bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shape analysis of hydrogen‐bonded networks in solvation clusters
Authors: Arteca Gustavo A. 
Published: January 2005

AbstractA procedure is developed and applied to characterize the global shape of the hydrogen‐bonded networks formed in solvent and solute‐solvent clusters. The methodology combines elements of geometry and topology of molecular chains, and it provides a description of the compactness and complexity of the entanglements formed by the network of hydrogen bonds between solute and solvent molecules. This approach complements others in the literature, where the hydrogen bonding is described in terms of the spatial distribution of bonds, their energetics and lifetimes, or the length hydrogen‐bonded walks in space. The results of the present technique do not depend too strongly on the details of the molecular geometry. Therefore, one can assess the extent to which large‐scale architecture is modified by rearrangements in the nuclear configuration, information which is important in molecular dynamics when estimating the persistence of essential structural features along dynamic trajectories. In this article we discuss the methodology and illustrate its application to the study of water clusters and solvated clusters of acetic acid. Expected qualitative features in the change of shape descriptors in actual reorganizations of hydrogen‐bonding patterns are discussed briefly. © 1994 by John Wiley & Sons, Inc.
Internal dynamics of a globular protein under external force field
Authors: Yoshioki Shuzo 
Published: January 2005

AbstractThe inelastic neutron‐scattering experiment of a small globular protein in powder form can present the density of states as a function of the frequency. This characterizes the internal dynamics of the protein, which (especially in the case of low‐frequency internal dynamics, < 200 cm−1) is required for an improved understanding of protein function. The theoretical frequency distributions of the internal dynamics of a protein have only been calculated in vacuo using the normal mode analysis. Here we show that frequency distributions of the internal motions of a protein in different environments can be provided by changing the magnitude of external force fields acting on the protein. Our test case is bovine pancreatic trypsin inhibitor (BPTI), consisting of 58 amino acid residues. To mimic the effect of intermolecular contacts in powders, external force fields formed by surrounding water molecules are forced to act on the protein. The neutron‐derived density of states of BPTI in powders is shown to be reproduced by the external force fields. In addition, the densities of states, shifted to low frequencies, are suggested to represent that of BPTI in solution. © 1994 by John Wiley & Sons, Inc.
Fast geometry optimization using a modified extended Hückel method: Results for molecules containing H, C, N, O, and F
Authors: Dixon Steven L. , Jurs Peter C. 
Published: January 2005

AbstractA semiempirically parameterized version of the extended Hückel molecular orbital method has been combined with an efficient quasi‐Newton Broyden‐Fletcher‐Goldfarb‐Shannon (BFGS) optimization algorithm to obtain accurate geometries for compounds containing H, C, N, O, and F. The requirement of only one matrix diagonalization per energy evaluation makes the EHNDO (Extended Hückel Neglect of Differential Overlap) method faster than semiempirical Hartree–Fock NDDO methods such as MNDO, AM1, and PM3. Geometrical results for EHNDO appear to be as good as or better than results for the widely used AM1 technique, and geometry optimization for EHNDO also requires only a fraction of the time. © 1994 by John Wiley & Sons, Inc.
High‐precision atomic computations from finite element techniques: Second‐order correlation energies for Be, Ca, Sr, Cd, Ba, Yb, and Hg
Authors: Flores Jesús R. , Redondo P. 
Published: January 2005

AbstractWe have applied the FEM‐MP2 method (an implementation of the p‐version finite element technique within the framework of second‐order Møller–Plesset perturbation theory, [J. Chem. Phys., 98, 5642 (1993), and references therein]) to calculate second‐order correlation energies for the atoms Be, Ca, Sr, Ba, Yb, Cd, and Hg and thus to complete our studies on closed‐shell elements. The FEM‐MP2 method permits the use of virtual orbitals of very high angular momentum (lmax = 12) in combination with radial basis sets which are very close to completeness, in such a way that we are able to obtain results that could be the most accurate published so far and, in some cases, the only values available in the literature. We hope they may be useful as a reference for basis set saturation tests and for new methods to calculate correlation energies. © 1994 by John Wiley & Sons, Inc.
D‐CICADA: A software for conformational PES elucidation on network of workstations
Authors: Matyska Luděk , Koča Jaroslav 
Published: January 2005

AbstractThe methodology of conformational potential energy (hyper)surface (PES) elucidation is the subject of this article. The decomposition of the recently developed software CICADA and its implementation in the distributed environment using PVM (parallel virtual machine) is presented. CICADA has been chosen for the parallelization because of its ability to elucidate systematically the low‐energy areas of PES in polynomial time. This makes the method applicable on larger systems which are beyond the scope of the grid search. To show the level of parallelization, conformational PES of two molecules, cyclohexane and terminally blocked alanine, have been studied by the distributed version, D‐CICADA, and results have been compared to those of the sequential version. D‐CICADA was tested on several virtual machines composed of DEC and Sun workstations. The timing shows good efficiency for both the decomposition of the original algorithm and the PVM environment. © 1994 by John Wiley & Sons, Inc.
Conformational study of dipeptides: A sensitivity analysis approach
Authors: Susnow Roberta , Schutt Clarence , Rabitz Herschel , Subramaniam Shankar 
Published: January 2005

AbstractThis article studies the backbone influence on the side chains of N‐methyl N′‐acetyl amides (dipeptides) of alanine, valine, phenylalanine, leucine, isoleucine, glutamine, and lysine. Several local minima corresponding to protein ϕ, ψ, and χ values for each dipeptide are determined through optimization in the MM2 force field. These local minima are located in various regions on the Ramachandran map related to particular protein secondary structures. The dipeptide backbone influence on the side chain is explored via the sensitivity of the side chain torsion angles χ with respect to the backbone ϕ and ψ angles. Sensitivity coefficients are calculated, describing the χ response to an externally imposed change in ϕ or ψ. The χ response, which depends on the backbone conformation in a particular region, is induced primarily by the van der Waals and dipole interactions between the backbone and the side chain, which change with a deviation in ϕ or ψ. Various sensitivity trends are observed in the particular Ramachandran regions, revealing the subtle relationships between the dipeptide backbone and the side chain. © 1994 by John Wiley & Sons, Inc.
On the calculation of ab initio quantum molecular similarities for large systems: Fitting the electron density
Authors: Mestres Jordi , Solà Miquel , Duran Miquel , Carbó Ramon 
Published: January 2005

AbstractA set of procedures for rapid calculation of quantum molecular similarities from ab initio wave functions is discussed. In all cases a density fitting is carried out to eliminate the need of calculating costly four‐centered integrals. It is proved that this methodology can be applied to large systems to reproduce exact quantum molecular similarity measures at an extremely low computational cost. © 1994 by John Wiley & Sons, Inc.
Algorithm to infer the structures of molecular formulas within a reaction pathway
Authors: Valdés‐Pérez Raúl E. 
Published: January 2005

AbstractMECHEM is a computer aid for elucidation of reaction pathways that was developed over the last 5 years. The program searches systematically and comprehensively for the simplest multistep reaction pathways (or mechanisms) that are consistent with the experimental constraints formulated by the experimentalist, any ad hoc assumptions, and the program's internal theory. Previous articles have reported the basic pathway‐generation algorithm and another algorithm that tests the structural soundness of individual steps. This article introduces an algorithm to solve another basic problem: Given a multistep pathway containing a mixture of molecular structures and formulas, assign possible structures to the formulas while obeying (and exploiting) the constraint imposed by the pathway steps. With this new algorithm, MECHEM is now approaching competence as an interactive tool for elucidating some catalytic reaction pathways, which is the current chemical focus. © 1994 by John Wiley & Sons, Inc.
Anisotropy of atom–atom repulsions
Authors: Stone A. J. , Tong C.‐S. 
Published: January 2005

AbstractWe describe investigations of the short‐range repulsion part of the intermolecular potential using a test particle approach. This approach provides an economical method of constructing reasonably accurate model repulsion potentials and demonstrates the importance of anisotropy in describing the short‐range repulsion. © 1994 by John Wiley & Sons, Inc.
Heats of formation of organic molecules calculated from ab initio theory and a group equivalent scheme: Alkenes
Authors: Schmitz Lawrence R. , Chen Yi Ren 
Published: January 2005

AbstractA bond and group equivalent scheme that allows the calculation of heats of formation of alkenes from ab initio 6‐31G* energies has been developed. For a group of 26 compounds, the root mean square (rms) error for the calculated heat of formation was 0.78 kcal/mol. Heats of formation have been predicted for an additional nine compounds for which the experimental values are either unknown or suspect. The heats of hydrogenation of barrelene and related compounds are discussed. © 1994 by John Wiley & Sons, Inc.
On the evaluation of the solvent polarization apparent charges in the polarizable continuum model: A new formulation
Authors: Coitiño Elena L. , Tomasi Jacopo , Cammi Roberto 
Published: January 2005

AbstractA new formulation (CLS‐PCM) for the calculation of the apparent surface charges in the framework of the ab initio polarizable continuum model of the solvent (PCM) is introduced. Its performance is compared with that of the original iterative version (ITER‐PCM) of the method as well as with a matricial alternative formulation (matrix‐BEM‐PCM) of the same problem. Both CLS‐PCM and matrix‐BEM‐PCM have shown to be computationally more efficient than ITER‐PCM without presenting any problems associated with the convergence of the process. Although for small and medium‐size solutes the use of matrix‐BEM‐PCM is recommended, for neutral solutes of larger size the use of CLS2 becomes computationally more convenient. Finally, for very large‐size systems, compromise between matrix storage requirements, time of calculation, and exactness of the results may make preferable the use of the more approximate CLS1 formalism, possibly in conjunction with semiempirical or semiclassical descriptions of the solute. © 1995 by John Wiley & Sons, Inc.
A vibrational molecular force field of model compounds with biological interest. IV. Parameters for the different glycosidic linkages of oligosaccharides
Authors: Dauchez Manuel , Derreumaux Philippe , Lagant Philippe , Vergoten Gérard 
Published: January 2005

AbstractThe force field previously obtained for both anomers of glucose has been applied to six disaccharides that are molecules of D‐glucopyranosyl residues. These six disaccharides have different types of glycosidic linkages—that is, α, α trehalose dihydrate (1‐1), sophorose monohydrate (β, 1‐2), laminarabiose (β, 1‐3), maltose monohydrate (α, 1‐4) and cellobiose (β, 1‐4), and gentiobiose (β, 1‐6). From a careful analysis of the infrared and Raman spectra and from harmonic dynamics calculations in the crystalline state, the results show the reliability and the transferability of the set of parameters previously obtained for different carbohydrates. Below 1500 cm−1, observed data and the corresponding calculated frequencies agreed within 5 cm−1 for each of the six disaccharides. The vibrational density of states are well reproduced by these calculations for each molecule, particularly for the fingerprint regions. Moreover, as found by other workers who used sophisticated potential energy functions, no additional terms are needed to express the exoanomeric effect. Specific force constants characteristic of each glycosidic linkage have been derived, particularly for the glycosidic angle bending. More interesting are the values of the internal rotation barriers. It is shown that they are of the same size for both sides of the glycosidic linkage: VC1O1 = VO1Cx′ = 3.29 kcal/mol for an alpha residue and 2.64 kcal/mol for a beta unit (x = 1–6 depends on the position of the glycosidic linkages of the considered disaccharide). © 1995 by John Wiley & Sons, Inc.
Generalized alteration of structure and parameters: A new method for free‐energy perturbations in systems containing flexible degrees of freedom
Authors: Severance Daniel L. , Essex Jonathan W. , Jorgensen William L. 
Published: January 2005

AbstractA modified derivation of the free energy perturbation (FEP) equation leads to a more general interpretation of the procedures for generating the geometry of a perturbed molecule from the reference one in FEP simulations of flexible systems. Using this form of the equation, it is possible to implement a wide variety of procedures which heretofore would have been considered impossible. A new method, generalized alteration of structure and parameters (GASP), has been implemented in the BOSS program and has been found to be more efficient for perturbations of harmonic degrees of freedom than the commonly adopted procedure. Additionally, an extreme example for which the new procedure proves less satisfactory is presented, and a more efficient method which is also derived from the new form of the FEP equation is devised and tested. It is concluded that the key to a convergent FEP method is efficient sampling of low‐energy configurations of the perturbed state; the new form of the equation suggests ways of generating such configurations. © 1995 by John Wiley & Sons, Inc.
Symplectic integrators and the conservation of angular momentum
Authors: Zhang Mei‐Qing , Skeel Robert D. 
Published: January 2005

AbstractIn this article we observe that generally symplectic integrators conserve angular momentum exactly, whereas nonsymplectic integrators do not. We show that this observation extends to multiple timesteps and to constrained dynamics. Both of these devices are important for efficient molecular dynamics simulations. © 1995 by John Wiley & Sons, Inc.
Ab initiocalculation of molar volumes: Comparison with experiment and use in solvation models
Authors: Wong Ming Wah , Wiberg Kenneth B. , Frisch Michael J. 
Published: January 2005

AbstractA simple and efficient procedure of calculating molecular volume (VM) based on the Monte Carlo method is presented. The volume of a molecule is defined by the volume occupied by the 0.001‐au electron density envelope. We have employed this method to compute the molecular volumes (VM) of a large selection of organic molecules and compare them with the corresponding molar volumes (Vm) measured in the liquid state. A strong correlation is found to exist between theVMandVmvalues (VM/Vm≈ 0.75). Using this linear relationship, the calculated molecular volume may provide an estimate of the cavity‐volume parameter in solvent‐effect calculations. As a chemical application of molecular volume, we have investigated the conformational equilibrium of 1,2‐difluoroethane in the liquid state using the self‐consistent reaction field theory. © 1995 by John Wiley & Sons, Inc.
The extended law of corresponding states and the intermolecular potentials for HeHe and NeNe
Authors: Behnejad H. , Maghari A. , Najafi M. 
Published: January 2005

AbstractA direct inversion procedure is used to obtain the pair interaction potentials for He and Ne from the extended law of corresponding states over the temperature range from absolute zero to the onset of ionization. We have used the experimentally reduced viscosity collision integrals obtained from the corresponding states correlation and performed an INVERT to determine the reduced potential energy curve corresponding to the collision integral. This directly determined potential is in excellent agreement with the potential independently obtained from molecular beam scattering measurements. © 1995 by John Wiley & Sons, Inc.
A molecular mechanics/grid method for evaluation of ligand–receptor interactions
Authors: Luty Brock A. , Wasserman Zelda R. , Stouten Pieter F. W. , Hodge C. Nicholas , Zacharias Martin , McCammon J. Andrew 
Published: January 2005

AbstractWe present a computational method for prediction of the conformation of a ligand when bound to a macromolecular receptor. The method is intended for use in systems in which the approximate location of the binding site is known and no large‐scale rearrangements of the receptor are expected upon formation of the complex. The ligand is initially placed in the vicinity of the binding site and the atomic motions of the ligand and binding site are explicitly simulated, with solvent represented by an implicit solvation model and using a grid representation for the bulk of the receptor protein. These two approximations make the method computationally efficient and yet maintain accuracy close to that of an all‐atom calculation. For the benzamidine/trypsin system, we ran 100 independent simulations, in many of which the ligand settled into the low‐energy conformation observed in the crystal structure of the complex. The energy of these conformations was lower than and well‐separated from that of others sampled. Extensions of this method are also discussed. © 1995 by John Wiley & Sons, Inc.
The exponents method for calculating equilibrium concentrations of complex species in solution
Authors: Campos Frederico F. , Rollett John S. 
Published: January 2005

AbstractThe exponents method for calculating the concentrations of species in multimetal‐multiligand systems is introduced. This method uses the Newton‐Raphson method with restricted step iteration, which guarantees a monotonically decreasing objective function. Variable transformation and scaling are performed to avoid underflows and overflows during the calculations. A special linear solver using the eigenvalues and eigenvectors of the Jacobian matrix is implemented for overcoming disastrous singularity of this matrix, and the singular value decomposition method is applied for setting the initial guess. In addition, polynomial extrapolation is used for improving the performance when simulating a diagram of concentrations of species. The method was tested with 14 systems of different sizes over the whole pH range and presented robust and efficient behavior. © 1995 by John Wiley & Sons, Inc.
Development of optimized MST/SCRF methods for semiempirical calculations: The MNDO and PM3 Hamiltonians
Authors: Orozco Modesto , Bachs M. , Luque F. J. 
Published: January 2005

AbstractThe self‐consistent reaction field (SCRF) method proposed by Miertus, Scrocco, and Tomasi (MST) has been optimized for MNDO and PM3 semiempirical Hamiltonians. Different algorithms used to compute the molecular electrostatic potential (MEP) and different solute cavities have been investigated. The ability of the optimized models to reproduce experimental free energies of solvation and to mimic the solvent effect in several chemical processes has been compared with the ab initio and AM1 versions of the MST method as well as with experimental data. © 1995 by John Wiley & Sons, Inc.
The role of the carboxylate ion in models of acyl‐chymotrypsin
Authors: Tong Weida , D'Souza Valerian T. 
Published: January 2005

AbstractTwo exquisite models of the acyl‐chymotrypsin intermediate, one designed by Bruice and another by Bender, were studied to elucidate the role of the carboxylate ion in the catalytic triad of serine proteases. However, opposing conclusions were drawn from these studies. Computational chemistry analysis of these models indicates that the carboxylate ion plays an insignificant role in the former model because of the correct orientation and the distance of the imidazole group without the carboxylate ion. However, in the latter model, the carboxylate ion serves to orient and place the imidazole group at the correct position. This analysis suggests that an important role of the carboxylate ion in serine proteases is to position the imidazole group to be an effective general base catalyst. © 1995 by John Wiley & Sons, Inc.
The electronic structure of weakly bound systems. II. NeX+ and ArX+(X = H2O, HCl, and HF) bimolecular cations
Authors: López Gustavo E. 
Published: January 2005

AbstractThe theoretical framework developed and tested in our previous study of weakly bound systems is applied to a sequence of bimolecular cations: (NeX)+ and (ArX)+, where X = HF, H2O, and HCl. The equilibrium structure, binding energies, and vibrational frequencies for this sequence of bimolecular cations are computed using several post‐Hartree‐Fock methods and triple zeta basis sets. In all cases, the absolute minima in the potential energy surface involves a hydrogen bond. The existence and stability of the aforementioned systems are established with binding energies ranging from 0.1 eV to 1.0 eV. The stability for the systems is explained in terms of the possible dissociative channels and changes in the electron density of the constituent monomers. © 1995 by John Wiley & Sons, Inc.
Comparison of potential‐derived charge and atomic multipole models in calculating electrostatic potentials and energies of some nucleic acid bases and pairs
Authors: Ritchie James P. , Copenhaver Ann S. 
Published: January 2005

AbstractWe compare the electrostatic potential surrounding several natural and synthetic nucleic acid bases calculated using an atom‐centered multiple expansion (ACME) derived from integration of the charge distribution with that from potential‐derived charges (PDCs) obtained using the CHELPG procedure. When the multipole expansions are carried out to octapoles, the root mean square (rms) error in the potential is always less than that from PDCs. Electrostatic interactions in pairs of these nucleic acid bases were also evaluated using ACMEs up to octapoles and PDCs. The electrostatic interaction energies from ACMEs were found always to be larger than those from PDCs or the total self‐consistent field (SCF) interaction energy. The value of the electrostatic energy differs by as much as approximately 19 or as little as approximately 8 kJ/mol between the ACME and PDC methods. The rank ordering provided by the electrostatic models is grossly similar but differs in the ranking of systems with two and three hydrogen bonds. A rigid twist about the NH ⃛ N axis of the pairs was examined using SCF calculations and the electrostatic models. It was found that with ACMEs the energy required for a 90‐degree rotation was always higher than that found from SCF calculations. With PDCs, similar results are obtained, except with the adenine/thymine and 9‐methyl‐adenine/1‐methyl‐thymine pairs. In these instances, the barrier is about 4 kJ/mol lower than that found with SCF calculations. These results demonstrate that integration of the charge density can provide convergent multipole expansions that provide a more accurate description of the electrostatic potential than the commonly used PDC model. In addition, the description of electrostatic interactions during twisting of AT and mAmT given by this model is shown to be somewhat anomalous. © 1995 by John Wiley & Sons, Inc.