bluuebunny/crossref_metadata_2025 huggingface dataset:
The basis set dependence of structures and energies of various states of cyclodisiloxane
Authors: Brenstein Robert J. , Scheiner Steve
Published: December 2004

Several common basis sets, ranging from minimal to double‐zeta, are applied to study the neutral singlet and triplet as well as positive‐ and negative‐ion doublet states of cyclodisiloxane. The effect of d‐polarization function exponents on the equilibrium geometries and energies is analyzed. The d‐type functions seem to be essential in the basis set of silicon, whereas their presence on oxygen is less critical. The optimum exponents (with respect to SCF energy) are determined to be 0.45 for Si and 0.60 for O, very close to those recommended for the 6–31G** basis set. The best structural predictions are obtained with the 6–31G(2d, p) basis set, which contains two sets of d functions on the heavy atoms. The predicted SiO bond length is 166 pm; the SiSi and OO distances are 237 and 232 pm, respectively, which correspond to an O—SiO angle of 88.6°. The ground state is found to be a singlet. All higher states have longer SiO bonds and Si—Si distances, whereas O—O distances are shorter. The energy separation between the singlet and other states is modified by electron correlation (MP treatment) by only a few kcal/mol.
Rayleigh–Schrödinger perturbation theory for many‐electron systems with partitioning of configurations by orders of excitation. II. Analysis of the ground state wavefunction and energy
Authors: Taylor William J.
Published: December 2004

Rayleigh‐Schrödinger perturbation theory has been rederived by an extension of Löwdin's partitioning method in which excited configurations are partitioned by their orders. The resulting equations show explicityly how first‐, second‐, and third‐order configurations contribute to the first three orders of perturbative corrections to the ground‐state wavefunction, and the first seven orders of corrections to the groundstate energy. The corrections to the energy have also been expressed in terms of the coefficients in the wavefunction by an independent derivation; this yields more compact expressions for the energy corrections. The results are summarized in three convenient tables. The relation of the results for the energy to the requirement of size consistency, and the linked cluster theorem of many‐body perturbation theory, is discussed.
Simple geometric generation of special points in brillouin‐zone integrations. Two‐dimensional bravais lattices
Authors: Ramíarez Rafael , Böhm Michael C.
Published: January 2005

A clear tabulation of sets of special points in numerical integrations over Brillouin zones (BZ) is given for the five two‐dimensional Bravais lattices. The special points derived on the basis of plain geometrical criteria coincide with a special case of the large unit cell (LUC) method. This similarity is also found for other generation procedures of k‐grids reported in the literature; that is, the corresponding techniques have their common origin in the LUC approach. The underlying integration procedure of the described scheme is based on the discrete summation, which implies that the weighting factors at the k‐points are only determined by the point symmetry in reciprocal space not by details of the adopted numerical integration formalism. The method can be applied to semiconducting and insulating solids—that is, to materials with finite band gaps. Grids in reciprocal space are generated on the basis of simple geometric criteria. The numerical effort of the present geometrical approach is negligible in comparison to the computational steps necessary in generation procedures of optimized k‐grids that have been published in the literature. The application of the suggested integration procedure is extremely simple; the generation of the k‐grids is only based on a few definitions and plain geometrical formulas. Modifications of the grid size are possible without difficulties. A collection of weighting factors ωi and special and general positions in the BZ is given; different grids are tabulated together with their geometrical efficiencies. The generated integration domains are compared with the results of elaborate schemes of finding grids with maximal efficiency.
Structure of MCSCF electronic energy domain
Authors: Panin A. I. , Khait Yu. G. , Gorinchoy N. N.
Published: January 2005

The modern version of the process of removing redundant variables in an MCSCF optimization problem is studied on the basis of the manifold theory. It is shown that there exists a simple parametrization of the MCSCF orbital manifold that is convenient for computer implementation of quasi‐Newton optimization schemes. A sequential unconstrained optimization technique for minimizing electronic energy with respect to local coordinates is described.
Exact results on homopolar singlet excitation energies of the hubbard model for linear polyenes
Authors: Hashimoto Katsufumi
Published: January 2005

The Lieb–Wu equations for homopolar singlet excited states of the Hubbard model of linear polyenes are formulated in a form tractable by numerical calculation. They are solved to obtain exact excitation energies of the lowest two excited states, corresponding to the 1B and 1E states of the benzene molecule, for systems with up to 50 and 30 electrons, respectively. These results may be particularly useful for checking accuracy of approximate methods for the homopolar states for which the conventional CI method is very difficult to apply. Calculation is also carried out for the 1B+ ionic excited state involving a spin excitation, which corresponds to the 1B state of the benzene molecule. The length dependence of the excitation energies is examined and shown to have no N−1 dependence for large N, where N is the number of electrons. This supplements the result on the 1E ionic state obtained in our previous paper.
The quality of s‐orbitals determined by least‐squares fitting and constrained variational methods
Authors: Robertson Donald D. , Smith Vedene H. , Simas Alfredo M. , Thakkar Ajit J.
Published: January 2005

Calculations of a wide range of position and momentum space properties of 23 orbital basis sets for atomic helium are performed to supplement our previous work. The combined results on 94 orbital basis sets are used to demonstrate that, as in the case of d‐orbitals, the least squares error is not as discriminating as other information theoretic measures of overall quality for s‐orbitals. Detailed comparisons suggest that constrained variation can improve the overall quality of the resulting orbital provided that the constraints are selected carefully to complement the bias inherent in the energy expectation value and the functional form of the basis functions.
The dirac second‐order equation and an improved quasirelativistic theory of atoms
Authors: Karwowski J. , Kobus J.
Published: January 2005

A transformation decoupling the Dirac second‐order equations for the large and small components of the radial atomic wavefunction has been derived. The decoupling procedure is exact for one‐electron atoms and approximate, though very accurate, for a general case of an atomic spherical potential. Its connection with the quasirelativistic theory of atoms has been discussed. The transformation has been applied to deriving an optimized quasirelativistic equation and to establishing relations between the quasirelativistic and the Dirac wavefunctions. Formulas resulting from these considerations allow improvement of quasirelativistic expectation values of operators so that the error, relative to the Dirac values, is reduced by a factor of 10.
The correlation effects at a local level. CI partitions
Authors: Largo‐Cabrerizo A. , Largo‐Cabrerizo J.
Published: January 2005

Making use of the local pair distribution function, h(r12+;r1, α), we have carried out a detailed study of the local mean values of r obtained from a CI wavefunction and from its different possible partitions for the helium isoelectronic series. Through comparison of these results with those provided by Hartree‐Fock and Hylleraas‐type explicitly correlated wavefunctions, we reached several conclusions concerning the relative importance of different partitions of the CI wavefunction in order to get a proper description of local correlation effects.
Some recent experiments on inelastic electron‐molecule collisions at low energies
Authors: Allan Michael
Published: January 2005

This work describes a novel trochoidal electron spectrometer and illustrates its properties on a few examples. In the first example vibrational excitation in the small molecules H2 and N2 is measured. Comparison of the results with theoretical work points to the neccessity of using non local methods for correct treatment of near‐threshold region and of extremely short‐lived resonances. In the second example the observation of resonant autodetachment of Feshbach resonances in many organic molecules is reported.
A molecular orbital study ofcisandtransdiaminodichloroplatinum(II)
Authors: El‐Issa B. D. , Makhyoun M. A. , Salsa' B. A.
Published: January 2005

The relativistic multiple scatteringXα method has been applied in order to calculate the eigenvalues and the charge densities of cis and trans diaminodichloroplatinum(II). The activity of the cis isomer as an antitumor agent is discussed in terms of the possible modes of coordination of certain fragments of the DNA molecule through the LUMO state of the cis Pt complex. Although possible, coordination of the trans isomer is rendered unlikely as a result of possible strain effects.
On the contribution of A. C. Hurley to theoretical chemistry
Authors: Maslen V. W.
Published: January 2005

Andrew Crowther Hurley was born in Melbourne, Australia, on 11 July 1926 and received his early education at Melbourne Church of England Grammar School. He graduated from the University of Melbourne with high honors in mathematics and natural philosophy and, in 1949, was awarded his M.A. with first class honors in the school of mathematics for his thesis “The Irreducible Crystal Classes in Four Dimensions,” his supervisor being Dr. Hans Schwerdtfeger. From 1950–1952 he was a member of Trinity College, Cambridge, and was awarded a Ph.D. for his research in theoretical chemistry under Sir John Lennard‐Jones. In 1953 he returned to Melbourne and joined what was to become the Division of Chemical Physics of the Commonwealth Scientific and Industrial Research Organization (CSIRO). The award of a fellowship by Trinity College enabled him to spend two more years, 1954–1956, in the Theoretical Chemistry Department of the University of Cambridge, and this was followed by a year with Professor J.C. Slater's solid state and molecular theory group at the Massachusetts Institute of Technology. In 1957 Andrew again returned to the Division of Chemical Physics in Melbourne, where he has remained, except for the academic year 1962–1963, when he was Visiting Professor in Theoretical Chemistry at Iowa State University.
Diabatic surfaces which permute into one another
Authors: Hall G. G.
Published: January 2005

Some of the problems, discussed recently, with the idea that every molecule has a structure can be removed by adopting the idea that some molecules have several structures with probabilities of transfer between them. This is supported theoretically by using diabatic energy surfaces and wave functions. Since these are not easy to define in general, their definition is given in the special case where the surfaces permute into one another. Two kinds of permutation operations are required. The analysis is given more fully for two intersecting diabatic surfaces. The analogy to the double‐valued property of the wave function near a conical intersection is given.
The 3‐21G(N*) basis set: An economical polarized basis set for ab initio studies on nitrogen‐containing molecules
Authors: Riggs Noel V. , Radom Leo
Published: January 2005

The 3‐21G basis set shares with its older cousin, the 4‐31G basis set, a tendency to overestimate valence angles at nitrogen atoms and to underestimate seriously barriers to inversion at such atoms. The 6‐31G* basis set generally yields greatly improved results in these respects. It is here shown that, for a variety of molecules, supplementation of the 3‐21G basis set at three‐ or two‐coordinate nitrogen atoms with a set of six d‐functions having exponent 1.0 leads to optimized geometries and inversion barriers at such nitrogen centers in good agreement with results obtained with the 6‐31G* basis set. This supplemented basis set, designated as 3‐21G(N*), also leads to calculated vibrational frequencies in good agreement with those calculated with the 6‐31G* basis set. The 3‐21G(N*) basis set offers an economical alternative to the 6‐31G* basis set, particularly for molecules containing several first‐row atoms other than nitrogen.
Unified analytical evaluation of the two‐center coulomb and hybrid integrals over slater‐type orbitals
Authors: Guseinov I. I.
Published: January 2005

Two‐center Coulomb and hybrid integrals are combined into a single expression by use of the formulas given by the author for the expansion of real and complex STO's about a point displaced from the orbital center. The final results are expressed in terms of the overlap integrals between STO's. Analytical formulas for the evaluation of these integrals have been established recently by the author.
A unified theory of the stability of benzenoid hydrocarbons
Authors: Cioslowski J.
Published: January 2005

The spectral density operator technique is proved to be a convenient tool for derivation of approximate topological formulae for total pi‐electron energy (Epi) of benzenoid hydrocarbons (BHs). Developed mathematical formalism points out a common origin of three different measures for the stability of BHs, namely: resonance energy (RE), number of Kekule structures (K) and HOMO‐LUMO separation (XHL). In turn, a novel topological invariant corresponding to “normalized” RE is derived. Numerical calculations for a representative set of BHs demonstrate effectiveness of the present approach. Various approaches to an estimation of BH stabilities are discussed.
Resonance energies of large conjugated hydrocarbons by a statistical method
Authors: Randić Milan , Solomon Vasanth , Grossman Stuart C. , Klein Douglas J. , Trinajsti Nenad
Published: January 2005

We developed a theoretical method for studying the aromatic stability of large molecules, molecules having a dozen and more fused benzene rings. Such molecules have so far often been outside the domain of theoretical studies. Combining the statistical approach and a particular graph theoretical analysis, it is possible to derive the expressions for molecular resonance energy for molecules of any size. The basis of the method is enumeration of conjugated circuits in random Kekulé valence structures. The method has been applied to evaluation of the resonance energies of conjugated hydrocarbons having about a dozen fused benzene rings. The approach consists of (1) construction of random Kekulé valence structures, (2) enumeration of conjugated circuits within the generated random valence structures, and (3) application of standard statistical analysis to a sufficiently large sample of structures. The construction of random valence forms is nontrivial, and some problems in generating random structures are discussed. The random Kekulé valence structures allow one not only to obtain the expression for molecular resonance energies (RE) and numerical estimates for RE, but also they provide the basis for discussion of local molecular features, such as ring characterization and Pauling bond orders.
Fixed closest distance of approach dipole potential mapping: An effective alternative to the monopole isopotential approach
Authors: Mishra P. C. , Tewari R. D.
Published: January 2005

It has been shown that an easier procedure to the study of molecular electrostatic potentials than the prevalent monopole isopotential approach is to use a dipole as the mapping device: allow the dipole to move on a geometrical surface enclosing the molecule such that the distance between the surface and the nearest atoms of the molecule (closest distance of approach) is fixed, say at 2 Å, calculate the electrostatic interaction energy between the molecule and the dipole at different points of the surface, and let the dipole orient itself along the minimum energy direction and treat these minimum energies as the desired electrostatic potentials. Thus the favorable binding sites of a given molecule for other species along with their relative orientations can be obtained. This procedure has been applied to the nucleic acid bases using the necessary input data from two independent sources. Thus success of the procedure in predicting important features of molecular electrostatic potentials has been demonstrated.
The effect of “full” and “limited” counterpoise corrections with different basis sets on the energy and the equilibrium distance of hydrogen bonded dimers
Authors: Alagona Giuliano , Ghio Caterina , Cammi Roberto , Tomasi Jacopo
Published: January 2005

A detailed analysis of the ΔE(R) curves for nine hydrogen bonded dimers involving HF, H2O, and NH3 as partners, computed with five basis sets (STO‐3G, MINI‐1, 3‐21G, 4‐31G, and 6‐31G**) and subjected to counterpoise (CP) corrections with three different methods is reported. Using several criteria and tests, the positive effect of full CP corrections for the description obtained with all the basis sets (with the exception of the STO‐3G one) is pointed out. The CP correction at the 6‐31G** levels is still sizable and improves the results with respect to the estimated Hartree–Fock limits of ΔE(Req) and Req. The results obtained with the application of the full CP correction to the MINI‐I energies are of relatively good quality. The STO‐3G energies at the SCF level are, on the contrary, overcorrected by the full CP correction and slightly improved by “limited” CP corrections: this basis set, however, is not recommended for calculations of geometries and stabilization energies of H‐bonded dimers of this size.
A gauge‐variational calculation of molecular diamagnetic susceptibility
Authors: Sinha S. K. , Ghosh R.
Published: January 2005

In order to avoid the determination of the perturbed wave function in the susceptibility calculation of closed shell molecules, several authors have developed gauge‐variation methods based on Rebane's work. The present work illustrates that introduction of a certain restriction in the gauge‐variation method makes the susceptibility calculations exceptionally simple. The restriction involves the use of the Coulomb gauge so that the gauge‐function satisfies Laplace's equation. The restriction was dictated by the demonstration of gauge‐invariance of the Rayleigh–Schrouml;dinger perturbation theory of diamagnetism. The method with the prescribed restriction has been applied to the H2O molecule, as an example, to demonstrate the advantages.
Variational construction of diabatic states
Authors: Pavlović Milica , Kučar Jasna , Hendeković Josip
Published: January 2005

The previously proposed local variational algorithm for generating diabatic states from adiabatic states is tested numerically for the simplest case of avoided potential curve crossing in a diatomic. The obtained results fully agree with those found by an interpolation scheme.
The complexes of phenyl acetylene with HF, H2O, and NH3: An ab initio study
Authors: Sapse A. M. , Jain Duli C.
Published: January 2005

Phenyl acetylene complexes with HF, H2O, and NH3 are investigated with ab initio molecular orbital calculations using the 6‐31G Gaussian basis set. HF is found to form a π complex, whereas H2O and NH3 form σ complexes. Observations of experimental spectroscopic shifts are rationalized.
EHMO Calculations for a pyridine molecule adsorbed on a Ag adatom: Implications for surface enhanced Raman spectroscopy
Authors: Tian Bogang , Wu Guozhen
Published: January 2005

Extended Hückel molecular orbital calculations have been made for the silver adatom‐pyridine complex in order to reveal the very chemical nature of the surface‐enhanced Raman scattering. The variation of the behaviors of the bond orders and charge densities as functions of the AgN distance and the net charge on the Ag atom, which is applied voltage dependent, is demonstrated. The calculated optical transition of the system can accommodate the experimental observation that as the wavelength of the exciting line shifts from 4880 to 6328 Å, the surface‐enhanced Raman signal is enhanced more. Most interesting is the fact that the calculations reproduce well the experimental observation that there is an applied voltage on the electrode at which the surface‐enhanced Raman signal is a maximum. The calculations show that the charge transfer enhanced mechanism is mostly due to the transfer of electrons from the silver atom to the pyridine molecule. Several useful overlap integrals involving d orbitals not available in the literature before are listed in the appendices for convenient reference.
A regular periodic table of the elements and its quantum mechanical requirement
Authors: Purdela D.
Published: January 2005

By using the n + (1/2)l filling rule of the atomic Aufbau principle, where n is the principal quantum number and l is the azimuthal quantum number, a new periodic table is presented, its periods having, in order, 8, 18, 18, 32, 42, 50, … elements. The mentioned rule is proposed instead of the n + l rule (or Madelung's rule) which constitutes the quantum mechanical basis of the current periodic table and predicts periods having, in order, 2, 8, 8, 18, 18, 32, 32, 50, … elements. The new periodic table is called “regular” because its groups are formed according to a single rule (namely, the first elements of each period are placed in the same order as the elements of the preceding period), in contrast with the current periodic table, where no simple rule can be applied for the same purpose. The most characteristic feature of the regular periodic table is the fact that its groups are also related in a periodic manner.
C. A. Coulson and the surface energy of metals: A further comment
Authors: Hall George G.
Published: January 2005

The role of the boundary conditions is emphasized in determining the relation between the counting problem, posed by Coulson and solved by the number theorists, and the physical problem from which it arises. The surface energy term, which Coulson sought, does exist, but only when the periodic boundary conditions, which he used, are replaced by the finite box conditions.
Particle‐hole symmetry and complementary quantum systems
Authors: Živković T. P.
Published: January 2005

It is well known that positive and negative ions derived from the same alternant hydrocarbon have almost indistinguishable electron spectra. Effective charges, bond orders, and many other properties also correlate between the two systems. These «alternancy» properties are due to the particle‐hole symmetry, and they can be generalized far beyond alternant hydrocarbons. In general, with each quantum system one can associate a «complementary» system. The eigenstates of the complementary system are related to the eigenstates of the original system in the same way as the anionic eigenstates of an alternant hydrocarbon are related to the cationic eigenstates of this hydrocarbon. In particular, the (N + k)‐electron spectrum of the complementary system is the same, up to the uniform shift, as the (N − k)‐electron spectrum of the original system; the effective charges in the complementary system are opposite to the corresponding effetive charges in the original system; bond orders in the two systems between vertices of the same and of the opposite parity are, respectively, opposite and the same, etc. Each particle‐hole symmetry operator associates with the original system one such complementary system. There is hence a large number of the systems complementary to the same original system. In the PPP model and in various generalizations of this model, systems complementary to conjugated hydrocarbons are Möbius‐type alterations of original hydrocarbons. In the case of conjugated heterocompounds, there is a formal replacement of all heteroatoms with some other heteroatoms, with or without an additional Möbius‐type change. Such complementary systems may correspond to entirely different molecules, and they also may describe some transition states of these molecules.
Total π‐electron energy in the “variable β” Hückel method
Authors: Cioslowski J.
Published: January 2005

It is demonstrated that the total π‐electron energy calculated within the “variable β” Hückel method is almost entirely determined by the total π‐electron energy computed within the ordinary (topological) Hückel method and the number of the carbon‐carbon bonds. This explains the fact that the topological Hückel method is capable of predicting relative stabilities of various molecules, even if they possess different bond lengths.
Supercomputing and supercomputers for science and engineering in general and for chemistry and biosciences in particular
Authors: Clementi E. , Chin S. , Corongiu G. , Detrich J. H. , Dupuis M. , Folsom D. , Lie G. C. , Logan D. , Sonnad V.
Published: January 2005

We start by pointing out relationships between production of information, global simulation, and supercomputing, thus placing our research activities in today's society context. Then we detail the evolution in hardware and software for 1CAP, our experimental supercomputer, which we claim to be especially well suited for supercomputing in science and engineering. A preliminary discussion of 1CAP/3090 (our latest experimental effort) is included. Many examples from different disciplines are provided to verify our assertions. We “prove” our point by presenting an example of global supercomputing. Starting with 3 nuclei and 10 electrons, building up to a single water molecule, then to a few hundred, we learn, for example, about Raman, infrared, and neutron scattering; we then move up to a few hundred thousand molecules to analyze particle flow and obstructions; finally we experiment, but only preliminarily, with a few million particles to learn more on nonequilibrium dynamics as in the Rayleigh‐Benard systems. In this way, quantum mechanics is overlapped with statistical mechanics and expanded into microdynamics. The entire paper is finally reanalyzed from a different perspective, presenting rather systematically, even if most briefly, our ideas on “modern” computational chemistry, where quantum mechanics is as much needed as fluid dynamics and graphics. In this section the main computational techniques are analyzed in terms of computer programs and their associated flow diagrams to solve the basic equations using parallel supercomputers.
Conformational implications of some nucleotide sequences
Authors: Poltev V. I. , Teplukhin A. V.
Published: January 2005

The conformational properties of some nucleotide sequences result in their ability to bind specifically some ligands or tobe recognized by specific proteins. In order to investigate the dependence of conformational behavior of the DNA duplex on nucleotide sequence, we analyzed the interaction energy of nucleic acid bases as a function of conformational parameters and base sequence. Extended regions of minimum energy values were found for different sequences. Although these regions (valleys) largely overlap, each one shows specificity for a particular sequence. This suggests that a specific pathway of changes in conformational parameters exists for each sequence. the changes may be accompanied by considerable shifts (2–3 Å) of the atom positions and an only slight variation (1–2 kcal/mol) of energy. Even small shifts in other directions can cause a drastic energy increase. For some nucleotide sequences, the energetically preferable conformations are the B‐like ones (e.g., ApA, TpA), whereas for others the A‐like ones are preferable (e.g., GpG, ApT). IN general, Pyr‐Pur sequences have a tendency to a larger τ and smaller H and D than Pur‐Pyr sequences. A large body of experimental data on nucleic acid structure in fibers and in solutions can be explained by results obtained.
Molecular interactions in aqueous solutions: The role of random fluctuations of external parameters and of thermodynamic instabilities
Authors: Palma‐Vittorelli M. B.
Published: January 2005

A biological system usually operates under nonstable values of relevant parameters, such as pH, temperature, and ionic strength. The question therefore poses whether such fluctations do affect its relevant processes. Experimental studies on the role of random temperature fluctuations on functional encounters of biostructural polymer molecules, and consequent self‐assembly of supramolecular structures, have evidenced an additional, noise‐induced order of these structures. This type of effect is the result of nonlinearity in physical systems, and the case of a biosystem is especially interesting. As recent experiments have shown, spinodal decomposition resulting from thermodynamic instability may favor the onset of the supramolecular ordering process. If the random fluctuations of temperature are imposed in such conditions of thermodynamic instability, their ordering effect is further enhanced.
A comparative analysis of the active site properties of the resting states of cytochrome c peroxidase, metmyoglobin, and catalase
Authors: Axe Frank U. , Waleh Ahmad , Chantranupong Lek , Loew Gilda H.
Published: January 2005

Quantum chemical studies (INDO‐RHF‐SCF) have been made for the resting state active sites of three closely related heme proteins, cytochrome c peroxidase (CCP), metmyoglobin (MMB), and catalase (CAT). The relative energies of the germane sextet, quartet, and doublet spin‐states of each active site were calculated. Both CCP and MMB have similar heme units, consisting of an Fe(III)‐protoporphyrin‐IX with an imidazole and water as axial ligands. Our calculations show that the larger doming of the porphyrin, greater out‐of‐planarity of the iron, and the shorter iron‐water distance in MMB leads to a sextet ground state with a low‐lying quartet state. By contrast, the order of these two states is reversed in CCP, when a neutral imidazole is used as the endogenous axial ligand. An imidazolate ligand, on the other hand, which is an extreme representation of the H‐bonding believed to occur in CCP with a nearby aspartate residue, leads to a sextet ground state with a low‐lying quartet state. Assuming at least a partially anionic ligand in the intact protein, it follows that the quartet contribution to the ground state properties will be larger in CCP than in MMB. These predictions are consistent with the observed differences in the temperature‐dependent magnetic susceptibility for these two proteins. The present results suggest that the experimentally observed Mössbauer resonance spectra of CCP should be reinterpreted in terms of sextet and quartet state contributions to the electric field gradient. Calculations for catalase, which has a single phenolate ligand, result in a sextet ground state with a low‐lying quartet state consistent with available Mössbauer and magnetic susceptibility data. Our calculations of the Im− form of CCP show that it more closely resembles CAT. Thus, the effect of proton transfer in CCP can account at least in part for the similarities between CCP and CAT function. Minor differences in ground spin‐state and electronic properties calculated for CCP and MMB, however, cannot explain why MMB does not have significant peroxidase activity. The different functions of MMB and CCP must then be due in part to other known differences in their protein environment such as polar residues around the distal ligand binding pocket of CCP, which are absent in MMB, and could help its transformation to an active oxidizing state.
Noncovalent interactions of medium strength. A revised interpretation and examples of its applications
Authors: Alagona G. , Cammi R. , Ghio C. , Tomasi J.
Published: January 2005

Recent studies performed in our group on a classical problem of quantum chemistry, with strong implications for theoretical biochemistry and pharmacology, are here summarized. Ab initio descriptions of noncovalent interactions, and in particular H bonds and acid‐base couples, have been reexamined using as novel tools the decomposition of ΔE with the inclusion of CP corrections and a further decomposition of the ΔE components into group contributions. Some results of systematic analyses performed over H‐bonded dimers are reported, supplemented by a successful application of this approach to a problem of noticeable economic importance (the identification of catalysts for the industrial synthesis of tensioactives). A new feature, presented here for the first time, is the extension of the CP‐corrected decomposition of ΔE to bimolecular interactions in solution.
A many‐body diagrammatic theory of rotation–vibration spectra
Authors: Biskupič Stanislav , Kvasnička Vladimír
Published: January 2005

A many‐body diagrammatic perturbation theory of rotation–vibration spectra is elaborated. The present approach is based on two many‐body techniques, namely on the second quantization formalism (a rotating–vibrating molecule is formally treated here as a system of interacting vibrons, obeying the Bose–Einstein statistics) and the many‐body diagrammatic theory of a model Hamiltonian, initially suggested in the microscopic theory of nuclei and in the last decade very frequently exploited in the accounting for the correlation effects in many electron systems. In the framework of this theory, the rotation–vibration energies are determined as the eigenvalues of a finite‐dimensional model eigenproblem.
A configuration‐averaged Hartree–Fock procedure
Authors: Zerner Michael C.
Published: January 2005

A configuration‐averaged Fock (CAHF) operator is developed within the restricted open‐shell formulation (ROHF) for the case of any number of open‐shell orbitals containing any number of electrons. The resulting orbitals and energies should be useful for those cases where there is a great degeneracy of states, either preventing self‐consistent field convergence, or negating the value of a pure state description itself. This procedure is compared with the hyper‐Hartree–Fock method of Slater and the grand canonical Hartree–Fock ansatz of Abdulnar, Linderberg, Öhrn, and Thulstrup.
Improved treatment for matrix elements of spin‐dependent operators
Authors: Qianer Zhang , Xiangzhu Li
Published: January 2005

In this paper a general method for the evaluation of the matrix elements of spin‐dependent operators is proposed to improve the treatment primitively suggesteed by Cooper and Musher. This approach is largely based on the recent results which the present authors have achieved in the representation theory for the inner‐ and outer‐product reduction of the symmetric group. It is shown that the so‐called outer‐product coupling coefficients (OPCC) can be used to generalize the method for constructing the irreducible tensor operators of group Sn. Together with the use of inner‐product coupling coefficients (IPCC), an expression for the matrix elements of spin‐dependent operators is presented as the product of a Racah coefficient for Sn and a reduced matrix element which can be expressed in terms of IPCC, OPCC, and the related integrals. The treatment for one‐ and two‐electron spin‐dependent operators is discussed in detail.
The local orbital energy and density functional theory
Authors: Pearson Ralph G. , Palke William E.
Published: January 2005

From the viewpoint of density functional theory, an expression is derived which improves the average energy of a trial density. Applications to atoms and molecules are made using wave function methods and are based on properties of the variance, which is defined as \documentclass{article}\pagestyle{empty}\begin{document}$ (\overline {\varepsilon ^2 } - (\overline \varepsilon)^2)^{1/2} $\end{document}, where ϵ is the local orbital energy. Calculated results for both Hartree‐Fock and correlated wave functions are quite encouraging.
Approximate density matrices and wigner distribution functions from density, kinetic energy density, and idempotency constraints
Authors: Morrison Robert C. , Yang Weitao , Parr Robert G. , Lee Chengteh
Published: January 2005

The Wigner distribution function and the corresponding density matrix are calculated using a form for the distribution function suggested by maximization of the entropy. Wigner functions and density matrices are determined by imposing conditions of idempotency on the density matrix. Exchange energies and Compton profiles calculated from density matrices obtained by imposing the idempotency constraints are compared with the results of calculations using the Hartree–Fock density matrix and a Gaussian approximation for the density matrix for H and the noble gases He through Xe. Compton profiles from Wigner functions with idempotency constraints show improvements over the Gaussian approximation for the lighter atoms, but do not show significant changes for the heavier atoms. Exchange energies from density matrices with idempotency constraints show improvements over the Gaussian approximation except for the heavier atoms Kr and Xe.
Second‐order polarization propagator calculations of dynamic dipole polarizabilities and C6 coefficients
Authors: Sauer Stephan P. A. , Diercksen Geerd H. F. , Oddershede Jens
Published: January 2005

The frequency‐dependent dipole polarizability, α(E), is calculated using the second‐order polarization propagator approximation (SOPPA). We have shown how to express α(E) as a function of E2 and thus obtained a form of α(E) that can be used to compute C6‐coefficients without invoking complex arithmetic. For He we find that SOPPA recovers a large fraction of the correlation contribution for all frequencies, whereas for H2 where the correlation contributions are much smaller and also basis set‐dependent, we find a less definite trend of SOPPA relative to RPA.
Energy deposition mechanisms and biochemical aspects of DNA strand breaks by ionizing radiation
Authors: Chatterjee Aloke , Holley William R.
Published: January 2005

A theoretical model based on physical, chemical, and biochemical mechanisms has been presented to evaluate the yields of DNA strand breaks (single and double) as a function of linear energy transfer (LET) or −dE/dx. Energetic heavy charged particles are considered explicitly to provide a general theory for low‐ as well as for high‐LET radiation. There are three main features of the calculation: (a) track structure considerations for the energy deposition pattern, (b) three‐dimensional structure of DNA molecules to provide information on the exact location of damage, and (c) a Monte‐Carlo scheme to simulate the diffusion processes of water radicals. To avoid the complexities of a cellular medium, an aqueous solution of DNA is considered in the calculation. When the results of the calculations are compared with experimental measurements of the yields of strand breaks in mammalian DNA (exposed in a cellular complex), reasonable agreement is obtained. However, only those experimental data have been compared where there were no enzyme repair processes. The method of calculation has also been extended to study breaks in higher‐order structures of DNA molecules such as chromatin. Specific limitations of the present model have been pointed out for making further improvements.
An ab initio study of the unimolecular decomposition mechanism of formamidine. 4‐31G Characterization of potential energy hypersurface
Authors: Andrés Juan , Krechl Jiría , Carda Miguel , Silla Estanislao
Published: January 2005

Ab initio MO calculations have been carried out for the unimolecular decomposition of formamidine. The Hartree–Fock method in LCAO approximation with the 4‐31G basis set was used. The 4‐31G potential hypersurface has been further studied. The stationary points (R, TS, and P) were localized. A reaction analysis by correlation of bond‐order indices and localized molecular orbitals demonstrated that the decomposition is an asynchronous process. The TS can be described as four‐membered ring.
The elements of Flatland: Hartree‐Fock atomic ground states in two dimensions for Z = 1–24
Authors: Pyykkö Pekka , Zhao Yongfang
Published: January 2005

The Hartree–Fock problem in two dimensions (2D) has been solved for 1 ≤ Z ≤ 24 using a Gaussian basis and assuming r−1 Coulomb interactions. The order of occupation of the one‐electron states is

like in the 3D case. The 1s shell is found to be particularly small and strongly bound, making the 2D hydrogen a “superhalogen” and the 2D He a “superinert gas.” In contrast to 3D, 4s13d2 and 4s23d3 configurations are preferred for the 2D “Sc” and “Cu,” respectively. The six first 2D atoms have stronger and the later ones weaker valence‐bonding energies than do their 3D analogs. It is noted that the 2D Dirac energy expression for a hydrogenlike atom for mj = l + 1/2 agrees with the 3D Klein–Gordon one.
Study of the substituent effect on conjugated chain polymers by quantitative PCO method
Authors: He Huang Yuan , Zhuang Liu Ruo
Published: January 2005

The recently developed quantitative perturbational crystal orbital method was applied to study the band structures of substituted polyacetylene (PMCA and PMFA), and the interpretations given are satisfactory.
Linear depedence of total π‐electron energy of benzenoid hydrocarbons on Kekulé structure count
Authors: Gutman Ivan , Hall George G.
Published: January 2005

It is an empirically established fact that the total π‐electron energy (E) of benzenoid hydrocarbons is a linear function of the number of Kekulé structures (K). A general class of approximate formulas for E is shown to exhibit the required linear dependency on K. The condition for this is that the highest occupied molecular orbitals (MOS) are nondegenerate and well separated from the second highest occupied MOS.
A Dirac–Fock self‐consistent field method for closed‐shell molecules including Breit interaction
Authors: Mohanty Ajaya K.
Published: January 2005

We present a method for including the Breit interaction in relativistic self‐consistent field calculations for closed‐shell molecular systems using atomic basis spinors of kinetically balanced Gaussian‐type functions. The method extends the formalism described in a previous paper [A. Mohanty and E. Clementi, Int. J. Quantum Chem. 39, 487–517 (1991)] that dealt with the two‐electron effect due to Coulomb interaction only. It is shown that both frequency‐dependent and frequency‐independent Breit interactions can be treated on equal footing, and the corresponding matrix elements are evaluated following the well‐known Fourier transform technique applied to electron repulsion integral evaluation in nonrelativistic molecular calculations.
Advances in automatic speech recognition by combining information theory and neural network algorithms
Authors: Rigoll Gerhard
Published: January 2005

This paper presents some of the newest developments in the field of automatic speech recognition. It concentrates on describing the efforts of combining the two so‐far most successful approaches in automatic speech recognition, namely, information theory and neural network techniques, in order to obtain more improved speech recognition algorithms. An overview of the various approaches to the combination of these two basic technologies is given and the arising problems, such as the choice of the appropriate neural network paradigms, the best possible combination strategies and possibilities for an integrated training of the neural network, and the Markov model parameters, are discussed.
A theoretical study of the ground‐state potential surface of guanine and its binding with oxygen and water
Authors: Santhosh C. , Mishra P. C.
Published: January 2005

A molecular orbital geometry optimization study of the potential surface of guanine, guanineO2, and guanineO2water reaction products in the ground state has been carried out. The origin of the asymmetric double‐well potential surface of guanine suggested earlier on the basis of experimental observations has been explained. The most stable binding of O2 with guanine (G) is found to occur at the C4C5 double bond of the latter molecule. In the case of GO2water reaction product (HOOGOH), the groups OOH and OH bind at C4 and C8, respectively. The possiblity of a polymeric reaction product of the type R1(GOOG)nR2 (R1, R2 = H, OH) has also been suggested. These results are broadly supported by experimental observations. The mechanism of spectral oscillations observed in UV‐irradiated guanine solutions has been discussed.
Matrix elements of the U(2n) generators in the spin‐orbit basis
Authors: Titov A. V.
Published: January 2005

An algorithm for the evaluation of the matrix elements of the U(2n) generators in the spin‐orbit basis [induced by the U(n) ⊗ U(2) subgroup] is proposed. This algorithm can be used for calculations with spin‐dependent Hamiltonians for many‐electron problems.
A gauge symmetric band model of the Woodward–Hoffmann rules
Authors: Squire A. E. , Squire R. H.
Published: January 2005

The Woodward–Hoffmann (WH) Rules for the prediction of relative rates and stereochemistry of concerted reactions are based on considerations of the orbital symmetry of the reactants and products. Literally hundreds of reactions have been successfully categorized by these remarkably simple‐appearing Rules. This paper develops a one‐dimensional band model of these Rules. By explicit inclusion of the effects of an electromagnetic field in a standard gauge‐invariant fashion, it can be shown that at certain levels of field strength the model suggests that the Rules may be reversed. This is because the Rules appear in the model as a consequence of a centrifugal angular momentum barrier that can be shifted by an electromagnetic field. This barrier could account for “aromatic” stabilization. As an additional effect, the model predicts flux‐dependent oscillations and persistent currents for “aromatic” molecules due to the Aharonov–Bohm effect. The possible health effects of electromagnetic fields are speculated. The likelihood of experimental observations to verify the applicability of the model is discussed.
On the combination of two methods for the calculation of multicenter integrals using exponential–type orbitals
Authors: Perevozchikov V. I. , Maslov I. V. , Niukkanen A. W. , Homeier H. H. H. , Steinborn E. O.
Published: January 2005

The possible combination of two methods for the calculation of multicenter two‐electron integrals using STO and B function basis sets is discussed. The first method (Method I), which is of approximate nature, is based on a simplified version of the so‐called Σ‐factorization method [A. W. Niukkanen and L. A. Gribov, Theor. Chim. Acta 62, 443 (1983)], where the radial part of the two‐center one‐electron density ρab(r) is represented as a sum of two radial functions fa(r) and fb(r), placed on two different centers a and b. After such a transformation, the calculation of the two‐electron integrals boils down to the calculation of some type of Coulomb integrals. The second method (Method II), which calculates each integral separately to a given accuracy, is based on Mobius‐type quadrature used for a three‐dimensional integral representation for the two‐electron integral of B functions [E. O. Steinborn and H. H. H. Homeier, Int. J. Quantum Chem. Symp. 24, 349 (1990)]. In Method I, the choice of the radial functions placed on the different centers has an essential influence on the final value of the multicenter integrals. In the present study of Method I, a rather simple approximation of the radial part was made that reproduced the qualitative behavior of the molecular integral curves as function of the geometry rather well. At the present state of development, Method I produces fast order‐of‐magnitude estimates that are useful for screening purposes, i.e., to decide which integrals have to be evaluated more accurately by other methods like Method II. Method II reproduces data given in the literature [R. M. Pitzer and D. P. Merrifield, J. Chem. Phys. 52, 4782 (1970)] correctly. © 1992 John Wiley & Sons, Inc.