bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of localized molecular orbitals using group theory methods and its approach to the many‐electron correlation problem. IV. The symmetry‐adaptation of many‐center integrals and hamiltonian matrix elements in MCSCF calculations
Authors: Zhou Taijin , Liu Aimin 
Published: January 2005

AbstractGroup theoretic methods are presented for the transformations of integrals and the evaluation of matrix elements encountered in multiconfigurational self‐consistent field (MCSCF) and configuration interaction (CI) calculations. The method has the advantages of needing only to deal with a symmetry unique set of atomic orbitals (AO) integrals and transformation from unique atomic integrals to unique molecular integrals rather than with all of them. Hamiltonian matrix element is expressed by a linear combination of product terms of many‐center unique integrals and geometric factors. The group symmetry localized orbitals as atomic and molecular orbitals are a key feature of this algorithm. The method provides an alternative to traditional method that requires a table of coupling coefficients for products of the irreducible representations of the molecular point group. Geometric factors effectively eliminate these coupling coefficients. The saving of time and space in integral computations and transformations is analyzed. © 1994 by John Wiley & Sons, Inc.
Molecular mechanics (MM3) parameterization of hydroxylamine and methyl derivatives
Authors: Liang Guyan , Bowen J. Phillip , Bentley James A. 
Published: January 2005

AbstractBased on results of electron diffraction, gas phase infrared spectroscopy (IR), and MP2/6‐31 + G* ab initio calculations, a set of molecular mechanics (MM3) parameters was developed for molecules containing the N(sp3)—O(sp3) moiety. Using this set of parameters, MM3 is able to reproduce structures (bond lengths and bond angles) and vibrational spectra satisfactorily. © 1994 by John Wiley & Sons, Inc.
Triazene proton affinities: A comparison between density functional, Hartree–Fock, and post‐Hartree–Fock methods
Authors: Schmiedekamp Ann M. , Topol Igor A. , Burt Stanley K. , Razafinjanahary Holy , Chermette Henry , Pfaltzgraff Timothy , Michejda Christopher J. 
Published: January 2005

AbstractThe consistency of three density functional computational implementations (DMol, DGauss, and deMon) are compared with high‐level Hartree–Fock and Møller–Plesset (MP) calculations for triazene (HNNNH2) and formyl triazene (HNNNHCOH). Proton affinities on all electronegative sites are investigated as well as the geometries of the neutral and protonated species. Density functional calculations employing the nonlocal gradient corrections show agreement with MP calculations for both proton affinities and geometries of neutral and protonated triazenes. Local spin density approximation DMol calculations using numerical basis sets must employ an extended basis to agree with other density functional codes using analytic Gaussian basis sets. The lowest energy conformation of triazene was found to be nonplanar; however, the degree of nonplanarity, as well as some bond lengths, is dependent on the basis set, electron correlation treatment, and methods used for the calculation. © 1994 by John Wiley & Sons, Inc.This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
Structure of disiloxane: A semiempirical and Post‐Hartree–Fock study
Authors: Csonka Gábor I. , Erdösy Miklós , Réffy József 
Published: January 2005

AbstractThe semiempirical (MNDO, AM1, and PM3) and ab initio predicted structure of disiloxane is studied with a series of basis sets and inclusion of electron correlation at MP2, MP3, MP4, CCD, CCSD, and CCSD(T) levels. The calculated molecular geometry and barrier to linearization of the SiOSi bond angle are compared with previous theoretical and experimental values. Our results show that the calculated barrier to linearization is very sensitive to the number of polarization functions in the basis set. We also investigate the coupling between the SiOSi bond angle and the SiO bond length and calculate the Mulliken and electrostatic potential‐derived charges. For comparison purposes we also calculate the molecular geometry, the barrier to linearization of the SiOSi bond angle, and the atomic charges in hexamethyldisiloxane. © 1994 by John Wiley & Sons, Inc.
Potential energy surfaces for RhCO from DFT calculations
Authors: Biemolt W. , Jansen A. P. J. 
Published: January 2005

AbstractWe present potential energy surfaces for RhCO obtained from density functional theory for two electronic states of RhCO. We have performed local spin‐density calculations including relativistic as well as gradient corrections. The construction of a reasonably accurate atom–atom potential for RhCO is not possible. We were much more successful in constructing the potential energy surfaces by representing the potential as a spherical expansion. The expansion coefficients, which are functions of the distance between the rhodium atom and the carbon monoxide center of mass, can be represented by Lennard‐Jones, Buckingham, or Morse functions, with an error of the fit within 10 kJ/mol. The potential energy surfaces, using Morse functions, predict that the electronic ground state of RhCO is 2Σ+ or 2Δ. This is a linear structure with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.253 nm. The bonding energy is −184 kJ/mol. Further, Morse functions predict that the first exicted state is 4A′. This is a bent structure (∠RhCO = 14°) with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.298 nm. The bonding energy of this state is −60 kJ/mol. Both these predictions are in good agreement with the actual density functional calculations. We found 0.250 nm with −205 kJ/mol for 2Σ+ and 0.253 nm with −199 kJ/mol for 2Δ. For 4A′, we found 0.271 nm, ∠RhCO = 30°, with −63 kJ/mol. The larger deviation for 4A′ than for 2Σ+ or 2Δ is a consequence of the fact that the minimum for 4A′ is a very shallow well. © 1994 by John Wiley & Sons, Inc.
The natural atomic orbital point charge model for PM3: Multipole moments and molecular electrostatic potentials
Authors: Beck Bernd , Rauhut Guntram , Clark Timothy 
Published: January 2005

AbstractThe natural atomic orbital/point (NAO‐PC) model originally developed to calculate molecular electrostatic potentials (MEPs) and multiple moments based on the AM1 wave function has been extended to PM3. As for AM1, NAO‐PC/PM3 reproduces dipole moments calculated by the standard PM3 method very well. There is also a surprisingly good correlation between experimental and calculated quadrupole moments. The MEPs calculated using PM3/NAO‐PC are found to be in better agreement with those given by RHF/6‐31G* than those obtained from the PM3 wave function using Coulson charges. On the other hand, the NAO‐PC model is often slightly worse then the method implemented in MOPAC‐ESP. The MEPs calculated using our model based on the PM3 wave function are often in better agreement with those given by RHF/6‐31G* than those obtain with AM1. © 1994 by John Wiley & Sons, Inc.
Conformational sensitivity analysis of FKBP–FK506/rapamycin complexes
Authors: Susnow Roberta , Senko Nancie , Ocain Timothy 
Published: January 2005

AbstractSensitivity analysis techniques are applied to the FKBP–FK506 and FKBP–rapamycin complexes to quantify the conformational relationships between FKBP and its ligands. Crystal structures of the two FKBP complexes are energy minimized in the Amber force field using a continuum solvent model, and derived Green's function sensitivity coefficients are developed to describe the relationship between the ϕ, ψ, and χ1 torsional angles of the FKBP residues and the bound ligand macrocycle torsional angles. Sensitivity analysis is applied to the entire FKBP structure and reveals that the local conformation of the residues of the 80s and 50s loops and of the active site are sensitive to the ligand conformation. The analysis also reveals that the torsional angles controlling the orientation of the amide and keto carbonyls of FK506 are sensitive to the aromatic side chains in the FKBP carbonyl binding pocket. © 1994 by John Wiley & Sons, Inc.
Efficient parallelization of the energy, surface, and derivative calculations for internal coordinate mechanics
Authors: Totrov Maxim , Abagyan Ruben 
Published: January 2005

AbstractAn efficient algorithm for parallelization of a molecular mechanics program operating in the space of internal coordinates such as dihedral angles, bond angles, and bond lengths is described. The iterative procedure to calculate analytical energy derivatives with respect to the internal coordinates was modified to allow parallelization. Computationally intensive modules that calculate energy and its derivatives, solvent‐accessible surface, electrostatic polarization energy and that update lists of interactions were parallelized with nearly 100% efficiency. The proposed strategy for the shared‐memory computer architecture is easily scalable and requires minimum changes in a program code. The overall speedup for a realistic calculation minimizing the energy of a myoglobin reaches a factor of 3 for 4 processors. © 1994 by John Wiley & Sons, Inc.
The use of Fraga's potential with AM1 atomic point charges in the evaluation of spectral shifts: Application to TICT molecules
Authors: Gorse Alain‐Dominique , Pesquer Michel 
Published: January 2005

AbstractFraga potential calculations with atomic point charges and geometrical parameters calculated from AM1 calculations have been used to calculate spectral shifts upon electronic excitation in twisted intramolecular charge transfer (TICT) systems due to intermolecular interactions. Changes of atomic polarizabilities have also been taken into account. Present calculations deal with absorption transitions of the p‐N,N‐dimethylaminobenzonitrile (DMABN) surrounded by methane, water, acetone, or acetonitrile solvent molecules. The methodology permits us to evaluate the influence of the solvent molecule on DMABN dimethylamino motions and to find the most stable conformation of a cluster configuration which can lead to a blue or red shift. The results have been compared with the experimental work of Warren et al.7 and confirm their analysis. © 1994 by John Wiley & Sons, Inc.
A computational study of azine, azoethene, and diimine linkages in the poly/oligoazine system
Authors: Schmitz Brian K. , Euler William B. 
Published: January 2005

AbstractHartree‐Fock (HF) and molecular mechanics calculations were performed on linear azine oligomers and model compounds. The rotational energy curves for the model compounds formaldazine, H2C = NN = CH2, ethenyl diazene, H2C = CHN = NH, and ethanediimine, HN = CHCH = NH were calculated for a variety of basis sets at the HF and MP2 level. In all of these cases the rotational energy barriers are quite different from butadienes or aza‐substituted butadienes because of the lone pair–lone pair interaction of the adjacent nitrogen atoms. The results on the model compounds were used to generate a set of molecular mechanics (MM) parameters that are appropriate for linear oligo‐ and polyazines. Comparison of the geometries of the HF results and MM results for the oligoazines showed that the two methods gave comparable results. © 1994 by John Wiley & Sons, Inc.
A variational biorthogonal valence bond method
Authors: Malcolm Nathaniel O. J. , McDouall Joseph J. W. 
Published: January 2005

AbstractThe details of a simple and efficient scheme for performing variational biorthogonal valence bond calculations are presented. A variational bound on the energy functional is obtained through the use of a complete configuration expansion in a well‐chosen subset of orbitals. The resultant wave functions are clearly dominated by the covalent (spin‐coupled) structures, with a negligible contribution from ionic structures. The orbitals obtained compare favorably with overlap enhanced atomic orbitals obtained by other valence bond approaches. The method is illustrated by calculations on water and dioxygen difluoride. © 1994 by John Wiley & Sons, Inc.
Implementation of artificial intelligence for automatic drug design. I. Stepwise computation of the interactive drug‐design sequence
Authors: Cohen Alexander A. , Shatzmiller Shimon E. 
Published: January 2005

AbstractIn this article we represent the development of an artificial‐intelligence‐based method for the automatic design of valid chemical structures (AISD). The key feature of the proposed algorithm is its ability to mimic many decision‐making processes carried by the human drug designer during a design session. The manual drug‐design process is analyzed and transformed into a computerized form by associating a weight factor with each term. These weights enable the translation of the drug designer's intution into probabilities that control the flow of the design process. The input required to initiate a design session might be as minimal as the geometry of a previously existed pharmacophoric model, up to the three‐dimensional geometry of the host receptor. A design application is demonstrated by the implementation of the proposed algorithm for the design of new potent sweeteners. © 1994 by John Wiley & Sons, Inc.
ToBaD: A method for the estimation of torsion barriers from crystal structure data; conformational analysis of N,N‐dimethylaniline and derivatives
Authors: Verdonk M. L. , Tjerkstra R. W. , Ridder I. S. , Kanters J. A. , Kroon J. , van der Kemp W. J. M. 
Published: January 2005

AbstractA new method for the estimation of torsion barriers and its application to conformational analysis is presented. This method, the ToBaD method (method of the torsion barrier derivative), makes use of crystal structure data. It is based on the assumption that the conformation of a compound in the crystalline phase must be very close to a (local) minimum energy conformation of this compound in the gas phase. The ToBaD method is demonstrated for the rotation of the phenyl‐N bond in N,N‐dimethylaniline. Two geometries of this compound are handled separately: one in which the nitrogen substituents are in a pyramidal or sp3 geometry, and the other in which the nitrogen atom and its substituents are coplanar (the sp2 geometry). It is predicted, by means of the ToBaD method, that for both geometries the conformation in which the nitrogen lone pair or p orbital is perpendicular to the aromatic ring is the lowest energy conformation. © 1994 by John Wiley & Sons, Inc.
Propella[34] prismane and its congeners: A MO‐theoretical study
Authors: Gleiter Rolf , Pfeifer Karl‐Heinz , Koch Wolfram 
Published: January 2005

AbstractThe geometries of a fourfold bridged tricyclo[4.2.0.02,5]octa‐3,7‐diene (1) and its photoproducts 2 and 3 were calculated by Hartree‐Fock ab initio (3‐21G and DZP basis) and semiempirical (MNDO, AM1, MINDO /3) methods. It was found that due to the smaller distance between the double bonds in 1 (2.65 Å) as compared to the parent tricyclo[4.2.0.02,5]octa‐3,7‐diene (4) (2.91 Å), the sequence of the frontier orbitals is different. In the case of 1, the photochemical [2 + 2]cycloaddition is allowed, whereas in 4 it is forbidden. © 1995 by John Wiley & Sons, Inc.
Implementation of reaction field methods in quantum chemistry computer codes
Authors: De Vries A. H. , Van Duijnen P. Th. , Juffer A. H. , Rullmann J. A. C. , Dijkman J. P. , Merenga H. , Thole B. T. 
Published: January 2005

AbstractThe embedding of a quantum mechanically described subsystem by classical representations of its surroundings is reviewed. The choices for a distributed monopole representation and a distributed (group) polarizability representation, as well as the continuum approach to model bulk effects, are discussed. Focus is on the practical implementation of the classical description in quantum chemistry codes (in particular, HONDO8.1). Expressions are given for the self‐consistent coupling between the classical partitions (dipole polarizabilities and boundary surface dipoles and charges) and for the coupling between classical and quantum partitions. The latter is mediated through expanded, rather than exact, potentials and fields. In this way, the computation of only a limited number of formal interactions between unit charge distributions located at the expansion centers suffices to evaluate the reaction field contributions. The electronic part of the coupling can be included in the Hamiltonian via the Fock matrix. The field operators, as well as the one‐ and two‐electron matrix elements over the basis functions, are simple. The expressions for these are given explicitly.Nonequilibrium potentials and Monte Carlo sampling over classical degrees of freedom have been added to better mimic experimental conditions. © 1995 by John Wiley & Sons, Inc.
Force field parameters for sulfates and sulfamates based onab initiocalculations: Extensions of AMBER and CHARMm fields
Authors: Huige Cornelis J. M. , Altona Cornelis 
Published: January 2005

AbstractAb initioself‐consistent field (SCF) Hartree‐Fock calculations of sulfatesROSO3(−1) (R= Me, Et, i‐Pr) and sulfamatesRNHSO3(−1) (R= H, Me, Et, i‐Pr) were performed at the 4‐31G(*S*N) //3‐21G(*S*N) basis set levels, where asterisks indicatedfunctions on sulfur and nitrogen atoms. These standard levels were determined by comparing calculation results with several basis sets up to MP2/6‐31G*//6‐31G*. Several conformations per compound were studied to obtain molecular geometries, rotational barriers, and potential derived point charges. In methyl sulfate, the rotational barrier around the CO bond is 1.6 kcal/mol at the MP2 level and 1.4 kcal/mol at the standard level. Its ground state has one of three HCOS torsion angles trans and one of three COSO torsion angles trans. Rotation over 60° around the single OS bond in the sulfate group costs 2.5 kcal/mol at the MP2 and 2.1 kcal/mol at the standard level. For ethyl sulfate, the calculated rotational barrier in going from the ground state, which has its CCOS torsion angle trans, to the syn‐periplanar conformation (CCOS torsion angle cis) is 4.8 kcal/mol. However, a much lower barrier of 0.7 kcal/mol leads to a secondary gauchelike conformation about 0.4 kcal/mol above the ground state, with the CCOS torsion angle at 87.6°. Again, one of the COSO torsion angles is trans in the ground state, and the rotational barrier for a 60° rotation of the sulfate group amounts to 1.8 kcal/mol. For methyl sulfamate, the rotational barriers are 2.5 kcal/mol around the CN bond and 3.3 kcal/mol around the NS bond. This is noteworthy because sulfamate itself has a calculated rotational barrier around the NS bond of only 1.7 kcal/mol. These and other data were used to parameterize the well‐known empirical force fields AMBER and CHARMm. When the new fields were tested by means of vibrational frequency calculations at the 6‐31G*//6‐31G* level for methyl sulfate, sulfamate, and methyl sulfamate ground states, the frequencies compared favorably with the AMBER and CHARMm calculated frequencies. The transferability of the force parameters to β‐D‐glucose‐6‐sulfate and isopropyl sulfate appears to be better than to isopropyl sulfamate. © 1995 by John Wiley & Sons, Inc.
The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
Authors: Eisenhaber Frank , Lijnzaad Philip , Argos Patrick , Sander Chris , Scharf Michael 
Published: January 2005

AbstractThe double cubic lattice method (DCLM) is an accurate and rapid approach for computing numerically molecular surface areas (such as the solvent accessible or van der Waals surface) and the volume and compactness of molecular assemblies and for generating dot surfaces. The algorithm has no special memory requirements and can be easily implemented. The computation speed is extremely high, making interactive calculation of surfaces, volumes, and dot surfaces for systems of 1000 and more atoms possible on single‐processor workstations. The algorithm can be easily parallelized. The DCLM is an algorithmic variant of the approach proposed by Shrake and Rupley (J. Mol. Biol., 79, 351–371, 1973). However, the application of two cubic lattices—one for grouping neighboring atomic centers and the other for grouping neighboring surface dots of an atom—results in a drastic reduction of central processing unit (CPU) time consumption by avoiding redundant distance checks. This is most noticeable for compact conformations. For instance, the calculation of the solvent accessible surface area of the crystal conformation of bovine pancreatic trypsin inhibitor (entry 4PTI of the Brookhaven Protein Data Bank, 362‐point sphere for all 454 nonhydrogen atoms) takes less than 1 second (on a single R3000 processor of an SGI 4D/480, about 5 MFLOP). The DCLM does not depend on the spherical point distribution applied. The quality of unit sphere tesselations is discussed. We propose new ways of subdivision based on the icosahedron and dodecahedron, which achieve constantly low ratios of longest to shortest arcs over the whole frequency range. The DCLM is the method of choice, especially for large molecular complexes and high point densities. Its speed has been compared to the fastest techniques known to the authors, and it was found to be superior, especially when also taking into account the small memory requirement and the flexibility of the algorithm. The program text may be obtained on request. © 1995 by John Wiley & Sons, Inc.
Uncoupled Hartree–Fock calculations of the polarizability and hyperpolarizabilities of nitrophenols
Authors: Bursi R. , Lankhorst M. , Feil D. 
Published: January 2005

AbstractThe polarizability and hyperpolarizabilities of nitrophenols as model compounds for studying nonlinear optics have been investigated at the Hartree‐Fock level of approximation by means of the Dalgarno Uncoupled Hartree‐Fock (DUHF) or Sum Over Orbitals (SOO) method. The additive character and the charge transfer effects in α, β, and γ have been analyzed in terms of the σ and π molecular orbital contributions, the contribution of the individual π molecular orbitals, and the contribution of the highest occupied and the lowest unoccupied molecular orbitals. Within the SOO approach, the reliability of the Two‐Level Model has been tested and the influence of the rotation of the nitro group and of the presence of the intramolecular hydrogen bonding in ortho‐nitrophenol have been studied. The results show that the present method is a reliable and efficient tool for the prediction of trends in the molecular polarizability and hyperpolarizabilities of large molecules. © 1995 by John Wiley & Sons, Inc.
INDO parameters for the elements of the I and II transition rows
Authors: Sizova O. V. , Baranovski V. I. 
Published: January 2005

AbstractIt is shown that with the use of published one‐center INDO parameters for transition metals M, it is not possible to reproduce experimental relative energies of the electronic states of M, M+, and M2+ accurately enough. Two new sets of INDO parameters for the elements of the I and II transition rows are developed. These parameters are obtained by the method which ensures that the calculated energy differences between atomic electron states are in agreement with the experimental data. The results of some molecular test calculations are presented. © 1995 by John Wiley & Sons, Inc.