organic compounds
2,2,2-Trifluoro-N-(isoquinolin-5-ylmethyl)acetamide
aDepartment of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland
*Correspondence e-mail: a.r.kennedy@strath.ac.uk
The molecular structure of the title compound at 123 K, C12H9F3N2O, presents a rotationally disordered CF3 group. Hydrogen bonds between the amide NH group and the N atom of the isoquinoline form a chain in the b-axis direction. The packed structure forms alternate layers of isoquinoline and amide groups parallel to the ab plane.
Related literature
In the search for biologically active compounds in the area of anti-inflammatory and pain relief drugs, we have found a class of compounds that act as potent antagonists or agonists of the vanilloid VR1 receptor. These have been shown to be useful in the treatment and prevention of inflammatory and other pain conditions in mammals, see: Jetter et al. (2007, 2008); Codd et al. (2003). The title compound was prepared as a precursor for more complex compounds. For analysis of the structures of analogous naphthalenes, see: Weinstein & Leiserowitz (1980). For a discussion on disorder in crystal structures, see: Müller (2009).
Experimental
Crystal data
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Refinement
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Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.
Supporting information
10.1107/S1600536809052994/tk2599sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809052994/tk2599Isup2.hkl
Isoquinoline (1.29 g, 10 mmol) in concentrated sulfuric acid (50 ml) was cooled to 293 K. n-Hydroxymethyl trifluoroacetamide (1.43 g, 10.00 mmol) was added in portions. After 15 min, the reaction mixture was allowed to warm to room temperature and stirred for 16 h. The clear light-brown reaction mixture was then poured onto 200 g of ice, then concentrated ammonium hydroxide was added dropwise until the reaction mixture was basic to pH paper. After extraction with 100 ml of dichloromethane, the organic layer was washed (2 x 100 ml brine), dried over MgSO4 and then evaporated under reduced pressure. The residue was applied to a silica gel column and eluted with 1:2 ethyl acetate:hexane [RF = 1/5]. This gave the product as a crystalline solid (2.03 g, 80%), m.p. 435 - 438 K. IR (KBr): 1716, 1624, 1563, 1380, 1211, 1141, 1034, 832, 755, 707 cm -1. 1H NMR (DMSO-d6): 10.08 (1H, s), 9.35 (1H, d, J = 0.8 Hz), 8.57 (1H, d, J = 6.0 Hz), 8.10 (1H, dd, J = 6.9 & 1.9 Hz), 7.96 (1H, d, J = 6.0 Hz), 7.71–7.65 (2H, m), 4.85 (2H, s) ppm.
The F atoms of the CF3 group are disordered by rotation about the C2—C1 bond. After several trial calculations, a model with three separate groups of F atom positions was adopted. Site occupancy factors are 0.5 for F1 to F3, 0.3 for F4 to F6 and 0.2 for F7 to F9. Only F1 to F3 were refined anisotropically. Restraints were placed on the C—F distances (1.33 Å) and to encourage similarity in the F atom Uij values (Müller, 2009).
The amide-H atom was found by difference synthesis and refined isotropically. All other H atoms were positioned geometrically at distances of 0.95 and 0.99 Å from the parent C atom for CH and CH2 groups respectively. For these atoms, a riding model was used with Uiso(H) values constrained to be 1.2 times Ueq of the parent C atom.
Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell
CrysAlis CCD (Oxford Diffraction, 2007); data reduction: CrysAlis RED (Oxford Diffraction, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).C12H9F3N2O | F(000) = 520 |
Mr = 254.21 | Dx = 1.540 Mg m−3 |
Monoclinic, P21/c | Melting point = 435–438 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 7.2308 (7) Å | Cell parameters from 1879 reflections |
b = 8.3498 (11) Å | θ = 2.7–30.1° |
c = 18.157 (2) Å | µ = 0.14 mm−1 |
β = 90.583 (9)° | T = 123 K |
V = 1096.2 (2) Å3 | Blade, colourless |
Z = 4 | 0.45 × 0.12 × 0.02 mm |
Oxford Diffraction Xcalibur S diffractometer | 2071 independent reflections |
Radiation source: fine-focus sealed tube | 1346 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.031 |
Detector resolution: 16.0268 pixels mm-1 | θmax = 26.0°, θmin = 2.7° |
ω scans | h = −8→8 |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007) | k = −10→9 |
Tmin = 0.717, Tmax = 1.000 | l = −21→22 |
4377 measured reflections |
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)] = 0.051 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.133 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0703P)2 + 0.0571P] where P = (Fo2 + 2Fc2)/3 |
2071 reflections | (Δ/σ)max < 0.001 |
191 parameters | Δρmax = 0.30 e Å−3 |
111 restraints | Δρmin = −0.45 e Å−3 |
C12H9F3N2O | V = 1096.2 (2) Å3 |
Mr = 254.21 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 7.2308 (7) Å | µ = 0.14 mm−1 |
b = 8.3498 (11) Å | T = 123 K |
c = 18.157 (2) Å | 0.45 × 0.12 × 0.02 mm |
β = 90.583 (9)° |
Oxford Diffraction Xcalibur S diffractometer | 2071 independent reflections |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007) | 1346 reflections with I > 2σ(I) |
Tmin = 0.717, Tmax = 1.000 | Rint = 0.031 |
4377 measured reflections |
R[F2 > 2σ(F2)] = 0.051 | 111 restraints |
wR(F2) = 0.133 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.30 e Å−3 |
2071 reflections | Δρmin = −0.45 e Å−3 |
191 parameters |
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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
F1 | −0.3651 (5) | 0.3984 (6) | 1.0372 (2) | 0.0468 (10) | 0.50 |
F2 | −0.3741 (5) | 0.3253 (6) | 0.92452 (18) | 0.0266 (10) | 0.50 |
F3 | −0.3909 (5) | 0.1505 (5) | 1.0096 (3) | 0.0490 (10) | 0.50 |
F4 | −0.3837 (11) | 0.2632 (9) | 0.9261 (3) | 0.042 (2)* | 0.30 |
F5 | −0.3858 (10) | 0.2219 (12) | 1.0445 (4) | 0.0590 (19)* | 0.30 |
F6 | −0.3263 (9) | 0.4512 (6) | 1.0002 (4) | 0.0530 (17)* | 0.30 |
F7 | −0.3639 (12) | 0.3146 (15) | 1.0568 (3) | 0.031 (2)* | 0.20 |
F8 | −0.3620 (17) | 0.3826 (12) | 0.9363 (5) | 0.044 (3)* | 0.20 |
F9 | −0.3770 (13) | 0.1449 (9) | 0.9730 (6) | 0.043 (2)* | 0.20 |
O1 | −0.0083 (3) | 0.3065 (3) | 1.04575 (11) | 0.0574 (7) | |
N1 | −0.0214 (3) | 0.2113 (3) | 0.92904 (12) | 0.0269 (5) | |
N2 | 0.2036 (3) | 0.5534 (3) | 0.69021 (12) | 0.0323 (6) | |
C1 | −0.3025 (3) | 0.2895 (3) | 0.98984 (12) | 0.0345 (7) | |
C2 | −0.0925 (4) | 0.2699 (3) | 0.99042 (14) | 0.0323 (7) | |
C3 | 0.1779 (3) | 0.1840 (3) | 0.92121 (13) | 0.0291 (6) | |
H3A | 0.2135 | 0.0859 | 0.9485 | 0.035* | |
H3B | 0.2465 | 0.2752 | 0.9431 | 0.035* | |
C4 | 0.2312 (3) | 0.1660 (3) | 0.84124 (13) | 0.0248 (6) | |
C5 | 0.2834 (3) | 0.0198 (3) | 0.81357 (14) | 0.0285 (6) | |
H5 | 0.2895 | −0.0697 | 0.8458 | 0.034* | |
C6 | 0.3287 (3) | −0.0013 (4) | 0.73828 (13) | 0.0297 (6) | |
H6 | 0.3651 | −0.1039 | 0.7211 | 0.036* | |
C7 | 0.3203 (3) | 0.1237 (3) | 0.69074 (13) | 0.0294 (6) | |
H7 | 0.3497 | 0.1090 | 0.6403 | 0.035* | |
C8 | 0.2672 (3) | 0.2763 (3) | 0.71693 (13) | 0.0249 (6) | |
C9 | 0.2235 (3) | 0.2993 (3) | 0.79266 (13) | 0.0230 (6) | |
C10 | 0.1718 (3) | 0.4552 (3) | 0.81438 (13) | 0.0264 (6) | |
H10 | 0.1419 | 0.4768 | 0.8642 | 0.032* | |
C11 | 0.1651 (3) | 0.5738 (3) | 0.76334 (14) | 0.0305 (6) | |
H11 | 0.1314 | 0.6780 | 0.7794 | 0.037* | |
C12 | 0.2528 (3) | 0.4093 (4) | 0.66921 (14) | 0.0306 (6) | |
H12 | 0.2805 | 0.3935 | 0.6187 | 0.037* | |
H1N | −0.089 (4) | 0.189 (4) | 0.8928 (16) | 0.038 (8)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
F1 | 0.0389 (18) | 0.068 (3) | 0.0337 (18) | 0.0250 (19) | 0.0054 (15) | −0.022 (2) |
F2 | 0.0278 (17) | 0.020 (2) | 0.0314 (19) | 0.0033 (19) | 0.0001 (12) | 0.0036 (17) |
F3 | 0.0405 (18) | 0.048 (2) | 0.058 (2) | −0.0050 (16) | 0.0009 (18) | 0.038 (2) |
O1 | 0.0464 (13) | 0.094 (2) | 0.0313 (11) | 0.0251 (12) | −0.0109 (9) | −0.0248 (12) |
N1 | 0.0266 (11) | 0.0317 (14) | 0.0223 (11) | 0.0007 (10) | 0.0021 (9) | −0.0017 (11) |
N2 | 0.0275 (11) | 0.0318 (16) | 0.0376 (13) | −0.0004 (10) | 0.0000 (9) | 0.0053 (12) |
C1 | 0.0418 (16) | 0.0372 (19) | 0.0247 (14) | 0.0078 (14) | 0.0052 (11) | 0.0029 (13) |
C2 | 0.0382 (15) | 0.0337 (18) | 0.0250 (14) | 0.0089 (13) | 0.0028 (11) | 0.0004 (13) |
C3 | 0.0300 (13) | 0.0301 (17) | 0.0271 (13) | 0.0042 (12) | 0.0006 (10) | 0.0016 (12) |
C4 | 0.0197 (12) | 0.0290 (17) | 0.0258 (13) | 0.0025 (11) | −0.0001 (9) | −0.0002 (12) |
C5 | 0.0279 (13) | 0.0236 (16) | 0.0340 (14) | 0.0044 (11) | 0.0000 (10) | 0.0032 (13) |
C6 | 0.0286 (14) | 0.0272 (16) | 0.0335 (14) | 0.0035 (11) | 0.0035 (10) | −0.0048 (13) |
C7 | 0.0263 (13) | 0.0356 (18) | 0.0263 (13) | 0.0000 (12) | 0.0042 (10) | −0.0055 (13) |
C8 | 0.0203 (12) | 0.0283 (15) | 0.0262 (13) | −0.0023 (11) | 0.0014 (9) | 0.0011 (12) |
C9 | 0.0182 (11) | 0.0253 (15) | 0.0255 (13) | −0.0007 (10) | −0.0007 (9) | −0.0004 (12) |
C10 | 0.0235 (13) | 0.0270 (16) | 0.0286 (13) | 0.0004 (11) | −0.0003 (10) | −0.0024 (12) |
C11 | 0.0246 (13) | 0.0273 (17) | 0.0396 (15) | 0.0002 (11) | 0.0001 (10) | −0.0013 (13) |
C12 | 0.0264 (13) | 0.0371 (18) | 0.0284 (13) | −0.0021 (12) | 0.0013 (10) | 0.0029 (13) |
F1—C1 | 1.334 (3) | C3—H3A | 0.9900 |
F2—C1 | 1.324 (4) | C3—H3B | 0.9900 |
F3—C1 | 1.374 (4) | C4—C5 | 1.374 (4) |
F4—C1 | 1.311 (5) | C4—C9 | 1.421 (4) |
F5—C1 | 1.295 (5) | C5—C6 | 1.420 (3) |
F6—C1 | 1.375 (5) | C5—H5 | 0.9500 |
F7—C1 | 1.316 (5) | C6—C7 | 1.356 (4) |
F8—C1 | 1.314 (5) | C6—H6 | 0.9500 |
F9—C1 | 1.356 (5) | C7—C8 | 1.414 (4) |
O1—C2 | 1.209 (3) | C7—H7 | 0.9500 |
N1—C2 | 1.326 (3) | C8—C12 | 1.412 (4) |
N1—C3 | 1.467 (3) | C8—C9 | 1.427 (3) |
N1—H1N | 0.84 (3) | C9—C10 | 1.411 (4) |
N2—C12 | 1.312 (3) | C10—C11 | 1.357 (4) |
N2—C11 | 1.370 (3) | C10—H10 | 0.9500 |
C1—C2 | 1.527 (4) | C11—H11 | 0.9500 |
C3—C4 | 1.514 (3) | C12—H12 | 0.9500 |
C2—N1—C3 | 121.9 (2) | C4—C3—H3B | 109.3 |
C2—N1—H1N | 121 (2) | H3A—C3—H3B | 108.0 |
C3—N1—H1N | 117.2 (19) | C5—C4—C9 | 118.5 (2) |
C12—N2—C11 | 117.0 (2) | C5—C4—C3 | 120.8 (2) |
F5—C1—F4 | 113.3 (6) | C9—C4—C3 | 120.6 (2) |
F8—C1—F7 | 118.6 (8) | C4—C5—C6 | 122.0 (2) |
F2—C1—F1 | 106.9 (3) | C4—C5—H5 | 119.0 |
F8—C1—F9 | 103.5 (7) | C6—C5—H5 | 119.0 |
F7—C1—F9 | 102.3 (7) | C7—C6—C5 | 120.5 (3) |
F2—C1—F3 | 104.2 (3) | C7—C6—H6 | 119.7 |
F1—C1—F3 | 104.2 (3) | C5—C6—H6 | 119.7 |
F5—C1—F6 | 105.3 (5) | C6—C7—C8 | 119.4 (2) |
F4—C1—F6 | 103.3 (5) | C6—C7—H7 | 120.3 |
F5—C1—C2 | 114.7 (4) | C8—C7—H7 | 120.3 |
F4—C1—C2 | 115.1 (4) | C12—C8—C7 | 121.4 (2) |
F8—C1—C2 | 112.7 (6) | C12—C8—C9 | 118.0 (2) |
F7—C1—C2 | 110.8 (4) | C7—C8—C9 | 120.6 (2) |
F2—C1—C2 | 114.2 (2) | C10—C9—C4 | 123.9 (2) |
F1—C1—C2 | 114.4 (2) | C10—C9—C8 | 117.1 (2) |
F9—C1—C2 | 107.4 (5) | C4—C9—C8 | 119.0 (2) |
F3—C1—C2 | 111.9 (3) | C11—C10—C9 | 119.3 (2) |
F6—C1—C2 | 103.3 (3) | C11—C10—H10 | 120.3 |
O1—C2—N1 | 126.5 (3) | C9—C10—H10 | 120.3 |
O1—C2—C1 | 118.1 (2) | C10—C11—N2 | 124.4 (3) |
N1—C2—C1 | 115.3 (2) | C10—C11—H11 | 117.8 |
N1—C3—C4 | 111.6 (2) | N2—C11—H11 | 117.8 |
N1—C3—H3A | 109.3 | N2—C12—C8 | 124.2 (2) |
C4—C3—H3A | 109.3 | N2—C12—H12 | 117.9 |
N1—C3—H3B | 109.3 | C8—C12—H12 | 117.9 |
C3—N1—C2—O1 | −0.3 (5) | N1—C3—C4—C9 | 69.5 (3) |
C3—N1—C2—C1 | −179.4 (2) | C9—C4—C5—C6 | −0.3 (4) |
F5—C1—C2—O1 | −52.4 (6) | C3—C4—C5—C6 | 178.1 (2) |
F4—C1—C2—O1 | 173.4 (5) | C4—C5—C6—C7 | −0.4 (4) |
F8—C1—C2—O1 | 122.9 (6) | C5—C6—C7—C8 | 0.5 (4) |
F7—C1—C2—O1 | −12.8 (7) | C6—C7—C8—C12 | −178.7 (2) |
F2—C1—C2—O1 | 148.2 (4) | C6—C7—C8—C9 | 0.3 (3) |
F1—C1—C2—O1 | 24.5 (5) | C5—C4—C9—C10 | 179.9 (2) |
F9—C1—C2—O1 | −123.8 (5) | C3—C4—C9—C10 | 1.5 (4) |
F3—C1—C2—O1 | −93.7 (4) | C5—C4—C9—C8 | 1.0 (3) |
F6—C1—C2—O1 | 61.6 (4) | C3—C4—C9—C8 | −177.4 (2) |
F5—C1—C2—N1 | 126.8 (6) | C12—C8—C9—C10 | −1.0 (3) |
F4—C1—C2—N1 | −7.4 (5) | C7—C8—C9—C10 | −180.0 (2) |
F8—C1—C2—N1 | −57.9 (7) | C12—C8—C9—C4 | 178.0 (2) |
F7—C1—C2—N1 | 166.4 (6) | C7—C8—C9—C4 | −1.0 (3) |
F2—C1—C2—N1 | −32.7 (4) | C4—C9—C10—C11 | −178.6 (2) |
F1—C1—C2—N1 | −156.3 (4) | C8—C9—C10—C11 | 0.3 (3) |
F9—C1—C2—N1 | 55.4 (5) | C9—C10—C11—N2 | 0.8 (4) |
F3—C1—C2—N1 | 85.5 (4) | C12—N2—C11—C10 | −1.1 (3) |
F6—C1—C2—N1 | −119.2 (4) | C11—N2—C12—C8 | 0.3 (4) |
C2—N1—C3—C4 | −162.6 (2) | C7—C8—C12—N2 | 179.7 (2) |
N1—C3—C4—C5 | −108.9 (3) | C9—C8—C12—N2 | 0.8 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···N2i | 0.84 (3) | 2.05 (3) | 2.847 (3) | 158 (3) |
Symmetry code: (i) −x, y−1/2, −z+3/2. |
Experimental details
Crystal data | |
Chemical formula | C12H9F3N2O |
Mr | 254.21 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 123 |
a, b, c (Å) | 7.2308 (7), 8.3498 (11), 18.157 (2) |
β (°) | 90.583 (9) |
V (Å3) | 1096.2 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.14 |
Crystal size (mm) | 0.45 × 0.12 × 0.02 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur S diffractometer |
Absorption correction | Multi-scan (CrysAlis RED; Oxford Diffraction, 2007) |
Tmin, Tmax | 0.717, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4377, 2071, 1346 |
Rint | 0.031 |
(sin θ/λ)max (Å−1) | 0.617 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.051, 0.133, 1.06 |
No. of reflections | 2071 |
No. of parameters | 191 |
No. of restraints | 111 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.30, −0.45 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2007), CrysAlis RED (Oxford Diffraction, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···N2i | 0.84 (3) | 2.05 (3) | 2.847 (3) | 158 (3) |
Symmetry code: (i) −x, y−1/2, −z+3/2. |
Acknowledgements
The authors thank the BBSRC for funding [grant No. BB/EO 13929/1].
References
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In the search for novel biologically active compounds in the area of anti-inflammatory and pain relief drugs, we have found a class of compounds acting as potent antagonists or agonists of the vanilloid VR1 receptor. These have been shown to be useful in the treatment and prevention of inflammatory and other pain conditions in mammals (Jetter et al., 2007; Jetter et al., 2008; Codd et al., 2003). The title compound was prepared as an important precursor for more complex compounds. Surprisingly, reaction of n-hydroxymethyl trifluoroacetamide with isoquinoline in the presence of sulfuric acid afforded a single positional isomer after purification by column chromatography.
The plane of the quinolene ring forms a dihedral angle of 76.2 (2) ° with the amide plane, see Fig. 1. Similar conformations were found in a study of similar naphthalene derivatives - though the analogous CF3 compound had an angle of 89 ° (Weinstein & Leiserowitz, 1980). The CF3 group is disordered by rotation about the C—CF3 bond (Müller, 2009).
A major difference between the naphthalene derivatives and the present compound is seen in the intermolecular contacts. The naphthalenes bond through amide to amide (N—H···O) hydrogen bonds. However, in the quinolene, the presence of a hetero atom enables N—H···N bonds. These form extended chains running along the b direction, see Fig. 2.
The packing diagram, Fig. 3, illustrates the layered nature of this structure. Traveling along the c direction there are alternate quinolene layers and amide layers. The closest π interaction, connecting molecules along the a direction, in the quinolene layer is slightly outside the sum of van der Waals distances (C5···C12 3.486 (4) Å).