Search results for "Intermolecular"
showing 10 items of 396 documents
On the structure of 3-acetylamino-5-methyl-1,2,4-oxadiazole and on the fully degenerate rearrangements (FDR) of its anion: a stimulating comparison b…
2009
An accurate crystal structure determination has provided evidence for a planar conformation for 3-acetylamino-5-methyl-1,2,4-oxadiazole (5), in agreement with quantum-mechanical calculations in the gas phase. In the crystal, a series of strong intermolecular N7H7….O9 hydrogen bonds link the amido groups of different molecules, causing the formation of infinite parallel ordered chains. The effect of the DMSO solvent on the energy and charge distribution of compound 5 and on its relevant 5− anion, involved in a fully degenerate rearrangement (FDR), has been deepened by quantum-mechanical DFT calculations. The calculated energy barrier for the FDR increases in going from in vacuo to DMSO, in a…
Intra- and intermolecular forces dependent main chain conformations of esters of α,β-dehydroamino acids
2013
Abstract Esters of dehydroamino acids occur in nature. To investigate their conformational properties, the low-temperature structures of Ac-ΔAla-OMe, Ac-ΔVal-OMe, Z-(Z)-ΔAbu-OMe, and Z-(Z)-ΔAbu-NHMe were studied by single-crystal X-ray diffraction. The ΔAla ester prefers the fully extended conformation C5. Both the ΔVal and (Z)-ΔAbu esters assume the conformation β, whereas the amide analogue of the latter prefers the conformation α. For the conformations found, DFT calculations using B3LYP/6-311++G(d,p) with the SCRF-PCM and M062X/6-311++G(d,p) with the SCRF-SMD method were applied to mimicking chloroform and water environment. The tendency of the ΔVal and (Z)-ΔAbu esters towards the confo…
Energetics of conformational conversion between 1,1,2-trichloroethane polymorphs
2008
Pressure-induced transformations between gauche-, gauche+ and transoid conformations have been evidenced by X-ray single-crystal diffraction for 1,1,2-trichloroethane, and the energies of intermolecular interactions, conformational conversion, and the latent heat have been determined.
Columnar supramolecular architecture of crystals of 2-(4-Iodophenyl)-1,10-phenanthroline derived from values of intermolecular interaction energy
2011
Using results of X-ray diffraction study supramolecular architecture of crystals of 2-(4-iodophenyl)-1,10-phenanthroline has been analyzed on the basis of quantum-chemical calculations of intermolecular interactions energy. It is demonstrated that these crystals have three levels of organization. Molecules form stacked dimers with the highest binding energy (first level). These dimers represent basic unit of infinite columns stabilized by stacking interactions between dimers (second level). The energy of intermolecular interactions between neighbouring stacked columns is very close. This does not allow to figure out any layers in the crystal. Therefore crystals of this compound have columna…
Revisiting the charge density analysis of 2,5-dichloro-1,4-benzoquinone at 20 K
2017
A high-resolution X-ray diffraction measurement of 2,5-dichloro-1,4-benzoquinone (DCBQ) at 20 K was carried out. The experimental charge density was modeled using the Hansen–Coppens multipolar expansion and the topology of the electron density was analyzed in terms of the quantum theory of atoms in molecules (QTAIM). Two different multipole models, predominantly differentiated by the treatment of the chlorine atom, were obtained. The experimental results have been compared to theoretical results in the form of a multipolar refinement against theoretical structure factors and through direct topological analysis of the electron density obtained from the optimized periodic wavefunction. The si…
A noncentrosymmetric crystal structure of a zwitterionic compound, pyridinium 5,7-dihydro-5,7-dioxo-6H-cyclopenta[b]pyridin-6-ylide, realized by weak…
2009
Abstract Crystal structures of pyridinium 1,3-dihydro-1,3-dioxo-2 H -inden-2-ylide (PI) of a zwitterionic molecule and its nitrogen substituted compounds, 4N-PI and 5N-PI, were solved with X-ray diffraction analyses. Whereas PI and 5N-PI showed centrosymmetric crystal structures, 4N-PI demonstrated a noncentrosymmetric crystal structure where all the molecules orient to almost the same direction. To elucidate the stability of such a polarized structure, we examined interatomic close contacts among the nearest neighbor molecules in the crystals and calculated intermolecular interaction energies with relation to those contacts. As a result, the noncentrosymmetric crystal structure of 4N-PI tu…
Competition between inter- and intra- molecular energy exchanges in a simple quantum model of a dimer
2006
Abstract We propose a fully quantum model to describe the dynamics of a possible radiationless energy transfer process between identical and nearly localized molecules or monomers coupled through a dipole–dipole term. The system is studied as an environmentally isolated dimeric pair and we find that its dynamics exhibits a competition between the process ruling out the transfer of energy among different degrees of freedom of a given monomer and the one steering the intermolecular passage of excitations from a monomer to the other one. Such a competition is quantitatively characterized investigating on the temporal behaviour of quantum covariances of some couples of appropriate observables h…
Inter- and intramolecular bonding in 1,3,5-triamino-2,4,6-trinitrobenzene: An experimental and theoretical quantum theory of atoms in molecules (QTAI…
2017
Chemical bonding in the triclinic phase of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) has been analyzed based on the experimental electron density derived from X-ray diffraction data obtained at 20 K. The results have been compared with those from solid state theoretical calculations. The total electron density has been analyzed in terms of the Quantum Theory of Atoms in Molecules (QTAIM). Features of the covalent bonds demonstrate the presence of multiple bonds of various order. Strong intramolecular hydrogen bonds and weaker intermolecular bonds within the layer structure are characterized by the properties of their (3, −1) critical points. Weaker interactions, predominantly O···O, betwe…
Hydrogen-Bond Cooperative Effects in Small Cyclic Water Clusters as Revealed by the Interacting Quantum Atoms Approach
2013
The cooperative effects of hydrogen bonding in small water clus- ters (H2O)n (n = 3-6) have been studied by using the partition of the electronic energy in accordance with the interact- ing quantum atoms (IQA) approach. The IQA energy splitting is comple- mented by a topological analysis of the electron density (1(r)) compliant with the quantum theory of atoms-in-mole- cules (QTAIM) and the calculation of electrostatic interactions by using one- and two-electron integrals, thereby avoiding convergence issues inherent to a multipolar expansion. The results show that the cooperative effects of hy- drogen bonding in small water clusters arise from a compromise between: 1) the deformation energ…
Similarities and differences between crystal and enzyme environmental effects on the electron density of drug molecules
2021
Abstract The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low‐molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. Howeve…