Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison withab initio SCF computations

An additive procedure (SIBFA) is developed for the rapid computation of conformational energy variations in very large molecules. The macromolecule is built out of constitutive molecular fragments and the intramolecular energy is computed as a sum of interaction energies between the fragments. The electrostatic and the polarization components are calculated using multicenter multipole expansions of theab initio SCF electron density of the fragments. The repulsion component is obtained as a sum of bond and lone pair interactions.Tests of the procedure on a series of model compounds containing ether oxygens and pyridine-like nitrogens are reported and compared with the results of correspondingab initio SCF calculations. The resulting methodology is compatible with the simultaneous computation of intermolecular interactions.     

The electrostatic field of B-DNA

The electrostatic field associated with one complete turn of B-DNA is presented. Two base sequences poly (dG) · poly (dC) and poly (dA) · poly (dT) are studied and the effects of sodium counterions bound to the nucleic acid are investigated. The contrasts between the electrostatic potential and the electrostatic field of the macromolecules are discussed and the possible applications of the field are considered.     

Molecular orbital studies on the conformation of GABA (γ-aminobutyric acid)

In distinction to Extended Hückel Theory which predicts as the most stable conformation of free zwitterionic GABA a totally extended form, PCILO and SCF ab initio studies show that the intrinsically preferred conformation of the isolated molecule is a highly folded one, resulting from strong interactions between the two charged ends. Computations are also carried out for hydrated GABA in the supermolecule approach allowing moreover for the flexibility of binding of some of the water molecules of the first hydration shell. They predict the coexistence in solution of a large number of conformations showing different degrees of folding (or extension), a result confirmed by recent NMR studies. This and a number of similar results show that we have to adapt our thinking on the role of conformations in pharmacological activity to this situation, which was frequently obscured by the more abundant results of X-ray crystallography yielding a single conformation.     

Ab initio study of a purine nucleoside: Adenosine

The ab initio SCF LCAO-MO method is used to compute the main electronic properties of a purine nucleoside, adenosine, in two specific conformational arrangements (3′-endo conformation of the ribose, gt orientation of the extracyclic CH₂OH group, anti orientation of the base with respect to the sugar and 3′-endo conformation of the ribose, gg orientation of the extra-cyclic CH₂OH group, syn orientation of the base with respect to the sugar). The results are compared with those performed for the isolated component fragments, adenine and 3′-endo riboses.     

Studies of solvent effects

The effect of water on the conformational preferences of acetylcholine has been studied within the discrete, the continuum and the combined discrete-continuum models described in parts I and II of this series. All the models lead to the conclusion that the trans-gauche form which is, following refined quantum-mechanical computations, the intrinsically preferred one and the one observed in the crystal of acetylcholine and of a number of analogues should remain also the preferred conformation in water. This result agrees with NMR studies. The results of the empirical discrete model used here compare favorably to those obtained by an ab initio super-molecule treatment. The continuum model utilized here represents a net improvement above such models utilized in other works.     

On the affinities of ammonia and water for Li, Na and K

The affinities of ammonia for Na⁺ and K⁺, recently determined experimentally, have been computed by the ab initio SCF method using ended polarized gaussian basis sets and shown to be satisfactory Furthermore, the corresponding values computed at the same level of accuracy for the three cations Li⁺, Na⁺, K⁺ and the two ligands NH₃ and H₂O are shown to yield the order Li⁺ > Na⁺ > K⁺ for each ligand and NH₃ > H₂O for each ion, in agreement with experiment. An analysis of the factors involved in the binding provides a consistent rationalization of these regularities and of some observed correlations.     

Hydration scheme of uracil and cytosine

The comparison of a pure electrostatic approximation and complete supermolecule SCF ab initio computations on the hydration scheme of uracil and cytosine shows that the electrostatic procedure is capable to reproduce the general aspects of the results of the supermolecule treatment provided that different distances of shortest approach be adopted for the distances between the oxygen of water and the nitrogen of NH₂ or NH groups or the oxygen of C-O groups on the one hand and the oxygen of water and pyridine-type nitrogens on the other hand.     

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%.     

Molecular orbital calculations on the conformation of nucleic acids and their constituents

The conformational properties of the furanose ring of purine- and pyrimidine--nucleosides and-nucleotides are studied quantum-mechanically with the help of the PCILO method, using the pseudorotational concept. The computations point to the existence of two stable conformational zones centered around the C(3)-endo and C(2)-endo conformations which in the isolated furanose ring are separated by barriers of the order of 4 kcal/mole. In nucleosides one of the barriers (the one running through the O(1)-exo-C(2)-exo path) becomes very high. A detailed study is made of the relation between the phase angle of pseudorotation, P, and the torsion angle about the glycosyl bond, _CN. A very satisfactory agreement with the available experimental data is observed.

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Zusammenfassung Die Konformationseigenschaften des Furanoserings in -Nucleosiden und Nucleotiden von Purin und Pyrimidin werden nach der PCILO-Methode unter Berücksichtigung der pseudorotatorischen Betrachtungsweise studiert. Die Rechnung läßt auf die Existenz zweier stabiler Konformationszonen schließen, die in der Umgebung der C(2)-endo und der C(3)-endo Konformationen liegen, und die im isolierten Furanosering durch Energiebarrieren der Größenordnung von 4 kcal/mol voneinander getrennt sind. In Nucleosiden wird eine der Barrieren (die durch den Weg O(1)-exo-C(2)-exo gekennzeichnete) sehr hoch. Die Relation zwischen dem Phasenwinkel der Pseudorotation, P, und dem Drehwinkel um die Glycosylbindung, _CN, wird einer eingehenden Untersuchung unterworfen. Man beobachtet eine sehr zufriedenstellende Übereinstimmung mit den verfügbaren experimentellen Daten.

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Résumé Les propriétés conformationnelles du noyau furanose des -nucleosides et nucleotides des purines et pyrimidines sont étudiées par la méthode PCILO en faisant appel au concept de la pseudorotation. Les calculs indiquent l'existence de deux zones de conformations stables, centrées autour des conformations C(2)-endo et C(3)-endo, qui sont dans le sucre isolé séparées par des barrières de l'ordre de 4 kcal/mole. Dans les nucleosides, l'une de ces barrières (celle qui passe par le chemin O(1)-exo-C(2)-exo) devient très élevée. Une étude détaillée est effectuée sur la relation entre l'angle de phase de la pseudorotation P et l'angle de torsion autour de la liaison glycosylique, _CN. Un excellent accord avec les données expérimentales disponibles est observé.

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This research was supported by the R.C.P. 173 and the A.T.P. A 655-2303 of the C.N.R.S.     

Molecular orbital calculations on the conformation of polypeptides and proteins

The conformational energy maps are computed for the lysyl and the arginyl residues with the help of the quantum-mechanical method PCILO. Because of the relatively very large number of the possible combinations of the side chain rotational angles, sub-maps are constructed only for the most common such combinations as indicated from the X-rays study of ten globular proteins. These submaps are then combined for the construction of the general conformational energy map. The comparison of the theoretically allowed and experimentally observed values of backbone dihedral angles and for the lysyl and arginyl residues in the globular proteins indicates a very satisfactory agreement among the two. These results confirm that the contour of the stable zone on the conformational energy map depends primarily on ¹ but indicate also that its fine structure is sensitive to the remaining 's in particular to ².

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Zusammenfassung Diagramme der Konformationsenergie werden für den Lysyl- sowie den Arginylrest mit Hilfe der quantenmechanischen PCILO-Methode berechnet. Wegen der großen Zahl möglicher Kombinationen der Rotationswinkel der Seitenketten werden Teildiagramme nur für die wichtigsten derartigen Kombinationen, die bei Untersuchungen nach der Röntgenstrahlmethode an zehn globulären Proteinen gefunden wurden, konstruiert. Diese Teildiagramme werden dann zum Gesamtdiagramm der Konformationsenergie kombiniert. Die Übereinstimmung zwischen experimentellen und theoretisch erlaubten Winkeln und der Hauptkette und den Lysyl- und Arginylresten ist sehr zufriedenstellend. Diese Ergebnisse bestätigen, daß der stabile Bereich des Diagramms der Konformationsenergie hauptsächlich von ¹ abhängt; sie zeigen aber auch, daß seine genaue Struktur von den übrigen -Werten beeinflußt wird, insbesondere von ².

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Résumé Les cartes d'énergie conformationelle des résidus lysyle et arginyle sont construites à l'aide de la méthode PCILO de la Chimie Quantique. A cause du nombre très élevé des combinaisons possibles des angles rotationnels de la chaîne latérale, des sous-cartes sont construites pour les plus fréquentes seulement de ces combinaisons (selon les indications de l'étude aux rayons X de dix protéines globulaires). Ces sous-cartes sont ensuite combinées pour la construction de la carte générale d'énergie conformationnelle. La comparaison des valeurs théoriques et expérimentales des angles et de la chaîne principale pour les résidus lysyle et arginyle des protéines indique un accord très satisfaisant entre les deux. Ces résultats confirment que le contour de la zone stable sur la carte d'énergie conformationnelle est déterminé principalement par la valeur de ₁ mais indiquent aussi que la structure fine de cette zone est sensible aux valeurs des supérieurs, en particulier de ².

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This work was supported by grant n 67-00-532 of the Délégation Générale à la Recherche Scientifique et Technique (Comité de Biologie Moléculaire).