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An unpredicted fourfold screw N—H
O hydrogen bond
C(4) motif in a primary dicarboxamide (
trans-cyclohexane-1,4-dicarboxamide, C
8H
14N
2O
2) was investigated by single-crystal X-ray diffraction and IR and Raman spectroscopies. Electron-density topology and intermolecular energy analyses determined from
ab initio calculations were employed to examine the influence of weak C—H
O hydrogen-bond interactions on the peculiar arrangement of molecules in the tetragonal
P4
32
12 space group. In addition, the way in which the co-operative effects of those weak bonds might modify their relative influence on molecular packing was estimated from cluster calculations. Based on the results, a structural model is proposed which helps to rationalize the unusual fourfold screw molecular arrangement.
Supporting information
CCDC reference: 1586317
Data collection: CrysAlis PRO (Agilent, 2014); cell refinement: CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis PRO (Agilent, 2014); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and
Mercury (Macrae et al., 2008); software used to prepare material for publication: PLATON (Spek, 2009) and PARST (Nardelli, 1995) within
WinGX (Farrugia, 2012).
trans-Cyclohexane-1,4-dicarboxamide
top
Crystal data top
C8H14N2O2 | Dx = 1.236 Mg m−3 |
Mr = 170.21 | Cu Kα radiation, λ = 1.54184 Å |
Tetragonal, P43212 | Cell parameters from 854 reflections |
Hall symbol: P 4nw 2abw | θ = 4.7–69.5° |
a = 6.9584 (2) Å | µ = 0.74 mm−1 |
c = 18.8979 (6) Å | T = 293 K |
V = 915.02 (6) Å3 | Frag, colourless |
Z = 4 | 0.25 × 0.12 × 0.12 mm |
F(000) = 368 | |
Data collection top
Agilent Xcalibur Eos Gemini diffractometer | 890 independent reflections |
Radiation source: Enhance (Cu) X-ray Source | 837 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.014 |
Detector resolution: 16.0604 pixels mm-1 | θmax = 72.0°, θmin = 6.8° |
ω scans | h = −8→8 |
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2014) | k = −6→7 |
Tmin = 0.893, Tmax = 1 | l = −11→23 |
1745 measured reflections | |
Refinement top
Refinement on F2 | Hydrogen site location: difference Fourier map |
Least-squares matrix: full | Only H-atom displacement parameters refined |
R[F2 > 2σ(F2)] = 0.044 | w = 1/[σ2(Fo2) + (0.075P)2 + 0.1598P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.130 | (Δ/σ)max < 0.001 |
S = 1.07 | Δρmax = 0.23 e Å−3 |
890 reflections | Δρmin = −0.13 e Å−3 |
68 parameters | Absolute structure: Flack x determined using 278 quotients [(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013) |
0 restraints | Absolute structure parameter: −0.1 (3) |
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. The measurements were performed on a Rigaku Oxford Diffraction EOS CCD
diffractometer with graphite-monochromated Cu Kα (λ = 1.54184 Å)
radiation. X-ray diffraction intensities were collected (ω scans with θ and
κ offsets), integrated and scaled with CrysAlis PRO (Agilent, 2014)
suite of programs. The unit-cell parameters were obtained by least-squares
refinement (based on the angular settings for all collected reflections with
intensities larger than seven times the standard deviation of measurement
errors) using CrysAlis PRO. Data were corrected empirically for
absorption employing the multi-scan method implemented in CrysAlis PRO.
The molecular structure was solved by direct methods with SHELXS and
the molecular model refined by full-matrix least-squares procedure with
SHELXL, both codes belong to the SHELX suite of programs (2008).
After non-hydrogen atoms were anisotropically refined, hydrogen atoms were
localized from Fourier difference maps and refined riding on bound atoms.
ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Macrae et al.,
2006) programs were used for structure analysis and to prepare material for
publication. Details of data collection and structure refinement are
summarized in Table 1. PLATON (Spek, 2009) and PARST (Nardelli,
1995) programs were used within WinGX (Farrugia, 2012) to prepare
tables for publication. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O5 | 0.3771 (3) | 1.0600 (3) | 0.54566 (9) | 0.0602 (6) | |
N6 | 0.3328 (4) | 1.0717 (4) | 0.42891 (11) | 0.0549 (7) | |
H62 | 0.367 (5) | 1.033 (6) | 0.3894 (17) | 0.067 (10)* | |
H61 | 0.245 (6) | 1.159 (6) | 0.4352 (17) | 0.070 (10)* | |
C4 | 0.4181 (3) | 1.0038 (3) | 0.48545 (11) | 0.0425 (6) | |
C1 | 0.5696 (4) | 0.8512 (4) | 0.47394 (12) | 0.0458 (6) | |
H11 | 0.5774 | 0.8366 | 0.4274 | 0.051 (8)* | |
C3 | 0.7604 (4) | 0.9142 (4) | 0.5055 (2) | 0.0696 (9) | |
H31 | 0.7398 | 0.9341 | 0.5572 | 0.072 (10)* | |
H32 | 0.7948 | 1.0401 | 0.4778 | 0.135 (18)* | |
C2 | 0.5077 (4) | 0.6614 (4) | 0.5047 (2) | 0.0694 (10) | |
H21 | 0.4976 | 0.6845 | 0.5572 | 0.073 (10)* | |
H22 | 0.3798 | 0.6212 | 0.481 | 0.084 (12)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O5 | 0.0700 (13) | 0.0727 (13) | 0.0379 (8) | 0.0316 (10) | −0.0028 (8) | −0.0087 (8) |
N6 | 0.0645 (14) | 0.0621 (14) | 0.0381 (10) | 0.0287 (12) | −0.0010 (9) | −0.0008 (9) |
C4 | 0.0455 (12) | 0.0434 (12) | 0.0387 (11) | 0.0097 (9) | −0.0002 (9) | −0.0026 (9) |
C1 | 0.0520 (14) | 0.0484 (13) | 0.0371 (10) | 0.0170 (11) | 0.0020 (10) | −0.0034 (9) |
C3 | 0.0443 (14) | 0.0422 (14) | 0.122 (3) | 0.0028 (12) | 0.0018 (17) | −0.0071 (16) |
C2 | 0.0384 (13) | 0.0478 (16) | 0.122 (3) | 0.0028 (12) | 0.0023 (17) | −0.0006 (17) |
Geometric parameters (Å, º) top
O5—C4 | 1.237 (3) | C1—H11 | 0.8876 |
N6—C4 | 1.311 (3) | C3—C3i | 1.528 (6) |
N6—H62 | 0.83 (3) | C3—H31 | 0.9969 |
N6—H61 | 0.87 (4) | C3—H32 | 1.0476 |
C4—C1 | 1.511 (3) | C2—C2i | 1.523 (5) |
C1—C2 | 1.506 (4) | C2—H21 | 1.0078 |
C1—C3 | 1.520 (4) | C2—H22 | 1.0349 |
| | | |
C4—N6—H62 | 119 (2) | C1—C3—C3i | 110.9 (2) |
C4—N6—H61 | 117 (2) | C1—C3—H31 | 107.4 |
H62—N6—H61 | 123 (3) | C3i—C3—H31 | 109.3 |
O5—C4—N6 | 122.1 (2) | C1—C3—H32 | 104.2 |
O5—C4—C1 | 121.1 (2) | C3i—C3—H32 | 111 |
N6—C4—C1 | 116.9 (2) | H31—C3—H32 | 113.9 |
C2—C1—C4 | 111.2 (2) | C1—C2—C2i | 111.7 (2) |
C2—C1—C3 | 110.6 (2) | C1—C2—H21 | 105.1 |
C4—C1—C3 | 110.5 (2) | C2i—C2—H21 | 106 |
C2—C1—H11 | 107.5 | C1—C2—H22 | 108.4 |
C4—C1—H11 | 105.4 | C2i—C2—H22 | 111.3 |
C3—C1—H11 | 111.6 | H21—C2—H22 | 114.2 |
| | | |
O5—C4—C1—C2 | 65.6 (4) | C2—C1—C3—C3i | 56.2 (4) |
N6—C4—C1—C2 | −114.0 (3) | C4—C1—C3—C3i | 179.6 (3) |
O5—C4—C1—C3 | −57.5 (4) | C4—C1—C2—C2i | −178.4 (3) |
N6—C4—C1—C3 | 122.8 (3) | C3—C1—C2—C2i | −55.3 (4) |
Symmetry code: (i) y, x, −z+1. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H62···O5ii | 0.83 (3) | 2.14 (4) | 2.955 (3) | 169 (4) |
N6—H61···O5iii | 0.87 (4) | 2.02 (4) | 2.889 (3) | 175 (4) |
N6—H62···O5ii | 0.83 (3) | 2.14 (4) | 2.955 (3) | 169 (4) |
N6—H61···O5iii | 0.87 (4) | 2.02 (4) | 2.889 (3) | 175 (4) |
C1—H11···O5ii | 0.89 | 2.68 | 3.492 (3) | 152.5 |
C2—H22···O5iv | 1.03 | 2.84 | 3.811 (4) | 155.6 |
C3—H32···O5v | 1.05 | 3.02 | 3.956 (4) | 149.7 |
Symmetry codes: (ii) −y+3/2, x+1/2, z−1/4; (iii) y−1, x+1, −z+1; (iv) y−1, x, −z+1; (v) y, x+1, −z+1. |
Geometries of selected intermolecular interaction calculated from full
optimized dimers at PBE/6-31G** theory level. X-ray difraction data in
parenthesisa topContact | Comp | H···O (Å) | X—H···O (°) | H···O═C (°) | X···O (Å) | N—C—O···H (°) |
N—Hs···O | 1 | 1.8091 [1.878] | 176.47 [174.2] | 120.05 [122.8] | 2.8377 [2.890 (3)] | -1.29 [5.9] |
| 2 | 1.7999 [1.907 (1)] | 176.06 [164.0] | 119.62 [118.8] | 2.8290 [2.897 (2)] | 0.00 [18.4] |
N—Ha···O | 1 | 1.9230 [1.956] | 175.98 [167.5] | 137.49 [135.0] | 2.9378 [2.955 (3)] | -164.96 [-137.8] |
| 2 | 1.9501 [1.935] | 167.70 [154.8] | 131.32 [126.5] | 2.9551 [2.886 (2)] | 160.58 [-138.3 (1)] |
C—Hin···O | 1 | 2.8655 [2.504] | 140.67 [150.1] | 121.90 [138.2] | 3.7803 [3.492 (3)] | 130.32 [140.2] |
| 2 | 2.5068 [2.654] | 146.42 [144.8] | 115.00 [129.5] | 3.4678 [3.599 (3)] | 123.58 [-146.8] |
C—Hout···O | 1 | 2.4895 [2.795 / 2.982] | 148.80 [155.3 / 150.1] | 109.22 [87.1 / 81.4] | 3.4730 [3.811 (4) / 3.957 (4)] | 85.15 [-81.8 / 78.3] |
| 2 | 2.2870 [2.612] | 177.59 [154.5] | 125.24 [93.4] | 3.3769 [3.625 (2)] | 87.27 [86.1] |
Note: (a) H-atom positions are corrected after normalizing
X—H bond lengths to neutron diffraction standard values. Hout and
Hin denote H atoms bonded to residue C atoms lying perpendicular and
parallel to the carboxamide plane, respectively. |
Values of the most relevant topological parameters of intermolecular (3,-1)
charge density CPs, evaluated at PBE/6-31G** theory level for clusters
I and IIa topContacts | Comp | ρ (e A-3) | \nabla2 (eA-5) | λ3 (eA-5) |
N—Hs···O | 1 | 0.2247 | 2.2884 | 4.5124 |
| 2 | 0.2314 | 2.4308 | 4.7490 |
N—Ha···O | 1 | 0.1566 | 1.7486 | 3.1217 |
| 2 | 0.1718 | 1.8356 | 3.3832 |
C—Hin···O | 1 | 0.0469 | 0.5597 | 0.8408 |
| 2 | 0.0803 | 0.8597 | 1.4336 |
C—Hout···O | 1 | 0.0453 | 0.5792 | 0.8289 |
| 2 | 0.0455 | 0.5647 | 0.8433 |
(a) ρ(r) electron density, its Laplacian,
\nabla2ρ(r),
and positive principal curvature, λ3, evaluated at the corresponding
(3,-1) critical points. |
Intermolecular energy calculated at MP2 and HF/aug-cc-pVDZ theory level using
the supermolecule and NBODel methods for dimers I, II and
III optimized at the PBE/6-31G** theory levela top | | | | | ΔE (kcal mol-1) | |
Cluster | Contacts | Nb | Comp | EMP2 | EHF | ENBOc |
I | N—Hs···O | 2 | 1 | -7.3 | -5.9 | -21.3 |
| | 2 | 2 | -7.5 | -6.2 | -22.2 |
II | N—Ha···O/C—Hin ···O | 2/2 | 1 | -10.1 | -4.9 | -14.6 |
| | 2 / 2 | 2 | -10.9 | -4.7 | -16.1 |
III | C—Hout···O | 4 | 1 | -1.8 | 0.0 | -3.0 |
| | 2 | 2 | -2.2 | -0.8 | -5.7 |
Notes: (a) intermolecular hydrogen bonds are labelled as
N—Hx···O and C—Hy···O, where subscript x =
a or s for antiplanar or synplanar carboxamide H atoms and y = in or
out for C—H groups oriented in or out of the carboxamide plane.
(b) The number of hydrogen bonds per molecule.
(c) Calculated as the dimer energy variation when the interacting
orbital are deleted, see text for further details. |
Electron acceptor and donor orbital population change topOverlapping orbitals | Δndonor (e)a | Δnacceptor (e)a |
| Dimer I | |
n(O) → σ*(Hs—N) | -0.03 | 0.03 |
| Dimer II | |
n(O) → σ*(Ha—N)/σ*(Hin—C) | -0.017 | 0.016/0.000b |
| Dimer III | |
π(C═O) → σ*(Hout–C)c | -0.002 | 0.002 |
(a) Population variations when interacting orbitals are deleted.
(b) As explained in the text, in the optimized geometry of the dimer
II, the H···O distance is too long as to alter significantly the
population of the σ*(Hin–C) antibonding orbital, but in the crystal
geometry it changes by about 0.002 e. (c) Optimized in the Ci
point group. |
Co-operative contribution to the interaction energy as a function of the
cluster size, calculated at MP2/6-31G(d,p) theory level. In parenthesis are
listed the calculated values at PBE/6-31G(d,p). topClusters series | Hydrogen bonds | Cluster size | |
| | Trimer | Tetramer |
I | N—Hs···O | -0.05 (-0.04) | -0.10 (-0.11) |
II | N—Ha···O + C—Hin···O | -1.02 (-0.92) | -2.40 (-2.42) |
III | C—Hout···O | 0.2 (0.3) | 0.6 (1.1) |
Topological analysis of selected contacts calculated at PBE/6-31G** theory
level for clusters I and IIa topContact | Comp | ρ | \nabla2 (e A-3) | λ3 (e A-3) | G (kcal mol-1) | V (kcal mol-1) | H (kcal mol-1) |
N—Hs···O | 1 | 0.2247 | 2.2884 | 4.5124 | 15.5 | -16.1 | -0.6 |
| 2 | 0.2314 | 2.4308 | 4.7490 | 16.3 | -16.7 | -0.4 |
N—Ha···O | 1 | 0.1566 | 1.7486 | 3.1217 | 11.6 | -11.9 | -0.3 |
| 2 | 0.1718 | 1.8356 | 3.3832 | 12.4 | -12.9 | -0.5 |
C—Hin···O | 1 | 0.0469 | 0.5597 | 0.8408 | 3.2 | -2.8 | 0.4 |
| 2 | 0.0803 | 0.8597 | 1.4336 | 5.6 | -5.5 | 0.1 |
C—Hout···O | 1 | 0.0453 | 0.5792 | 0.8289 | 3.3 | -2.7 | 0.6 |
| 2 | 0.0455 | 0.5647 | 0.8433 | 3.2 | -2.7 | 0.5 |
(a) ρ(r) electron density, its Laplacian,
\nable2ρ(r),
positive principal curvature, λ3, G(r) kinetic, V(r) potential and H(r)
total energy densities evaluated at the corresponding (3,-1) critical
points. |
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