bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discrete spatial symmetries: Redundant coordinates and search for stationary points in reduced spaces
Authors: Banerjee Ajit 
Published: January 2005

AbstractGiven the invariance of an N‐body system under discrete operations of reflection, inversion, a rotation by 2π/n, and the corresponding relations among the derivatives of energy, we have constructed through an invertible transformation a set of active and redundant coordinates. Movement along the active coordinates preserves all symmetry relations. We show that algorithms for locating stationary points or for calculating reaction paths are exactly separable in these active and redundant coordinates. We further show that this formalism is equally applicable when equations of constraints among coordinates are specified for the movement of particles. This includes geometrical constraints on bond lengths, angles, substituent group internal rotations, etc. This formalism enhances the efficiency since (laborious) cartesian derivatives need to be calculated only for the active variables and that the problem is reduced in term of m(⩽3N) variables. We apply this procedure to obtain the equilibrium geometry of H2O molecule within the subspace of C2v symmetry configurations ab initio derivatives.
Ab initio studies on the catalytic mechanism of ester hydroloysis by serine proteases
Authors: Stamato Fulvia M. L. G. , Tapia O. 
Published: January 2005

AbstractSome aspects of the catalytic mechanism of the serine proteases were submitted to ab initio RHF MO studies at a 3‐21G basis set level. Analytical gradients were used to optimize the geometry of the molecular partners and to sense the interactions among them when they make up for the active site in chymotrypsin. Reaction fields of graded strengths were used to sense the response of the active site to protein surrounding effects. The catalytic triad (Asp‐His‐Ser) is reduced to a model dyad represented by ammonia and methyl alcohol. Methyl acetate represents a substrate. One water molecule is added to the model as a local solvation effect. (This molecule plays a central role in the rupture of the acylated enzyme, which was not studied here). The reaction pathways of MeAc interacting with the alcohol and alcoholate were studied to determine the intrinsic properties of this system in the present level of wave function representation. The presence of the dyad alters the interaction potential of the reacting system. The canonical form in vacuo is significantly more stable than the diionic one. The reaction field produces stabilizing effects favoring the catalytic diionic form. The effect of the tetrahedralization in the substrate has been studied. A planar substrate is strongly repelled at distances shorter than 3.0 Å, whereas a tetrahedral substrate can approach the catalytic dyad in the native configuration without apparent steric hindrance.
Molecular orbital calculations on tumor‐inhibitory nitrosoureas: QSARs
Authors: Lewis David F. V. 
Published: January 2005

AbstractMolecular Orbital (MO) calculations by the MINDO/3 method on tumor‐inhinbitory nitrosoureas is reported. Electronic structures for 18 chlorethyl nitrosoureas and 30 cyclohexyl nitrosoureas (CCNUS) are related to biological activity in the form of toxicity, therapeutic activity, and increase in life span and chemical reactivity in the form of alkylating and carbamoylating activity. Hydrophobicity, as measured by the logarithm of the partition coefficient (octan‐1‐o1/water), shows a parallelism with calculated bulk molecular properties. Mechanisms of alkylation and other reactions related to biological action are proposed and discussed.
Adiabatic perturbation theory for the degenerate case. III. Adiabatic formalism by Gell‐Mann and low with an arbitrary switching function
Authors: Dmitriev Yuri Yu. , Solnyshkina Olga V. 
Published: January 2005

AbstractAn adiabatic formalism in the degenerate or quasidegenerate subspaces, which does not depend on the particular form of the switching function g(α, t), is outlined. A general factorization theorem for the dynamic operator Sα(t, t0 | g) is proved. This theorem enables one to formulate the perturbation expansion for the effective Hamiltonian and the wave operator which is free from the adiabatic divergencies.
The concept of the topological atom within the MO‐LCAO approach. II. On the nature of the nephelauxetic effect
Authors: Proinov E. , Neshey N. , Andreev A. 
Published: January 2005

AbstractA new MO‐LCAO description of the nephelauxetic effect is proposed based on the concept of the topological atom and on the method of reduced density matrices. This approach allows one to overcome some conceptual difficulties of ligand‐field theory and to derive effective parameters of d‐d electron repulsion of a bound transition‐metal in a proper way. The two ligand‐field mechanisms of the nephelauxetic effect—the central field covalency and the symmetry‐restricted covalency—are clarified and generalized. In addition, a new factor, important for the nephelauxetic effect is found: its size‐dependence on the region of the topological atom.
The sequential product of geminals and the ground states of some atoms
Authors: Jiang X. Q. , Jin B. Y. , Zeng Z. H. , Sun C. C. , Coleman A. J. 
Published: January 2005

AbstractBy means of the SPG function which is associated with an extreme point of the set of N‐representable second‐order reduced density matrices, an attempt is made to perform the calculations of the ground states of some atoms with four electrons such as Be. The results show that the SPG function is as suitable as the well‐known AGP function for approximating the ground states of atoms and molecules.
A sequential product of geminals and its applications
Authors: Jin B. Y. , Jiang X. Q. , Zeng Z. H. , Sun C. C. , Coleman A. J. 
Published: January 2005

AbstractIn this paper, an SPG function, which is associated with an extreme point of the set of N‐representable second‐order reduced density matrices, is used to perform the calculation of the ground state energy of LiH with the variation of internuclear separation. The result of our calculation essentially is in accordance with that of AGP function.
A Crystal Orbital approach for two‐ and three‐dimensional solids on the basis of CNDO/INDO Hamiltonians. Basis equations
Authors: Ramírez Rafael , Böhm Michael C. 
Published: January 2005

AbstractA Hartree–Fock (HF) self‐consistent field (SCF) crystal orbital (CO) formalism for two‐ and three‐dimensional (2D/3D) solids on the basis of semiempirical CNDO/INDO (complete neglect of differential overlap; intermediate neglect of differential overlap) Hamiltonians is presented. The employed SCF variants allow for the treatment of atomic species up to bromine under the inclusion of the first (i.e., 3d) transition metal series. Band structure investigations of 2D and 3D materials containing more than 30 atoms per unit cell are feasible by the present SCF HF CO formalism. The theoretical background of the computational scheme is given in this contribution. Special emphasis is placed on physically reliable truncation criteria for the lattice sums, the adaptation of the crystal symmetry in k space, as well as the suitable choice of domains in Brillouin zone (BZ) integrations required in the determination of charge‐density matrices. The capability and limitations of the semiempirical SCF HF CO approach is demonstrated for some simpler solids by comparing the present computational results with those of ab initio CO schemes as well as conventional numerical methods in soid‐state theory. The employed model solids are graphite and BN (2D and 3D networks for both solids) as well as diamond, silicon, germanium, and TiS2.
The two‐dimensional band structure of (polyphthalocyaninato)Ni(II)
Authors: Ramírez Rafael , Böhm Michael C. 
Published: January 2005

AbstractThe two‐dimensional (2D) band structure of (polyphthalocyaninato)Ni(II), Ni(ppc), has been analyzed by a self‐consistent field (SCF) Hartree–Fock (HF) crystal orbital (CO) formalism based on an INDO (intermediate neglect of differential overlap) type Hamiltonian. The calculated HF band gap of Ni(ppc) amounts to 0.24 eV. The highest filled band is a ringlike a1u combination (D4h symmetry label) localized at the carbon sites of the organic fragment. Remarkable hybridization in the valence band leads to the considerable band width Δϵv of 2.92 eV. This value is close to the Δϵv numbers which are conventionally encountered in one‐dimensional metallomacrocycles. The effective width of the states in Ni(ppc) is 13.8 eV. In graphite a net π interval of 13.0 eV is predicted by the present CO formalism; i.e., the energetic distribution of the π electrons is roughly comparable in both 2D solids. The Ni 3d states in Ni(ppc) are far below the Fermi level which is calculated at −4.9 eV; they are predicted between −12.2 and −16.4 eV in the mean‐field approximation. Quasi‐particle corrections lead to a significant shift of these strongly metal‐centered states. Important electronic structure properties of Ni(ppc) are compared with those of 1D metallomacrocycles with similar molecular stoichiometry. The total density of states distribution of Ni(ppc) has been fragmented into projected (ligand π and σ, Ni 3d) contributions in order to allow for a transparent interpretation of the 2D band structure.
Simplified expansion of Slater orbitals about displaced centers
Authors: Rico J. Fernández , Lóapez R. , Ramíarez G. 
Published: January 2005

AbstractA new and very simple one‐range expansion of the 0s function is derived and employed as the starting point of three recurrence relations which allow the expansion of arbitrary Slater functions over displaced centers. Convergence of the expansions, both pointwise and in norm, are analyzed, and three‐center nuclear attraction integrals are chosen for a further test of the formal developments and the numerical behavior of these expansions.
Control over theoretical descriptions of atoms and molecules. An information theoretic approach to the automatic classification and systematic improvement of approximate wave functions
Authors: Maroulis George 
Published: January 2005

AbstractA rigorous approach to the study of the quality of theoretical descriptions of atoms and molecules is proposed. Theoretical descriptions, i.e., collections of atomic or molecular properties obtained via quantum chemical methods, are associated with information quantities defined with respect to reference theoretical or experimental data. In this way the comparison of two theoretical descriptions is reduced to the comparison of the respective information quantities. An increase in information is interpreted as improvement of the theoretical description. The aforementioned approach should be useful in problems related to classifications and systematic improvements of approximate wave functions and consequently for comparing the performance of quantum chemical methods in calculations of atomic and molecular properties. This approach should also constitute a powerful tool for the construction of suitable basis sets for use in calculations of atomic and molecular properties.
Structure and properties of nonclassical polymers. VII. Polymers with heteroatoms
Authors: Tyutyulkov N. N. , Ivanov C. I. , Schopov I. , Polansky O. E. , Olbrich G. 
Published: January 2005

AbstractIt is shown that the Coulson–Rushbrooke theorem for odd alternant hydrocarbons [15] can be generalized for some classes of nonclassical systems containing heteroatoms. The energy spectrum of such conjugated polymers containing heteroatomic groups, in particular a nitroxide group >NO, is analogous to that studied [1–4] in homonuclear alternant nonclassical polymers, whose ground state is characterized by maximum spin multiplicity. Their band structure is characterized by a wide energy gap, in the middle of which there is a band of degenerate or nearly degenerate quantum states.The presence of a narrow band of degenerate quantum states, the Hund rule, and the alternant character of the polymers of this group determine the maximum multiplicity of their ground state and may give rise to the creation of magnetic order in such compounds, if interchain correlations occur. This is in line with the investigations in Refs. 1–11.
A measure of the error in wave functions
Authors: Fraga Serafin 
Published: January 2005

AbstractThe quantity ϵ = (Φ||(H − E)Φ|) gives a measure of the error in the approximate solution, Φ (with corresponding energy expectation value E), to an eigenfunction of the Hamiltonian operator H of the system under consideration; this quantity vanishes for the exact function ψ. In a percentage scale (with 0% error for the exact function and 100% for a reference, approximate function), the error of Φ may be expressed as 100(ϵ/ϵr), where ϵr corresponds to the reference function (e.g., obtained with a minimal basis set). This approach eliminates the need of knowing beforehand the exact solution in order to have an estimate of the error of an approximate solution.
Thomas–Fermi theory from a perturbative treatment of the hydrogenic limit energy density functional: A possible link to local density functional theory
Authors: Bartolotti Libero J. , Parr Robert G. , Tal Yoram 
Published: January 2005

AbstractA perturbation expansion which connects the hydrogenic limit energy density functional to the Thomas–Fermi functional is discussed. This perturbation series, where the Coulomb energy density functional is treated as the perturbation to the hydrogenic limit functional, is, in fact, the q = (N/Z) expansion of Thomas–Fermi theory. A truncated form of the first‐order correction to the functional provides further insight into the model which treats the ground state energy as a local functional of the electron density.
An interaction potential between an alanine zwitterion and a water molecule based on ab initio calculations
Authors: Ni Xiangshan , Shi Xiufan , Ling Lunjiang 
Published: January 2005

AbstractInteraction energies between an alanine zwitterion and a water molecule at 150 different positions and orientations have been calculated using the ab initio method with the minimal basis set and employing the counterpoise method to eliminate the basis set superposition error. Dispersion energies are estimated using the Slater–Kirkwood formula. Out of a total of 150 computed interaction energies, 140 whose SCF interaction energies are below 5 kcal/mol have been fitted with a summation of atom‐atom pair potentials in the form of the Lennard–Jones potential plus an electrostatic term. The standard deviation for this fitting is 0.49 kcal/mol.A sampling scheme regarding geometrical configurations is presented. Twenty rays are uniformly drawn from the origin of coordinates, a floatable division with equal ratios is made along each ray, and one of 60 orientations is randomly taken as the orientation of a water molecule. A nonlinear fitting method is used with a restriction on the sign change of fitting coefficients.
The use of symmetry in reciprocal space integrations. Asymmetric units and weighting factors for numerical integration procedures in any crystal symmetry
Authors: Ramirez Rafael , Böhm Michael C. 
Published: January 2005

AbstractA systematic collection of spatial domains for reciprocal space integrations is derived for all possible crystal symmetries. This set can be used as a simpler alternative to the conventional Brillouin zones. The analysis is restricted to integrations where the function in the integrand satisfies inversion symmetry in k space. In this case only 24 different spatial domains have to be defined in order to allow for k space integrations in the 230 different crystal symmetries. A graphic representation of the asymmetric unit for each of the 24 integration domains is given. Special positions and the associated weighting factors required for numerical integrations in theoretical solid‐state approaches are tabulated.
Hydrophobic effect in biological associates: A Monte Carlo simulation of caffeine molecules stacking
Authors: Danilov Victor I. , Shestopalova Anna V. 
Published: January 2005

AbstractResults of a Monte Carlo simulation of the hydration of caffeine (1,3,7‐trimethyl‐2,6‐dioxipurine) and three different configurations of its stacked dimer are presented. Simulations were performed in a cluster approximation; the system contained 200 water molecules. The nature of the stabilization of caffeine stacking associates in water was considered. A hydrophobic behavior of methyl groups during association of caffeine molecules in water is shown. Results of the simulation of caffeine hydration are compared with experimental data from the study of the system of caffeine–water.
Conformational analysis of oligosaccharides in solution
Authors: Tvaroška Igor 
Published: January 2005

AbstractA complete understanding of the role of carbohydrates in biological systems is to a large extent dependent on the information available about the equilibrium mixture and about the preferred conformation of the carbohydrate molecules in solution. The conformational analysis offers a tool which can determine all possible conformations which influence the solution behavior of carbohydrates.This paper attempts to survey the progress in the theoretical conformational analysis of saccharides in solution. The conformational analysis will be discussed in detail both with respect to the strategy for the investigation of conformational properties but also with regard to the quality of the method used for calculations of the energy of the isolated molecule and free energy of solvation.Finally, examples will be given to illustrate how the methods of conformational analysis can be used to estimate the solution behavior of cyclic model compounds of carbohydrates 2‐methoxytetrahydropyran, monosaccharide D‐glucopyranose, and two disaccharides; β‐maltose and β‐cellobiose.
Interaction model for the antiinflammatory action of benzoic and salicylic acids and phenols
Authors: Mehler E. L. , Gerhards J. 
Published: January 2005

AbstractAb initio, quantum chemical methods have been used to develop an interaction model for the binding of benzoic and salicylic acids and phenols to cyclooxygenase, leading to their antiinflammatory action. The model is based on a regression analysis of the energy of the highest occupied molecular orbital with the potency of the active substances to inhibit prostaglandin production in mouse macrophages and on an analysis of the frontier orbital charge distributions and electrostatic potentials of active and inactive compounds. The model suggests that binding is controlled by an electrostatic orientational factor and a charge transfer or polarization contribution. The observed relative potencies of the phenols and acids can be rationalized with the help of the proposed interaction model.
Generalized statistical approach to the study of interatomic interactions
Authors: Santamaría R. , Berrondo M. , Novaro O. , Kryachko E. S. 
Published: January 2005

AbstractWe present a simple model for calculating the interatomic interaction energies in the electron gas approximation. We use a generalization of the supermolecular electronic density which includes a density overlap term. We present numerical calculations for the He‐He interaction as an illustration of the method.
Nonlocal and nonlinear electromagnetic effects at surfaces
Authors: Lundqvist S. 
Published: January 2005

AbstractThe reflected and transmitted electric fields generated by s‐ and p‐polarized incident radiation are discussed using a microscopic approach that matches the solution of Maxwell's equation (obtained by integration over the surface region) to the incident and the reflected fields in the vacuum and to the transmitted fields in the bulk. At positions where the dielectric response is varying rapidly, the parallel components of the oscillating polarization are the sources of reflected as well as transmitted fields, and the corresponding perpendicular components (which exist only for p‐polarized incident radiation) lead to charge oscillations that are the source of both longitudinal and transverse fields. The presence of the surface makes possible the generation of transverse and longitudinal excitations with large normal components of the wave vector, whose propagation directions are given by the conservation of the parallel component of the wave vector. This formulation does not make use of additional surface boundary conditions (ABC) but requires an explicit model for the nonlocal dielectric function in the surface region. Besides discussing the fields, we discuss the choice of electromagnetic potentials. We also discuss nonlinear properties with applications to second harmonic generation.
Some remarks on the perturbation and variation–perturbation calculations of the free energy for quantum systems
Authors: Löwdin Per‐Olov , Nagel Bengt 
Published: January 2005

AbstractA generalization of the Gibbs–Bogoliubov inequality F ⩽ F0 + 〈H − H0〉0 for the free energy F is studied which leads to a variation principle for this quantity that may be of importance in certain computational applications to quantum systems. This approach is coupled with a study of the perturbation expansion of the free energy for a canonical ensemble with H = H0 + λV in the general case when H0 and V do not commute. The second‐ and high‐order derivatives of the free energy with respect to the perturbation parameter λ are calculated. From the second‐order term is finally obtained a second‐order correction to the previous variational minimum for the free energy.
Explicit representation of Gel'fand–Tsetlin states in clifford algebra unitary group approach
Authors: Li Xiangzhu , Paldus Josef 
Published: January 2005

AbstractA explicit expression for the unitary group Clebsch–Gordan coefficients, which couple two fully antisymmetric single‐column states into the two‐column Gel'fand–Tsetlin states, is given in terms of isoscalar factors for the canonical subgroup chain U(n) ⊃ U(n – 1) ⊃ …︁ ⊃ U(1). The isoscalar factors are expressed through the step numbers labeling canonical basis states and enable a straightforward construction of Gel'fand–Tsetlin states in the Clifford algebra unitary group approach, without the use of the tables for the symmetric group outer‐product reduction coefficients.
Electric field variant ket for the calculation of dynamic polarizabilities. Application to H2O and N2
Authors: Rérat M. 
Published: January 2005

AbstractThe use of a new time‐dependent ket, variationally determined as a linear combination of Slater determinants associated with an electric field variant factor, provides an efficient technique for the calculation of dynamic polarizability tensors. Including electron correlation, the method is applied to the evaluation of the frequency‐dependent polarizability of H2O and N2 and can be used even when the photon energy is near the excitation energy. With relatively small basis sets, calculated polarizabilities and resonance frequencies are in good agreement with experimental values for H2O but have to be improved for N2.
Charge density by the use of the hiller–sucher–feinberg identity. Perturbative corrections and configuration interaction effects
Authors: Ishida Kazuhiro 
Published: January 2005

AbstractConfiguration interaction (CI) calculations are carried out for He atom and H2, LiH, and BH molecules in order to obtain the value of the charge density at the nucleus by the use of the Hiller–Sucher–Feinberg (HSF) identity. The HSF density also can be calculated with the double perturbation theory based on the Møller–Plesset‐type theory and also on the Epstein–Nesbet type. It is found that each value of the HSF density for these perturbative corrections is very similar to the corresponding value by the CI with single‐ and double‐electron excitations. Especially for the He atom, the HSF density value by the full‐CI wave function coincides with the exact value of the charge density in three significant figures. The electron correlation effects are found to be small but cannot be ignored in the HSF density. It can be shown that the superiority of the HSF density over the usual delta‐function‐type density is excellently confirmed.