bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational analysis of 4h‐1,3,2‐benzodioxaphosphorin 2‐sulfides with ab initio molecular orbital calculations
Authors: Kurita Yasuyuki , Takayama Chiyozo , Sasaki Mitsuru 
Published: January 2005

AbstractAmong some 2‐substituted 4H‐1,3,2‐benzodioxaphosphorin 2‐sulfides, the 2‐OMe derivative has the sulfur atom mainly in the quasiequatorial position. On the other hand, the conformation in which the sulfur is quasiaxial is favored in the 2‐NHMe and 2‐Et derivatives. We have done ab initio molecular orbital calculations for the model compounds, and such a substituent effect was reproduced. Moreover, the effect was discussed in terms of the intramolecular electrostatic interactions and the degree of charge distribution.
Improvements to the distance geometry algorithm for conformational sampling of cyclic structures
Authors: Peishoff Catherine E. , Dixon J. Scott 
Published: January 2005

AbstractModifications to the distance geometry algorithm as embodied in the program DGEOM have been made to improve sampling capabilities. Specifically, torsion angle sampling replaces distance sampling for 1,4 atomic relationships and correlated distance sampling is disabled. The effects of these modifications are illustrated by comparing the different sets of conformations produced for butane. In addition, these changes are shown to increase the conformational sampling of two medium‐sized rings, cycloheptadecane and caprylolactam. The current results for these molecules are compared to those of other conformational searching methods.
Powerful simulated‐annealing algorithm locates global minimum of protein‐folding potentials from multiple starting conformations
Authors: Snow Mark E. 
Published: January 2005

AbstractProtein‐folding potentials, designed with the explicit goal that the global energy minimum correspond to crystallographically observed conformations of protein molecules, may offer great promise toward calculating native protein structures. Achieving this promise, however, depends on finding an effective means of dealing with the multiple‐minimum problem inherent in such potentials. In this study, a protein‐folding‐potential test system has been developed that exhibits the properties of general protein‐folding potentials yet has a unique well‐defined global energy minimum corresponding to the crystallographically determined conformation of the test molecule. A simulated‐annealing algorithm is developed that locates the global minimum of this potential in four of eight test runs from random starting conformations. Exploration of the energy‐conformation surface of the potential indicates that it contains the numerous local minima typical of protein‐folding potentials and that the global minimum is not easily located by conventional minimization procedures. When the annealing algorithm is applied to a previously developed actual folding potential to analyze the conformation of avian pancreatic polypeptide, a new conformer is located that is lower in energy than any conformer located in previous studies using a variety of minimization techniques.
Alternative expressions for energies and forces due to angle bending and torsional energy
Authors: Swope William C. , Ferguson David M. 
Published: January 2005

AbstractWe have derived alternative expressions for computing the energies and forces associated with angle bending and torsional energy terms commonly used in molecular mechanics and molecular dynamics computer programs. Our expressions address the problems of singularities that are intrinsic in popular angle energy functions and that occur from other chain rule derivations of force expressions. Most chain rule derivations of expressions for Cartesian forces due to angle energies make use of relations such as

where ϕ is a bond or torsion angle, E(ϕ) is energy, and ∂/∂x represents a derivative with respect to some Cartesian coordinate. This expression leads to singularities from the middle term, −1/sin ϕ, when ϕ is 0 or π. This is a problem that prevents the use of torsional energy expressions that have phase angles, ϕ°, other than 0 or π, such as in E(ϕ) = κ[1 + cos(nϕ − phsi;°)]. Our derivations make use of a different, but equivalent, form of the chain rule:

This form still possesses singularities for the bond angle forces since the last factor is undefined when ϕ is 0 or π. However, the alternate form may be used to great advantage for the torsional angle forces where no such problem arises. The new expressions are necessary if one desires the use of torsional energy expressions with general phase angles. Even for energy expressions in common use, i.e., with phase angles of 0 or π, our force expressions are as computationally efficient as the standard ones. The new expressions are applicable to all molecular simulations that employ restrained, or phase‐shifted, torsional angle energy expressions.
An ab initio and molecular mechanical investigation of ureas and amide derivatives
Authors: Kontoyianni Maria , Phillip Bowen J. 
Published: January 2005

AbstractAb initio molecular orbital theory with the 6‐31G* basis set has been used to investigate the geometries and preferred conformations for urea, derivatives of urea, and a few complicated amide derivatives. The results from the ab initio calculations provide insight into the gas‐phase rotational barrier about the CN bond and have been used to generate parameters for the MM2(87) molecular mechanics program. When applicable, theoretical structures are compared with corresponding previously reported experimental geometries. Urea is predicted to be nonplanar with pyramidal amino groups.
Effective internal rotation potential energy function of acryloyl fluoride, CH2  CH  CF O
Authors: Bock Charles W. , Abramenkov Alexander V. , De Maré George R. , Panchenko Yurii N. 
Published: January 2005

AbstractThe geometry of acryloyl fluoride was optimized completely at the RHF/6‐31G* level of theory at 10 points on the theoretical potential energy curve for internal rotation. The energies obtained were used to determine a six term cosine expansion of the torsional potential energy function. This function was then refined using the experimental torsional transition frequencies in the s‐trans and s‐cis wells in conjunction with the geometrical parameters optimized at the RHF/6‐31G* level. The effective potential function obtained is compared with previous results. The necessity of accounting for relaxation of the geometry upon internal rotation is stressed. © 1992 by John Wiley & Sons, Inc.
Long time dynamics of a polymer with rigid body monomer units relating to a protein model: Comparison with the rouse model
Authors: Knapp E.W. 
Published: January 2005

AbstractSimulation data from an off‐lattice polymer model are compared with data from the Rouse model. The polymer model is built of sequentially connected rigid monomer units that represent the amide planes of a protein backbone. The time propagation of the dynamics of the polymer model is performed by a Monte Carlo method. The elementary Monte Carlo steps correspond to local confomational changes in a window of three consecutive monomer units. The time autocorrelation functions of end‐to‐end distances from segments within the linear chain molecule are considered in detail. Both models exhibit a stretched exponential decay pattern. A comparison of the data from the Rouse model and the computer simulation provide an estimate of the time unit of 15 ps for a full scan of the algorithm for local conformational changes along the chain. With a conservative estimate of the parameters governing the Rouse model this time unit is four orders of magnitude longer than the elementary time step of a conventional computer simulation of polymer dynamics based upon the classical equations of motion for all atoms. © 1992 by John Wiley & Sons, Inc.
Conformational analysis of carbonyl and thiocarbonyl ethyl esters: The HC(X) (X, Y = O or S) internal rotation
Authors: Fausto R. , De Carvalho L.A.E. Batista , Teixeira‐Dias J.J.C. 
Published: January 2005

AbstractThe internal rotation in the HC(X)YCH2CH3 (X, Y = O or S) series of molecules was studied by the ab initio SCF‐MO method using 3‐21G and 3‐21G + d(ζ = 0.65S) basis sets. Energies and structures of several conformations of these molecules, determined by gradient geometry refinement, are reported and used to assess the effects of oxygen‐by‐sulphur substitution on molecular properties. The nature and relative importance of intramolecular interactions involving both the CH2CH3 and the HC(X)Y (X, Y = O or S) fragments are also discussed. © 1992 by John Wiley & Sons, Inc.
NDDO fragment self‐consistent field approximation for large electronic systems
Authors: Ferenczy György G. , Rivail Jean‐Louis , Surján Péter R. , Náray‐Szabó Gábor 
Published: January 2005

AbstractA semi‐empirical NDDO method, generalized from a similar scheme at the CNDO/2 level developed previously, is presented to treat very large molecules. The extended molecular system is divided into a relatively small subsystem where substantial chemical changes take place and an environment remaining more‐or‐less unperturbed during the process. Expanding the wave function on an atomic hybrid basis an SCF procedure is performed for the subsystem in the field of the iteratively determined electronic distribution of the environment. A computer program has been written for the IBM RISC System/6000 530 computer and several test calculations were done for a variety of large classical molecules, like substituted aliphatic hydrocarbons, water oligomers, and a heptapeptide. Protonation energies, proton transfer potential curves, rotational barriers, atomic net charges, and HOMO and LUMO energies, as computed by the exact version of the NDDO method, are fairly well reproduced by our approximation if the subsystem is appropriately defined. © 1992 by John Wiley & Sons, Inc.
Heats of formation of organic molecules by Ab Initio calculations: Carboxylic acids and esters
Authors: Allinger Norman L. , Schmitz Lawrence R. , Motoc Ioan , Bender Charles , Labanowski Jan K. 
Published: January 2005

AbstractA bond and group equivalent scheme that allows the calculation of heats of formation for carboxylic acids and esters from ab initio 6‐31G* energies has been developed. For a group of 16 compounds, the rms error for the calculated heats of formation was 0.64 kcal/mol. Heats of formation have been predicted for an additional seven compounds for which the experimental values are either unknown or suspect. © 1992 by John Wiley & Sons, Inc.
Molecular mechanics study of conformational trends in simple alcohols and ethers. II. Intramolecular hydrogen bonding
Authors: Vázquez Saulo A. , Ríos Miguel A. , Carballeira LuíS 
Published: January 2005

AbstractIn this article we present an extension of our modified MM2(80) force field MM2MOD in which a potential function for hydrogen bonding in alcohols and ethers is included. The results of applying MM2(85), MM2(87), and MM2MOD on ethylene glycol, 2‐methoxyethanol and 1,3‐propanediol are reported and compared with available experimental data and ab initio results. It is concluded that hydrogen bonding plays an important role in determining the molecular conformations of these systems. © 1992 by John Wiley & Sons, Inc.
Semiempirical study of electronic and bonding properties of cobalt silicide clusters
Authors: Urbina‐Villalba German , Rodriguez Leonardo J. , Castro German R. , Ruette Fernando 
Published: January 2005

AbstractThe electronic structure of cobalt silicide clusters Co7Si7 and Si7Co7 was studied in comparison to that of Co19 and Si17 clusters under the scope of the MINDO/SR method. Clusters Co7Si7 and Si7Co7 represent the environment of a cobalt atom and that of a silicon atom in the cobalt monosilicide bulk, respectively. It is found that the CoSi bond is essentially sp in character with an indirect participation (by electrostatic interaction) of the cobalt d orbitals. Our calculations show a charge transfer from silicon to the d orbitals of cobalt via sp–sp interaction with an internal sp–d hybridization. The theoretical density of states for cobalt silicide clusters are reported and compared with experimental results of surface spectroscopies. © 1992 by John Wiley & Sons, Inc.
Localized electron pair theory for the calculation of ground state energies of large molecules
Authors: Cullen J.M. 
Published: January 2005

AbstractThe quantum mechanical energy is examined in which groups of one, two, three, and four localized electron pairs found within a molecule are separately computed. From these results, the interaction energies of the electron pairs taken one, two, three, and four at a time form the terms of a convergent molecular mechanics like expansion of the molecular ground state energy. This procedure can be used with any size consistent quantum mechanical method. The computational time for large molecules depends chiefly upon the order needed in the energy expansion to obtain sufficient convergence and not on the particular quantum mechanical method used. Preliminary results within the framework of a semiempirical CNDO/2 model Hamiltonian show at the Hartree–Fock and Møller–Plesset perturbation levels that relative energies converge to within a few tenths of a kcal/mol of the exact values at the four body level for molecules that have little delocalization. In strained ring and aromatic systems, convergence is however not nearly as rapid. Results can be improved somewhat by using larger interacting fragments containing two or more electron pairs over three or more atomic centers. © 1992 by John Wiley & Sons, Inc.
Electronegativity and Bader's bond critical point
Authors: Hati Sanchita , Datta Dipankar 
Published: January 2005

AbstractThe electronegativities () of some 36 atoms/groups (including some 6 ionic ones) X are calculated from the atomic charges in the corresponding methyl species CH3X that were obtained by applying Bader's theory of atoms in molecules. The numerical values of the for the various groups studied are reasonable and correlate linearly with the two existing experimental scales for group electronegativity, Inamoto's i scale and the 1JCC (ortho‐ipso) coupling constants in the monosubstituted benzenes, to satisfactory extents. The relations between the values and some “critical properties” of the various CH3X molecules considered are also studied. It is suggested that in a molecule PX, rP/R where rP is the distance of Bader's critical point on the bond PX of length R from the atom P or the binding atom of the group P can be a very good measure of the electronegativity of the atom/group X. © 1992 by John Wiley & Sons, Inc.
Correlated molecular and multicenter multipole moments in ground and excited states from multiple reference double‐excitation configuration interaction calculations
Authors: Roszak Szczepan , Sokalski W. Andrzej , Kaufman Joyce J. 
Published: January 2005

AbstractCorrelated molecular mulitpole moments and compact correlated cumulative atomic multipole moment (CCAMM) representation of molecular charge distribution in ground as well as in excited states have been derived directly from multiple reference double‐excitation configuration interaction (MRD‐CI) wave functions for BH and H2CO molecules using several extended basis sets with multiple polarization functions. This approach extends previously introduced uncorrelated and correlated CAMMs, and allows obtaining inexpensive modeling of electrostatic effects involving molecules in excited electronic states. © 1992 by John Wiley & Sons, Inc.
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
Authors: Kumar Shankar , Rosenberg John M. , Bouzida Djamal , Swendsen Robert H. , Kollman Peter A. 
Published: January 2005

AbstractThe Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen's Multiple Histogram Technique, has been applied for the first time on complex biomolecular Hamiltonians. The method is presented here as an extension of the Umbrella Sampling method for free‐energy and Potential of Mean Force calculations. This algorithm possesses the following advantages over methods that are currently employed: (1) It provides a built‐in estimate of sampling errors thereby yielding objective estimates of the optimal location and length of additional simulations needed to achieve a desired level of precision; (2) it yields the “best” value of free energies by taking into account all the simulations so as to minimize the statistical errors; (3) in addition to optimizing the links between simulations, it also allows multiple overlaps of probability distributions for obtaining better estimates of the free‐energy differences. By recasting the Ferrenberg–Swendsen Multiple Histogram equations in a form suitable for molecular mechanics type Hamiltonians, we have demonstrated the feasibility and robustness of this method by applying it to a test problem of the generation of the Potential of Mean Force profile of the pseudorotation phase angle of the sugar ring in deoxyadenosine. © 1992 by John Wiley & Sons, Inc.
Treatment of redundancies among internal coordinates in optimizing molecular mechanics force constants
Authors: Palmö K. , Pietilä L. ‐O. , Krimm S. 
Published: January 2005

AbstractThe use of redundant coordinate bases in the construction of molecular mechanics force fields is discussed. It is shown that the intrinsic indeterminacy in a force field in redundant coordinates in general stems from the squares of the first‐order redundancy relations. The necessity to use constraints in such a force field is pointed out, and a method to check whether or not a set of constraints makes the force field determinate is described. It is also explained how force fields corresponding to different sets of constraints can be transformed into one another. To facilitate the utilization of ab initio or other spectroscopic force fields, a procedure is given by which force constants pertaining to a nonredundant coordinate basis can be optimized in molecular mechanics calculations where redundant coordinates are used. © 1992 by John Wiley & Sons, Inc.
Theoretical studies of organometallic compounds. III. Structures and bond energies of FeCHn and FeCH (n = 1, 2, 3)
Authors: Veldkamp Achim , Frenking Gernot 
Published: January 2005

AbstractThe geometries and dissociation energies for the FeC and CH bonds of FeCHn and FeCH (n = 1, 2, 3) have been calculated by ab initio quantum mechanical methods using different effective core potential models and Møller–Plesset perturbation theory. The HW3 ECP model, which has a configuration [core] (n−1)s2, (n−1)p6, (n−1)d1, (n)sm for the transition metals, is clearly superior to the larger core LANL1DZ ECP model with the configuration [core] (n−1)d1, (n)sm. The FeC bond energies calculated at correlated levels using the HW3 ECP are in much better agreement with experiment than the LANL1DZ results. This effect is mainly due to the higher number of correlated electrons rather than the inclusion of the outermost core electrons in the Hartree–Fock calculation. At the PMP4/HW3TZ/6‐31G(d)//MP2/HW3TZ/6‐31G(d) level, the theoretically predicted FeC bond energies for FeCH are in the range of 80% of the experimental values and have nearly the same accuracy as all‐electron calculations using large valence basis sets and the MCPF method for the correlation energy. © 1992 by John Wiley & Sons, Inc.
Conformational sampling by a general linearized embedding algorithm
Authors: Crippen Gordon M. , Smellie Andrew S. , Richardson Wendy W. 
Published: January 2005

AbstractLinearized embedding is a variant on the usual distance geometry methods for finding atomic Cartesian coordinates given constraints on interatomic distances. Instead of dealing primarily with the matrix of interatomic distances, linearized embedding concentrates on properties of the metric matrix, the matrix of inner products between pairs of vectors defining local coordinate systems within the molecule. We developed a pair of general computer programs that first convert a given arbitrary conformation of any covalent molecule from atomic Cartesian coordinates representation to internal local coordinate systems enforcing rigid valence geometry and then generate a random sampling of conformers in terms of atomic Cartesian coordinates that satisfy the rigid local geometry and a given list of interatomic distance constraints. We studied the sampling properties of this linearized embedding algorithm vs. a standard metric matrix embedding program, DGEOM, on cyclohexane, cycloheptane, and a cyclic pentapeptide. Linearized embedding always produces exactly correct bond lengths, bond angles, planarities, and chiralities; it runs at least two times faster per structure generated, and is successful as much as four times as often at refining these structures to full agreement with the constraints. It samples the full range of allowed conformations broadly, although not perfectly uniformly. Because local geometry is rigid, linearized embedding's sampling in terms of torsion angles is more restricted than that of DGEOM, but it finds in some instances conformations missed by DGEOM. © 1992 by John Wiley & Sons, Inc.
Rotational barrier in phosphatriafulvene: An MCSCF study
Authors: Schoeller Wolfgang W. , Strutwolf Jörg , Haug Wilfried , Busch Thilo 
Published: January 2005

AbstractAs probed by ab initio calculations at SCF and MCSCF levels, the rotational barrier of the PC double bond in the title compound is similar in magnitude to the corresponding one in methylenephosphane. The transition state for rotation is dipolaric in nature. On this basis, a combination of electron releasing and electron accepting substituents reduces the magnitude of the rotational barrier in phosphatriafulvene. It is supported by experimental investigations. © 1993 John Wiley & Sons, Inc.
Supplementary d and f functions in molecular wave functions: Optimum and nonoptimum exponents
Authors: Magnusson Eric 
Published: January 2005

AbstractEnergy optimization calculations have been carried out to determine the variability of optimum p, d, and f polarization function exponents in molecules containing first‐ and second‐row elements and in normal valency and hypercoordinate species. Optimum exponents were determined for single sets of higher‐order functions at both Hartree–Fock and correlated (Moller–Plesset) levels of theory using the Dunning–Hay double zeta and the McLean–Chandler triple zeta basis sets. More detailed calculations were used to test the response to nonoptimum d and f function exponents of the total energy, the optimum geometry, and harmonic stretching frequencies. The variability in optimum exponents and the size of the energy penalties incurred by adopting nonoptimum values reduces the utility of standard exponents for p, d, and f polarization functions. © 1993 John Wiley & Sons, Inc.
Supplementary d and f functions in molecular wave functions at large and small internuclear separations
Authors: Magnusson Eric 
Published: January 2005

AbstractThe CO, CO2, CS, CIF, and SO2 molecules were used to test the dependence of supplementary d and f function exponents to changes in bond lengths and bond angles in MO calculations utilizing Gaussian basis sets in Hartree–Fock and Moller–Plesset calculations. Using Dunning–Hay double zeta basis sets, optimizations were performed at internuclear separations from 100–200 pm and beyond. The energy cost of not reoptimizing d function exponents when bonds are stretched or compressed is much smaller for correlated calculations than for those at the Hartree–Fock level and is greatest at the lower end of the range of internuclear distances. The problem is much less serious at all levels when multiple sets of d functions are used. © 1993 John Wiley & Sons, Inc.