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.     

PICOSECOND FLUORESCENCE STUDY OF PHOTOSYNTHETIC MUTANTS OF Chlamydomonas reinhardii: ORIGIN OF THE FLUORESCENCE DECAY KINETICS OF CHLOROPLASTS

Abstract— The fluorescence decay kinetics of photosynthetic mutants of Chlamydomonas reinhardii which lack photosystem II (PS II), photosystem I (PS I), and both PS II and PS I have been measured. The PS II mutant strain8–36C exhibits fluorescence decay lifetime components of 53, 424 and 2197 ps. The fluorescence decay of a PS I mutant strain12–7 contains two major fluorescence decay components with lifetimes of 152 and 424 ps. The fluorescence decay of mutant strain C2, which lacks both PS II and PS I, is nearly single exponential with a lifetime of 2561 ± 222 ps. In simulations in which it is assumed that wild-type decays are a simple sum of the major decay components of the isolated parts of the photosynthetic unit as measured in the mutants, curves are obtained that fit the wild-type C. reinhardii fluorescence decay data when the absorption cross-sections of PS II and PS I are weighted approximately equally. The 89 ps lifetime component in the wild-type is an average of 53 and 152 ps components arising from excitation transfer to and trapping in PS I and PS II. The single step transfer time in PS I is estimated to be between 100 and 700 fs depending on assumptions about array size. We find that between two and four visits to the PS I reaction center are required before final trapping.     

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%.     

The effect of σ and π singly-excited configurations in the calculation of excited states by the CNDO and INDO approximations

The CNDO/2 and INDO approximations (with their original parametrization) are utilized for the calculation of transition energies. The effect of including all ( and ) singly excited configurations is assessed in C₂H₄, H₂CO, HCOOH and HCONH₂, and the results are compared to experimental transitions and to the available non-empirical calculations. The effect of extensive mixing is then considered in larger molecules.

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Zusammenfassung Die Näherungen CNCO/2 und INDO (mit ihrer ursprünglichen Parametrisierung) werden für die Berechnung von Übergangsenergien benutzt. Der Effekt des Einschlusses aller ( und ) einfach angeregter Konfigurationen wird untersucht für C₂H₄, H₂CO, HCOOH und HCONH₂ und die Ergebnisse werden mit experimentellen Übergängen und den verfügbaren nicht-empirischen Rechnungen verglichen. Die Überlegungen werden dann auf größere Moleküle ausgedehnt.

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Résumé Les procédés CNDO/2 et INDO (avec leur paramétrisation originale) sont utilisés pour calculer des énergies de transition. L'effet du mélange de toutes les configurations monoexcitées ( et ) est étudié pour C₂H₄, H₂CO, HCOOH et HCONH₂, les résultats sont comparés aux transitions expérimentales et aux calculs non-empiriques disponibles. L'étude est étendue à de plus grandes molécules.

     

Quantum-mechanical exploration of the properties of the sugar rings

Theab initio SCF method is used for computing the main electronic properties of the ribose unit of the nucleic acids. The present study is devoted to the ribose in the C₃-endo,gg conformation. The properties investigated include the distribution of the electronic charges, the electrostatic molecular potential around the four oxygens of the unit, the hydration and the Na⁺ binding schemes studied in the supermolecule approximation. The possibilities of through-water binding of the cation to the sugar are also explored. The predictions of the computation in particular with regard to cation binding to the ribose ring are correlated with recent experimental results.     

On the affinity of cytosine towards electrophiles

Ab initio SCF computations on the intrinsic preferences of the H⁺, CH ₃ ⁺ and C₂H ₅ ⁺ cations towards the two principal sites of protonation or alkylation on cytosine, N₃ or O₂, show that this preference undergoes a continuous modification with the increase in size and complexity of the cation. N₃ is the preferred site of fixation of H⁺, O₂ the preferred site of C₂H ₅ ⁺ , while CH ₃ ⁺ has no marked preference. The exchange repulsion term of the binding energy appears responsible for the preference of C₂H ₅ ⁺ for O₂.This work was supported by the Ligue Francaise contre le Cancer and the National Foundation for Cancer Research (USA)     

Theoretical studies of molecular conformation. II: Application of the SIBFA procedure to molecules containing carbonyl and carboxylate oxygens and amide nitrogens

The SIBFA procedure (Sum of Interactions Between Fragments computedAb initio, Ref [1]) is extended to the study of the conformational behavior of representative molecules containing amide nitrogens and carbonyl and carboxylate oxygens. The molecules studied are C- and N-ethylammonium formamide, C- and N-ethanol-formamide, ethylammonium formate and ethanolformate. The cases investigated include interactions of the types which occur between functional groups in proteins or ionophores. The accuracy of the procedure, assessed by comparing the results to those of correspondingab initio SCF computations, is very satisfactory. An application of the procedure to study the conformation of the glycyl and alanyl dipeptides as a function of the backbone torsional angles and is presented.     

Configuration mixing involving σ and π orbitals

The effect (on the energy of the different states) of including doubly excited configurations in a - plus -configuration interaction treatment, is studied within the CNDO/2 framework. For moderately large molecules the problem of the choice of the type ( or ) of configurations taken into account is examined. When possible, comparison is made with similar non empirical calculations.

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Zusammenfassung Im Rahmen der CNDO/2 Methode wird der Einfluß (auf die Energien verschiedener Zustände) des Einschlusses doppelt angeregter Konfigurationen in einer - und -Konfigurationswechsel-wirkungs-Behandlung studiert. Für nicht allzu große Moleküle wird das Problem der Wahl der Art ( oder ) der berücksichtigten Konfigurationen untersucht. Soweit möglich, werden die Resultate mit denen ähnlicher nichtempirischer Rechnungen verglichen.

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Résumé L'effet (sur l'énergie des différents états) de l'introduction de configurations diexcitées dans une interaction de configuration plus , est étudié dans le cadre de la méthode CNDO/2. Pour des molécules de taille moyenne le problème du choix du type ou des configurations est examiné. Les résultats obtenus sont comparés aux calculs non-empirique similaires disponibles.