Recensio

Sans résumé     

Theoretical study of the electronic properties of the purine and pyrimidine components of the nucleic acids

A semi-empirical self-consistent field calculation has been carried out for the purine and pyrimidine bases of the nucleic acids after an appropriate optimization of the integral values using reference compounds. Special emphasis has been laid upon results concerned with the ionization potentials, electron affinities, spectral transitions, triplet states, dipole moments and basicities of the compounds. They enable in particular a detailed interpretation of both the individual ultra-violet absorption spectra of the bases and of their interrelations.

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Zusammenfassung Ein semiempirisches SCF-Verfahren wurde zur Berechnung von Purin- und Pyrimidinbasen von NucleinsÄuren herangezogen, wobei besonderes Gewicht auf Ionisierungspotentiale, ElektronenaffinitÄten, spektrale übergÄnge, TriplettzustÄnde, Dipolmomente und BasizitÄten gelegt wurde. Insbesondere ist eine eingehende Interpretation der UV-Absorptions-spektren möglich, und zwar sowohl hinsichtlich der einzelnen Basen als auch deren Beziehungen untereinander.

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Résumé Un calcul self-consistent semi-empirique a été effectué pour les bases puriques et pyrimidiques des acides nucléiques, à l'aide d'un jeu d'intégrales déterminées de facon optimum pour une série de molécules de référence. L'accent a été mis en particulier sur les résultats relatifs aux potentiels d'ionisation, affinités électroniques, transitions ^*, états triplets, moments dipolaires et basicités. Il a été possible d'interpréter tant les spectres individuels des bases que leurs interrelations.

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This work was supported by grant No. GM 12289–01 of the United States Public Health Service (National Institute of General Medical Sciences).     

An SCFab initio investigation of the “through-water” interaction of the phosphate anion with the Na+ cation

SCFab initio computations in the supermolecule approach were carried out for the study of the hydration scheme of the dihydrogen phosphate anion, of the sodium cation and for the investigation of the direct and the through-water interaction of these two charged species. It is found that the energy balances of the direct phosphate-Na⁺ binding, involving their prior dehydration, or their through-water binding, allowing them to conserve their hydration shells, are of the same order of magnitude, indicating the competitivity of the two processes. This situation results in the existence of multiple possibilities for phosphate-Na⁺-water association. Appreciable energies of interaction exist between the different subunits of such systems. The Na⁺ cation and to a somewhat lesser extent the phosphate anion have a polarizing effect upon the charge distribution in the system over relatively appreciable distances. On the contrary, the charge transfers between the different components of the system are interpretable essentially in terms of displacements between adjacent units only.     

Steric accessibility of reactive centers in B-DNA

A method for calculating the “static” steric accessibilities of atoms within macromolecules for various probes is presented and an application is made to the accessibility of atoms within B-DNA. Changes in accessibility in passing from the individual subunits of the nucleic acid to a single helical strand and then to a double helix are discussed. The influence of various base sequences is also investigated. The present methodology and results are compared to earlier attempts at the calculation of steric accessibilities and their significance for the interpretation of chemical reactivity is substantiated by an illustrative example.     

An ab initio study of the hydration of alkylammonium groups

Ab initio STO 3G calculations of the electronic structure and interaction energies with water of methyl and ethylammonium ions are reported. It is shown that the calculations predict a preferential attack at the -group (relative to the nitrogen), in agreement with experimental facts, and that successive ethylation reduces the favorable energy of hydration.Further calculations show that due to the large positive charges on the hydrogens, direct C–H... O hydrogen bond formation is possible. Thus a water molecule forms such a hydrogen bond of - 10kcal/mole in NMe ₄ ⁺ ; of –9kcal/mole at an position in the ethylated ions and of –6 kcal/mole at a position. The a preference noted above is thus preserved. It seems unlikely that such interactions significantly change the overall hydration described above. Although twelve sites for H-bonding exist in NMe ₄ ⁺ , they approach each other rather closely and after addition of four water molecules further water molecules introduce such intermolecular repulsions as to reduce rather than increase the total hydration energy which remains always slightly lower than that obtained with water in the axial type of site described above [14].     

The calculation of molecular electrostatic potential from a multipole expansion based on localized orbitals and developed at their centroids: Accuracy and applicability for macromolecular computations

An improvement of a multipole expansion based on localized orbitals and termed LMTP is presented and its ability to generate accurate electrostatic potentials is demonstrated. The possibilities of using this expansion in studying the potential of different conformational states of a molecule without the necessity of recalculating its molecular wavefunction is described and the construction of macromolecular potentials by the superposition of the potentials of subunits is reconsidered.     

On the molecular electrostatic potentials obtained with CNDO and INDO wave functions

Molecular electrostatic potentials computed with CNDO/2 and INDO wave functions are shown to present systematic differences with respect to ab initio potentials in the case of out-of-plane potentials and in-plane vicinal hetero atoms in planar hetero molecules.     

Molecular electrostatic potentials of hydrogen-bonded systems: The oligomers of formamide

The modifications of the electrostatic molecular potential of formamide upon hydrogen bonding into various dimers and oligomers are presented and the predictive value of these potentials for assessing the strength of further hydrogen bonding is discussed. The potentials of long linear chains allow an understanding of the disposition of the molecules in the crystal.     

On the sites and mechanisms of alkylation in the nucleic acids

The intrinsic capacity (computed by ab initio molecular orbital techniques) of ethyl and methyl cations to bind to the anionic oxygens of the phosphate groups of the nucleic acids is found to be larger than their affinity for the carbonyl oxygens or for the nitrogens of the bases cytosine and guanine. Analysis of the components of the binding energies indicates that the preference of the ethyl cation for the oxygens of the phosphate or for those of the bases is due to different reasons. The results are discussed in connection with the available experimental observations.     

Ab initio molecular electrostatic potentials

The ab initio isopotential map of guanine is given and compared to that of adenine. It shows that in contrast to the situation in adenine, the most basic site of guanine is N₇ with a secondary potential minimum at O₆. These results as well as those concerning the secondary out-of-plane attractive regions over the NH₂ group and C₈ H bonds of the two molecules are discussed in connection with the available experimental knowledge concerning the bonding of alkylating carcinogens and mutagens.