Non-bonded interactions of atoms in organic crystals and molecules

Abstract

E O S , U L . V A V I L O V A 2 8 , M O S C O W -V -3 1 2 , U . S . S . R . Mechanical Model of MoleculesThe word 'molecule' may be used in two different meanings. Speaking about a 'common salt molecule' we have in mind the finest representative of this substance: one sodium atom and one chlorine atom make up a common salt molecule. However, a common salt particle consisting of one sodium and one chlorine atom does not exist in nature. When dissolved, this substance dissociates into ions. In solids, each positively or negatively charged ion has six neighbouring ions of the opposite sign located at equal distances. The same happens in the melted substance, the only difference being that the co-ordination number of six is realized here 'on the average'.Speaking about a 'naphthalene molecule' we also mean the smallest representative of this substance, but unlike the previous example a naphthalene molecule, composed of ten carbon atoms and eight hydrogen atoms, exists as a separate particle in solids, solutions, or melts and in a gaseous state.Most inorganic substances behave as common salt. In inorganic substances we do not have, as a rule, to subdivide interactions into valence and non-valence (non-bonded) types. On the contrary, in the okerwhelming majority of organic substances this distinction is completely obvious.Experimental studies of the structure and properties of organic molecules and crystals, as well as practical work on chemical synthesis, testify that the model of an organic molecule in the form of a set of atoms linked by 'springs' in conformity with a valence scheme is a very good approximation to its actual structure. This model, which may quite appropriately be called a mechanical model, has great predictability in almost all the spheres of physical chemistry and can be equally well applied to many problems of synthetic organic chemistry. About 30 years ago, approximarely at the same time and independently of one another, Hill,1 Westheimer,2 and the present author3 showed that a mechanical model may acquire quantitative characteristics. However, its 'computation value' for predicting the geometry of molecules and crystals and for calculating their properties was demonstrated only after the emergence of computers.The mechanical model is based on the concept that each atom in a molecule calculated the path of isomerization. The angles of rotation about the C-3-C-4 and C-2-C-3 bonds are plotted along the rotation axes. The displacements of 7 2 V. G . Dashevsky and A. A. Lugovsky, J . Mol. Structure, 1972, 12, 39. 153

Further justification for the exo-anomeric effect. Conformational analysis based on nuclear magnetic resonance spectroscopy of oligosaccharides

“…In the case of the PDGal units, the spacings that reflect J,,, = 7.8 Hz and J,,,, = 4.3 Hz require that the hydroxymethyl group exist largely in a conformer that has one of the hydrogen atoms at C6 in anti-periplanar relationship to H5; i.e., either 2(4)b or c. This situation was also observed for methyl P-D-galactopyranoside (2) (1). The signals for H6 and H6' could also be sufficiently resolved at 400 MHz to provide this information in the case of methyl a-D-galactopyranoside (4). ABX analysis of the H5, H6, and H6' protons gave J,,, = 8.2 Hz and J,,6, = 4.6Hz.…”

Crystal structures of polynuclear aromatic hydrocarbons. Classification, rationalization and prediction from molecular structure

“…Potential packing energies have been computed using atom-atom pairwise potentials as described previously (Gavezzotti & Desiraju, 1988) for all compounds for which a full structure determination is available. There has been a debate on whether the (6-exp) and similar formulations are adequate to quantitatively describe the intermolecular potential energy of aromatics, or whether the introduction of other terms in the potential expression is necessary (Kitaigorodskii, 1973(Kitaigorodskii, , 1978Williams, 1974;Williams & Starr, 1977). Our line of thought is in agreement with recent views (Pertsin & Kitaigorodskii, 1987) on nonbonded potentials in general; the use of optimized potentials which do not include explicit Coulomb terms does not mean that electrostatic interactions are altogether neglected.…”

Nonbonded potentials for azahydrocarbons: the importance of the Coulombic interaction

“…The decision whether to define element subtypes will depend on the amount of variation of the nonbonded characteristics of the element in different bonding situations and on the desired accuracy. Kitaigorodsky (1978) has emphasized the desirability of using the same nonbonded potential for each element regardless of its bonding environment in the molecule. In practice we have set up as our desired accuracy targets for prediction of crystal structures the following 'threshold' values (Hsu & Williams, 1980): 1% for the lattice constants, 1 ° in the cell angles, 2 ° in the molecular rotation in the cell, and 0.1 A in the molecular translation in the cell..The idea of threshold accuracy is that nonbonded potentials which give predictions better than the threshold are deemed to be fully satisfactory.…”