PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2010 January 1; 66(Pt 1): o135.
Published online 2009 December 12. doi:  10.1107/S1600536809052994
PMCID: PMC2980156

2,2,2-Trifluoro-N-(isoquinolin-5-ylmeth­yl)acetamide

Abstract

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 [triangle], 2008 [triangle]); Codd et al. (2003 [triangle]). The title compound was prepared as a precursor for more complex compounds. For analysis of the structures of analogous naphthalenes, see: Weinstein & Leiserowitz (1980 [triangle]). For a discussion on disorder in crystal structures, see: Müller (2009 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0o135-scheme1.jpg

Experimental

Crystal data

  • C12H9F3N2O
  • M r = 254.21
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o135-efi1.jpg
  • a = 7.2308 (7) Å
  • b = 8.3498 (11) Å
  • c = 18.157 (2) Å
  • β = 90.583 (9)°
  • V = 1096.2 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.14 mm−1
  • T = 123 K
  • 0.45 × 0.12 × 0.02 mm

Data collection

  • Oxford Diffraction Xcalibur S diffractometer
  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007 [triangle]) T min = 0.717, T max = 1.000
  • 4377 measured reflections
  • 2071 independent reflections
  • 1346 reflections with I > 2σ(I)
  • R int = 0.031

Refinement

  • R[F 2 > 2σ(F 2)] = 0.051
  • wR(F 2) = 0.133
  • S = 1.06
  • 2071 reflections
  • 191 parameters
  • 111 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.30 e Å−3
  • Δρmin = −0.45 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2007 [triangle]); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2007 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809052994/tk2599sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809052994/tk2599Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank the BBSRC for funding [grant No. BB/EO 13929/1].

supplementary crystallographic information

Comment

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).

Experimental

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.

Refinement

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.

Figures

Fig. 1.
The molecular structure and atomic labelling, showing 40% probability displacement ellipsoids. H atoms are shown as spheres of arbitrary radius. Minor disorder components are not shown.
Fig. 2.
Part of the hydrogen bonded chains formed along the b direction. O atoms are red, N atoms blue, F atoms pink and C-atoms are black. Hydrogen bonds are shown as dashed lines.
Fig. 3.
Packed structure viewed down the a-axis.

Crystal data

C12H9F3N2OF(000) = 520
Mr = 254.21Dx = 1.540 Mg m3
Monoclinic, P21/cMelting point = 435–438 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 7.2308 (7) ÅCell parameters from 1879 reflections
b = 8.3498 (11) Åθ = 2.7–30.1°
c = 18.157 (2) ŵ = 0.14 mm1
β = 90.583 (9)°T = 123 K
V = 1096.2 (2) Å3Blade, colourless
Z = 40.45 × 0.12 × 0.02 mm

Data collection

Oxford Diffraction Xcalibur S diffractometer2071 independent reflections
Radiation source: fine-focus sealed tube1346 reflections with I > 2σ(I)
graphiteRint = 0.031
Detector resolution: 16.0268 pixels mm-1θmax = 26.0°, θmin = 2.7°
ω scansh = −8→8
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007)k = −10→9
Tmin = 0.717, Tmax = 1.000l = −21→22
4377 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.051Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.133H atoms treated by a mixture of independent and constrained refinement
S = 1.06w = 1/[σ2(Fo2) + (0.0703P)2 + 0.0571P] where P = (Fo2 + 2Fc2)/3
2071 reflections(Δ/σ)max < 0.001
191 parametersΔρmax = 0.30 e Å3
111 restraintsΔρmin = −0.45 e Å3

Special details

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)

xyzUiso*/UeqOcc. (<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)
N20.2036 (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)
C30.1779 (3)0.1840 (3)0.92121 (13)0.0291 (6)
H3A0.21350.08590.94850.035*
H3B0.24650.27520.94310.035*
C40.2312 (3)0.1660 (3)0.84124 (13)0.0248 (6)
C50.2834 (3)0.0198 (3)0.81357 (14)0.0285 (6)
H50.2895−0.06970.84580.034*
C60.3287 (3)−0.0013 (4)0.73828 (13)0.0297 (6)
H60.3651−0.10390.72110.036*
C70.3203 (3)0.1237 (3)0.69074 (13)0.0294 (6)
H70.34970.10900.64030.035*
C80.2672 (3)0.2763 (3)0.71693 (13)0.0249 (6)
C90.2235 (3)0.2993 (3)0.79266 (13)0.0230 (6)
C100.1718 (3)0.4552 (3)0.81438 (13)0.0264 (6)
H100.14190.47680.86420.032*
C110.1651 (3)0.5738 (3)0.76334 (14)0.0305 (6)
H110.13140.67800.77940.037*
C120.2528 (3)0.4093 (4)0.66921 (14)0.0306 (6)
H120.28050.39350.61870.037*
H1N−0.089 (4)0.189 (4)0.8928 (16)0.038 (8)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
F10.0389 (18)0.068 (3)0.0337 (18)0.0250 (19)0.0054 (15)−0.022 (2)
F20.0278 (17)0.020 (2)0.0314 (19)0.0033 (19)0.0001 (12)0.0036 (17)
F30.0405 (18)0.048 (2)0.058 (2)−0.0050 (16)0.0009 (18)0.038 (2)
O10.0464 (13)0.094 (2)0.0313 (11)0.0251 (12)−0.0109 (9)−0.0248 (12)
N10.0266 (11)0.0317 (14)0.0223 (11)0.0007 (10)0.0021 (9)−0.0017 (11)
N20.0275 (11)0.0318 (16)0.0376 (13)−0.0004 (10)0.0000 (9)0.0053 (12)
C10.0418 (16)0.0372 (19)0.0247 (14)0.0078 (14)0.0052 (11)0.0029 (13)
C20.0382 (15)0.0337 (18)0.0250 (14)0.0089 (13)0.0028 (11)0.0004 (13)
C30.0300 (13)0.0301 (17)0.0271 (13)0.0042 (12)0.0006 (10)0.0016 (12)
C40.0197 (12)0.0290 (17)0.0258 (13)0.0025 (11)−0.0001 (9)−0.0002 (12)
C50.0279 (13)0.0236 (16)0.0340 (14)0.0044 (11)0.0000 (10)0.0032 (13)
C60.0286 (14)0.0272 (16)0.0335 (14)0.0035 (11)0.0035 (10)−0.0048 (13)
C70.0263 (13)0.0356 (18)0.0263 (13)0.0000 (12)0.0042 (10)−0.0055 (13)
C80.0203 (12)0.0283 (15)0.0262 (13)−0.0023 (11)0.0014 (9)0.0011 (12)
C90.0182 (11)0.0253 (15)0.0255 (13)−0.0007 (10)−0.0007 (9)−0.0004 (12)
C100.0235 (13)0.0270 (16)0.0286 (13)0.0004 (11)−0.0003 (10)−0.0024 (12)
C110.0246 (13)0.0273 (17)0.0396 (15)0.0002 (11)0.0001 (10)−0.0013 (13)
C120.0264 (13)0.0371 (18)0.0284 (13)−0.0021 (12)0.0013 (10)0.0029 (13)

Geometric parameters (Å, °)

F1—C11.334 (3)C3—H3A0.9900
F2—C11.324 (4)C3—H3B0.9900
F3—C11.374 (4)C4—C51.374 (4)
F4—C11.311 (5)C4—C91.421 (4)
F5—C11.295 (5)C5—C61.420 (3)
F6—C11.375 (5)C5—H50.9500
F7—C11.316 (5)C6—C71.356 (4)
F8—C11.314 (5)C6—H60.9500
F9—C11.356 (5)C7—C81.414 (4)
O1—C21.209 (3)C7—H70.9500
N1—C21.326 (3)C8—C121.412 (4)
N1—C31.467 (3)C8—C91.427 (3)
N1—H1N0.84 (3)C9—C101.411 (4)
N2—C121.312 (3)C10—C111.357 (4)
N2—C111.370 (3)C10—H100.9500
C1—C21.527 (4)C11—H110.9500
C3—C41.514 (3)C12—H120.9500
C2—N1—C3121.9 (2)C4—C3—H3B109.3
C2—N1—H1N121 (2)H3A—C3—H3B108.0
C3—N1—H1N117.2 (19)C5—C4—C9118.5 (2)
C12—N2—C11117.0 (2)C5—C4—C3120.8 (2)
F5—C1—F4113.3 (6)C9—C4—C3120.6 (2)
F8—C1—F7118.6 (8)C4—C5—C6122.0 (2)
F2—C1—F1106.9 (3)C4—C5—H5119.0
F8—C1—F9103.5 (7)C6—C5—H5119.0
F7—C1—F9102.3 (7)C7—C6—C5120.5 (3)
F2—C1—F3104.2 (3)C7—C6—H6119.7
F1—C1—F3104.2 (3)C5—C6—H6119.7
F5—C1—F6105.3 (5)C6—C7—C8119.4 (2)
F4—C1—F6103.3 (5)C6—C7—H7120.3
F5—C1—C2114.7 (4)C8—C7—H7120.3
F4—C1—C2115.1 (4)C12—C8—C7121.4 (2)
F8—C1—C2112.7 (6)C12—C8—C9118.0 (2)
F7—C1—C2110.8 (4)C7—C8—C9120.6 (2)
F2—C1—C2114.2 (2)C10—C9—C4123.9 (2)
F1—C1—C2114.4 (2)C10—C9—C8117.1 (2)
F9—C1—C2107.4 (5)C4—C9—C8119.0 (2)
F3—C1—C2111.9 (3)C11—C10—C9119.3 (2)
F6—C1—C2103.3 (3)C11—C10—H10120.3
O1—C2—N1126.5 (3)C9—C10—H10120.3
O1—C2—C1118.1 (2)C10—C11—N2124.4 (3)
N1—C2—C1115.3 (2)C10—C11—H11117.8
N1—C3—C4111.6 (2)N2—C11—H11117.8
N1—C3—H3A109.3N2—C12—C8124.2 (2)
C4—C3—H3A109.3N2—C12—H12117.9
N1—C3—H3B109.3C8—C12—H12117.9
C3—N1—C2—O1−0.3 (5)N1—C3—C4—C969.5 (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—C6178.1 (2)
F4—C1—C2—O1173.4 (5)C4—C5—C6—C7−0.4 (4)
F8—C1—C2—O1122.9 (6)C5—C6—C7—C80.5 (4)
F7—C1—C2—O1−12.8 (7)C6—C7—C8—C12−178.7 (2)
F2—C1—C2—O1148.2 (4)C6—C7—C8—C90.3 (3)
F1—C1—C2—O124.5 (5)C5—C4—C9—C10179.9 (2)
F9—C1—C2—O1−123.8 (5)C3—C4—C9—C101.5 (4)
F3—C1—C2—O1−93.7 (4)C5—C4—C9—C81.0 (3)
F6—C1—C2—O161.6 (4)C3—C4—C9—C8−177.4 (2)
F5—C1—C2—N1126.8 (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—C4178.0 (2)
F7—C1—C2—N1166.4 (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—C110.3 (3)
F9—C1—C2—N155.4 (5)C9—C10—C11—N20.8 (4)
F3—C1—C2—N185.5 (4)C12—N2—C11—C10−1.1 (3)
F6—C1—C2—N1−119.2 (4)C11—N2—C12—C80.3 (4)
C2—N1—C3—C4−162.6 (2)C7—C8—C12—N2179.7 (2)
N1—C3—C4—C5−108.9 (3)C9—C8—C12—N20.8 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N···N2i0.84 (3)2.05 (3)2.847 (3)158 (3)

Symmetry codes: (i) −x, y−1/2, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2599).

References

  • Codd, E. E., Dax, S. L., Jetter, M., McDonell, M., McNally, J. J. & Youngman, M. (2003). PCT Int. Appl. WO 2003097586 A1.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Jetter, M. C., McNally, J. J., Youngman, M. A., McDonnell, M. E., Dubin, A. E., Nasser, N., Zhang, S.-P., Codd, E. E., Colburn, R. W., Stone, D. R., Brandt, M. R., Flores, C. M. & Dax, S. L. (2008). Bioorg. Med. Chem. Lett.18, 2730–2734. [PubMed]
  • Jetter, M. C., Youngman, M. A., McNally, J. J., McDonnell, M. E., Zhang, S.-P., Dubin, A. E., Nasser, N., Codd, E. E., Flores, C. M. & Dax, S. L. (2007). Bioorg. Med. Chem. Lett.17, 6160–6163. [PubMed]
  • Müller, P. (2009). Crystallogr. Rev.15, 57–80.
  • Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED Oxford Diffraction Ltd, Abingdon, England.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Weinstein, S. & Leiserowitz, L. (1980). Acta Cryst. B36, 1406–1418.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography