Enamines I. Vinyl Amine,a Theoretical Study of its Structure,electrostatic potential,and proton affinity

The structure of vinyl amine and its reactivity towards a proton is studied by the PRDDO SCF MO method. The equilibrium structure is found to be non-planar and barriers to inversion- and rotation-dominated processes are calculated. Proton addition to vinyl amine, as a model of enamine protonation, is examined by means of electrostatic molecular potentials and C- versus N-proton affinities.     

SCF theory of molecular interactions

Perturbation theory is used to analyze the interactions between two closed-shell systems in the SCF approximation. The effects of orbital overlap are included. The dominant terms through second order are identified, including electrostatic, penetration, polarization, charge transfer, and SCF dispersion effects. The basis set limit is studied so that basis set superposition contributions may be identified. Calculations are presented for He? He and Na⁺? H₂O.     

Stereochemical and electronic structure of the free base,cation, and dication of porphin

The equilibrium stereochemical and electronic structure of the free base and the mono- and dications of porphin was calculated by the MO-LCAO SCF method in the CNDO/2 approximation. Successive protonation of the porphin molecule leads to an increase in the dimensions of the conjugation contour and to stage-by-stage exclusion of the nitrogen atoms. It was also established that single and double protonation of the free base does not lead to destruction of the coplanarity of the porphyrin macrocycle.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 24, No. 3, pp. 339–343, May–June, 1988.     

On the relation between the formal atomic charges and total molecular energies

It is shown that the total SCF molecular energies are fairly well reproduced by the sum of electrostatic potentials exerted on the nuclei calculated in the point-charge approximation. Hence, there is a very simple relation between the total energies and formal atomic charges in molecules. The semiempirical SCC-MO charges have the same performance as the ab initio DZ ones.     

Molecular electrostatic potentials and electron deformation densities from Xα calculations. The case of O2, O2− and O22−

A molecular-orbital study, performed using both multiple scattering Xα and ab initio SCF models, is reported for the protonation process of O₂, O₂⁻ and O₂²⁻. The main features of both molecular electrostatic potential and electron deformation density contour maps are compared and discussed.     

Quantum-chemical calculation of the hydroxylamine molecule and its complex with the proton

The cis and trans conformations of the hydroxylamine molecule were calculated by the SCF LCAO-MO method in the CNDO/2 approximation with optimization of the geometry. It was shown that the cis conformer is more stable in the free state; the barrier to internal rotation of the OH group about the N-O axis was determined. Various schemes for the protonation of hydroxylamine were investigated. The proton affinity of the molecule was calculated (for the N- and O-complexes). It was shown that protonation of NH₂OH at the nitrogen is more favorable, and the trans form of hydroxylamine has the strongest proton affinity.Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 24, No. 1, pp. 122–125, January–February, 1988.     

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.     

The molecular electrostatic potentials for the nucleic acid bases: Adenine,thymine, and cytosine

The electrostatic potentials arising from ab initio MO LCAO GTO SCF wave functions for adenine, thymine and cytosine are given and discussed.Well defined characteristic regions of immediate chemical significance are found. The analysis of such results aims at comparing different protonation sites in the same molecule as well as in different ones. Differences among the proton affinities of the nitrogen atoms (pyridine-like, amine and imine) are evidenced, as well as the distinction between oxygen and nitrogen atoms.

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Zusammenfassung Die mit Hilfe von ab initio MO LCAO GTO SCF Wellenfunktionen berechneten elektrostatischen Potentiale von Adenin, Thymin und Cytosin werden angegeben und diskutiert.Man findet genau bestimmte charakteristische Zonen von klarer chemischer Bedeutung. Durch die Analyse solcher Resultate können verschiedene Protonierungsplätze sowohl in ein und demselben Molekül als auch in verschiedenen Molekülen verglichen werden. Deutlich zeigen sich Unterschiede der Protonenaffinitäten der unterschiedlich chemisch gebundenen Stickstoffatome (pyridinartiger, Amin- und Iminstickstoff) und der Unterschied zwischen Stickstoff- und Sauerstoffatomen.

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Résumé Les potentiels electrostatiques moléculaires calculés à partir de fonctions d'onde ab initio MO SCF LCAO GTO sont donnés et discutés pour l'adénine, la thymine et la cytosine.Des régions bien définies sont obtenues dont la signification chimique apparait clairement. L'analyse de l'ensemble des résultats permet la comparaison des differents sites de protonation dans une même molécule ainsi que dans differentes molécules, ainsi que la distinction entre oxygene et azote d'une part, azotes de differents types d'autre part.

     

铂配位的腺嘌呤质子化的理论研究

用量子化学从头算研究一系列平面四方金属配体作用于腺嘌呤N₇位点对其质子化的影响。计算结果表明气相中，配合物质子化能力主要受长程静电效应影响，不同金属离子的影响差别甚微。综合考虑极性溶剂影响后长程静电效应影响显著降低。NBO电荷布居分析表明质子化位点电子云密度的变化直接影响该位点质子化能力。     

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.     

Theoretical studies of thiols and disulfides. Conformations,barriers and proton affinities

Results from an ab-initio MO LCAO SCF study of RSSR, RSH and RS^? (R = H, CH₃) in a minimal and a double zeta basis and cysteine [COO^?CH(NH⁺₃)CH₂SH] and cysteine anion in a minimal basis are reported. The barriers and conformational preference of the disulfides are discussed and it is suggested that their origin is more confined to the disulfide region than previously believed. The proton affinities of the different RS^? ions are calculated, whereas the protonation of the disulfide bond is studied by use of the molecular electrostatic potential. The good agreement of the results in the minimal and the double zeta basis is discussed.     

Counterpoise estimates of the BSSE in the evaluation of protonation energies

Counterpoise estimates of the BSSE in the evaluation of protonation energies have been calculated for basis sets ranging from minimal to split-valence plus polarization quality. Three-, five- and six-membered-ring heterocycles have been chosen as suitable model compounds for this study. Counterpoise corrections are significant, at the minimal basis set and 3–21G levels, when considering both, absolute and relative protonation energies and depend on the nature of the centre which undergoes protonation. In general, second- and third-order counterpoise corrections to the protonation energies are comparable to the corresponding SCF values. BSSE depend not only on the size of the basis sets but also on their quality. The presence in the basis of quite diffuse functions (either sp or d) leads to lower protonation energies and greater BSSE. Relative protonation energies are not substantially affected by BSSE or correlation effects.     

The validity of electrostatic predictions of the shapes of van der Waals dimers

The interaction energies of the van der Waals dimers H₂O-H₂O, Cl₂-HF, ClF-HF and N₂O-HF have been calculated for a range of geometries using ab initio SCF techniques. The SCF binding energies have been decomposed into electrostatic, exchange, polarisation and charge-transfer contributions and the intermolecular angles optimised with respect to various combinations of the above components. The effects of exchange, polarisation and charge transfer on the shape of a given dimer are found approximately to cancel, so that in each case a purely electrostatic model is capable of predicting intermolecular angles that agree well with those of a full SCF treatment, as well as with experiment. These findings are consistent with the proposals and earlier calculations of Buckingham and Fowler.     

A minimalist model for exploring conformational effects on the electrospray charge state distribution of proteins

The electrospray ionization (ESI) charge state distribution of proteins is highly sensitive to the protein structure in solution. Unfolded conformations generally form higher charge states than tightly folded structures. The current study employs a minimalist molecular dynamics model for simulating the final stages of the ESI process in order to gain insights into the physical reasons underlying this empirical relationship. The protein is described as a string of 27 beads ("residues"), 9 of which are negatively charged and represent possible protonation sites. The unfolded state of this bead string is a random coil, whereas the native conformation adopts a compact fold. The ESI process is simulated by placing the protein inside a solvent droplet with a 2.5 nm radius consisting of 1600 Lennard-Jones particles. In addition, the droplet contains 14 protons which are modeled as highly mobile point charges. Disintegration of the droplet rapidly releases the protein into the gas phase, resulting in average charge states of 4.8+ and 7.4+ for the folded and unfolded conformation, respectively. The protonation probabilities of individual residues in the folded state reveal a characteristic pattern, with values ranging from 0.2 to 0.8. In contrast, the protonation probabilities of the unfolded protein are more uniform and cover the range from 0.8 to 1.0. The origin of these differences can be traced back to a combination of steric and electrostatic effects. Residues exhibiting a small accessible surface area are less likely to capture a proton, an effect that is exacerbated by partial electrostatic shielding from nearby positive residues. Conversely, sites that are sterically exposed are associated with electrostatic funnels that greatly increase the likelihood of protonation. Unfolding enhances the steric and electrostatic exposure of protonation sites, thereby causing the protein to capture a greater number of protons during the droplet disintegration process.     

A semiclassical self-consistent field (SC SCF) approximation for eigenvalues of coupled-vibration systems

The self-consistent-field (SCF) approximation for coupled-vibron systems in the semiclassical limit yields Hartree-type equations, in which only the eigenenergies and turning points are self-consistently evaluated. Calculations yield vibrational energies in excellent agreement with quantum SCF and exact quantum results. Applications and extensions are briefly discussed.     

An ab initio method for approximation of the frozen molecular fragment

An ab initio method for calculation on many-electron molecular systems with the approximation of the inactive part of a molecule by frozen molecular fragment is presented. In the following method the SCF calculations are performed in two series. First the molecular orbitals resulting from the first SCF calculation (modest basis set) are localized. In the second SCF run, the basis set is extended for the active part of the molecule, while molecular orbitals of the inactive part, selected from the localized set, are kept frozen. The results are in good agreement with the extended basis set calculation.     

Accuracy and limitations of the pseudopotential method

Molecular model potential calculations have been performed within the SCF approximation on nine di- and triatomic molecules from the first row of the periodic table. We compare the molecular constants with ab initio SCF values and with model potential results obtained by other authors. Our results are accurate to a few per cent. The three most significant approximations in molecular model potential theory are: 1) The molecular model potential is the sum of atomic model potentials; 2) The atomic model potential is energy-independent; 3) The electron interaction model operator is l/r ₁₂. We arrive at the following general conclusions concerning these approximations: 1) The first approximation does not hold for strongly ionic molecules and for some highly excited molecular states. 2) Approximations 2 and 3 cancel to a large extent in molecules as they do in atoms, except in the case where approximation 1 breaks down. 3) Although various model- and pseudo-potentials yield reasonable results for atoms, not all of them are suitable for molecular calculations.     

Electrostatic Contribution to the Enthalpy of Charging at Hematite/Electrolyte Interface

A calorimetry study of hematite surface reactions is reported, with special emphasis on the estimation of the electrostatic contribution to the enthalpy of charging. The calorimetry titrations were performed outside the point of zero charge region where the electrostatic contribution is significant. The results were interpreted by the surface complexation model. The interpretation enabled the evaluation of standard protonation and deprotonation enthalpies as well as the electrostatic contribution to these quantities. Copyright 1999 Academic Press.