
343 parametersΔρmax = 0.31 e Å−3
0 restraintsΔρmin = −0.25 e Å−3
Crystal data top
C28H27FN4O3·H2OV = 2459.1 (4) Å3
Mr = 504.55Z = 4
Monoclinic, P21/cMo Kα radiation
a = 16.0640 (15) ŵ = 0.10 mm−1
b = 7.6562 (7) ÅT = 100 K
c = 20.1991 (19) Å0.35 × 0.33 × 0.21 mm
β = 98.163 (2)°
Data collection top
Bruker APEX Duo CCD area-detector
diffractometer		6502 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		5002 reflections with I > 2σ(I)
Tmin = 0.967, Tmax = 0.980Rint = 0.037
24841 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0420 restraints
wR(F2) = 0.113H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.31 e Å−3
6502 reflectionsΔρmin = −0.25 e Å−3
343 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
F10.00660 (5)1.18506 (11)0.02501 (4)0.0277 (2)
O10.89089 (5)0.94479 (13)0.30464 (5)0.0235 (2)
O20.92597 (6)0.83605 (14)0.20908 (5)0.0283 (2)
O30.29289 (7)0.45959 (15)0.01770 (6)0.0368 (3)
N10.52774 (6)0.76622 (14)0.16989 (5)0.0155 (2)
N20.56706 (6)0.87671 (14)0.27305 (5)0.0170 (2)
N30.31735 (7)0.78858 (16)0.31867 (6)0.0205 (2)
N40.32987 (6)0.73537 (15)−0.01162 (5)0.0182 (2)
C10.61471 (7)0.77837 (16)0.17809 (6)0.0160 (2)
C20.67326 (8)0.73151 (17)0.13630 (7)0.0184 (3)
H2A0.65680.67950.09380.022*
C30.75670 (8)0.76529 (17)0.16049 (7)0.0193 (3)
H3A0.79870.73580.13370.023*
C40.78115 (7)0.84195 (17)0.22350 (7)0.0178 (3)
C50.72238 (7)0.88486 (17)0.26539 (7)0.0170 (2)
H5A0.73900.93600.30810.020*
C60.63811 (7)0.84952 (16)0.24192 (6)0.0159 (2)
C70.50329 (7)0.82625 (16)0.22826 (6)0.0156 (2)
C80.41508 (7)0.83587 (16)0.24061 (6)0.0158 (2)
C90.39447 (8)0.77708 (17)0.30149 (6)0.0182 (3)
H9A0.43760.72600.33250.022*
C100.25739 (8)0.85882 (18)0.27371 (7)0.0191 (3)
H10A0.20250.86880.28570.023*
C110.26951 (7)0.91840 (16)0.21053 (6)0.0160 (2)
C120.35139 (7)0.90683 (16)0.19441 (6)0.0163 (2)
H12A0.36340.94710.15230.020*
C130.19944 (7)0.99304 (16)0.16271 (6)0.0166 (2)
C140.21604 (8)1.10604 (17)0.11189 (7)0.0187 (3)
H14A0.27261.13790.10890.022*
C150.15166 (8)1.17301 (18)0.06552 (7)0.0203 (3)
H15A0.16341.24980.03110.024*
C160.07029 (8)1.12430 (18)0.07115 (7)0.0206 (3)
C170.05031 (8)1.01864 (18)0.12132 (7)0.0223 (3)
H17A−0.00660.99140.12470.027*
C180.11554 (8)0.95205 (18)0.16728 (7)0.0201 (3)
H18A0.10290.87780.20220.024*
C190.47650 (7)0.68575 (17)0.11211 (6)0.0162 (2)
H19A0.41860.66890.12230.019*
H19B0.49990.56930.10400.019*
C200.47344 (8)0.79563 (18)0.04903 (6)0.0188 (3)
H20A0.53130.81230.03850.023*
H20B0.45000.91210.05690.023*
C210.41947 (7)0.70879 (19)−0.01050 (7)0.0206 (3)
H21A0.43610.7557−0.05240.025*
H21B0.43120.5818−0.00930.025*
C220.29024 (8)0.90041 (19)−0.03556 (7)0.0236 (3)
H22A0.31300.9429−0.07570.028*
H22B0.29880.9913−0.00040.028*
C230.19705 (9)0.8521 (2)−0.05240 (8)0.0296 (3)
H23A0.16060.9487−0.04100.035*
H23B0.18240.8238−0.10050.035*
C240.18793 (9)0.6929 (2)−0.00927 (9)0.0352 (4)
H24A0.14570.6107−0.03220.042*
H24B0.17090.72700.03410.042*
C250.27508 (8)0.6116 (2)0.00055 (7)0.0245 (3)
C260.87277 (8)0.87268 (17)0.24398 (7)0.0204 (3)
C270.97999 (8)0.9758 (2)0.32679 (8)0.0273 (3)
H27A1.00331.05410.29500.033*
H27B1.01130.86420.32910.033*
C280.98829 (9)1.0583 (2)0.39429 (8)0.0316 (3)
H28A1.04701.09170.40840.047*
H28B0.97070.97500.42640.047*
H28C0.95261.16250.39240.047*
O1W0.41361 (6)0.24454 (14)0.08944 (6)0.0233 (2)
H1W10.3772 (12)0.315 (3)0.0644 (10)0.043 (5)*
H2W10.4181 (12)0.291 (3)0.1303 (12)0.050 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.0204 (4)0.0310 (5)0.0289 (5)0.0040 (3)−0.0065 (3)0.0031 (4)
O10.0147 (4)0.0285 (5)0.0262 (5)−0.0030 (4)−0.0004 (4)−0.0006 (4)
O20.0175 (4)0.0359 (6)0.0329 (6)−0.0010 (4)0.0080 (4)−0.0008 (5)
O30.0320 (6)0.0305 (6)0.0450 (7)−0.0029 (4)−0.0040 (5)0.0121 (5)
N10.0140 (5)0.0197 (5)0.0124 (5)0.0003 (4)0.0010 (4)0.0001 (4)
N20.0157 (5)0.0201 (5)0.0153 (5)0.0006 (4)0.0021 (4)0.0003 (4)
N30.0188 (5)0.0269 (6)0.0161 (6)−0.0010 (4)0.0030 (4)0.0006 (5)
N40.0148 (5)0.0238 (6)0.0155 (5)0.0014 (4)0.0005 (4)−0.0001 (4)
C10.0148 (5)0.0173 (6)0.0155 (6)0.0005 (4)0.0011 (4)0.0031 (5)
C20.0191 (6)0.0211 (6)0.0151 (6)0.0021 (5)0.0027 (5)0.0015 (5)
C30.0182 (6)0.0211 (6)0.0197 (7)0.0028 (5)0.0059 (5)0.0043 (5)
C40.0154 (5)0.0180 (6)0.0196 (7)0.0009 (4)0.0012 (5)0.0046 (5)
C50.0166 (6)0.0177 (6)0.0160 (6)−0.0002 (4)−0.0006 (4)0.0016 (5)
C60.0161 (5)0.0163 (6)0.0153 (6)0.0008 (4)0.0020 (4)0.0022 (5)
C70.0163 (5)0.0168 (6)0.0135 (6)0.0011 (4)0.0017 (4)0.0022 (5)
C80.0150 (5)0.0178 (6)0.0147 (6)−0.0013 (4)0.0019 (4)−0.0030 (5)
C90.0187 (6)0.0224 (6)0.0134 (6)0.0000 (5)0.0013 (4)−0.0006 (5)
C100.0161 (6)0.0238 (6)0.0181 (6)−0.0015 (5)0.0043 (5)−0.0014 (5)
C110.0150 (5)0.0170 (6)0.0158 (6)−0.0014 (4)0.0014 (4)−0.0022 (5)
C120.0168 (5)0.0184 (6)0.0136 (6)−0.0011 (4)0.0021 (4)−0.0008 (5)
C130.0151 (5)0.0188 (6)0.0157 (6)−0.0004 (4)0.0014 (4)−0.0037 (5)
C140.0157 (5)0.0211 (6)0.0195 (7)−0.0008 (4)0.0030 (5)−0.0020 (5)
C150.0211 (6)0.0221 (6)0.0178 (7)0.0015 (5)0.0028 (5)0.0002 (5)
C160.0171 (6)0.0226 (6)0.0205 (7)0.0042 (5)−0.0031 (5)−0.0027 (5)
C170.0146 (5)0.0266 (7)0.0253 (7)−0.0002 (5)0.0009 (5)−0.0011 (6)
C180.0169 (6)0.0236 (7)0.0199 (7)−0.0019 (5)0.0026 (5)0.0006 (5)
C190.0162 (5)0.0188 (6)0.0131 (6)−0.0005 (4)0.0007 (4)−0.0013 (5)
C200.0162 (6)0.0258 (7)0.0141 (6)−0.0028 (5)0.0007 (4)0.0010 (5)
C210.0143 (5)0.0335 (7)0.0140 (6)0.0016 (5)0.0020 (4)−0.0020 (6)
C220.0247 (6)0.0231 (7)0.0225 (7)0.0036 (5)0.0009 (5)0.0001 (6)
C230.0215 (6)0.0345 (8)0.0306 (8)0.0084 (6)−0.0038 (6)−0.0057 (7)
C240.0166 (6)0.0444 (9)0.0438 (10)−0.0016 (6)0.0016 (6)0.0020 (8)
C250.0200 (6)0.0298 (7)0.0224 (7)−0.0022 (5)−0.0016 (5)0.0020 (6)
C260.0171 (6)0.0187 (6)0.0257 (7)−0.0005 (5)0.0034 (5)0.0047 (5)
C270.0143 (6)0.0300 (7)0.0361 (9)−0.0045 (5)−0.0017 (5)0.0020 (6)
C280.0267 (7)0.0277 (8)0.0370 (9)−0.0032 (6)−0.0068 (6)0.0037 (7)
O1W0.0215 (5)0.0276 (5)0.0209 (5)−0.0001 (4)0.0031 (4)−0.0023 (4)
Geometric parameters (Å, º) top
F1—C161.3642 (14)C13—C181.3996 (17)
O1—C261.3378 (17)C14—C151.3910 (18)
O1—C271.4571 (15)C14—H14A0.9500
O2—C261.2152 (16)C15—C161.3793 (18)
O3—C251.2358 (18)C15—H15A0.9500
N1—C71.3737 (16)C16—C171.370 (2)
N1—C11.3864 (15)C17—C181.3939 (18)
N1—C191.4652 (15)C17—H17A0.9500
N2—C71.3244 (15)C18—H18A0.9500
N2—C61.3946 (16)C19—C201.5216 (18)
N3—C91.3362 (16)C19—H19A0.9900
N3—C101.3391 (17)C19—H19B0.9900
N4—C251.3398 (18)C20—C211.5309 (18)
N4—C211.4506 (15)C20—H20A0.9900
N4—C221.4658 (17)C20—H20B0.9900
C1—C21.3968 (18)C21—H21A0.9900
C1—C61.4010 (18)C21—H21B0.9900
C2—C31.3844 (17)C22—C231.5327 (19)
C2—H2A0.9500C22—H22A0.9900
C3—C41.4060 (19)C22—H22B0.9900
C3—H3A0.9500C23—C241.517 (2)
C4—C51.3934 (18)C23—H23A0.9900
C4—C261.4899 (17)C23—H23B0.9900
C5—C61.3959 (16)C24—C251.519 (2)
C5—H5A0.9500C24—H24A0.9900
C7—C81.4751 (16)C24—H24B0.9900
C8—C91.3928 (18)C27—C281.491 (2)
C8—C121.3934 (17)C27—H27A0.9900
C9—H9A0.9500C27—H27B0.9900
C10—C111.3947 (18)C28—H28A0.9800
C10—H10A0.9500C28—H28B0.9800
C11—C121.4021 (17)C28—H28C0.9800
C11—C131.4891 (17)O1W—H1W10.90 (2)
C12—H12A0.9500O1W—H2W10.89 (2)
C13—C141.3968 (19)
C26—O1—C27115.15 (11)C18—C17—H17A120.8
C7—N1—C1106.33 (10)C17—C18—C13120.93 (13)
C7—N1—C19128.87 (10)C17—C18—H18A119.5
C1—N1—C19124.47 (10)C13—C18—H18A119.5
C7—N2—C6104.58 (10)N1—C19—C20112.47 (10)
C9—N3—C10117.03 (12)N1—C19—H19A109.1
C25—N4—C21125.03 (12)C20—C19—H19A109.1
C25—N4—C22113.87 (11)N1—C19—H19B109.1
C21—N4—C22120.64 (11)C20—C19—H19B109.1
N1—C1—C2131.62 (12)H19A—C19—H19B107.8
N1—C1—C6105.67 (11)C19—C20—C21111.41 (11)
C2—C1—C6122.71 (11)C19—C20—H20A109.3
C3—C2—C1116.11 (12)C21—C20—H20A109.3
C3—C2—H2A121.9C19—C20—H20B109.3
C1—C2—H2A121.9C21—C20—H20B109.3
C2—C3—C4121.97 (12)H20A—C20—H20B108.0
C2—C3—H3A119.0N4—C21—C20113.66 (11)
C4—C3—H3A119.0N4—C21—H21A108.8
C5—C4—C3121.45 (11)C20—C21—H21A108.8
C5—C4—C26121.46 (12)N4—C21—H21B108.8
C3—C4—C26117.08 (11)C20—C21—H21B108.8
C4—C5—C6117.14 (12)H21A—C21—H21B107.7
C4—C5—H5A121.4N4—C22—C23103.29 (11)
C6—C5—H5A121.4N4—C22—H22A111.1
N2—C6—C5129.37 (12)C23—C22—H22A111.1
N2—C6—C1110.07 (10)N4—C22—H22B111.1
C5—C6—C1120.55 (11)C23—C22—H22B111.1
N2—C7—N1113.34 (10)H22A—C22—H22B109.1
N2—C7—C8122.57 (11)C24—C23—C22103.74 (11)
N1—C7—C8124.09 (11)C24—C23—H23A111.0
C9—C8—C12118.26 (11)C22—C23—H23A111.0
C9—C8—C7119.18 (11)C24—C23—H23B111.0
C12—C8—C7122.53 (11)C22—C23—H23B111.0
N3—C9—C8123.60 (12)H23A—C23—H23B109.0
N3—C9—H9A118.2C23—C24—C25104.00 (12)
C8—C9—H9A118.2C23—C24—H24A111.0
N3—C10—C11124.86 (11)C25—C24—H24A111.0
N3—C10—H10A117.6C23—C24—H24B111.0
C11—C10—H10A117.6C25—C24—H24B111.0
C10—C11—C12116.70 (11)H24A—C24—H24B109.0
C10—C11—C13121.88 (11)O3—C25—N4125.84 (13)
C12—C11—C13121.41 (11)O3—C25—C24126.49 (13)
C8—C12—C11119.53 (12)N4—C25—C24107.66 (13)
C8—C12—H12A120.2O2—C26—O1123.17 (12)
C11—C12—H12A120.2O2—C26—C4123.42 (13)
C14—C13—C18118.25 (11)O1—C26—C4113.41 (11)
C14—C13—C11120.58 (11)O1—C27—C28107.83 (12)
C18—C13—C11121.16 (12)O1—C27—H27A110.1
C15—C14—C13121.46 (11)C28—C27—H27A110.1
C15—C14—H14A119.3O1—C27—H27B110.1
C13—C14—H14A119.3C28—C27—H27B110.1
C16—C15—C14117.87 (13)H27A—C27—H27B108.5
C16—C15—H15A121.1C27—C28—H28A109.5
C14—C15—H15A121.1C27—C28—H28B109.5
F1—C16—C17118.35 (11)H28A—C28—H28B109.5
F1—C16—C15118.63 (12)C27—C28—H28C109.5
C17—C16—C15123.02 (12)H28A—C28—H28C109.5
C16—C17—C18118.40 (12)H28B—C28—H28C109.5
C16—C17—H17A120.8H1W1—O1W—H2W1104.2 (18)
C7—N1—C1—C2177.83 (13)C13—C11—C12—C8−179.92 (11)
C19—N1—C1—C23.9 (2)C10—C11—C13—C14156.88 (13)
C7—N1—C1—C6−1.04 (13)C12—C11—C13—C14−22.24 (18)
C19—N1—C1—C6−174.99 (11)C10—C11—C13—C18−23.22 (19)
N1—C1—C2—C3178.99 (13)C12—C11—C13—C18157.65 (13)
C6—C1—C2—C3−2.30 (19)C18—C13—C14—C15−1.8 (2)
C1—C2—C3—C40.13 (19)C11—C13—C14—C15178.05 (12)
C2—C3—C4—C51.2 (2)C13—C14—C15—C160.0 (2)
C2—C3—C4—C26−179.73 (12)C14—C15—C16—F1−178.27 (12)
C3—C4—C5—C6−0.41 (19)C14—C15—C16—C172.3 (2)
C26—C4—C5—C6−179.42 (11)F1—C16—C17—C18178.03 (12)
C7—N2—C6—C5177.95 (13)C15—C16—C17—C18−2.5 (2)
C7—N2—C6—C1−1.19 (14)C16—C17—C18—C130.5 (2)
C4—C5—C6—N2179.24 (12)C14—C13—C18—C171.6 (2)
C4—C5—C6—C1−1.70 (18)C11—C13—C18—C17−178.31 (12)
N1—C1—C6—N21.40 (14)C7—N1—C19—C20115.93 (14)
C2—C1—C6—N2−177.59 (12)C1—N1—C19—C20−71.54 (15)
N1—C1—C6—C5−177.83 (11)N1—C19—C20—C21−179.93 (10)
C2—C1—C6—C53.18 (19)C25—N4—C21—C20−109.17 (15)
C6—N2—C7—N10.52 (14)C22—N4—C21—C2079.12 (15)
C6—N2—C7—C8−179.04 (11)C19—C20—C21—N480.43 (14)
C1—N1—C7—N20.34 (14)C25—N4—C22—C23−12.33 (16)
C19—N1—C7—N2173.93 (12)C21—N4—C22—C23160.26 (12)
C1—N1—C7—C8179.89 (11)N4—C22—C23—C2423.99 (15)
C19—N1—C7—C8−6.5 (2)C22—C23—C24—C25−26.92 (16)
N2—C7—C8—C9−45.73 (18)C21—N4—C25—O33.8 (2)
N1—C7—C8—C9134.76 (13)C22—N4—C25—O3176.05 (14)
N2—C7—C8—C12132.21 (13)C21—N4—C25—C24−177.20 (12)
N1—C7—C8—C12−47.30 (19)C22—N4—C25—C24−4.99 (17)
C10—N3—C9—C80.9 (2)C23—C24—C25—O3−160.64 (15)
C12—C8—C9—N3−1.57 (19)C23—C24—C25—N420.41 (17)
C7—C8—C9—N3176.45 (12)C27—O1—C26—O2−0.48 (19)
C9—N3—C10—C110.8 (2)C27—O1—C26—C4179.56 (11)
N3—C10—C11—C12−1.7 (2)C5—C4—C26—O2179.52 (13)
N3—C10—C11—C13179.17 (12)C3—C4—C26—O20.5 (2)
C9—C8—C12—C110.57 (18)C5—C4—C26—O1−0.52 (18)
C7—C8—C12—C11−177.39 (11)C3—C4—C26—O1−179.57 (11)
C10—C11—C12—C80.91 (18)C26—O1—C27—C28179.18 (12)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1W—H1W1···O30.90 (2)1.89 (2)2.7881 (16)174.3 (19)
O1W—H2W1···N2i0.89 (2)2.04 (2)2.9309 (16)175 (2)
C14—H14A···O1Wii0.952.493.4368 (17)173
C17—H17A···O2iii0.952.453.1768 (17)133
C27—H27A···O2iv0.992.453.2749 (18)141
C28—H28B···F1i0.982.433.2851 (18)145
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) x, y+1, z; (iii) x−1, y, z; (iv) −x+2, y+1/2, −z+1/2.

Experimental details

Crystal data
Chemical formulaC28H27FN4O3·H2O
Mr504.55
Crystal system, space groupMonoclinic, P21/c
Temperature (K)100
a, b, c (Å)16.0640 (15), 7.6562 (7), 20.1991 (19)
β (°) 98.163 (2)
V (Å3)2459.1 (4)
Z4
Radiation typeMo Kα
µ (mm−1)0.10
Crystal size (mm)0.35 × 0.33 × 0.21
Data collection
DiffractometerBruker APEX Duo CCD area-detector
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.967, 0.980
No. of measured, independent and
observed [I > 2σ(I)] reflections		24841, 6502, 5002
Rint0.037
(sin θ/λ)max (Å−1)0.682
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.113, 1.03
No. of reflections6502
No. of parameters343
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.31, −0.25

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1W—H1W1···O30.90 (2)1.89 (2)2.7881 (16)174.3 (19)
O1W—H2W1···N2i0.89 (2)2.04 (2)2.9309 (16)175 (2)
C14—H14A···O1Wii0.952.493.4368 (17)173
C17—H17A···O2iii0.952.453.1768 (17)133
C27—H27A···O2iv0.992.453.2749 (18)141
C28—H28B···F1i0.982.433.2851 (18)145
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) x, y+1, z; (iii) x−1, y, z; (iv) −x+2, y+1/2, −z+1/2.
 

Footnotes

‡Thomson Reuters ResearcherID: A-5599-2009.

Acknowledgements

The authors would like to express their gratitude to Pharmacogenetic and Novel Therapeutic Research, Institute for Research in Mol­ecular Medicine and Department of Pharmacology, School of Pharmaceutical Sciences, Universiti Sains Malaysia (USM). This work was funded through Research Grant No. RUC 1001/PSK/8620012 and HiCoE Research Grant No. 311.CIPPM.4401005. IAR also thanks USM for the Short Term Grant No. 304/PFIZIK/6312078.

References

First citationBruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationCoburn, R. A., Clark, M. T., Evans, R. T. & Genco, R. J. (1987). J. Med. Chem. 30, 205–208.  CrossRef CAS PubMed Web of Science Google Scholar
 First citationRao, A., Chimirri, A., Clercq, E. D., Monforte, A. M., Monforte, P., Pannecouque, C. & Zappala, M. (2002). Il Farmaco. 57, 819–823.  Web of Science CrossRef PubMed CAS Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationTanious, F. A., Hamelberg, D., Bailly, C., Czarny, A., Boykin, D. W. & Wilson, W. D. (2004). J. Am. Chem. Soc. 126, 143–153.  Web of Science CrossRef PubMed CAS Google Scholar
 First citationYoon, Y. K., Ali, M. A., Choon, T. S., Asik, S. I. J. & Razak, I. A. (2012). Acta Cryst. E68, o59.  Web of Science CSD CrossRef IUCr Journals Google Scholar

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ISSN: 2056-9890
Volume 69| Part 7| July 2013| Pages o1013-o1014
https://doi.org/10.1107/S1600536813014177
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