bluuebunny/crossref_metadata_2025 huggingface dataset:
Inner projection with and without perturbation theory: The anharmonic oscillator revisited and the quadratic Zeeman effect in ground‐state hydrogen
Authors: Cizek J. , Vrscay E. R.
Published: December 2004

This paper serves a twofold purpose. First, Löwdin's inner projection in both nonperturbative and perturbative forms is applied to the quartic anharmonic oscillator. Inner projection with perturbation theory yields rational approximations to Brillouin–Wigner‐type perturbation expansions. These lower bounds are compared with [N − 1, N] Padé approximants to the Rayleigh–Schrödinger perturbation series for this problem. These Padés are also expressible as the even convergents, w2N, of a Stieltjes‐type continued fraction. The latter representation has certain advantages with respect to its Padé counterpart. Inner projection without perturbation theory provides significantly better results than the perturbative version. The application of inner projection techniques to a perturbed hydrogen atom is not straightforward. The usual problems associated with the continuum spectrum of hydrogen are present. By means of a nonunitary “tilting” transformation associated with the Lie group SO(4, 2), these problems may be bypassed. In the SO(4, 2)‐reformulated eigenvalue problem, a reinterpretation of the basic variables, as developed by Silverstone and Moats, yields a new Hamiltonian that permits direct use of the inner projection method. This method has been applied to the ground state of the hydrogen atom in a magnetic field, using both four‐ and eight‐dimensional basis manifolds. This represents the first application of inner projection to this problem.
Cation–ligand interactions: Reproduction of extended basis set Ab initio SCF computations by the SIBFA 2 additive procedure
Authors: Gresh N. , Pullman A. , Claverie P.
Published: December 2004

In the framework of the additive SIBFA 2 procedure, the intermolecular interaction energy is computed as a sum of five terms: ΔE = EMTP + Erep + Epol + ECT + Edisp. In order to assess the accuracy of the procedure to compute cation–ligand interactions, the interaction of alkali (Na+, K+) and alkaline‐earth (Mg2+, Ca2+) cations with two representative ligands H2O and HCOO− has been studied and the results compared with those of ab initio SCF extended basis set computations. The additive procedure reproduces very satisfactorily the results of ab initio computations as concerns the numerical values of the interaction energies and the equilibrium cation–ligand distances, as well as the evolution of the energy components. A detailed study of these components at different distances helps, in particular, to delineate the relative weights of the charge‐transfer and polarization contributions within the second‐order energy.
Guanine and adenine‐amino acids interactions: An ab initio study
Authors: Sapse A. M. , Jain Duli C.
Published: December 2004

Ab initio calculations using an STO‐3G Gaussian basis set are performed in order to obtain the binding energy to the 06 and N7 of guanine of such amino acid models as the guanidinium ion for arginine, the ammonium ion for lysine, the methanol for serine, and the formamide for glutamic acid. The binding of formamide to adenine is also investigated. The charged ions exhibit a much higher binding energy to the bases, as expected, than the uncharged molecules. The order of binding strength is NH > guanidinium+ > formamide > methanol, and for formamide, guanine > adenine.
Simple constructive proof of Karadakov's extended pairing theorem
Authors: Mayer I.
Published: December 2004

A simple proof is given for Karadakov's recent extension of the pairing theorem to the virtual subspaces. The proof consists of an explicit construction of the virtual orbitals with the required pairing properties, utilizing the pairing of the occupied orbitals.
Method of local‐scaling transformations and density‐functional theory in quantum chemistry
Authors: Petkov Ivan Zh. , Stoitsov Mario V. , Kryachko Eugene S.
Published: December 2004

The method of local‐scaling transformations is developed with a view to applications of the nonrelativistic quantum mechanical variational principle in quantum chemistry. Some properties of local‐scaling transformations are studied. The method presented links local‐scaling transformations and one‐electron densities via the ordinary differential equation that provides a proof of the theorem on the existence of the energy density functional within any given orbit and its universality in a sense of the general theory of ordinary differential equations, and allows the construction of this functional explicitly.
[2 + 2] Cycloadditions. A concerted pathway for acetylene plus ethylene
Authors: Andes Hess B. , Schaad L. J. , Reinhoudt D. N
Published: December 2004

The [2s + 2a] cycloaddition of ethylene and acetylene has been studied. A transition structure of C2 symmetry was located on the potential surface. Activation energies for the process are also reported.
The conformation of o‐benzosemiquinone radical and its assignment of the proton hyperfine coupling constants by using the indo and the molecular geometry adjusting methods
Authors: Shinagawa Yasuko , Shinagawa Y.
Published: December 2004

The minimal energy conformations of o‐benzosemiquinone anion radical were calculated for several cases of assignments by using the INDO method and the molecular geometry adjusting method. In order to know the effect of lithium ion in the solvent, the minimal energy conformations of the system of LiOH and o‐benzosemiquinone anion radical were calculated. The calculations of the minimal energy conformations of this radical in t‐butyl alcohol, alkaline aqueous ethanol, alkaline water, neutral methanol, and acetonitrile were carried out. The total energies of the minimal energy conformations in the assignment |A3| > |A4| were lower than those in the assignment |A3| < |A4|.
Comments on the davydov hamiltonian for quasi‐one‐dimensional molecular chains
Authors: Tuszyński J. A.
Published: December 2004

The almost lossless transfer of energy and electronic charge along quasi‐one‐dimensional molecular substances such as peptide chains (H  N  C  O)n found an explanation in a model proposed by Davydov. The Davydov model is based on the dipole—dipole interactions between neighboring peptide groups and on the fact that the internal CO vibrations are coupled to the elastic deformations of the chain. The Davydov Hamiltonian is written in the position‐space representation and, on making a continuum transformation, leads to a nonlinear Schrödinger equation whose solutions are solitons. A Davydov soliton is a coupled pair of an exciton and a lattice deformation. In this paper, the Davydov Hamiltonian is transformed to the reciprocal lattice and its equivalent, second‐quantized Hamiltonian is investigated. Some important observations are made about the coupling constants, their dispersion relations, and the equation of motion for the ladder operators. Our procedure is free of semiclassical approximations but, instead, assumes the onset of Bose condensation. The resultant nonlinear Schrödinger equation is similar to that of Davydov, but a more complete set of solutions is found.
Correlation hole and physical properties: A model calculation
Authors: Cohen Leon , Lee Chongmoon
Published: December 2004

The correlation hole of Coulson and Nielson and its extension to momentum space by Banyard and Reed is studied by using an exactly solvable model. For this model all relevant quantities pertaining to the correlation hole have been calculated exactly. We use this model to study the relationship between the fit to the correlation hole for an approximate wave function and the closeness of the approximate energies to the exact ones. We show that, although in general the better the fit the closer are the approximate physical quantities to the exact ones, there are exceptions where that is not the case. Also, we present a convenient method for the calculation of the two particle distribution in momentum space and generalize the concept of the correlation hole by defining it in the pseudophase space of position and momentum.
Synchronism in the Diels‐Alder reaction
Authors: Burke Luke A.
Published: December 2004

Defined as the formation of two new bonds of equal length at the same time, synchronism has been shown to be not possible for the Diels‐Alder reaction when the products are not of strict Cs symmetry. This has been done in two steps. First, the SCF‐MO transition‐state structures for the cyclization reactions of ethylene with cyclopentadiene and furan have been calculated. The activation energies (and heat of reaction) with the STO‐3G, 3‐21G, and 4‐31G basis sets are as follows: with cyclopentadiene 35.0 (−80.7), 30.0 (−32.0), 38.4 (−19.9) kcal/mol; with furan 33.4 (−66.4), 34.6 (−16.5), 42.1 (−8.8) kcal/mol. Then, using a bond‐order‐bond‐length relationship, a value for the tendency toward asynchronism has been calculated for substituted reactants where the two new bonds are arbitrarily held equal. This tendency has been shown in all cases which break strict Cs symmetry. Further, inspection of the atomic‐orbital coefficients showed that the substituents cannot be considered as mere perturbations on the pi system in many cases.
Conformational behavior of azabiphenyls
Authors: Barone Vincenzo , Lelj Francesco , Russo Nino
Published: December 2004

The conformational behavior of biphenyl‐like compounds constituted by benzene and/or azabenzenes has been investigated at the STO‐3G Hartree‐Fock level. Although the STO‐3G basis set probably overstimates conjugative attraction, it seems able to provide reliable general trends. In this connection the analysis of over 30 molecules shows that compounds with the same ortho substituents (including nitrogen lone pairs) have very similar conformational behavior, irrespective of their composition. Furthermore, the comparison of different isomers shows that repulsive interactions decrease in the order hydrogen–hydrogen > lone pair – lone pair > hydrogen lone pair. Conjugative, electrostatic, and steric interactions have also been expressed by well known semiempirical functions, thus allowing a better analysis of the overall torsional potential.
Classical and quantum mechanical calculations of conformational probability density distributions. Two‐rotor molecules
Authors: Smeyers Yves G. , Hernández‐Laguna A.
Published: December 2004

In order to study the dynamical structure of a two‐rotor molecule, such as acetone, as a function of temperature, conformational probability density distributions are computed by using three different approaches: the so‐called current approach, the classical approach, and the quantum mechanical oscillator approach. It is found that the three procedures yield comparable results, at least at normal temperature (25°C), although the current and, especially, the classical approaches give rise to too sharp distributions when compared with the quantum mechanical results. Owing to its simplicity, the current approach may be used advantageously, and it is easily extendible to many‐rotor systems. Finally, it is verified that deuteration does not affect appreciably the conformation.
Thermal motion from monte carlo simulations of aqueous ionic solutions
Authors: Marchese Francis T. , Beveridge David L.
Published: December 2004

The statistical pattern recognition procedure of Marchese and Beveridge for the analysis of Monte Carlo simulations of aqueous ionic solutions [J. Am. Chem. Soc. 106, 3713 (1984)] has been extended to include average hydrogen positions as well as oxygen positions. In addition, thermal ellipsoids have been calculated for each atom and displayed graphically. Application of this procedure to the analysis of a dilute aqueous solution of Zn++ reveals an octahedral arrangement of water molecules within the ion's first hydration shell. The thermal ellipsoids show that most of the water motion is manifest in the hydrogen atoms.
The calculation of ligand‐field multiplet states from multiple‐scattering Xα wave functions
Authors: Daul C. , Goursot A.
Published: December 2004

A method is outlined for the calculation of the multiplet ligand‐field states of transition metal complexes. The procedure involves the use of MS‐Xα wave functions, in connection with irreducible tensor operators, and allows the calculation of the elements of the many‐electron CI matrices. Comparison of the calculated and experimental multiplet state energies of CrF, CrCl, and MnF allows one to conclude that the method is useful for the prediction of ligand‐field spectra of transition‐metal complexes.
Theoretical interpretation of infrared spectra of the ClH stretching vibration in the gaseous (Ch3)2O · · · HCl complex
Authors: Wójcik Marek J.
Published: December 2004

The paper presents a theoretical interpretation of the fine structure of infrared spectra of the ClH stretching region in the gaseous (CH3)2O ··· HCl complex. The idea of Millen and Schrems is adopted, in which the spectrum represents a vibrational progression of the hydrogen‐bond stretching mode, and each subband is formed by the progression of the hydrogen‐bond bending mode. The rotational structure is present in such defined fine bands. Theoretical bands are calculated for three different temperatures and for the complex with DCl using two coupling parameters evaluated from the bandwidth. Results show that the most intense peak is associated with the Oσ ← Oσ transition in the stretching O ··· Cl vibration. They also suggest that the complex is nonplanar.
Core–Valence correlations and relativistic effects in heavy atoms for molecular applications
Authors: Durand Ph.
Published: December 2004

Theoretical core effective potential methods are widely used in valence‐only electron molecular calculations. These methods, which imply the frozen‐core approximation, work well for the elements of the righthand side of the periodic table but are often unrealistic for metallic elements with highly polarizable cores. For these atoms one has to consider the polarization of the cores under the influence of the electric field created by the valence electrons. Moreover, relativistic corrections must be added for heavy atoms.

Various theoretical approaches of core–valence interactions (polarization and core–valence correlations) will be reviewed, with a special emphasis on practical methods of calculation. The problem of handling the relativistic effects will mainly be discussed within the two‐component Pauli formalism. It will be shown that the Foldy–Wouthuysen transformation is not the unique way for deriving relativistic corrections and that the second‐order Dirac equation also provides a good starting point for obtaining relativistic corrections. Analytical exact results are given for the hydrogen atom. The accuracy of this approach is tested on many‐electron atoms and molecules.

It is finally shown that the problem of the core‐valence separation is relevant to the general methodology of effective Hamiltonians that seems to provide the best promising way for filling the gap between the semiempirical and purely theoretical ab initio methods.
Interatomic interactions in density functional theory
Authors: Vela Alberto , Cedillo Andrés , Gázquez José L.
Published: December 2004

The concept of an atom in a molecule in the context of density functional theory is used to analyze different levels of approximation to the description of interatomic interactions. Such an approach strongly suggests the use of Kohn–Sham atomic densities as an alternative to Hartree–Fock atomic densities in the electron gas model of Gordon and Kim. The results for rare gases and ionic crystals show that both densities lead to similar results.
Multiple bonds and re(4f) binding energies of some rhenium halides
Authors: Katrib A. , El‐Issa B. D. , Ghodsian R.
Published: December 2004

Experimental results on the bombardment of some rhenium trihalides by argon ions in a photoelectron spectrometer have yielded lower‐valency rhenium halides. The presence of the compounds have been made evident by the destabilization of the Re(4f) and the relative decrease in the halogen spectral line intensities. A theoretical approach to the energy of the Re(4f) states have been studied by the MS X‐α method. The molecular model used in the calculations is made up of rhenium polyhalides in D4h symmetry having the structure Re2X (n = 2, 4, 6). A discussion is also presented on the formation of multiple bonds as a result of the overlap between the dxy orbitals of rhenium.
Structural features of some small carbonyls in the 1,3nπ states: An mcscf study
Authors: Das Kalyan Kumar , Mukherjee D. , Bhattacharyya S. P.
Published: December 2004

Structural features of a series of tetraatomic carbonyls in the 1,3nπ* states are studied by using a recently proposed MCSCF algorithm at the INDO/2 level. The computed geometrical parameters and the inversion barrier heights agree quite well with the available experimental or ab initio theoretical data. The calculated transition energies turn out to be somewhat lower than the experimental counterparts. The specific MCSCF algorithm used is found to have excellent convergence properties.
Calculation of SN 1 + N 2 ⊃ SN1 ⊗ sn 2 and U(n1 + n2) ⊃ u (n1) ⊗ u (n2) subduction coefficients by using spin graph
Authors: Zhenyi Wen
Published: December 2004

By use of the graphical method of spin algebra, simple, and closed expressions for SN1+N2 ⊃ SN1 ⊗ SN2 and U(n1 + n2) ⊃ U(n1) ⊗ U(n2), subduction coefficients are derived.
Slater determinant from atomic form factors
Authors: Frishberg C.
Published: December 2004

The electron densities and expectation values for several physical properties predicted by three single determinant wave functions for the beryllium atom are presented. The wave functions are the Hartree–Fock, the Best Density Matrix, and the X‐ray fitted. The X‐ray fitted electron density comes closest to reproducing the exact density for r < 8.0 a.u. and gives, in most cases, better values for the physical properties.
Composite exciton‐phonon states in molecular crystals
Authors: Singh Jai
Published: December 2004

It is known that the diagonalization of the exciton‐phonon Hamiltonian gives rise to the composite exciton‐phonon energy states. Within the single phonon approximation, two different diagonalized Hamiltonians are obtained for 0–0 and 0–1 phonon transitions in pure molecular crystals. The resulting secular equations are solved, and analytical expressions for the energy eigenvalues corresponding to the two transitions are derived. The thermal broadening due to the composite exciton‐phonon states interaction is also calculated at low temperatures, and the results agree with experiments.
Electron density near an impurity
Authors: Adawi I.
Published: December 2004

The behavior of the electron density n(r) [and potential energy V(r)] near an impurity of charge Z is studied by using the linear response theory of an electron gas at finite temperature and with exchange and correlation effects included. The odd powers series in the expansion of n(r) [and V(r)] are calculated exactly by using asymptotic methods, and the coefficients in the series are given in terms of moments taken over the Fermi–Dirac distribution function. In all linear response theories and at all temperatures, the derivative n'(0) = ‐2Zn0/a0, where n0 is the unperturbed electron density and a0 is the Bohr radius. The effects of exchange and correlation appear in the fifth‐ and higher‐order terms in nodd(r).
Correlation with independent particle orbitals
Authors: Esséan Hanno
Published: December 2004

A method is suggested for calculating the correlation energy within an independent particle or SCF approach. It is based on the fact that a correlation factor, depending explicitly on the electron‐electron distances, can be shown to yield an effective potential operator in a Schrödinger equation for the remaining (SCF) factor in the wave function. An explicit correlation factor with certain desirable properties is the basis for the discussion. The resulting effective operator is calculated, and an independent‐pair approximation is made to make it more tractable. Finally, it is argued that the essential effects of the operator is simply given by a short range electron‐electron attraction and electron‐nuclear repulsion. A qualitative justification for this is also given.
Unified treatment of the electronic structure of organic conjugated polymers
Authors: dos Santos M. C. , de Melo C. P. , Brandi H. S.
Published: December 2004

Theoretical calculations for polaron‐type defect structures on organic conjugated polymers are carried out by Green's function and transfer function formalism. Firstly, the renormalization concept is applied to mathematically convert the polymers PPP, PPY, and PTP to an equivalent (trans‐PA)‐like form. Then, it is shown that Green's functions and polaron wave functions are readily obtained from the equations for trans‐PA by the appropriate substitution of the renormalized parameters. It is suggested that the existence of defects such as polarons or bipolarons could be invoked to provide a unified treatment of electric conduction in organic conjugated polymers.
Investigation of the hydrogen bonds between formaldehyde and hydrogen halides by pseudopotential Ab Initio method
Authors: Yanbo (Y. B. Ding) Ding , Xiaoyuan (X. Y. Fu) Fu
Published: December 2004

The weak hydrogen bonded systems H2CO ⃛HX (X = F, Cl, Br, and I) have been studied by means of ab initio MO method with pseudopotential approximation. The stabilization energies of these hydrogen bonds are 8.96, 4.12, 3.00, and 2.21 kcal/mol, respectively. The interaction eneraction energies are farther decomposed according to Morokuma's energy decomposing scheme. It is found that the title complexes are mainly electrostatic, although the contribution of charge transfer is also significant.
Molecular electrostatic potential studies on antiepileptic drug: Troxidone
Authors: Jayasuriya Keerthi , Williams David J.
Published: December 2004

Ab initio SCF‐MO‐LCAO calculations of the molecular electrostatic potential (MEP) have been carried out on a seven‐member series related to the antiepileptic drug troxidone. The effect of the substituted alkyl groups on the bioactivity of these molecules is discussed. The substituted alkyl groups increase the negative potential found near the oxygen atoms in the molecular plane.
Size‐extensivity in multireference many‐body perturbation theories: A direct comparison between single‐reference and multireference perturbation theories in the nondegenerate case
Authors: Meissner L. , Jankowski K.
Published: December 2004

Linkage properties of the diagrammatic representation of the energies obtained in the multireference many‐body perturbation calculations with respect to the incompleteness or completeness of the model space are discussed. The case of not completely degenerate model space is considered for which a comparison with the standard single‐reference many‐body perturbation expansion is possible. The Hose–Kaldor type of graphical representation of the perturbation expansion for the effective Hamiltonian is used in this comparison. It is shown that for an incomplete model space the perturbation expansion is not size‐extensive. In this case, for a truncated expansion of the effective Hamiltonian, the energies obtained by diagonalization of the effective Hamiltonian matrix are represented by both linked and unlinked irreducible contributions. The unlinked ones do not appear when the complete model space is used.
Ab initio calculations of all‐trans octatetraene and eight isoelectronic conjugated chains: Semiempirical heats of formation and stabilization energies
Authors: Younang Elie , André Jean‐Marie , Delhalle Joseph
Published: December 2004

In the framework of our study of the changes of the electric polarizability upon substituting heteroatomic linkages in conjugated hydrocarbon backbones, we have been led to examine the relative stability of eight compounds isoelectronic to the all‐trans octatetraene using the Cox and Pilcher concept of stabilization energy (SE), SE = ΔHa – ΣNABEAB, where ΔHa is the heat of atomization of the species under consideration and the EAB's are bond‐energy terms. Full geometry optimizations at the 4‐31G level have been performed to obtain the equilibrium geometries needed to deduce reliable semiempirical heats of formation from appropriate isodesmic processes. Some of the compounds containing the  CHN and  NN  groups have electric polarizabilities and stabilization energies comparable to octatetrene.
Theoretical study of CO adsorption on the NiCu(110) system
Authors: Castellani Norberto J.
Published: December 2004

The electronic influence of the matrix on several adsorption sites of the CO/NiCu(110) system has been studied using a semiempirical molecular orbital calculation. A negative ligand effect of a copper matrix on monometallic nickel sites and a less important ligand effect of a nickel matrix on copper sites have been found and explained in base on the electronic structure. Bridge nickel–copper sites show an intermediate negative ligand effect within a Cu matrix. The results of the theoretical calculation are compared with the available experimental data.
Correlation energy calculations for infinite systems
Authors: Fulde Peter , Stollhoff Gernot
Published: December 2004

A survey is given of ab initio calculations for solids and polymers, which start from an SCF calculation and treat correlations by using local operators. The theory is formulated by employing a projection method. As regards applications, special attention is paid to elemental semiconductors and to polymers like polyethylene and polyacetylene. With the help of reduced Hamiltonians, insight can be gained into various correlation effects. This is demonstrated by a discussion of the problem of dimerization in polyacetylene. Finally, a formalism is described that allows for treating the effects of correlations on energy bands of solids. It is shown that qualitative new aspects of correlations enter when a quasiparticle in, e.g., a semiconductor is considered. The theory is applied to a calculation of the energy bands of silicon.
Electron correlation in one dimension: Coupled cluster approaches to cyclic polyene π‐electron models
Authors: Paldus J. , Piecuch P.
Published: December 2004

Methods accounting for correlation effects in quasi‐one‐dimensional π‐electron systems and based on the restricted Hartree–Fock (RHF) single determinantal reference state are briefly reviewed as well as their role in the bond length alternation (or dimerization) problem in polyactylene‐like systems, as described by the semiempirical Hamiltonians of the Pariser–Parr–Pople (PPP) type. Particular attention is given to the π‐electron model of cyclic polyene homologous series CNHN, N = 2n = 4v + 2, v = 1,2,…, which can be regarded as an idealized model of one‐dimensional metallic‐like systems with imposed Born–von Kármán boundary conditions when N ∞. These models provide a useful bridge between the typical aromatic systems, represented by benzene (N = 6) π‐electron model, and long linear polyenic chains, since the properties of these systems hardly change once a sufficiently large N (˜26 or 30) is reached. It is shown that due to the quasidegenerate character of the RHF reference employed, and the related prominence of connected quadruply excited cluster components in the exact wave function, most of the standard technieques suffer a singular behavior break down entirely for large enough systems, particularly in the strongly correlated regime. The approximate coupled pair theory that accounts for quadruply excited clusters (ACPQ method) is shown to be free of these shortcomings and is extended to include also approximately the effects of connected triexcited cluster components. These results are compared with other recently examined approximate methods accounting for the tri‐ and quadruply excited clusters and the proposed ACPQ+T(ACPQ) procedure is shown to provide the best results in the whole range of the coupling constant.
Theoretical prediction of sequence‐dependent DNA superstructures and their implications in recognition mechanisms with proteins
Authors: Boffelli D. , De Santis P. , Palleschi A. , Scipioni A. , Savino M.
Published: December 2004

Superstructures of biologically relevant DNA fragments were obtained from the sequence by integrating the theoretically evaluated local deviations from the canonical B‐DNA structure produced by the differential interactions in the 16 different dinucleotide steps.

The theoretical model was tested on 450 multimeric oligonucleotides different for sequence, periodicity, and length, and reproduced their electrophoretic behaviors with surprisingly good approximation. A very good agreeent was also obtained between the theoretical and experimental gel electrophoretic mobility changes following point mutations in a Sv40 DNA tract. The application to the set of the 177 different nucleosomal DNA tracts of Satchwell et al. revealed a very significant distribution pattern of the curvature phases along the sequence, which accounts for the main features of the nucleosome structure. This distribution allowed the localization of virtual nucleosome positions near the Sv40 origin of replication using the correlation function with the corresponding curvature diagrams in good agreement with the experimental map.
Enthalpic and entropic contributions of water molecules to the functional T → R transition of human hemoglobin in solution
Authors: Bulone D. , Palma‐Vittorelli M. B. , Palma M. U.
Published: December 2004

Generalized solvent‐mediated forces contribute to free energy at the functional T → R transition of human hemoglobin A (HbA). Their contribution is here sorted out quantitatively in both its enthalpic and entropic parts, along with the average number of water molecules involved. The latter (about 75 waters in average) must be considered together with HbA as one statistically defined functional unit for oxygen transport. Their configurations are expected to undergo frequent structural rearrangements. Lifetimes of statistically relevant configurations do not need to (although, of course, they may) exceed by more than a factor 5 the normal H‐bond lifetimes of the pure solvent. Compared to the bare protein, the “functional unit” here evidenced for the first time involves a larger, higher dimensionality region of the phase space. The study allows a microscopic view of solvent‐mediated generalized forces and evidences their qualitative and quantitative relevance to biomacromolecular function and stability.
Computational investigation of the role of hydration in nucleic acid structure and function
Authors: Poltev V. I. , Teplukhin A. V. , Malenkov G. G.
Published: December 2004

The results of the Monte Carlo Metropolis simulation of water structure and of the hydration of nucleic acid fragments, complementary base pairs and mispairs, base pair stacks, and duplex fragments have been summarized. Systematic investigations suggest some general conclusions: (1) the hydration shell structure of the major and minor grooves of the duplex depends significantly on DNA conformation (or stack configuration) and nucleotide sequence, while global hydration characteristics (average energy, the number of water–water and water–base H‐bonds) are only slightly dependent on these factors, (2) hydration economy takes place in the B–A transition due to an increase of the number of water molecules forming hydrogen bonds with two or more atoms of bases (water bridging), and (3) the hydration of the duplex could contribute to nucleic acid functioning via water‐bridged mispair formation and stabilization of specific conformations.
Some approaches to the multiple‐minima problem in the calculation of polypeptide and protein structures
Authors: Scheraga Harold A.
Published: December 2004

Various methods are used to surmount the multiple‐minima problem that is encountered in the multidimensional conformational energy surface of a polypeptide. A summary is given here of two of these methods: (i) The build‐up procedure that is modified to include statistical data on the positional frequencies of occurrence of amino acid residues along the chain, and (ii) the diffusion equation method that smoothes out the potential surface, leaving only the potential well containing the global minimum.
Computational studies on aspartic proteases. I. Active‐site protonation and hydration in the substrate‐free crystalline state
Authors: Turi László , Náray‐Szabó Gábor
Published: December 2004

We performed semiempirical molecular orbital calculations on the free and hydrated states of the HCOO−…HCOOH couple in crystals of an aspartic protease, rhizopuspepsin, in order to gain information not available by conventional X‐ray diffraction studies. The reliability of the MNDO/PM3 method was proven for the model system HCOO−…HOH, for which we could reproduce geometry and energetics of the complex, obtained by sophisticated ab initio calculations, with astonishing accuracy. Comparing the geometries of the active‐site models to experiment and their relative energies, we suggest that in the substrate‐free crystalline state the carboxyl–carboxylate–hydroxonium triad exists most probably in the neutral form. The carboxyl–carboxylate dyad attracts a hydroxonium ion better than does ammonium, indicating that the nonhydrogen atom, located by X‐ray crystallography near the active site, is oxygen and not nitrogen. We located the most probable hydrogen positions by geometry optimization.
Ab initio CI calculations on free‐base porphin
Authors: Yamamoto Yuichi , Noro Takeshi , Ohno Kimio
Published: December 2004

Ab initio configuration interaction (CI) calculations were carried out on low‐lying singlet and triplet π–π* states and ionized states of free‐base porphin. We take into account single and double excitations from σ and π electrons in the CI calculations. The composite natural orbitals were employed in order to reduce the size of orbital set to be used in the CI. The calculated excitation energies were in good agreement with experimental values. The use of split‐valence‐type basis and the inclusion of correlation effects of σ electrons were proved to be important to describe the low‐lying π–π* states, especially the Soret band.
Study on some metal–metal quadruple bonds
Authors: Li Ming
Published: December 2004

In the present paper, the role of (n − 1)ƒ orbitals in metal–metal quadruple bonds was studied. It was shown by the calculations that the probabilities for finding the σ‐, π‐, and δ‐electrons between two metal atoms, under the influence of the ƒ orbitals on the metal–metal quadruple bonds, increased while their mean kinetic energy components along the metal bond axis decreased. In addition, the effects of the ƒ orbitals upon the σ, π, and δ metal–metal bonds were different. In general, σ < π < δ.
Representation of square‐cell configurations in the complex plane: Tools for the characterization of molecular monolayers and cross sections of molecular surfaces
Authors: Walker P. Duane , Mezey Paul G.
Published: December 2004

Two numerical codes, a complex face vector F and a real face vector D are developed for the characterization of square‐cell configurations (lattice animals), used for representing the shapes of molecular monolayers and cross sections of molecular surfaces. The real face vector D represents all the intrinsic properties, size, and shape of the lattice animal. The complex face vector F contains complete information about the size, the shape, and also the placement of the particular lattice animal with respect to the lattice. Based on the properties of the face vectors, a method is developed for the classification of similar animals into equivalence classes. The face vector method is proposed for an algorithmic, nonvisual computer analysis of similarity of shapes of molecular monolayers and planar domains of cross sections of molecular surfaces, approximated by lattice animals.
Nonadiabatic theory of electron–vibrational coupling: New basis for microscopic interpretation of superconductivity
Authors: Svrček Michal , Baňacký Pavol , Zajac Anton
Published: December 2004

The electron–vibrational problem of the general nonadiabatic molecular systems has been solved by means of the quasi‐particle transformations. The SCF ab initio solution of the nonadiabatic fermion Hamiltonian yields stabilization of the electronic ground‐state energy due to electron–phonon interaction and it also gives the corrections to the one‐ and two‐particle terms. Two two‐particle correction yields effective attractive electron–electron interaction, but in the form different from Frölich's effective electron–electron interaction term. In contrast to the standard electron–phonon Hamiltonian of solid‐state physics that does not take into account the possible effects of nonadiabaticity of a system, the presented nonadiabatic theory yields also one‐particle corrections. The presence of this term in the Hamiltonian might play a crucial role in the theory of superconductivity since the superconductors are nonadiabatic systems.
Superconductivity–the phenomenon conditioned by nuclear microflows in nonadiabatic systems
Authors: Svrček Michal , Baňacký Pavol , Zajac Anton
Published: December 2004

Conditions for low and high Tc superconductors following from the nonadiabatic electron‐vibrational theory at ab initio level have been obtained. According to the presented results, the supercurrent is realized by the motion of the ground‐state electronic‐charge distribution of the fully occupied band. The motion of the electronic‐charge distribution is conditioned by the newly arisen, nondissipative degrees of freedom of nuclear, Jahn–Teller‐like, microflows. The Meissner effect is also interpreted.
The modified all‐valence INDO method with the inclusion of spin–orbit coupling
Authors: Roszak S. , Lipiński J.
Published: December 2004

The all‐valence INDO method has been modified for the inclusion of spin–orbit coupling effects. In the method presented, the Hamiltonian includes spin–orbit coupling and the basis set constitutes the singlet and triplet determinental wave functions constructed from molecular orbitals resulting from nonrelativistic calculations. Eigenvectors obtained are later used for the evaluation of transition probabilities among different states. The results presented include lifetimes of different states of organic molecules and transition energies for halogen molecules and they are in a good agreement with experimental results. © 1992 John Wiley & Sons, Inc.
Relativistic quantum defect calculations on the copper isoelectronic sequence
Authors: Lavin C. , Barrientos C. , Martin I.
Published: December 2004

The quantum defect orbital (QDO) method and its relativistic (RQDO) counterpart have been employed in this work to compute oscillator strengths for several fine‐structure transitions in members of the copper isoelectronic sequence up to Z = 92. The RQDO results are found to be in quite good agreement with the best estimates derived from other sources, whenever the comparison is possible. © 1994 John Wiley & Sons, Inc.
Theoretical evolution of the third‐order molecular polarizabilities as a function of chain length in thiophene and pyrrole oligomers
Authors: Beljonne D. , Shuai Z. , Brédas J. L.
Published: December 2004

On the basis of INDO (intermediate neglect of differential overlap)/MRD‐CI (multireference determinant–configuration interaction) calculations, the SOS (sum‐over‐states) formalism is applied to calculate the third‐order polarizabilities, γ, in thiophene and pyrrole oligomers. For both types of oligomers, the chain‐length dependence of γ can be divided into three regimes: Describing γ as a power law of the number of rings (N), we observe that the power value first strongly increases with N, than reaches a nearly constant value (power regime), and, finally, decreases toward one, indicating the appearance of a saturation regime. Very good agreement with the experimental evolution has been found in the case of the oligothiophenes. The comparison of the results obtained for the two types of oligomers indicates a lower polarizability in the oligopyrroles. © 1994 John Wiley & Sons, Inc.
On the determination of effective one‐electron Hamiltonians to be used for studying large molecules
Authors: Couty M. , Lévy B.
Published: December 2004

We studied the possibility of defining a one‐electron effective Hamiltonian in the form of a Hückel‐type matrix, taking into account the effect of the environment of the atoms in different molecules (the E2HT). It is found that the appropriate basis set in which this Hamiltonian is defined can be determined by using diatomic fragments. Concerning the matrix elements themselves, the appropriate information can be taken in fragments with a size similar to that of ethane. © 1994 John Wiley & Sons, Inc.
Core photoionization satellites in fullerence and related model systems
Authors: Lunell Sten , Enkvist Christer , Agback Martin , Svensson Svante , Brühwiler Paul A.
Published: December 2004

The so‐called shake‐up satellites accompanying C1s photoionization in C60 have been studied theoretically by means of INDO/CI. It is found that the lowest shake‐up satellites in C60 correspond to global charge‐transfer excitions that move charge from the opposite side of the fullerence cage to the core‐hole region, whereas higher‐energy satellites tend to move charge from regions nearer to the core hole. Analogies are drawn, with, on the one hand, smaller model molecules such as napthalene and acenaphtylene and, on the other hand, infinite systems such as graphite. © 1994 John Wiley & Sons, Inc.
A theoretical approach to the complexation and decomplexation processes in the reaction C60 + He ⇌ (He@C60)
Authors: Xu Zhijin , Yan Jimin
Published: December 2004

To theoretically investigate the complexation and decomplexation processes in the reaction C60 + He ⇌ (He@C60), four possible reaction paths are assumed, so that while He approaches and penetrates the C60 cage (a) a pentagon, (b) a hexagon, (c) a short bond, or (d) a long bond will be expanded on its original sphere or plane to form a window. The computation is performed by the quantum chemical method EHMO/ASED. The results show that the probability of completing this reaction in terms of the tunnel effect can be neglected and the reaction is completed by overcoming a potential barrier of the reaction. It is easily completed by opening a planar window than by opening a shperical window. The probability through reaction path (b) with a barrier of 1247.94 kJ/mol is larger than that through reaction path (a) with a barrier of 1438.26 kJ/mol. The probability through reaction path (d) is the largest with a barrier of 1076.78 kJ/mol, when the planar expansion forming a window of a 9‐membered ring is at the optimized value of 0.40 å. When He deviates the center and approaches the C60 cage, there will be a charge distribution on C60 with changing in size and even in sign along the longitude corresponding to the symmetry axis, but the absolute value gradually decreases. This situation is similar to the charge transfer on carbons in sraight‐chain polyene. © 1995 John Wiley & Sons, Inc.
Characterization of structural transitions from aqueous solution to a lipid phase for α‐MSH
Authors: Jacchieri Saul G. , Ito Amando S.
Published: December 2004

Fluorescence spectroscopy results show that the α‐melanocyte‐stimulating hormone peptide (α‐MSH) interacts with acidic lipid vesicles. Detectable structural changes are concomitant with the passage of a tryptophan residue from aqueous to lipidic media. The observed multiexponential decay of fluorescence, rationalized as originating from three rotameric populations of the tryptophan residue, has been used together with a matrix algorithm to find the most probable conformational families of α‐MSH in water and lipid environments. A model is discussed in which the same conformational families occur in various phases, although with different probabilities. A conformational family in which χ1 of the Trp9 side chain is in the trans‐rotameric conformation is shown to have structural features highly appropriate to interact with negatively charged biological membranes, which are also in accordance with previous molecular dynamics simulations and with structures engineered in α‐MSH analogs that show an increased potency in biological essays. The gauche minus and gauche plus side‐chain conformations of Trp9, on the other hand, yield conformations more likely to predominate in aqueous solution. NMR spectroscopy measurements of α‐MSH analogs indicate the existence in aqueous solution of a β strand in the vicinity of Trp9. A similar structural feature was found in the present conformational analysis for the gauche minus and gauche plus side‐chain rotamers of Trp9. © 1995 John Wiley & Sons, Inc.
Local quantum chemistry: The local space approximation for Møller–Plesset perturbation theory
Authors: Kirtman Bernard
Published: December 2004

The local space approximation is an accurate technique for describing a relatively small cluster embedded within an extended system. It has previously been developed for the Hartree‐Fock, local density functional, configuration interaction, and coupled cluster electronic structure methods. Here it is extended to Møller‐Plesset perturbation theory. © 1995 John Wiley & Sons, Inc.
Accurate CI expansion in a spline basis of the helium ground‐state wave function
Authors: Decleva Piero , Lisini Adriana , Venuti Marco
Published: December 2004

Careful study of radial spline basis‐set convergence on the angular limits of the He 1s 2 state has been performed. Improvement of algorithm allows reaching the full ci limit in a large radial (79 spline functions) and angular (Imax=80) expansion. A variational energy of − 2.903724299061 au, with an error of 7.8 × 10−8 au is obtained, improving by over two orders of magnitude the previous available limit. Accurate angular momentum limits (1 × 10−8 au) are obtained up to l = 25. Analysis of the behavior of two‐particle radial wave functions reveals a sharply peaked behavior which allows effective truncation of the two‐electron radial basis for high angular momentum values. A reasonable estimate of computational resources required indicate that an accuracy below 1 × 10−8 au is presently feasible and about 1 × 10−9 au possible in the near future. © 1995 John Wiley & Sons, Inc.
Theoretical investigation of the conrotatory ring opening of cyclobutene and 1, 2‐dihydro‐1, 2‐diazacyclobutadienes with ab initio and density functional Gaussian‐type‐orbital approach
Authors: Jursic Branko S. , Zdravkovski Zoran
Published: December 2004

The theoretical study of the thermally allowed conrotatory opening of cyclobutene (1) and cis‐ (2) and trans‐1,2‐dihydro‐1,2‐diazacyclobutadiene (3) were performed with ab initio and density functional calculations. The reactants and the transition states were fully optimized by using the 6‐31 + G** basis set with RHF, MP2, SVWN, and BLYP methods. The calculated activation barriers for the ring opening of 1 with both MP2 and SVWN incorporating ZPVF correction give extraordinary agreement with the experimental value. The predicted activation energies for 2 and 3 are lower than in the case of the cyclobutene ring opening. Of the two 1,2‐dihydro‐1,2‐diazacyclobutadiene isomers, the trans isomer has a lower activation barrier. The structural and energy differences and the trend among these compounds are interpreted in terms of orbital overlap and steric interactions in the course of the conrotatory ring opening. © 1995 John Wiley & Sons, Inc.