Andreas
Lemmerer
and
Joseph P.
Michael
*
Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO Wits 2050, Johannesburg, South Africa. E-mail: joseph.michael@wits.ac.za; Fax: +27 11 717 6749; Tel: +27 11 717 6753
First published on 13th September 2007
Single-crystal structures of five 1-arylcycloalkanecarboxamides, viz.1-phenylcyclopentanecarboxamide (1), 1-phenylcyclohexanecarboxamide (2), 1-(2-fluorophenyl)cyclohexanecarboxamide (3), 1-(2-chlorophenyl)cyclohexanecarboxamide (4) and 1-(2-bromophenyl)-cyclohexanecarboxamide (5), are reported. The primary hydrogen-bonded motif consists of centrosymmetric or non-centrosymmetric R22(8) dimers between the carboxamide functional groups. In compound 1, the dimers are further linked by hydrogen bonds to form infinite two-dimensional sheets, while in 4 and 5 additional hydrogen bonding with molecules not involved in dimer formation links the dimers into infinite chains. The cycloalkane rings in the five compounds adopt noticeably different conformations. As a consequence of these various effects, none of the five compounds is isostructural.
Our interest in the title compounds originated from synthetic investigations first performed in the 1980s, when we prepared several 1-(2-halophenyl)cyclohexanecarboxamides as part of a model study to identify suitable precursors for the construction of oxindoles bearing spirocyclic rings at C-3.11,12 These spiro-oxindoles in turn served as models for developing methodology aimed at the total synthesis of the complex spiro-oxindole alkaloid gelsemine.13 Related 1-phenylcycloalkanecarboxamides have been tested for neuroprotective activity.14 In this article we report a range of distinctly different hydrogen bonding patterns in five representatives of the title compound, 1–5 (Scheme 1), as revealed by single-crystal X-ray diffraction studies.
Scheme 1 Structures of compounds 1–5, showing the primary hydrogen-bonded dimeric motif. |
Fig. 1 The contents of the asymmetric unit for structures 1–5, showing the atomic numbering scheme. Displacement ellipsoids are shown at the 50% probability level. H atoms not involved in hydrogen bonding interactions are omitted in 4 and 5 for clarity. Atoms labelled with small letters a, b or c refer to molecules A, B and C in the asymmetric unit. |
1 | 2 | 3 | 4 | 5 | |
---|---|---|---|---|---|
Formula | C12H15NO | C13H17NO | C13H16FNO | C13H16ClNO | C13H16BrNO |
M r | 189.25 | 203.28 | 221.27 | 237.72 | 282.18 |
Temperature/K | 173 | 173 | 173 | 173 | 173 |
Crystal size/mm | 0.30 × 0.20 × 0.10 | 0.40 × 0.36 × 0.14 | 0.40 × 0.32 × 0.08 | 0.56 × 0.26 × 0.20 | 0.38 × 0.32 × 0.16 |
Crystal system | Monoclinic | Orthorhombic | Monoclinic | Monoclinic | Triclinic |
Space group | P21/c | Pca21 | P21/c | P21/c | P |
a/Å | 14.140(2) | 13.8232(19) | 11.792(5) | 13.314(2) | 8.9257(13) |
b/Å | 7.3843(11) | 6.1326(8) | 8.646(4) | 9.3311(13) | 10.8387(16) |
c/Å | 10.2066(15) | 26.176(4) | 12.170(5) | 29.104(4) | 13.7825(19) |
α/° | 90 | 90 | 90 | 90 | 69.877(10) |
β/° | 109.291(10) | 90 | 111.510(7) | 90.109(10) | 87.223(11) |
γ/° | 90 | 90 | 90 | 90 | 82.095(11) |
V/Å3 | 1005.8(3) | 2219.0(5) | 1154.4(8) | 3615.6(9) | 1240.1(3) |
Z | 4 | 8 | 4 | 12 | 4 |
D calc/g cm–3 | 1.250 | 1.217 | 1.273 | 1.310 | 1.511 |
µ(Mo-Kα)/mm–1 | 0.079 | 0.077 | 0.091 | 0.295 | 3.294 |
θ range/° | 1.53 to 28.00 | 1.56 to 28.00 | 1.86 to 28.00 | 1.40 to 28.00 | 2.02 to 28.00 |
No. unique data | 2430 | 2731 | 2791 | 8724 | 5986 |
No. data with I ≥ 2σ(I) | 1963 | 2282 | 2003 | 6264 | 4856 |
R 1 | 0.0459 | 0.0434 | 0.0436 | 0.0471 | 0.0319 |
wR 2 (all data) | 0.1184 | 0.1126 | 0.1190 | 0.1576 | 0.0958 |
Absolute parameter17 | — | –10(10) | — | — | — |
D–H⋯A | D–H/Å | H⋯A/Å | D⋯A/Å | <(D–H⋯A)/° | Symmetry transformations |
---|---|---|---|---|---|
1 | |||||
N(1A)–H(1As)⋯O(1A) | 0.91(2) | 2.15(2) | 3.047(1) | 169(1) | –x + 1, –y + 2, –z + 1 |
N(1A)–H(1Aa)⋯O(1A) | 0.89(2) | 2.23(2) | 3.104(1) | 165(1) | x, –y + 3/2, z – 1/2 |
2 | |||||
N(1A)–H(1As)⋯O(1B) | 0.85(4) | 2.09(4) | 2.933(3) | 172(4) | — |
N(1B)–H(1Bs)⋯O(1A) | 0.99(5) | 1.95(4) | 2.921(3) | 169(4) | — |
3 | |||||
N(1A)–H(1As)⋯O(1A) | 0.87(2) | 1.99(2) | 2.860(2) | 174(2) | –x + 1, –y + 1, –z |
4 | |||||
N(1A)–H(1As)⋯O(1B) | 0.85(3) | 2.03(3) | 2.881(2) | 176(2) | — |
N(1B)–H(1Bs)⋯O(1A) | 0.88(3) | 2.13(3) | 2.999(2) | 172(2) | — |
N(1B)–H(1Ba)⋯O(1C) | 0.83(3) | 2.13(3) | 2.903(2) | 157(2) | x, y + 1, z |
N(1C)–H(1Ca)⋯O(1B) | 0.87(3) | 2.22(3) | 3.043(2) | 159(2) | — |
5 | |||||
N(1A)–H(1As)⋯O(1A) | 0.88(3) | 2.11(3) | 2.981(2) | 174(2) | –x + 1, –y, –z + 1 |
N(1A)–H(1Aa)⋯O(1B) | 0.86(3) | 2.08(3) | 2.874(2) | 153(2) | — |
N(1B)–H(1Ba)⋯O(1A) | 0.84(3) | 2.21(3) | 2.959(3) | 149(3) | x + 1, y, z |
The structure of 1-phenylcyclopentanecarboxamide (1), which has one molecule (labelled A) in the asymmetric unit, contains two unique hydrogen bonds. The first, N(1A)–H(1As)⋯O(1A), forms the expected R22(8) dimers that point alternately in the [–110] and [110] directions (Fig. 2a); while the second, N(1A)–H(1Aa) ⋯O(1A), results in the formation of a C(4) chain along the c-axis. The unitary GS notation is N1 = C(4)R22(8), and the binary GS notation is N2 = C12(4)C22(8). The combination of the two types of hydrogen bonds creates a larger ring, a hexamer with GS notation R46(16). The net result is the formation of a 2-D network of alternating R22(8) and R46(16) rings parallel to the bc-plane (Fig. 2b). This 2-D network has a wave-like pattern in which adjacent R22(8) dimers along the b-axis are related by a centre of inversion (Fig. 2c). As a consequence of the inversion centre, both N(1A)–H(1As)⋯O(1A) hydrogen bond distances are equal [d(H⋯O) = 2.15(2) Å].
Fig. 2 Hydrogen bonding in 1-phenylcyclopentanecarboxamide (1). (a) The two unique hydrogen bonds, shown as dashed red and green lines, forming the R22(8) centrosymmetric hydrogen-bonded dimer and the R46(16) ring. (b) The 2-D hydrogen-bonded pattern formed by the R22(8) and R46(16) rings. (c) Side-on view of the wave-like hydrogen bonded pattern. Atoms marked with a superscript (i) are at the symmetry position (1 – x, 2 – y, 1 – z). H atoms not involved in hydrogen bonding interactions are omitted for clarity. |
The structure of 1-phenylcyclohexanecarboxamide (2) has two molecules (labelled A and B) in the asymmetric unit. The two molecules are related by a pseudo inversion centre and the unitary GS notation is N1 = DD. As a consequence, the N2 = R22(8) dimers, connected by N(1A)–H(1As)⋯O(1B) and N(1B)–H(1Bs)⋯O(1A) hydrogen bonds, are non-centrosymmetric. These stack along the direction of the a-axis and point alternately in the [–101] and [101] directions (Fig. 3a). The H⋯O bond distances for N(1A)–H(1As)⋯O(1A) and N(1B)–H(1Bs)⋯O(1B) differ by 0.19 Å. The two anti-orientated H atoms, H(1Aa) on molecule A and H(1Ba) on molecule B, do not participate in hydrogen bonding.
Fig. 3 Hydrogen bonding in 1-phenylcyclohexanecarboxamide (2). (a) The two unique hydrogen bonds, shown as dashed red lines, forming the R22(8) non-centrosymmetric hydrogen bonded dimer. (b) Packing diagram of 2. |
The asymmetric unit in the crystal structure of 1-(2-fluorophenyl)cyclohexanecarboxamide (3) contains only one molecule. The centrosymmetric R22(8) dimers are joined by N(1A)–H(1As)⋯O(1A) hydrogen bonds (Fig. 4a). These dimers stack in a parallel head-to-head fashion along the c-axis; and they themselves point approximately along the [101] direction (Fig. 4b). Atom H(1Aa) does not participate in any hydrogen bonding interactions. The unitary GS motif is N1 = R22(8). In contrast to the halogen-containing analogues 4 and 5 (vide infra), structure 3 has no C–H⋯π interactions.
Fig. 4 Hydrogen bonding in 1-(2-fluorophenyl)cyclohexanecarboxamide (3). (a) The single unique hydrogen bonds, shown as dashed red lines, forming the R22(8) centrosymmetric hydrogen bonded dimer. (b) Packing diagram of 3. Atoms marked with a superscript (i) are at the symmetry position (1 – x, 1 – y, –z). |
The comparatively simple crystal structure of 3 contrasts markedly with the complexity shown by that of 1-(2-chlorophenyl)cyclohexanecarboxamide (4), which has no fewer than three molecules (labelled A, B and C) in its asymmetric unit (Z′ = 3)—the most among all of the compounds reported in this study. Molecules A and B form non-centrosymmetric R22(8) dimers that result from the N(1A)–H(1As)⋯O(1B) and N(1B)–H(1Bs)⋯O(1A) hydrogen bonds (Fig. 5a). These dimers extend along the crystallographic a-direction. Adjacent dimers are linked by molecule C to form an infinite 1-D chain, GS notation C22(8), along the b-axis (Fig. 5b and 5c). The hydrogen bonds creating the chain are N(1B)–H(1Ba)⋯O(1C) and N(1C)–H(1Ca)⋯O(1B). The unitary GS motif is N1 = DDDD and the binary GS pattern is N2 = C22(8)R22(8). Hydrogen atoms H(1Aa) on molecule A and H(1Cs) on molecule C are not involved in any hydrogen bonded interactions. Additionally, there is a weak C–H⋯π interaction present between molecules B and C, with atom C(6B) interacting with the centroid Cg3 of the aromatic group C(8C)–C(13C) through atom H(6B1) [d(C–H⋯Cg3 = 2.76 Å; ∠(C–H⋯Cg3) = 141°; cf.Fig. 5a]. However, there appear to be no significant C–H⋯Cl interactions.
Fig. 5 Hydrogen bonding in 1-(2-chlorophenyl)cyclohexanecarboxamide (4). (a) The three types of hydrogen bonds observed in 4. The non-centrosymmetric R22(8) dimer hydrogen bonds are shown as dashed red lines, the hydrogen bonds in the C22(8) chain are shown as dashed green lines and the C–H⋯π hydrogen bond as dashed blue lines. (b) The dimers connected to form an infinite 1-D chain along the b-axis. (c) Packing diagram shown down the b-axis. Atoms marked with a superscript (i) are at the symmetry position (x, 1 + y, z). H atoms not involved in hydrogen bonding interactions are omitted for clarity in (a) and (b). |
The crystal structure of 1-(2-bromophenyl)cyclohexanecarboxamide (5) has two molecules (labelled A and B) in the asymmetric unit. Two molecules of A form centrosymmetric R22(8) dimers pointing along the c-axis (Fig. 6a). Neighbouring dimers are linked by molecule B to form a C22(8) chain of hydrogen bonds. The same hexamer with GS notation R46(16) is formed as in (1). The unitary and binary GS notations are N1 = DDR22(8) and N2 = C22(8) respectively. Together, the R22(8) dimer and R46(16) hexamer form an infinite hydrogen bonded ribbon along the a-axis (Fig. 6b and 6c). Atom H(1Bs) plays no part in the hydrogen bonding interactions, i.e. the C12(4) chain observed in 1 is absent and hence no 2-D network is created. However, there is a weak C–H⋯π interaction present between molecules A and B, with atom C(6A) interacting through atom H(6A1) with centroid Cg2 of the aromatic group C(8B)–C(13B) [d(C–H⋯Cg2) = 2.88 Å; ∠(C–H⋯Cg2) = 142°; cf.Fig. 6a]. There is no apparent involvement of the bromine atoms in hydrogen bonding.
Fig. 6 Hydrogen bonding in 1-(2-bromophenyl)cyclohexanecarboxamide (5). (a) The three types of hydrogen bonds observed in 5. The centrosymmetric R22(8) dimer hydrogen bonds are shown as dashed red lines, the hydrogen bonds in the C22(8) chain are shown as dashed green lines and the C–H⋯π hydrogen bond as dashed blue lines. (b) The R22(8) and R46(16) rings connected to form an infinite ribbon pattern along the b-axis. (c) Packing diagram shown down the a-axis. Atoms marked with superscripts (i), (ii) and (iii) are at the symmetry positions (1 – x, –y, 1– z), (–1 + x, y, z) and (2 – x, –y, 1 – z) respectively. H atoms not involved in hydrogen bonding interactions are omitted for clarity in (a) and (b). |
1 | 2 | 3 | 4 | 5 | |
---|---|---|---|---|---|
Hydrogen bonding pattern | Centrosymmetric dimers connected to form 2-D network | Non-centrosymmetric discrete dimer | Centrosymmetric discrete dimer | Non-centrosymmetric dimers connected to form 1-D chain | Centrosymmetric dimers connected to form 1-D ribbon |
Graph set notation | N 1 = C(4)R22(8) | N 1 = DD | N 1 = R22(8) | N 1 = DDDD | N 1 = DDR22(8) |
N 2 = C12(4)C22(8) | N 2 = R22(8) | N 2 = C22(8)R22(8) | N 2 = C22(8) | ||
Number of molecules in the asymmetric unit (Z′) | 1 | 2 | 1 | 3 | 2 |
Position of carboxamide | Equatorial (A) | Axial (A and B) | Equatorial (A) | Equatorial (A and B); axial (C) | Equatorial (A); axial (B) |
Position of aryl ring | Axial (A) | Equatorial (A and B) | Axial (A) | Axial (A and B); equatorial (C) | Axial (A); equatorial (B) |
Torsion angle between carboxamide and aryl ring/° | C(7A)–C(1A)–C(6A)–O(1A) = 97.52(12) | C(8A)–C(1A)–C(7A)–O(1A) = –93.4(3); C(8B)–C(1B)–C(7B)–O(1B) = 91.7(3) | C(8A)–C(1A)–C(7A)–O(1A) = 155.82(12) | C(8A)–C(1A)–C(7A)–O(1A) = 148.2(2); C(8B)–C(1B)–C(7B)–O(1B) = –147.13(18); C(8C)–C(1C)–C(7C)–O(1C) = –134.91(19) | C(8A)–C(1A)–C(7A)–O(1A) = –143.24(18); C(8B)–C(1B)–C(7B)–O(1B) = –128.48(19) |
Packing efficiency25 (%) | 70.7 | 69.7 | 68.4 | 68.5 | 68.0 |
Compounds 2 and 3 both form isolated R22(8) dimers. However, while the dimers in 2 are arranged in a non-centrosymmetric fashion, those in 3 are centrosymmetric. This is reflected in the asymmetric unit in 2 being twice that of 3. Most interestingly, the replacement of an ortho-hydrogen atom in 2 by a fluorine atom in 3 results in a surprising conformational inversion of the cyclohexane ring: the orientations of the carboxamide and aryl rings have switched to equatorial and axial, respectively, making the molecular disposition more like 1 than like 2. Notwithstanding the more spacious arrangement of the dimeric supramolecular synthon that results in the equatorial location of the carboxamide groups, there are no additional hydrogen-bonding interactions between the dimers. In addition, the dihedral angle between the carboxamide and aryl substituents changes substantially upon halogenation of the latter, as one might expect from the greater degree of steric interference; for 1 and 2 the angle is a little greater than ±90°, while for 3–5 it is around ±145° for the molecules involved in dimer formation (Table 3).
The structures of the chloro and bromo analogues 4 and 5 are even more unexpected, as they now contain extra hydrogen-bonded interactions. As described above, the non-centrosymmetric R22(8) dimers in 4 (molecules A and B) are linked through a third, independent, molecule (C) to create a chain-type motif (Fig. 5b); and in 5, the centrosymmetric dimers (molecules A) are linked by non-dimeric molecules (B) to give a larger hexameric hydrogen-bonded motif (Fig. 6b) that associates further to form ribbons. Once again, the changes appear to be related to the conformations adopted by the cyclohexane rings. In all three of the halogen-containing compounds, the molecules that form the dimers have their carboxamide functional groups in equatorial positions. However, the cyclohexane ring is again inverted in the non-dimeric molecules in 4 and 5. In the chloro compound 4, the molecule that links the dimers into chains (molecule C) has an axial carboxamide functional group; and the same holds for the molecule in the bromo compound 5 (molecule B) that links the dimers into hexameric units. The torsion angle between the carboxamide and aryl substituents deviates correspondingly between the molecules that form dimers and the molecules that link the dimers (Table 3). In both 4 and 5, the aryl ring of the non-dimeric linking molecules further rigidifies the crystal structure by C–H⋯π association with an axial hydrogen atom adjacent to the substituted carbon atom on the cyclohexane ring; but in none of the halogenated compounds is the halogen atom involved in hydrogen bonding.
The crystal structure was solved by direct methods using SHELXS-97.22 Non-hydrogen atoms were first refined isotropically followed by anisotropic refinement by full matrix least-squares calculations based on F2 using SHELXL-97.22Hydrogen atoms were first located in the difference map and all CH hydrogen atoms were then positioned geometrically and allowed to ride on their respective parent atoms. NH hydrogen atom positions were allowed to refine freely and their isotropic thermal parameters were assigned as 1.2 times those of their parent atoms. Diagrams and publication material were generated using WinGx,23 ORTEP,24 PLATON25 and DIAMOND.26 Graph set notations were assigned using the program RPLUTO.27 Further crystallographic data are summarised in Table 1.
Footnote |
† CCDC reference numbers 649368–649372. For crystallographic data in CIF or other electronic format see DOI: 10.1039/b708333e |
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