Conformational analysis: crystallographic, molecular mechanics and quantum chemical studies of C—H...O hydrogen bonding in the flexible bis(nosylate) derivative of catechol

Abstract

The single-crystal X-ray diffraction analysis of 2-[[(4-nitrophenoxy)sulfonyl]oxy]phenyl 4-nitrophenyl sulfate (4) reveals that an interesting intermolecular or extended structure (a one-dimensional hydrogen-bonded polymer) is formed because of pairs of intermolecular (aryl)C--H...O(nitro) hydrogen bonds between the C(2) symmetry monomer units. The axis of the hydrogen-bonded polymer runs co-linear with the [101] face diagonal of the monoclinic unit cell. Molecular mechanics calculations using a modified version of the MM+ force field and a random conformational search algorithm have been used to locate the important low-energy in vacuo conformations of (4). The MM-calculated conformation of (4) that most closely matches the X-ray structure lies some 26.5 kJ mol(-1) higher in energy than the global minimum-energy conformation, consistent with the notion that the crystallographically observed molecular architecture of (4) is a local energy minimum in the absence of its crystal lattice environment. Since the X-ray conformation of (4) was correctly calculated only when all of the neighbouring molecules in the crystal lattice were included in the simulation, hydrogen bonding and other non-bonded interactions in the crystal lattice clearly dictate the experimentally observed conformation of (4). Quantum chemical calculations (AM1 method) confirm the critical role played by the intermolecular (aryl)C--H...O(nitro) hydrogen bonds in controlling the crystallographically observed conformation of (4) and show that self-recognition in this system by hydrogen bonding is favoured on electrostatic grounds. Collectively, the molecular simulations suggest that because the lowest-energy molecular conformation of (4) does not permit the formation of an extended hydrogen-bonded 'supramolecular' structure, it is not the preferred conformation in the crystalline solid state.

Crystal Structure and Stereochemistry Study of 2-Substituted Benzoxazole Derivatives

“…This is in agreement with what was reported in the literature showing that the effects of hydrogen-bonding and van der Waals interactions in the crystal structure cause the molecules to adopt higher-energy conformations, which correspond to local minima in the molecular potential energy surface [28]. This result in consent with the reported notation, which states that the crystallographically observed molecular architecture is a local energy minimum in the absence of its crystal lattice environment [29]. …”

Crystal Structure and Molecular Mechanics Modelling of 2-(4-Amino-3-benzyl-2-thioxo-2,3-dihydrothiazol-5-yl)benzoxazole

“…This variation may be due to the experimental structure of the investigated compounds in crystal conditions; that is, the neighbouring molecules, hydrogen bonding, and other nonbonded interactions in the crystal lattice environment are taken into account, in agreement with what was reported in literature showing that the effects of hydrogen-bonding and van der Waals interactions in the crystal structure cause the molecules to adopt higher energy conformations, which correspond to local minima in the molecular potential energy surface [24]. Also, in consent with the notation, which states that the crystallographically observed molecular architecture is a local energy minimum in the absence of its crystal lattice environment [25].…”

Molecular Recognition: Preorganization of a Bis(pyrrole) Schiff Base Derivative for Tight Dimerization by Hydrogen Bonding

“…Finally, the self-association constant K D measured from the fit of the data for the imine C À H proton resonance (Figure 6 a) is experimentally equivalent to that measured from the concentration dependence of the pyrrole N À H resonance, thus implying an internally consistent method for quantifying the self-association constant in this system. Molecular simulations: Semi-empirical quantum mechanics simulations using methods such as AM1 are not only computationally efficient, but are widely recognized as being sufficiently accurate for simulations on medium to large hydrogen-bonded supramolecular species with both strong [11,14,38] and weak [39,40] hydrogen bonds. Using this method, our computational objectives were to: 1) fully map the region of conformational space encompassing the X-ray conformations for 4 in an effort to further understand the marked nonplanarity of each monomer conformation observed in the crystal lattice, 2) determine the structures and energies of the global and local minima accessible to 4, 3) determine the in vacuo enthalpy of association of the dimer- …”