bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of cholesky‐like matrix decomposition methods to the evaluation of atomic orbital integrals and integral derivatives
Authors: O'neal Douglas W. , Simons Jack 
Published: December 2004

AbstractWhen viewed as a square two‐indexed matrix, the array of atomic orbital‐based, two‐electron integrals (ij|kl) is a positive semidefinite array. Beebe and Linderberg showed, in 1977, that actual or near linear dependencies often exist within the types of atomic orbital basis sets employed in conventional quantum chemical calculations. In fact, large (i.e., higher quality) bases were shown to be substantially more redundant than smaller or more spatially separated bases. In situations where there exists significant basis near redundancy, the rank (r) of the (ij|kl) ≡ Vl,J matrix of integrals will be significantly smaller than the matrix dimension M. When this occurs, it proves computationally tractable to decompose the M‐dimensional matrix V into components L (V = LLT) which contain all of the information needed to form the full V matrix. The Cholesky algorithm allow such a decomposition to be carried out and forms the basis of the work described here. The method is found to be highly successful in reducing the number of integrals and integral derivatives that must actually be calculated. In particular, results on the C2 molecule indicate that the algorithm can be superior to traditional methods of integral derivative generation if the orbital basis is large enough to contain appreciable near redundancy. In contrast, results on benzene with a more spatially delocalized basis show that conventional methods are preferred whenever substantial basis (near) redundancy is not present.
Approximate density–external potential relation and the pauli potential for systems with coulombic interaction
Authors: Kozlowski P. M. , March N. H. 
Published: December 2004

AbstractEarlier work on the Pauli potential VPauli, which allows the square root of the electron density to be calculated directly from a Schrödinger equation, is generalized from two‐level (radial) systems such as the Be atom to the n‐level case in one dimension. This is achieved using hyperspherical functions, in terms of which the first‐ and second‐order density matrices are expressed. It is confirmed that VPauli can be constructed from the ground‐state density ρ (x) and its first two derivatives, plus the functional derivative of the single‐particle kinetic energy with respect to ρ. Finally, contact is made with the Harriman construction, but now using approximate one‐body orbitals.
The effect of penetration on the multipole and multistreak expansions of molecular electrostatic potentials
Authors: Berrondo M. , Eggleston S. W. , Larson E. G. 
Published: December 2004

AbstractWe have separated the electrostatic potential of a molecule into two parts: an atomic‐like part, which is expanded in spherical harmonics around each nucleus, plus an overlap part, expanded in ellipsoidal harmonics around each pair of nuclei. Neglect of the penetration effect in these expansions yields a superposition of point and line multipoles. We have studied the penetration effect for the case of the hydrogen molecules and suggest an approximation for the elliptical penetration effect as a screening factor in the electrostatic potential.
Variational calculations of vibrational and vibration‐rotational properties of ozone
Authors: Anmin Tian , Ruifeng Liu , Zemin Sun , Xuefeng Zhou , Guosen Yan 
Published: December 2004

AbstractVibrational and vibration‐rotational energy levels of ozone and its isotopic substitutes have been calculated variationally by the ladder operator method. Thirty vibrational band origins and rotational energies of vibrational ground states for these molecules have been given. The good agreement between the calculated results and the observed values shows that the calculation method is a promising one for variational studies of vibrational and vibration‐rotational properties of nonlinear polyatomic molecules.
Evaluation of two‐center, two‐ and three‐electron integrals involving correlation factors over Slater‐type orbitals. II. Kinetic and potential energy integrals and examples of numerical results
Authors: Budziński Jan , Firszt Mirosława , Woźnicki Wiesław 
Published: December 2004

AbstractThis article is concerned with the construction of the general algorithm for evaluating two‐center, two‐ and three‐electron integrals occurring in matrix elements of one‐electron operators in the basis of variational correlated functions. This problem has been solved here in prolate spherical coordinates, using the modified and extended form of the Neumann expansion of the interelectronic distance function rkij derived in Part I of this series for k = −1, 0, 1, 2. This work expands the method proposed by one of us in the preceding paper for integrals of the types mentioned above. The results of numerical calculations for different types of the two‐ and three‐electron integrals are presented. The problem of convergence of the proposed procedures used is also discussed.
Ab initio studies of parts of the potential surface for the system C3H6 + HO2
Authors: Skancke Per N. 
Published: December 2004

AbstractThe addition reactions between HO2 and propene leading to the radical intermediates CH3CHCH2OOH and CH3CHOHCH2 have been studied by ab initio molecular orbital calculations using a 6‐31G* basis set and including electron correlation through fourth‐order Møller–Plesset calculations. The intermediates are predicted to have energies of about 5 kcal/mol below the total reactant energies, the complex resulting from the HO2 attack on the central carbon of propene being slightly preferred. The activation energies for the addition to the terminal carbon and the central carbon are predicted to be 8.5 and 8.0 kcal/mol, respectively, at the highest level of calculation [MP4(SDTQ)] with corrections for spin contamination. Spin contamination corrections are found to be very important in the calculation of these values. Referring to previous calculations at the same level for the addition of HO2 to ethylene [12], we assume that the addition step is the rate‐determining one in the reaction leading to HO and propene oxide. The observed activation energy for this reaction, 14.2 kcal/mol [2], is significantly higher than the predicted one for the addition step. The discrepancy found, 6.2 kcal/mol, is virtually the same as the one encountered in the ethylene case, 6.6 kcal/mol [12]. The barrier to intramolecular hydrogen migration leading to the intermediate radical CH2CH2CH2OOH is found to be 42.6 kcal/mol at the highest level of calculation. Spin contaminiation corrections are not important for this energy.
Exact and approximate Hartree–Fock calculations for extended metallic systems
Authors: Calais Jean‐Louis , Delhalle Joseph 
Published: December 2004

AbstractStarting out with the electron gas, we make a survey of the reasons for the singularity in the derivative of the orbital energy with respect to the wave number at the Fermi level for a realistic extended metallic system. Some properties of the occupation function are reviewed and it is pointed out that the direct reason for the singularity resides in a divergent lattice sum originating in the exchange part of the orbital energy. Numerical aspects are discussed, in particular with reference to the difficulty in detecting this singularity in actual computations.
Strategies for electron correlation calculations on large molecular systems
Authors: Saebø Svein 
Published: December 2004

AbstractThe two main problems in applying common methods for electron correlation to large systems are (1) the steep dependency of the computational task with the size of the system and (2) the large and often prohibitive number of two‐electron integrals that must be stored and retrieved during the calculation. The direct local correlation method eliminates both these problems. This method is a combination of the local correlation method that eliminates the steep computational dependency with the size of the system and extension of the direct SCF approach to electron correlation methods. The latter method eliminates external storage of the electron repulsion integrals. In this review, the direct local correlation approach and its computer implementation will be described in detail, including computational examples and comparisons to similar methods developed in other groups. The feasibility of future applications to extended systems is discussed.
Theoretical study of the hydrogen chemisorption on a ZnO surface
Authors: Nakatsuji H. , Fukunishi Y. 
Published: December 2004

AbstractReactions of a hydrogen molecule with a ZnO surface are studied by an ab initio method. For simulating the ZnO (10 1 0) surface, one ZnO molecule both with and without a Madelung potential is used. Since the electrostatic potential due to the ionic layer decreases exponentially, the effect of the layers deeper than the second one can be neglected. The Madelung potential is, therefore, expressed by the 32 point charges of ±0.5 situated on the first and second layers. Several low‐lying states of ZnO and the ZnO + H2 system have been calculated by the symmetry‐adapted cluster (SAC) and SAC–CI methods. It is found that the 1Σ+ state of ZnO is the ground state and catalytic active and the other states are inactive. ZnO (1Σ+) reacts with H2 and dissociatively adsorbs it with making ZnH and OH bonds. This occurs both with and without the Madelung potential. Without the Madelung potential, the heat of reaction is 81.3 kcal/mol and the reaction barrier is 14.0 kcal/mol. With the Madelung potential, the heat of reaction decreases to 73.5 kcal/mol and the barrier decreases to 11.5 kcal/mol. The mechanism of this reaction is the electron donation from the 2pπ orbital of O to the antibonding σu MO of H2 and the back‐donation from the bonding σg MO of H2 to the LUMO of ZnO. In the intermediate stage of the reaction, the dipole of ZnO works to increase the overlap of the active MOS to make the reaction easier. Throughout the reaction, the in‐plane 2pπ orbital of O and the HOMO of ZnO are inactive and work to keep the ZnO bond stable during the catalytic process.
A molecular dynamics study of large‐scale reversible aggregation of anisotropic particles
Authors: Brugè F. , Martorana V. , Fornili S. L. , Palma‐Vittorelli M. B. 
Published: December 2004

AbstractWe report findings of 1000 ps molecular dynamics simulations of a bidimensional system of 4050 Lennard–Jones particles with electric dipoles, undergoing spinodal separation. This simple system is used to model the reversible aggregation of building blocks bearing specific and fixed adhesion sites at their surface. Aggregation regions so obtained resemble images of self‐assembled biological structures. Statistical analyses of these regions evidence the interplay of thermodynamic instability and of interaction range between the attachment sites. They also illustrate some basic aspects of the morphogenesis of extended biomolecular/cellular structures, self‐organized from initially homogeneous solutions.
Comments on the carbon cluster C60 and on its complexes with alkaline elements
Authors: Corongiu G. , Clementi E. 
Published: December 2004

AbstractWe have analyzed in the Hartree–Fock approximation the carbon cluster C60 with a single‐zeta [(9,5)/(2,1)] basis set and a double‐zeta [(9,5)/(4,2)] basis set, the latter with and without 3d polarization functions. Estimates of the correlation energy correction were obained either using Becke's density functional theory or the Clementi–Chakravorty's electron–pair density approximation. The cluster's positive ion and singly and doubly charged negative ions have also been studied (doublets for C and C and singlet and triplet for C) and computed both with a doublezeta basis set and defferent geometries or a double‐zeta plus polarization basis set. The geometries considered include the one obtained by quantum molecular dynamics using the Car–Parrinello approximation and two additional near this minimum. The computed ionization potential and electron affinity are in reasonable agreement with the experiments considering the basis sets adopted. A lithium, a sodium, or a potassium atom or the corresponding positive ions have been placed at the center of the cluster and have been shown to form stable complexes: C60Li+, C60Li, C60Na+, C60Na, C60K+, and C60K. In addition, preliminary data with a calcium atom are reported. Computations on model cluster C5, C6, and C9 are also reported to show that one needs large basis sets, extended use of polarization functions, and correlation corrections for quantitative results, more accurate than ∼5 kcal/mol per carbon atom, in the total energy, as in this work.
Ab initio SCF molecular dynamics: Exploring the potential energy surface of small silicon clusters
Authors: Maluendes S. A. , Dupuis M. 
Published: December 2004

AbstractA few classical nuclear trajectories at finite temperature have been calculated from ab initio SCF energy gradients. They have been used as an alternative means to search for local minimum energy structures on the Born–Oppenheimer surfaces for some elemental silicon clusters. The approach is found to be beneficial in yielding different structures of silicon clusters. In other cases, the trajectories stay trapped in only one region of the phase space.
Monte Carlo simulation of liquid hydroxylamine using ab initio intermolecular potential functions
Authors: Michopoulos Yanos , Rode Bernd M. 
Published: December 2004

AbstractA potential model for intermolecular interactions between hydroxylamine (NH2OH) molecules based on ab initio quantum mechanical calculations is reviewed and critically assessed by analyzing results from a Monte Carlo simulation of liquid hydroxylamine. The liquid structure is studied in detail using radial, energy, and angular distribution functions, coordination numbers, and their distribution. Results indicate a large first solvation shell (5.3 Å), which contains 13 molecules, out of which only 4 are truly bonded by nonlinear, low‐energy hydrogen bonds. These are of either the OH…O or the OH…N type, as NH…O and NH…N linear bonds are considerably suppressed, and no cyclic dimers are found. The dependence of the structural and physical properties on the simulation characteristics has also been investigated.
Cobalt spectroscopy and the structure of the active site of carbonic anhydrase
Authors: Garmer D. R. , Krauss M. 
Published: December 2004

AbstractTheoretical models of divalent cobalt bound to the active site of the enzyme, carbonic anhydrase, are constructed to study the effect of the first‐shell geometry and coordination number on the experimentally observed visible spectra. Favorable comparisons of the ab initio calculations of the hexa‐aquo complex of Co(II) with experimental results provides a test of the method. The d–d spectra variation with pH in the enzyme is found to be determined by the first‐shell complex geometry as obtained from energy optimization. The low pH complex is predicted to be predominantly five‐coordinate with two waters in the first‐shell, whereas the high pH complex is predominantly four‐coordinate. Equilibria between the four‐ and five‐coordinate structures at low pH is not indicated by the calculation.
Inter‐ and intramolecular motions in proteins
Authors: Parak Fritz 
Published: December 2004

AbstractThe use of 57Fe Mössbauer radiation allows the study of protein crystal dynamics by a time‐resolved analysis of X‐ray scattering. In myoglobin cystals, the main source of the root mean squared amplitude of motions comes from intramolecular protein dynamics. Segments of the size of an α‐helix move collectively. Long‐range correlated motions give only a minor contribution. Comparison with Mössbauer absorption spectroscopy shows that protein‐specific dynamics is frozen out below 200 K and the lattice dynamics is mainly responsible for the low‐temperature behavior.
Studies of protein hydration in aqueous solution by high‐resolution nuclear magnetic resonance spectroscopy
Authors: Wüthrich Kurt , Otting Gottfried 
Published: December 2004

AbstractIndividual hydration water molecules in aqueous protein solutions have been observed using experimental schemes for homonuclear two‐dimensional and heteronuclear three‐dimensional NMR experiments in H2O solution, which do not require suppression of the solvent line by presaturation. In these experiments, the location of the hydration waters is determined from their nuclear Overhauser effects (NOEs) with individual hydrogen atoms of distinct amino acid residues. In the basic pancreatic trypsin inhibitor (BPTI), four internal water molecules that had been reported in three different crystal forms were also found to be in the same locations in the solution structure, with lifetimes with respect to exchange of the water protons in excess of 0.3 ns. Additional NOEs with polypeptide protons located on the protein surface may involve either hydration water molecules or hydroxyl protons of amino acid side chains. Their total number is small compared to the number of NOEs expected from the hydration water molecules identified in the crystal structures of BPTI.
Saddle‐point expansion in molecular‐orbital theory
Authors: Marañón Julio 
Published: December 2004

AbstractWe propose a novel method for calculation of the electronic correlation energy of molecular systems in the path integral formalism. The procedure consists of saddle‐point expansion of the path integral around the Hartree–Fock energy. By one loop‐expansion of the molecular path integral into the generalized space phase of the molecular orbitals, the shift energy is obtained.
Algorithmic tools in the study of semiempirical potential surfaces
Authors: Liotard Daniel A. 
Published: December 2004

AbstractThe most efficient optimization methods implemented in the semiempirical package AMPAC are presented. They concern the minimization of the energy or of the gradient norm by either pseudo‐Newton or quadratic procedures, the search for transition states, and the intrinsic reaction coordinate in conjunction with variational transition‐state theories. Nonlocal methods such as simulated annealing are also introduced. © 1992 John Wiley & Sons, Inc.
On the implications of the structure of 3′‐azido‐3′‐deoxythymidine and related compounds to antiviral activity
Authors: Da Motta Neto Joaquim Delphino , Zerner Michael C. , De Alencastro Ricardo Bicca 
Published: December 2004

AbstractWe report structure–activity relation studies on 3′‐azido‐3′‐deoxythymidine (AZT) and the implications to the biological activity of this class of compounds. The adiabatic potential surface (APS) of the title compound has been examined with the LCAO–MO–SCF method within the AMI approximation. This study has shown at least 13 minima, all separated by small energy differences and barriers. We have found that the equilibrium favors the anti,gg conformations, in variance to previous studies that predicted the syn,gg conformers to be the most stable forms. The most stable conformation (A) is favored by about 0.5 kcal/mol. However, calculations simulating a bulk‐water environment suggest that the three lowest energy conformations (A, B, and C) become almost degenerate in solution. We suggest that the crystallographic conformation (L), characterized by a high dipole moment, and analogous to C, undergoes a strong stabilization upon rotation of the 3′‐azido group and that these two conformers, C and L, are the only ones in which the hydroxyl proton is free of steric hindrance. This last point has some relevance from the biological point of view since it is generally accepted that this site must be phosphorylated in order for AZT to achieve its therapeutic effects. The above results suggest that, once in solution, conformer L isomerizes to C, which is the bioactive form of AZT. © 1992 John Wiley & Sons, Inc.
A combined quantum chemical/molecular mechanical study of hydrogen‐bonded systems
Authors: Vasilyev V. V. , Bliznyuk A. A. , Voityuk A. A. 
Published: December 2004

AbstractA computational approach, which involves the combination of the OPLS force field and molecular orbital MNDO, AM1, and PM3 methods, has been developed to describe the effects of a large, molecular mechanically simulated environment on the Hamiltonian of a quantum chemical system. To test the validity of the combined quantum mechanical/molecular mechanical (QM/MM) potential, a systematic study of the structures and energies of neutral and charged hydrogen‐bonded complexes has been carried out, including comparisons with pure semiempirical calculations and available experimental and ab initio data. It is shown that, in many cases, the hybrid QM/MM potential behaves better than do related MNDO/M, AM1, and PM3 methods. As a case in point, the draw‐back of AM1 favoring bifurcated H‐bonded structures over single ones is not presented in the combined AM1/OPLS scheme. Possible ways of improvement of the combined QM/MM potential are discussed. © 1992 John Wiley & Sons, Inc.
The C2‐DIIS convergence acceleration algorithm
Authors: Sellers Harrell 
Published: December 2004

AbstractWe present a theoretical and numerical comparison between two DIIS algorithms to which we refer herein as C1‐DIIS and C2‐DIIS. The C2‐DIIS algorithm is shown to be equivalent to the traditional C1‐DIIS algorithm near convergence and more stable numerically as regards the accumulation of round‐off error when the C1‐DIIS equations become (nearly) singular. The C2‐DIIS algorithm also offers alternative solutions to the DIIS equations when anharmonicities or numerical difficulties are problematic. These properties of the C2‐DIIS algorithm allow the use of much larger DIIS spaces, obviating the need for truncation of the DIIS space, which, when done, usually results in a loss of information contained in the iterated subspace. The C2‐DIIS method can be considered to be a variant of the singular value decomposition method. © 1993 John Wiley & Sons, Inc.
Multiple time scale Hartree–Fock molecular dynamics
Authors: Hartke Bernd , Gibson Douglas A. , Carter Emily A. 
Published: December 2004

AbstractThis is the first application of a rigorous, established multiple time‐step method to ab initio molecular dynamics. The resulting algorithm is conceptually simple and easy to implement, but very effective. It translates the large mass differences present in ab initio molecular dynamics into substantial savings in computer time while retaining high accuracy. This transforms ab initio molecular dynamics from a desirable but prohibitively expensive possibility into a viable method, at least for short‐time phenomena in small systems or for otherwise inaccessibly complicated potential energy surfaces. © 1993 John Wiley & Sons, Inc.
Spatially confined simple quantum mechanical systems
Authors: Zicovich‐Wilson C. , Planelles J. H. , Jaskóalski W. 
Published: December 2004

AbstractA study of two simple quantum mechanical system, i.e., harmonic oscillator (HO) and hydrogen atom (H) trapped inside the wells is performed. The influence of the spatial confinement on the energy spectra of both systems is investigated. An analytically solvable model of the well potential is presented in the case of the HO. A central and noncentral localization of HO in the well is discussed. The results are used to explain some reported anomalous experimental data on the porphine IR spectrum. The case of hydrogen atom is studied by solving the problem of the electron in the potential V = Z/R cot r/R. An exact formula for the energy is derived for s states. For others, analytically nonsolvable symmetries, a formula with correct asymptotic behavior is proposed. The results are compared with some numerical calculations for spherical rectangular well and an extension to many‐electron atoms is also presented. The effect of breaking degeneracy and of ordering energies of H in a different way than in the case of many‐electron systems is broadly discussed. © 1994 John Wiley & Sons, Inc.