Publisher Summary This chapter discusses a model that relies on the knowledge of the molecular electrostatic potential, which is derived from a molecular wavefunction by using the usual methods for calculating the mean expectation value of an operator. In its basic premises the model employs quantum mechanics, with only the approximations necessary in molecular quantal calculations. The model is also discussed regarding its relationships with the Hellmann–Feynman theorem. The electrostatic potential V itself is examined in order to show how the electrostatic potential reflects the characteristics of the electronic distribution of a molecule and then the reliability of V is discussed as a reactivity index. The shape of the electrostatic potential and its relationship to the electronic molecular structure is discussed with the aid of various examples. One of them includes the glycine tautomers and the corresponding anion example. The chapter also discusses the electrostatic molecular potential in terms of local group contributions.

Electronic Molecular Structure, Reactivity and Intermolecular Forces: An Euristic Interpretation by Means of Electrostatic Molecular Potentials

In this work, we present a sound modified implementation of the noniterative approach for the inclusion of solvent effects for molecular-shaped cavities in conventional ab initio gas phase computations. This model will serve as the starting point from which to add additional influences such as nonelectrostatic and correlation effects, as well as optimization of cavity radii. The improvement over recent dielectric continuum models is (a) the utilization of distributed multipoles up to hexadecapoles for the generation of the potential on the cavity boundary to the dielectric and the calculation of surface charges, and (b) an accurate assessment of outlying charge effects. The new method is tested in calculations of solvation energies and geometries for a number of neutral and charged molecules.

First Principles Implementation of Solvent Effects Without Outlying Charge Error

A dynamic technique, using radioactivity as a means of detection, makes it possible to measure the partial pressures of highly polar compounds in dilute aqueous solution. The results can be expressed in terms of the dimensionless distribution coefficient for transfer of a compound from dilute aqueous solution to the vapor phase. For acetic acid this coefficient is 1.1 X 10(-5), for acetamide 7.6 X 10(-8), for N-methylacetamide 4.1 X 10(-8), and for N,N-dimethylacetamide 5.4 X 10(-7). Thus acetamide is much more strongly solvated than the uncharged acetic acid molecule. The results suggest: (1) that the peptide bond represents an extreme among uncharged functional groups in the degree to which it is stabilized by solvent water; (2) that the very great hydrophilic character of the peptide bond may be associated mainly with hydrogen bonding of the solvent to the carbonyl oxygen atom (rather than the N-H group); and (3) that the observed equilibria of biosynthesis and hydrolysis of peptide bonds in aqueous solution are largely determined by differences between reactants and products in their free energies of solvation. It is anticipated that where "bound" water is found in proteins, it will often be found to be associated with peptide bonds, and will tend to be associated with the C-O group rather than with the N-H group.

Interaction of the peptide bond with solvent water: a vapor phase analysis.

This review is devoted to the presentation of recent developments in a field of theoretical molecular biophysics which seem to open large possibilities for progress in a hitherto relatively unexplored although very important direction. It is concerned with the establishment of a new methodology in the molecular orbital approach to the problem of the solvation of biological molecules. The methodology is still in an initial stage, susceptible of many refinements and its practical applications may also be considered as being in their beginnings. Nevertheless the successes obtained so far and the interest which they aroused in a number of laboratories incite us to present already now the general principles and the available results so as to offer a possibility of evaluating the advantages, present-day limitations and future potentialities of the procedure, which could then be explored by all those interested. This review may thus be said to be to a large extent oriented towards the future, with the acknowledged aim of producing an acceleration and widening of researches in this field. Possible progress in this respect is interesting from a double point of view.

New paths in the molecular orbital approach to solvation of biological molecules.

Ab initio calculations of hydrogen bond energies for a number of water–formamide and methanol–formamide complexes are reported at both the SCF and correlated levels. Full gradient optimizations of these structures have been performed for basis sets of double zeta and double zeta plus polarization quality. For both water and methanol, the most stable 1:1 complex is found to be a cyclic double hydrogen bonded structure. Basis set effects on the calculated hydrogen bond energies were investigated as was the magnitude of the basis set superposition error. In all cases investigated, the addition of polarization functions to the basis set is found to decrease the calculated binding energy by approximately 2–4 kcal/mol, while correlation is found to increase the binding energy by ≂1 kcal/mol. Calculations on dihydrated formamide indicate a small three‐body contribution to the total binding energy.

Ab initio study of the hydrogen bonding interactions of formamide with water and methanol

As a first step in a general quantum-mechanical investigation of environmental effects on the structure and properties of biomolecules, the non-empirical ab initio self-consistent field molecular orbital method has been employed for the determination of the principal hydration sites of formamide and of the essential characteristics of the monohydrates. In view of the extension of the study to more complex systems, the validity of a simplified treatment taking into account only the electrostatic parts of the interaction energy between formamide and water has also been investigated.

Quantum-mechanical studies of environmental effects on biomolecules. I. Hydration of formamide.

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Quantum-mechanical studies of environmental effects on biomolecules. I. Hydration of formamide.