bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applications of an optimization technique in submolecular biology
Authors: Sundaram K. 
Published: December 2004

AbstractSome applications of an optimization technique due to Levenberg in theoretical submolecular biology are described. This technique has proved a very useful tool for the generation of three‐dimensional structures of molecules having cyclic components or other constrained regions. The generated molecular structures provide the starting point for quantum chemical calculations of great value in solving problems of biological interest. The mechanism of transport of alkali metal cations by valinomycin is one such example and this paper describes briefly how various conformations of valinomycin were obtained using the optimization technique. A variant of the same method has been suggested as a new technique for the detection of topographical similarities between apparently dissimilar molecules which are substrates for the same enzyme or receptor site. The technique is illustrated with a comparison of a tricyclic antidepressant with norepinephrine both of which have been postulated to compete for a common receptor site in the “amine pump” of peripheral adrenergic nerve cell membranes. Another area in which the optimization technique has proved useful is in developing an optimum separable localized bond function method designed for rigorous calculations on large saturated molecules. This method is briefly described.
A variational principle for transition and density matrices and approximations to the equations‐of‐motion
Authors: Dmitriev Yuri , Roos Björn 
Published: December 2004

AbstractA general variational principle for transition and density matrices is proposed. The principle is closely related to Rowe's variational treatment of the equations‐of‐motion method. It permits the simultaneous construction of coupled approximations for two eigenstates, and it is a straightforward extension of the usual variational method.
Generation of genealogical spin eigenfunctions
Authors: Grabenstetter J. E. , Tseng T. J. , Grein F. 
Published: December 2004

AbstractA method is given for generating the Yamanouchi‐Kotani genealogical spin eigenfunctions which requires neither storage of eigenfunctions for smaller numbers of electrons, nor summations of large order, nor explicit use of results from the theory of representations of the symmetric group. An explicit formula is given for the coefficients of expansion in terms of spin products.
Equivalent spherical harmonics
Authors: Schmelzer A. 
Published: December 2004

AbstractIt is known that the 2l+1 spherical harmonics Ylm can be transformed into cyclically equivalent orbitals, of which only a few examples have so far been given explicitly. In this article the totality of such cyclic sets is derived.It is demonstrated that other kinds of equivalent spherical harmonics do not exist.Finally a set of five equivalent d orbitals related to icosahedral symmetry is introduced.
Uniform quality gaussian basis sets for organo‐silicon compounds
Authors: Mezey P. G. , Yates K. , Theodorakopoulos G. , Csizmadia I. G. 
Published: December 2004

AbstractBy applying the powerful direct optimization technique of conjugate gradients as adapted for the optimization of an open shell energy functional, a uniformly balanced (15s 10p) Gaussian basis set was obtained for the silicon atom. The quality of this basis set, as defined in terms of “exponent forces” or energy gradient |g|, is compatible with the quality of suitably chosen (10s 5p) carbon and (5s) hydrogen basis sets. Contractions better than double zeta were determined for all three bases of Si, C, and H. Using the primitive and contracted bases, ab initio SCF MO calculations were carried out on molecules of SiH4, CH4, and H2. Some of the computed results obtained for H2C = SiH2 are also included as an illustration for organo‐silicon compounds.
Variational localized‐site cluster expansions. VII. Higher ansätze and the linear heisenberg model
Authors: Garcíaa‐bach M. A. , Klein D. J. 
Published: December 2004

AbstractThe localized‐site cluster expansion technique is applied to the infinite linear Heisenberg model with both nearest‐neighbor and next nearest‐neighbor interactions. These cluster ansätze are systematically studied and improved, up to the so‐called 5‐site approximation. Generally we find the present cluster ansätze yield the most accurate variational results yet available.
Electronic structure calculation of [Fe(CN)6]−3 by the SCF‐MSXα method: Study of optical transitions, X‐ray photoelectron spectrum, and Mössbauer isomer shifts
Authors: Guenzburger Diana , Maffeo Bruno , Larsson Sven 
Published: December 2004

AbstractThe SCF‐MSXα method is used to determine the electronic structure of [Fe(CN)6]−3. Optical transition energies and valence electron ionization potentials are calculated and compared with experimental measurements. The electronic charge density at the Fe nucleus is calculated; this result and available electron densities at the Fe nucleus obtained by the same method for other Fe complexes are used to discuss the mechanisms involved in the interpretation of Mössbauer isomer shift values.
Level crossings and branch points studied by the multidimensional partitioning technique
Authors: Brändas Erkki , Froelich Piotr 
Published: December 2004

AbstractThe possibility of level crossings is discussed from a general multidimensional partitioning viewpoint. By extending the traditional motion of a self‐adjoint Hamiltonian to a self‐adjoint analytic family of operators, it is found that level intersections that appear fall into two mutually exclusive categories: the conventional diagonal one corresponding to Jordan blocks of order m = 1, and the nondiagonal one with m ≥ 2. Consequences with respect to some recent examples, such as Longuet‐Higgins “sign‐reversing loop” construction and the 1II near degeneracy in SiO, are discussed and examined.
Additivity model for calculations of UHF spin densities in some aza‐aromatic radical anions
Authors: Sharma K. K. 
Published: December 2004

AbstractThe additivity model suggested by Moss et al. has been applied for predicting spin densities in aza‐aromatic radical anions. The core‐resonance integrals (βrs) have been evaluated using Linderberg's relation. The spin‐density values calculated using the additivity model, have been found to be in good agreement with unrestricted Hartree–Fock (UHF) spin‐density values.
On the approximation of potential‐energy functions for two‐center systems
Authors: Barnsley Michael F. , Aguilar Jacques G. 
Published: December 2004

AbstractLet E(R) be a potential‐energy function for a neutral or ionic diatom in the Born‐Oppenheimer approximation. Then the approximation of E(R) for 0 < R < ∞ starting from finite and typically small sets of given information is considered. The approach is based on the fact that the scaled potential curves F(R) = R2E(R) derive from an eigenvalue problem which depends linearly on R. The nature of the curves F(R) is examined in detail. The results include the discovery of various approximants, some of which display rigorous bounding properties and others, closely related, whose behavior with respect to the approximated function appears to be predictable.
Intermolecular correlation in a new approximation scheme
Authors: Aronowitz S. 
Published: December 2004

AbstractIt is demonstrated for a spin‐free, nonrelativistic, complete molecular Hamiltonian that there is an optimal solution to the separation of electronic and nuclear motions. The adiabatic approximation is obtained as a special limiting case. A fruitful interpretation of intermolecular correlation results from the assumption that such correlation involves the degeneracy of a molecular‐energy state of one molecule with that of another chemical species, e.g., cubane and cyclooctatetraene. As a consequence, rigorous relationships are established for the influence of nodal patterns of the electronic functions on intermolecular correlation. Also derived are stringent symmetry rules which both electronic and nuclear functions involved in the correlation must obey. Throughout the treatment is a many‐electron one.
Orbital optimization techniques: Comparative study in a semiempirical framework
Authors: Adnan S. S. Z. , Bhattacharya S. , Mukherjee D. 
Published: December 2004

AbstractIn this paper, MC‐SCF and CI methods have been explored for the calculation of ground‐ and excited‐state energies of some aromatic heterocycles in the PPP framework. A new algorithm for solving the orbital equations in MC‐SCF theory has been suggested and its performance has been compared with the conventional gradient optimization technique. Energies of first few transitions have been calculated and compared with rather extensive CI results.
On the adequacy of the molecular‐orbital picture for describing ionization processes
Authors: Cederbaum L. S. , Schirmer J. , Domcke W. , Von Niessen W. 
Published: December 2004

AbstractGeneral arguments concerning the adequacy of the molecular‐orbital (MO) ionization picture are given. Whereas the MO ionization picture is found to be valid for both outer valence and core electrons, it may completely break down in the inner valence region. The general considerations are supported by many‐body calculations on methane, acetylene, hydrogen cyanide, and dinitrogen tetroxide. It is demonstrated that the breakdown of the MO ionization picture is a common phenomenon.
Conformational analysis of double‐helical polynucleotides
Authors: Khutorsky V. E. , Poltev V. I. 
Published: December 2004

AbstractThe intramolecular interaction energy of the regular double‐helical polynucleotide as a function of variables that determine the mutual position of base pairs and sugar pucker was calculated using atom–atom potentials. The calculations showed the existence of two valley‐like regions with minimal values on the energetic surface. One of them corresponds to the A family of nucleic acids, the other to the B family. The points that correspond to the models constructed by means of x‐ray data are placed in a conformational space near the lines that describe the position of the bottom of the valleys.
Theoretical model study of the reactivity of benzo(a)pyrene diol epoxide with the amino groups of the nucleic acid bases
Authors: Lavery Richard , Pullman Bernard 
Published: December 2004

AbstractA quantum‐mechanical model study, aided by classical potential calculations, of the formation of adducts between the candidate ultimate carcinogen benzo(a)pyrene diol epoxide and the amino groups of guanine, adenine, and cytosine is presented. An explanation for the preferential reactivity of guanine is proposed and conformational aspects of adduct formation are discussed for both nucleosides and B‐DNA.
Theoretical conformational analysis considering solvent effects
Authors: Hofmann Hans‐Jörg , Peinel Gustav , Weller Thilo 
Published: December 2004

AbstractThe conformational structure of some biologically important compounds (formamide, 1‐methyl‐1,4‐dihydronicotinamide, and chlorocholine) was examined using quantum‐chemical methods. For each of the systems studied a theoretical model (supermolecule approximation, classical continuum model, or hydration shell model) was selected to estimate the influence of solvents on the conformational structure.
Intermolecular interactions of globular proteins in the crystal state
Authors: Makarov A. A. , Monaselidze D. R. , Esipova N. G. 
Published: December 2004

AbstractThe present work is devoted to investigation of thermal transitions in the crystals of seven proteins to compare the protein globule stability in crystal and solution. Calorimetry methods, electron and optical microscopy, as well as x‐ray diffraction studies are used. It is found that protein crystals do not melt and that the destruction of the crystal lattice is a result of protein globule denaturation within the crystal. It is demonstrated that during the heating of pepsin and DF‐trypsin crystals it is possible to observe phase transition of the first order. Equilibrium temperatures of protein denaturation in crystals and in solution coincide. The peculiarities of the crystal state are revealed in the increasing thermal transition cooperativity and the system relaxation period.
Molecular orbital study of molecular nitrogen fixation
Authors: Turi Nagy L. , Pelikán P. , Liška M. , Haring M. , Čeppan M. , Breza M. 
Published: December 2004

AbstractThe model systems of molecular nitrogen fixation [N2 + H]⋅, [N2 + H]+, [N2 + H]−, [N2 + H2], [N2 + H2]+, and [N2 + H2]− were studied by the semiempirical INDO method. The study was based on the formal analogy between the catalytic reactions and the photochemical, radical, and ionic reactions on the other side. Symmetrical and donor‐acceptor properties of necessary catalytic systems were proposed using the dependence of energy characteristics and electron structure on reaction coordinate. On the basis of this MO study we have proposed the appropriate symmetry types of catalysts for each of acceptable models of nitrogen fixation. For one of the proposed systems there was realised a model MO computation with explicit inclusion of atoms of transition metals (Fe, V).
Influence of annelation by benzene ring on electronic absorption spectra and on character of the singlet π‐π* transitions at polynuclear p‐quinones
Authors: Nepraš Miloš , Titz Miloš 
Published: December 2004

AbstractAromatic polynuclear p‐quinones and their derivatives have been studied using their electronic absorption and luminescence spectra and their basicity. The data were used to provide a basis for the study of the relationships between the structure and the spectral characteristics.
Influence of intermolecular interactions on the DNA conformation
Authors: Malenkov G. G. , Gagua A. V. , Timofeev V. P. 
Published: December 2004

AbstractOf the two known families of double‐stranded DNA conformations, A is stable in less‐polar, and B in more‐polar solutions. In some water‐nonelectrolyte solutions, B to A transition occurs when water activity in the system is near 0.8. In such systems, however, as water‐methanol, water‐ethylene glycol, etc., B conformation is stable at very low water activity. Hyperfine splitting constant of a spin label (A), a widely used criterion of the solvent polarity, was measured by EPR method in the solutions, in which B to A transition takes place at 25°C. A values in solutions of different compositions are close to each other. A method for quantitative estimation of Van der Waals and hydrogen‐bond contributions to A values is proposed. A values in water‐methanol solutions show that their polarity is too high for the A form to be stable. Decreasing temperature shifts the B‐A equilibrium to the B form, which correlates with increasing polarity of the water‐alcohol solutions, as measured by the EPR method. Thus B to A transition is mainly determined by the polarity of the environment, which, in turn, is determined by the ability of the solvent molecules to participate in Van der Waals interactions and hydrogen bonding.
Bose condensation of phonons in biological systems
Authors: Moskalenko S. A. , Pokatilov E. P. , Miglei M. F. , Kiselyova E. S. 
Published: December 2004

AbstractUsing the Bogolyubov's rate equation from the theory of superfluidity the possibility of Bose condensation of phonons in biological systems and the validity of Fröhlich's hypothesis has been proved. We took into account both the third and the fourth anharmonism in the rate equation. All the processes with active phonons (from one to four) of biological active modes have been investigated. Taking into account these processes the expression for the chemical potential is shown to be changed, but the conditions for Bose condensation of phonons still exist. For the first time we point out the possibility of soliton wave packet propagation in the coherent systems of phonons and photons. The possibility of Bose condensation of excitons in biological systems is also discussed.
Modeling of the short‐range order for polymers by the ideal peak method
Authors: Shilov V. V. , Kruglyak N. E. , Lipatov Yu. S. 
Published: December 2004

AbstractThe method of the modeling of the radial distribution function for liquid and amorphous polymers is described. The method consists in the use of pair functions of the radial distribution (ideal peaks) for the construction of the distribution function of intramolecular distances and the comparison of the theoretical function with the experimental one. The theoretical functions for two possible conformations of the poly(tetramethylene glycol) macromolecule were computed. It follows from comparison of the computed theoretical functions with the experimental one that the intramolecular distances do not become apparent in the experimental curve. The differential functions containing the contributions of the intermolecular distances only were obtained by subtraction of the theoretical function from the experimental. Comparison of the differential functions of the two conformational states which were taken as models proved that there are large numbers of gauche conformations in the liquid polymer in contrast to the crystalline polymer. On the basis of the analysis of the differential functions for liquid and crystalline poly(tetramethylene glycol), we concluded that the short‐range order of the polymer is distorted during the melting in that the basic plane of the poly(tetramethylene glycol) paracrystal becomes almost hexagonal.
Theoretical study of electronic spectra of the DNA bases
Authors: Kuprievich V. A. , Shramko O. V. 
Published: December 2004

AbstractExcited π‐electronic states of cytosine and uracil are calculated by the CI method. The effects of a transition from the single‐excited configuration set to the set involving all double‐excited configurations are considered. The set expansion is shown to affect essentially the transition energies and oscillator strengths, in particular, an additional electron transition related to the first absorption band occurs in the singlet uracil spectrum. When doubly excitations are taken into account the triplet transition energies considerably increase and become practically insensitive to repulsion integral parametrization.
Solvation of nonpolar groups of biomacromolecules
Authors: Sarkisov G. N. , Agrafonov Yu. V. , Martynov G. A. 
Published: December 2004

AbstractThe method of correlation functions used in the theory of liquids is suggested for investigation of the solvation shell structure in the vicinity of nonpolar surfaces. An approach making it possible to obtain the molecule correlation functions in the solvation shell is worked out. In this approach the correlation functions are the product of the interatomic correlation functions.
Effective utilization of off‐diagonal hypervirial relations considering diagonal hypervirial relation: Harmonic oscillator case
Authors: Sakamoto Kazuyoshi , Terasaka Toshitaka 
Published: December 2004

AbstractThe effective utilization of hypervirial relations is scrutinized to improve the approximate excited‐state functions in the harmonic oscillator system. A new method is presented which simultaneously employs the off‐diagonal hypervirial relations with the diagonal hypervirial relation. In order to use these relations effectively, the following points are pointed out: (i) the presented method is useful to get better reasonable results for the excitation energies and the state functions; (ii) the ground state given must satisfy the virial theorem; (iii) in the hypervirial operator used here as xm, the smaller integers of m's present better results; and (iv) the employment of the comparatively small number of trial basis functions of the type exp (−γ|x|) is sufficient for reproducing the exact excited state. Especially among them, condition (ii) plays an important role. Applying all the proposals to the first and the second excited states, one gets a highly improved excitation energy, state function, and other physical quantities (e.g., transition moment and oscillator strength). The presented method is also found to be more effective than the employment of only the off‐diagonal hypervirial relations or the method of the scaling operation.
Second quantization for composite particles, reactive collisions, and unstable particles
Authors: Girardeau M. D. 
Published: December 2004

AbstractThe salient features of generalized second‐quantization representations for nonrelativistic systems of composite particles are reviewed and their application to a reformulation of the quantum theory of reactive collisions is discussed. Such representations allow the properties of the bound composite states to be built explicitly into the algebra of states and observables. A single unperturbed Hamiltonian simultaneously describes the free propagation of the various species of bound composites as well as of their unbound constituents, while the interaction Hamiltonian describes only true scattering and reaction processes. The inclusion of the binding of all composites in the unperturbed Hamiltonian cures the divergences in the Born series arising from bound‐state poles. Unstable composites can be included in a natural way, leading to an explicit representation for the kinematics and dynamics of their decay and their contribution to collision phenomena.
Quantum‐field theory and electrodynamics of superconducting systems
Authors: Fusco‐Girard M. , Mancini F. , Marinaro M. 
Published: December 2004

AbstractBy using quantum‐field theory techniques and the boson transformation method, we study systems that exhibit macroscopic ordered states. As an illustration, we apply the method to the study of superconducting systems by taking into account the quantization of the vector potential. The results of a dynamical calculation, performed in the pair approximation, are presented. The Higgs phenomenon is also discussed in the framework of a fully quantum theory.
Irreversibility, decay, and asymptotic dynamics
Authors: Emch Gérard G. 
Published: December 2004

AbstractThis paper contains the skeleton of one lecture, and of two raporteur's interventions, made at the Sanibel Symposium in February–March, 1979. The task asked of this lecturer was to present an outline of the program of nonequilibrium statistical mechanics, and to indicate some of the recent developments in our understanding of this program. Section I lists a few of the principal physical ingredients of the theory. The possible implementation of certain aspects of the program is demonstrated in Sec. II with the help of three exactly soluble models. Finally in Sec. III we extrapolate from these particular examples in two directions: the stochastic aspect of statistical mechanics, and some remarks on the theory of the quantum measurement process. The presence, at the Symposium, of several distinguished lecturers who presented their own original, and most interesting, contributions hopefully made appear less outrageous—at least at the time—the severe omissions due to the personal choices this particular speaker had to make to keep within the time limitations inherent to such a gathering. It is now hoped that, even when taken out of the full context of the Symposium, the rearranged text which follows might nevertheless help focusing attention on some of the important problems remaining to be solved. It is a pleasure to acknowledge here the stimulating hospitality of the Symposium Scientific Director, Professor P.‐O. Löwdin.
Nodeless wave function quantum theory
Authors: Hunter Geoffrey 
Published: December 2004

AbstractThe nodes where the wave function changes sign in conventional quantum theory can alternatively be regarded as places where the wave function descends to zero but rises again without changing its sign. This behavior is accomplished by adding delta function barriers to the potential energy wherever a node occurs in the wave function. This model is supported by the recognition that the wave functions of a subsystem, which is not truly isolated, are really marginal amplitudes which implicitly average out interactions of the system with its environment. The finite effect of these interactions is to replace the delta function barriers by barriers of finite width and height.