organic compounds
4-Methoxy-N-(pyridin-4-ylmethyl)-3-(trifluoromethyl)benzamide monohydrate
aDepartment of Studies and Research in Chemistry, Tumkur University, Tumkur, Karnataka 572 103, India, bSolid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India, cDepartment of Studies and Research in Physics, U.C.S., Tumkur University, Tumkur, Karnataka 572 103, India, and dDepartment of Studies and Research in Chemistry, U.C.S., Tumkur University, Tumkur, Karnataka 572 103, India
*Correspondence e-mail: pasuchetan@yahoo.co.in
In the title compound, C15H13F3N2O2·H2O, the dihedral angle between the benzene and pyridine rings is 74.97 (1)°. The –CF3 group attached to the benzene ring is syn to the C=O bond in the adjacent side chain. In the crystal, molecules are linked to one another through the water molecules by strong N—H⋯O, O—H⋯O and O—H⋯N hydrogen bonds, forming a ladder-type network. The benzamide molecules are also linked to one another through C—H⋯F interactions, forming C(6) chains parallel to the b-axis direction. Aromatic π–π stacking interactions [centroid–centroid separations = 3.7150 (1) and 3.7857 (1) Å] between adjacent pairs of pyridine and benzene rings are also observed, resulting in a three-dimensional architecture are also observed.
CCDC reference: 967883
Related literature
For hydrogen-bond motifs, see: Bernstein et al. (1995). For the biological activity of see: Manojkumar et al. (2013a,b); Sreenivasa et al. (2013c). For the importance of containing trifluoromethyl substituents as pharmacophores, see: Sreenivasa et al. (2013a) and for providing structural rigidity to the molecules, see: Sreenivasa et al. (2013b).
Experimental
Crystal data
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Data collection: APEX2 (Bruker, 2009); cell APEX2 and SAINT-Plus (Bruker, 2009); data reduction: SAINT-Plus and XPREP (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97.
Supporting information
CCDC reference: 967883
10.1107/S1600536813029103/sj5360sup1.cif
contains datablocks I, New_Global_Publ_Block. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536813029103/sj5360Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536813029103/sj5360Isup3.cml
3-Tri-fluoromethyl-4-methoxy benzoic acid (1 mmol) and 1,1-carbonyldiimidazole (1.5 mmol) were dissolved in dichloroethane (5 ml) and heated to 45 oC for 30 min. 4-Aminomethyl pyridine (1.5 mmol) was added and the heating was continued for 4 h. The reaction was monitored by TLC. The organic layer was washed with sodium bicarbonate, dried using sodium sulfate and concentrated to yield the crude compound. This was further purified by
using petroleum ether / ethyl acetate (7:3) as Fine colorless crystals were grown by slow evaporation of the solvent system: petroleum ether / ethyl acetate (4:1) at room temperature.The hydrogen atoms attached to O3 were located in difference maps and refined in a rigid group. The remaining H atoms were positioned with idealized geometry using a riding model with N–H = 0.86 and C—H = 0.93 - 0.97 Å. The isotropic displacement parameters for all H atoms were set to 1.2 times Ueq of the parent atom or 1.5 times that of the parent atom for CH3.
Data collection: APEX2 (Bruker, 2009); cell
APEX2 and SAINT-Plus (Bruker, 2009); data reduction: SAINT-Plus and XPREP (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).Fig. 1. Molecular structure of the title compound, showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level. | |
Fig. 2. Linking of molecules in the crystal structure via water molecules, generating a ladder type network. H-atoms not involved in H-bonding are omitted. | |
Fig. 3. Linking of molecules into C(6) chains parallel to the b axis through C—H···F interactions. | |
Fig. 4. Aromatic π–π stacking interactions observed in the crystal structure. |
C15H13F3N2O2·H2O | F(000) = 340 |
Mr = 328.29 | Prism |
Triclinic, P1 | Dx = 1.427 Mg m−3 |
Hall symbol: -P 1 | Melting point: 485 K |
a = 7.2687 (13) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 7.8758 (14) Å | Cell parameters from 1167 reflections |
c = 14.177 (3) Å | θ = 1.5–25.0° |
α = 104.071 (10)° | µ = 0.12 mm−1 |
β = 99.672 (10)° | T = 296 K |
γ = 97.21 (1)° | Prism, colourless |
V = 764.2 (2) Å3 | 0.34 × 0.28 × 0.22 mm |
Z = 2 |
Bruker APEXII CCD diffractometer | 11967 independent reflections |
Radiation source: fine-focus sealed tube | 9619 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.000 |
ϕ and ω scans | θmax = 25.0°, θmin = 1.5° |
Absorption correction: ψ scan (SADABS; Bruker, 2009) | h = −8→8 |
Tmin = 0.959, Tmax = 0.973 | k = −9→9 |
11967 measured reflections | l = −16→16 |
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)] = 0.048 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.135 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0568P)2 + 0.2647P] where P = (Fo2 + 2Fc2)/3 |
11967 reflections | (Δ/σ)max = 0.001 |
212 parameters | Δρmax = 0.36 e Å−3 |
0 restraints | Δρmin = −0.34 e Å−3 |
C15H13F3N2O2·H2O | γ = 97.21 (1)° |
Mr = 328.29 | V = 764.2 (2) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.2687 (13) Å | Mo Kα radiation |
b = 7.8758 (14) Å | µ = 0.12 mm−1 |
c = 14.177 (3) Å | T = 296 K |
α = 104.071 (10)° | 0.34 × 0.28 × 0.22 mm |
β = 99.672 (10)° |
Bruker APEXII CCD diffractometer | 11967 independent reflections |
Absorption correction: ψ scan (SADABS; Bruker, 2009) | 9619 reflections with I > 2σ(I) |
Tmin = 0.959, Tmax = 0.973 | Rint = 0.000 |
11967 measured reflections |
R[F2 > 2σ(F2)] = 0.048 | 0 restraints |
wR(F2) = 0.135 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.36 e Å−3 |
11967 reflections | Δρmin = −0.34 e Å−3 |
212 parameters |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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. |
x | y | z | Uiso*/Ueq | ||
C4 | 0.20712 (13) | −0.16715 (12) | 0.35758 (7) | 0.0408 (2) | |
C1 | 0.26262 (13) | 0.00741 (12) | 0.56032 (7) | 0.0417 (3) | |
C6 | 0.24913 (15) | 0.10202 (13) | 0.48940 (8) | 0.0468 (3) | |
H6 | 0.2589 | 0.2249 | 0.5092 | 0.056* | |
C5 | 0.22150 (14) | 0.01550 (13) | 0.39008 (8) | 0.0468 (3) | |
H5 | 0.2123 | 0.0812 | 0.3437 | 0.056* | |
C7 | 0.2577 (2) | −0.28518 (15) | 0.60207 (9) | 0.0678 (4) | |
C3 | 0.22117 (14) | −0.26116 (13) | 0.42910 (8) | 0.0471 (3) | |
H3 | 0.2120 | −0.3840 | 0.4090 | 0.057* | |
C11 | 0.32767 (14) | −0.24851 (13) | 0.04242 (7) | 0.0430 (3) | |
C12 | 0.49099 (15) | −0.13759 (13) | 0.09862 (7) | 0.0471 (3) | |
H12 | 0.4928 | −0.0702 | 0.1626 | 0.057* | |
C9 | 0.18106 (15) | −0.26938 (14) | 0.25155 (8) | 0.0488 (3) | |
C2 | 0.24823 (14) | −0.17729 (13) | 0.52871 (8) | 0.0452 (3) | |
C10 | 0.14376 (16) | −0.26534 (16) | 0.07791 (8) | 0.0605 (3) | |
H10A | 0.0539 | −0.2148 | 0.0390 | 0.073* | |
H10B | 0.0931 | −0.3906 | 0.0649 | 0.073* | |
C13 | 0.65231 (16) | −0.12678 (14) | 0.05948 (8) | 0.0538 (3) | |
H13 | 0.7607 | −0.0502 | 0.0988 | 0.065* | |
C8 | 0.30246 (17) | 0.26947 (13) | 0.69388 (8) | 0.0567 (3) | |
H8A | 0.4111 | 0.3276 | 0.6766 | 0.085* | |
H8B | 0.3154 | 0.3032 | 0.7648 | 0.085* | |
H8C | 0.1901 | 0.3042 | 0.6635 | 0.085* | |
C14 | 0.50371 (19) | −0.32623 (15) | −0.08476 (9) | 0.0641 (3) | |
H14 | 0.5059 | −0.3927 | −0.1484 | 0.077* | |
C15 | 0.33680 (17) | −0.34444 (14) | −0.05187 (8) | 0.0558 (3) | |
H15 | 0.2301 | −0.4212 | −0.0929 | 0.067* | |
N1 | 0.15688 (12) | −0.18044 (12) | 0.18228 (6) | 0.0520 (2) | |
HN1 | 0.1489 | −0.0696 | 0.2003 | 0.062* | |
N2 | 0.66248 (14) | −0.21897 (12) | −0.03090 (7) | 0.0586 (3) | |
O1 | 0.28861 (11) | 0.08100 (9) | 0.65917 (5) | 0.0556 (2) | |
O3 | 0.89123 (14) | −0.17560 (10) | −0.17013 (7) | 0.0713 (3) | |
H1O | 0.8411 | −0.1809 | −0.1207 | 0.107* | |
H2O | 0.8934 | −0.2802 | −0.2039 | 0.107* | |
O2 | 0.18367 (14) | −0.43033 (10) | 0.22891 (6) | 0.0790 (3) | |
F1 | 0.12080 (15) | −0.27319 (12) | 0.65342 (7) | 0.1170 (3) | |
F2 | 0.41714 (13) | −0.23917 (11) | 0.67010 (6) | 0.1046 (3) | |
F3 | 0.24329 (18) | −0.45486 (10) | 0.55973 (6) | 0.1459 (5) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C4 | 0.0431 (6) | 0.0365 (6) | 0.0412 (6) | 0.0039 (5) | 0.0103 (5) | 0.0078 (5) |
C1 | 0.0483 (6) | 0.0381 (6) | 0.0362 (6) | 0.0054 (5) | 0.0060 (5) | 0.0083 (5) |
C6 | 0.0653 (7) | 0.0322 (6) | 0.0415 (7) | 0.0077 (5) | 0.0093 (5) | 0.0091 (5) |
C5 | 0.0609 (7) | 0.0417 (6) | 0.0386 (7) | 0.0070 (5) | 0.0096 (5) | 0.0136 (5) |
C7 | 0.1090 (11) | 0.0452 (8) | 0.0500 (8) | 0.0187 (7) | 0.0111 (8) | 0.0155 (6) |
C3 | 0.0574 (7) | 0.0307 (6) | 0.0511 (7) | 0.0058 (5) | 0.0106 (5) | 0.0082 (5) |
C11 | 0.0548 (6) | 0.0382 (6) | 0.0346 (6) | 0.0066 (5) | 0.0068 (5) | 0.0092 (5) |
C12 | 0.0563 (7) | 0.0476 (6) | 0.0328 (6) | 0.0076 (5) | 0.0047 (5) | 0.0060 (5) |
C9 | 0.0508 (6) | 0.0430 (7) | 0.0475 (7) | 0.0026 (5) | 0.0119 (5) | 0.0045 (6) |
C2 | 0.0566 (7) | 0.0360 (6) | 0.0444 (7) | 0.0081 (5) | 0.0089 (5) | 0.0142 (5) |
C10 | 0.0565 (7) | 0.0739 (8) | 0.0378 (7) | −0.0006 (6) | 0.0064 (5) | −0.0013 (6) |
C13 | 0.0532 (7) | 0.0541 (7) | 0.0490 (7) | 0.0039 (5) | 0.0024 (6) | 0.0124 (6) |
C8 | 0.0814 (8) | 0.0411 (6) | 0.0421 (7) | 0.0100 (6) | 0.0077 (6) | 0.0048 (5) |
C14 | 0.0830 (9) | 0.0553 (8) | 0.0476 (7) | 0.0037 (7) | 0.0236 (7) | −0.0009 (6) |
C15 | 0.0655 (8) | 0.0478 (7) | 0.0425 (7) | −0.0041 (6) | 0.0120 (6) | −0.0029 (5) |
N1 | 0.0636 (6) | 0.0506 (5) | 0.0366 (5) | 0.0064 (4) | 0.0126 (4) | 0.0026 (4) |
N2 | 0.0638 (6) | 0.0549 (6) | 0.0572 (7) | 0.0086 (5) | 0.0185 (5) | 0.0120 (5) |
O1 | 0.0865 (6) | 0.0409 (4) | 0.0364 (4) | 0.0108 (4) | 0.0067 (4) | 0.0091 (3) |
O3 | 0.0933 (6) | 0.0590 (5) | 0.0690 (6) | 0.0117 (5) | 0.0364 (5) | 0.0185 (4) |
O2 | 0.1277 (8) | 0.0419 (5) | 0.0609 (6) | 0.0138 (5) | 0.0235 (5) | −0.0004 (4) |
F1 | 0.1480 (8) | 0.1277 (8) | 0.1152 (7) | 0.0268 (6) | 0.0619 (7) | 0.0820 (6) |
F2 | 0.1252 (7) | 0.1093 (7) | 0.0871 (6) | 0.0239 (5) | −0.0084 (5) | 0.0600 (5) |
F3 | 0.3145 (16) | 0.0451 (5) | 0.0806 (6) | 0.0383 (6) | 0.0229 (7) | 0.0305 (4) |
C4—C5 | 1.3843 (13) | C12—H12 | 0.9300 |
C4—C3 | 1.3914 (13) | C9—O2 | 1.2331 (12) |
C4—C9 | 1.4903 (14) | C9—N1 | 1.3392 (13) |
C1—O1 | 1.3506 (12) | C10—N1 | 1.4495 (13) |
C1—C6 | 1.3875 (14) | C10—H10A | 0.9700 |
C1—C2 | 1.3989 (13) | C10—H10B | 0.9700 |
C6—C5 | 1.3753 (14) | C13—N2 | 1.3295 (14) |
C6—H6 | 0.9300 | C13—H13 | 0.9300 |
C5—H5 | 0.9300 | C8—O1 | 1.4305 (12) |
C7—F3 | 1.3079 (13) | C8—H8A | 0.9600 |
C7—F2 | 1.3240 (15) | C8—H8B | 0.9600 |
C7—F1 | 1.3279 (16) | C8—H8C | 0.9600 |
C7—C2 | 1.4929 (15) | C14—N2 | 1.3319 (15) |
C3—C2 | 1.3746 (14) | C14—C15 | 1.3743 (16) |
C3—H3 | 0.9300 | C14—H14 | 0.9300 |
C11—C12 | 1.3750 (14) | C15—H15 | 0.9300 |
C11—C15 | 1.3832 (14) | N1—HN1 | 0.8600 |
C11—C10 | 1.5072 (15) | O3—H1O | 0.8499 |
C12—C13 | 1.3808 (15) | O3—H2O | 0.8500 |
C5—C4—C3 | 117.63 (9) | C3—C2—C1 | 119.91 (9) |
C5—C4—C9 | 124.51 (9) | C3—C2—C7 | 119.49 (9) |
C3—C4—C9 | 117.85 (9) | C1—C2—C7 | 120.59 (10) |
O1—C1—C6 | 124.57 (9) | N1—C10—C11 | 115.26 (9) |
O1—C1—C2 | 116.78 (8) | N1—C10—H10A | 108.5 |
C6—C1—C2 | 118.65 (9) | C11—C10—H10A | 108.5 |
C5—C6—C1 | 120.53 (9) | N1—C10—H10B | 108.5 |
C5—C6—H6 | 119.7 | C11—C10—H10B | 108.5 |
C1—C6—H6 | 119.7 | H10A—C10—H10B | 107.5 |
C6—C5—C4 | 121.53 (9) | N2—C13—C12 | 124.12 (10) |
C6—C5—H5 | 119.2 | N2—C13—H13 | 117.9 |
C4—C5—H5 | 119.2 | C12—C13—H13 | 117.9 |
F3—C7—F2 | 106.29 (11) | O1—C8—H8A | 109.5 |
F3—C7—F1 | 105.41 (12) | O1—C8—H8B | 109.5 |
F2—C7—F1 | 104.90 (11) | H8A—C8—H8B | 109.5 |
F3—C7—C2 | 112.39 (10) | O1—C8—H8C | 109.5 |
F2—C7—C2 | 113.54 (11) | H8A—C8—H8C | 109.5 |
F1—C7—C2 | 113.58 (10) | H8B—C8—H8C | 109.5 |
C2—C3—C4 | 121.74 (9) | N2—C14—C15 | 123.86 (11) |
C2—C3—H3 | 119.1 | N2—C14—H14 | 118.1 |
C4—C3—H3 | 119.1 | C15—C14—H14 | 118.1 |
C12—C11—C15 | 116.65 (10) | C14—C15—C11 | 119.91 (11) |
C12—C11—C10 | 123.31 (10) | C14—C15—H15 | 120.0 |
C15—C11—C10 | 120.02 (9) | C11—C15—H15 | 120.0 |
C11—C12—C13 | 119.61 (10) | C9—N1—C10 | 121.98 (10) |
C11—C12—H12 | 120.2 | C9—N1—HN1 | 119.0 |
C13—C12—H12 | 120.2 | C10—N1—HN1 | 119.0 |
O2—C9—N1 | 121.38 (10) | C13—N2—C14 | 115.85 (10) |
O2—C9—C4 | 120.76 (10) | C1—O1—C8 | 118.17 (7) |
N1—C9—C4 | 117.85 (9) | H1O—O3—H2O | 109.5 |
O1—C1—C6—C5 | −179.63 (9) | F3—C7—C2—C3 | 1.81 (18) |
C2—C1—C6—C5 | 0.23 (15) | F2—C7—C2—C3 | 122.49 (12) |
C1—C6—C5—C4 | −0.29 (16) | F1—C7—C2—C3 | −117.75 (12) |
C3—C4—C5—C6 | 0.15 (15) | F3—C7—C2—C1 | −179.53 (12) |
C9—C4—C5—C6 | −178.73 (10) | F2—C7—C2—C1 | −58.85 (15) |
C5—C4—C3—C2 | 0.05 (15) | F1—C7—C2—C1 | 60.90 (15) |
C9—C4—C3—C2 | 179.00 (9) | C12—C11—C10—N1 | −10.41 (15) |
C15—C11—C12—C13 | 0.16 (14) | C15—C11—C10—N1 | 171.11 (10) |
C10—C11—C12—C13 | −178.37 (9) | C11—C12—C13—N2 | −0.43 (16) |
C5—C4—C9—O2 | 174.51 (10) | N2—C14—C15—C11 | −0.26 (18) |
C3—C4—C9—O2 | −4.36 (15) | C12—C11—C15—C14 | 0.16 (15) |
C5—C4—C9—N1 | −4.80 (15) | C10—C11—C15—C14 | 178.74 (10) |
C3—C4—C9—N1 | 176.33 (9) | O2—C9—N1—C10 | −3.73 (16) |
C4—C3—C2—C1 | −0.10 (16) | C4—C9—N1—C10 | 175.58 (9) |
C4—C3—C2—C7 | 178.57 (10) | C11—C10—N1—C9 | −93.86 (12) |
O1—C1—C2—C3 | 179.83 (9) | C12—C13—N2—C14 | 0.33 (16) |
C6—C1—C2—C3 | −0.04 (15) | C15—C14—N2—C13 | 0.02 (17) |
O1—C1—C2—C7 | 1.17 (15) | C6—C1—O1—C8 | 0.32 (15) |
C6—C1—C2—C7 | −178.69 (10) | C2—C1—O1—C8 | −179.53 (9) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—HN1···O3i | 0.86 | 2.12 | 2.9119 (14) | 152 |
O3—H1O···N2 | 0.85 | 2.01 | 2.8402 (15) | 166 |
O3—H2O···O2ii | 0.85 | 2.20 | 2.9646 (13) | 149 |
C6—H6···F3iii | 0.93 | 2.46 | 3.3963 (15) | 173 |
Symmetry codes: (i) −x+1, −y, −z; (ii) −x+1, −y−1, −z; (iii) x, y+1, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—HN1···O3i | 0.86 | 2.12 | 2.9119 (14) | 152 |
O3—H1O···N2 | 0.85 | 2.01 | 2.8402 (15) | 166 |
O3—H2O···O2ii | 0.85 | 2.20 | 2.9646 (13) | 149 |
C6—H6···F3iii | 0.93 | 2.46 | 3.3963 (15) | 173 |
Symmetry codes: (i) −x+1, −y, −z; (ii) −x+1, −y−1, −z; (iii) x, y+1, z. |
Acknowledgements
The authors thank Professor T. N. Guru Row, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, for his help and valuable suggestions.
References
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Amides containing trifluoromethyl substituents have been considered as important pharmacophores (Sreenivasa et al. 2013a). Amide groups are very common in nature, form easily and provide structural rigidity to molecules (Sreenivasa et al. 2013b). Amides show a broad spectrum of pharmacological properties, including antibacterial (Manojkumar et al. 2013a), anti-inflammatory, antioxidant, analgesic and antiviral activity (Manojkumar et al. 2013b, Sreenivasa et al. 2013c). Keeping this in mind, the crystal structure of the title compound was determined.
In the title compound, C15H13F3N2O2·H2O, the dihedral angle between the benzene ring and the pyridine ring is 74.97 (1)°. The –CF3 group attached to the benzene ring is syn to the C=O bond in the adjacent side chain. Further, the conformation of the N—H bond in the chain is anti with respect to the C=O bond. In the crystal structure, the molecules are linked to one another via water molecules through strong N1—HN1···O3, O3—H2O···O2 and O3—H1O···N2 hydrogen bonds, forming a ladder type network. The benzamide molecules are also linked to one another forming C(6) chains (Bernstein et al., 1995) parallel to the b axis through intermolecular C6—H6···F3 interactions. Further, aromatic π–π stacking interactions [centroid-centroid separations Cg1···Cg1 = 3.7150 (1) Å and Cg2···Cg2 = 3.7857 (1) Å] are also observed in the crystal structure. Cg1 and Cg2 are the centroids of the C11···C13,N2,C14,C15 and C1···C6 rings respectively.