Non empirical quantum mechanical calculations of the1H,13C,15N and17O magnetic shielding constants and of the spin-spin coupling constants in formamide,hydrated formamide and N-methylformamide

The magnetic shielding constants of the different atoms of formamide, hydrated formamide and N-methylformamide are calculated by anab initio method. For the protons of formamide the measured differences between their chemical shifts are correctly reproduced by theory, provided that the molecular geometry used as input is carefully chosen. The differences between the values of the magnetic shielding constants calculated for formamide and hydrated formamide show that intermolecular hydrogen bonding produces variations of chemical shifts for all the atoms of the molecule except the formyl proton. The calculated chemical shift variations between formamide and N-methylformamide are compared to the experimental values and discussed in relation with different hydrogen bonding possibilities of the two molecules. The calculation of the contact term of the spin-spin coupling constants of formamide and hydrated formamide shows that in most cases the measured trends are satisfactorily reproduced and that the variations of these terms upon hydration are less than 3%.     

Theoretical study of the electronic properties of biological purines and pyrimidines

In view of a study of the atypical bases of the nucleic acids, the integral values appropriate for the methyl substituent have been determined in the SCF approximation previously described [1]. Both the inductive and the hyperconjugation effects have been introduced. An application to thymine is described.     

Cation-binding to biomolecules

Ab initio SCF MO computations are performed on the binding of the Na⁺ ion to the purine and pyrimidine bases of the nucleic acids. The results are compared in particular with those of previous studies on proton affinities. The computations indicate two principal differences between these two types of interactions: 1) the increased significance in cation binding of the individual oxygen binding sites in bases containing both oxygen and nitrogen; 2) the appearance in cytosine and guanine of bridged positions between a nitrogen and a carbonyl oxygen as the preferred binding sites. The theoretical results are compared with the available experimental data. Their general significance for cation binding is discussed.     

The molecular electrostatic potential of the B-DNA helix

The overlap multipole expansion procedure is utilized for the evaluation of the component of the electrostatic molecular potential of the B-DNA helix due to its sugar-phosphate backbone. The overall shape of the potential, its extension in space, the location of the minima and the differences in the values of the potential in particularly significant regions (minor and major grooves, vicinity of the phosphates) are indicated. The isopotential surfaces are practically cylindrical at distances larger than 15 Å from the helix axis but exhibit a more complex structure at shorter distances.This paper is dedicated to Professor H. Hartmann on the occasion of his 65th birthday.     

The electrostatic molecular potential of yeast tRNAPhe. III. The molecular potential and the steric acessibility associated with the phosphate groups

The molecular electrostatic potential of yeast tRNA^Phe is calculated at sites bridging the anionic oxygens of each of the 76 phosphate groups of the molecule. A quantitative measure of the steric accessibility of the anionic oxygens of the phosphates toward a spherical cation is presented. Both the resulting potentials and accessibilities are discussed in terms of the molecular and electronic structure of tRNA.     

Quantum-mechanical studies of environmental effects on biomolecules VI.Ab initio Studies on the hydration scheme of the phosphate group

Ab initio SCF computations using the STO 3G basis set have been performed on the hydration scheme of the dimethylphosphate anion (DMP^?) within the “supermolecule” approach. This model compound represents the phosphate group in nucleic acids, phospholipid components of membranes and a number of other important biological structures. In the first place the principal hydration sites for the fixation of a water molecule have been established and this was followed by the determination of the polyhydration scheme of the first solvation shell, which may involve up to six water molecules. The effect of hydration on the relative stabilities of thegg,gt andtt forms of (DMP^?) was evaluated. The study was extended to the computation of the energies of interaction in the second and third hydration shells and the conclusion was reached that organized hydration around (DMP^?) is essentially limited to two hydration shells with possible residual organization of a third shell around specific sites. The structure of the bound water was investigated. Charge transfer is observed from (DMP^?) to the bound water, the perturbation extending essentially to the first and with decreasing intensity, to the second hydration shell.     

An ab initio study of the effect of the 3d orbitals of phosphorus on the properties of the phosphate group

A large number of properties of the dimethylphosphate anion (DMP^?), model system for the phosphate group of the nucleic acids and the phospholipid components of membranes, has been investigated by the SCF ab initio procedure including the 3d orbitals of the phosphorus atom in the gaussian basis set and the results of the computations were compared with similar results obtained previously without taking these orbitals into account. The properties investigated include the conformational states of DMP with respect to the torsion about the P-O_ester bonds, the distribution of the electronic charges, the molecular electrostatic potentials generated by DMP^?, the characteristics of the molecular orbitals, particularly the electronic isodensity maps, the hydration scheme. Qualitatively, the introduction of the 3d orbitals modifies little the general aspects of the results obtained for most of the properties studied. On the quantitative level significant, although generally not great, modifications may be noticed with respect to some features of these properties. One of the strongest influences of the introduction of the 3d orbitals concerns the decrease of the net electronic charges in DMP^?.     

Cation-binding to biomolecules

Ab initio SCF computations indicate that Mg²⁺ should bind essentially to the oxygen atoms of uracil, the remaining part of the base being rather repulsive towards such an interaction. The Coulombic component predominates in the interaction, the essential feature of which may thus be deduced from the study of the molecular electrostatic potential of uracil. These ab initio results contradict an earlier CNDO prediction that the binding of uracil and Mg²⁺ should occur preferentially at the C₅=C₆ double bond of the base. It is shown that the CNDO result is an artifact due to an exaggeration by this method of the charge transfer between the ligand and the cation. The small amount of available experimental data seem in favor of the ab initio results.     

Quantum mechanical studies of environmental effects on biomolecules

LCAO SCF calculations with a (7s, 3p/3s) atomic basis are performed on urea and hydrated urea in order to determine the preferred sites of water fixation using the supermolecule approach. It appears that up to five water molecules can be directly bound to urea in the first hydration shell.