bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of solute cavities and van der Waals parameters in ab initio MST‐SCRF calculations of neutral molecules
Authors: Bachs M. , Luque F. J. , Orozco Modesto 
Published: January 2005

AbstractThe cavity used to represent the solute/water interface in Miertus–Scrocco–Tomasi self‐consistent reaction field (MST‐SCRF) calculations of neutral molecules has been optimized by fitting to experimental data. The study is focused on the refinement of the van der Waals radii of polar and apolar hydrogens and of the van der Waals parameters used to compute the dispersion/repulsion contribution to the total free energy of hydration. When a scaling coefficient of 1.25 is used to build the solute cavity, comparison of 6‐31G*/MST results with experimental data demonstrates that the optimum van der Waals radii for hydrogens are around 1.2 Å (apolar) and 0.9 Å (polar). The optimization of the solute cavity and the refinement of the van der Waals parameters lead to root mean square deviations in the computed free energy of hydration of only 0.9 kcal/mol for the 23 molecules considered in this study. © 1994 by John Wiley & Sons, Inc.
Parametrization of a force field for studying some beta‐lactams
Authors: Fernández Berta , Ríos Miguel A. 
Published: January 2005

AbstractA molecular mechanics force field for studying some beta‐lactams was developed from ab initio and experimental data. The optimized parameters allowed accurate calculation of the geometries of both the compounds on which the parametrization was based and others on which the validity of the predictions was checked. © 1994 by John Wiley & Sons, Inc.
ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
Authors: Abagyan Ruben , Totrov Maxim , Kuznetsov Dmitry 
Published: January 2005

AbstractAn efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) structure determination, and protein design. The method uses and further develops a previously introduced approach to model biomolecular structures in which bond lengths, bond angles, and torsion angles are considered as independent variables, any subset of them being fixed. Here we simplify and generalize the basic description of the system, introduce the variable dihedral phase angle, and allow arbitrary connections of the molecules and conventional definition of the torsion angles. Algorithms for calculation of energy derivatives with respect to internal variables in the topological tree of the system and for rapid evaluation of accessible surface are presented. Multidimensional variable restraints are proposed to represent the statistical information about the torsion angle distributions in proteins. To incorporate complex energy terms as solvation energy and electrostatics into a structure prediction procedure, a “double‐energy” Monte Carlo minimization procedure in which these terms are omitted during the minimization stage of the random step and included for the comparison with the previous conformation in a Markov chain is proposed and justified. The ICM method is applied successfully to a molecular docking problem. The procedure finds the correct parallel arrangement of two rigid helixes from a leucine zipper domain as the lowest‐energy conformation (0.5 Å root mean square, rms, deviation from the native structure) starting from completely random configuration. Structures with antiparallel helixes or helixes staggered by one helix turn had energies higher by about 7 or 9 kcal/mol, respectively. Soft docking was also attempted. A docking procedure allowing side‐chain flexibility also converged to the parallel configuration starting from the helixes optimized individually. To justdy an internal coordinate approach to the structure prediction as opposed to a Cartesian one, energy hypersurfaces around the native structure of the squash seeds trypsin inhibitor were studied. Torsion angle minimization from the optimal conformation randomly distorted up to the rms deviation of 2.2 Å or angular rms deviation of l0° restored the native conformation in most cases. In contrast, Cartesian coordinate minimization did not reach the minimum from deviations as small as 0.3 Å or 2°. We conclude that the most promising detailed approach to the protein‐folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. © 1994 by John Wiley & Sons, Inc.
Force field for computation of conformational energies, structures, and vibrational frequencies of aromatic polyesters
Authors: Sun H. 
Published: January 2005

AbstractA CFF931 all‐atom force field for aromatic polyesters based on ab initio calculations is reported. The force field parameters are derived by fitting to quantum mechanical data which include total energies, first and second derivatives of the total energies, and electrostatic potentials. The valence parameters and the ab initio electrostatic potential (ESP) derived charges are then scaled to correct the systematic errors originating from the truncation of the basis functions and the neglect of electron correlation in the HF/6‐31G* calculations. Based on the force field, molecular mechanics calculations are performed for homologues of poly(p‐hydroxybenzoic acid) (PHBA) and poly(ethylene terephthalate) (PET). The force field results are compared with available experimental data and the ab initio results. © 1994 by John Wiley & Sons, Inc.
Hybrid Monte Carlo: An efficient algorithm for condensed matter simulation
Authors: Clamp M. E. , Baker P. G. , Stirling C. J. , Brass A. 
Published: January 2005

AbstractA detailed comparison has been made of the performance of molecular dynamics and hybrid Monte Carlo simulation algorithms for calculating thermodynamic properties of 2D Lennard‐Jonesium. The hybrid Monte Carlo simulation required an order of magnitude fewer steps than the molecular dynamics simulation to calculate reproducible values of the specific heat. The ergodicity of the two algorithms was compared via the use of intermediate scattering functions. For classical systems the intermediate scattering functions should be real; however, a simple analysis demonstrates that this function will have a significant imaginary component when ergodicity breaks down. For q vectors near the zone boundary, the scattering functions are real for both algorithms. However, for q vectors near the zone center (i.e., harmonic, weakly coupled modes), the scattering function calculated via molecular dynamics had a significantly larger imaginary component than that calculated using hybrid Monte Carlo. Therefore, the hybrid Monte Carlo algorithm is more ergodic and samples phase space more efficiently than molecular dynamics for simulations of 2D Lennard‐Jonesium. © 1994 by John Wiley & Sons, Inc.
Explicitly correlated Gaussian functions with r factors for calculations of the ground state of the helium atom
Authors: Zhang Zhenghong , Adamowicz Ludwik 
Published: January 2005

AbstractExplicitly correlated Gaussian functions with r exp( − βr) factors have been used in variational calculations of the ground state of the helium atom. Additional correlation factors in the form of even powers of rij were introduced to the Gaussian functions with exponential correlation components by differentiating these functions with respect to the correlation exponent β. The algorithm of this method and its computational implementation is described. A number of calculations were performed for the ground state of helium atom to test the performance of the basis sets comparising different numbers of the Gaussians with the exp( − βr) and r exp( − βr) correlation factors. The numerical results indicate that including functions with r factors does not lead to improved results, contrary to what was anticipated initially. © 1994 by John Wiley & Sons, Inc.
GEPOL: An improved description of molecular surfaces. III. A new algorithm for the computation of a solvent‐excluding surface
Authors: Pascual‐ahuir J. L. , Silla E. , Tuñon I. 
Published: January 2005

AbstractTo understand and calculate the interactions of a solute with a solvent, a good method of computing the molecular surface is needed. Three kinds of surfaces may be used: the van der Waals Surface, the Accessible Surface, and the Molecular Surface. The latter is redefined in this article as the Solvent‐Excluding Surface. The new algorithm for computing the Solvent‐Excluding Surface included in the GEPOL93 program is described. GEPOL93 follows the same concept as former versions of GEPOL but with a full new algorithm. Thus, it computes the Solvent‐Excluding Surface by filling the spaces not accessible to the solvent with a set of new spheres. The computation is controlled by three parameters: the number of triangles per sphere, controlled by NDIV; the maximum overlap among the new spheres (OFAC); and the size of the smallest sphere that can be created (RMIN). The changes introduced for the computation of the ESURF make GEPOL93 not just a new version but a new program. An estimation is made of the error in the area and volume obtained in the function of the parameters. © 1994 by John Wiley & Sons, Inc.
Is the stereomutation of methane possible?
Authors: Pepper Melanie J. M. , Shavitt Isaiah , Schleyer Paul Von Ragué , Glukhovtsev Mikhail N. , Janoschek Rudolf , Quack Martin 
Published: January 2005

AbstractLarge basis set ab initio calculations at correlated levels, including MP2, single reference, as well as multireference configuration interaction, carried out on the methane potential energy surface, have located and characterized a transition structure for stereomutation (one imaginary frequency). This structure is best described as a pyramidal complex between singlet methylene and a side‐on hydrogen molecule with Cs symmetry. At the single reference CI level, it lies 105 kcal/mol above the methane Td‐ground state but is stable relative to dissociation into CH2(1A1) and H2 by 13 kcal/mol at 0 K (with harmonic zero point energy (ZPE) corrections for all structures). Dissociation of the transition state into triplet methylene and hydrogen also is endothermic (by 4 kcal/mol), but single bond rupture to give CH and H. is 3 kcal/mol exothermic. Thus, it does not appear likely that methane can undergo stereomutation classically beneath the dissociation limit. Confirming earlier conclusions, side‐on insertion of 1A1 CH2 into H2 in a perpendicular geometry occurs without activation energy. Planar (D4h) methane (130.5 kcal/mol) has four imaginary frequencies. Two of these are degenerate and lead to equivalent planar C2v structures with one three‐center, two‐electron bond and two two‐electron bonds and two imaginary frequencies. The remaining imaginary frequencies of the D4h form lead to tetrahedral (Td) and pyramidal (C4v) methane. The latter has three negative eigenvalues in the force‐constant matrix; one of these leads to the Td global minimum and the other to the Cs (parallel) stereomutation transition structure. Multireference CI calculations with a large atomic natural orbitals basis set produce similar results, with the electronic energy of the Cs stereomutation transition state 0.7 ± 0.5 kcal/mol higher than that of CH + H. dissociation products, and a ZPE‐corrected energy which is 5 ± 1 kcal/mol higher. Also considered are photochemical pathways for stereomutation and the possible effects of nuclear spin, inversion tunneling, and the parity‐violating weak nuclear interaction on the possibility of an experimental detection of stereomutation in methane. © 1995 by John Wiley & Sons, Inc.
An efficient simulation technique for electrostatic free energies with applications to azurin
Authors: Svensson Bo , Jönsson Bo 
Published: January 2005

AbstractWe present an efficient technique for Monte Carlo simulation of electrostatic free energy changes in biomolecular systems. It is a development of a recent method for the study of the influence of electrostatic interactions on the ion binding properties and redox potentials of biomolecules. The electrolyte solution is described by the primitive model, in which ions are treated as hard charged spheres and the solvent is replaced by a structureless continuum. The protein is kept fixed in the center of a spherical simulation cell, and the dielectric constant has the solvent value throughout the cell. By a multiparticle perturbation approach, it is possible to obtain a number of free energy changes within one simulation only. The usefulness of the method is illustrated with a study of the copper binding electron‐transport protein azurin (from Alcaligenes denitrificans). The change in acidity of the histidine residues upon changing the redox state of the copper ion is calculated. The theoretical predictions agree well with available experiments. © 1995 by John Wiley & Sons, Inc.
Improved methods for semiempirical solvation models
Authors: Liotard Daniel A. , Hawkins Gregory D. , Lynch Gillian C. , Cramer Christopher J. , Truhlar Donald G. 
Published: January 2005

AbstractWe present improved algorithms for the SMx (x = 1, 1a, 2, 3) solvation models presented previously [see the overview in C. J. Cramer and D. G. Truhlar, J. Comp.‐Aided Mol. Design, 6, 629 (1992)]. These models estimate the free energy of solvation by augmenting a semiempirical Hartree‐Fock calculation on the solute with the generalized Born (GB) model for electric polarization of the solvent and a surface tension term based on solvent‐accessible surface area. This article presents three improvements in the algorithms used to carry out such calculations, namely (1) an analytical accessible surface area algorithm, (2) a more efficient radial integration scheme for the dielectric screening computation in the GB model, and (3) a damping algorithm for updating the GB contribution to the Fock update during the iterations to achieve a self‐consistent field. Improvements (1) and (2) decrease the computer time, and improvement (3) leads to more stable convergence. Improvement (2) removes a small systematic numerical error that was explicitly absorbed into the parameterization in the SMx models. Therefore, we have adjusted the parameters for one of the previous models to yield essentially identical performance as was obtained originally while simultaneously taking advantage of improvement (2). The resulting model is called SM2.1. The fact that we obtain similar results after removing the systematic quadrature bias attests to the robustness of the original parameterization. © 1995 by John Wiley & Sons, Inc.
The relaxation of molecular crystal structures using a distributed multipole electrostatic model
Authors: Willock D. J. , Price S. L. , Leslie M. , Catlow C. R. A. 
Published: January 2005

AbstractWe describe a method for minimizing the lattice energy of molecular crystal structures, using a realistic anisotropic atom–atom model for the intermolecular forces. Molecules are assumed to be rigid, and the structure is described by the center of mass positions and orientational parameters for each molecule in the unit cell, as well as external strain parameters used to optimize the cell geometry. The resulting program uses a distributed multipole description of the electrostatic forces, which consists of sets of atomic multipoles (charge, dipole, quadrupole, etc.) to represent the lone pair, π electron density, and other nonspherical features in the atomic charge distribution. Such ab initio based, electrostatic models are essential for describing the orientation dependence of the intermolecular forces, including hydrogen bonding, between polar molecules. Studies on a range of organic crystals containing hydrogen bonds are used to illustrate the use of this new crystal structure relaxation program, DMAREL, and show that it provides a promising new approach to studying the crystal packing of polar molecules. © 1995 by John Wiley & Sons, Inc.
Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self‐consistent field supermolecular computations
Authors: Gresh Nohad 
Published: January 2005

AbstractDetailed investigations are performed of the binding energetics of Zn2+ to a series of neutral and anionic ligands making up the sidechains of amino acid residues of proteins, as well as ligands which can be involved in Zn2+ binding during enzymatic activation: imidazole, formamide, methanethiol, methanethiolate, methoxy, and hydroxy. The computations are performed using the SIBFA molecular mechanics procedure (SMM), which expresses the interaction energy under the form of four separate contributions related to the corresponding ab initio supermolecular ones: electrostatic, short‐range repulsion, polarization, and charge transfer. Recent refinements to this procedure are first exposed. To test the reliability of this procedure in large‐scale simulations of inhibitor binding to metalloenzyme cavities, we undertake systematic comparisons of the SMM results with those of recent large basis set ab initio self‐consistent field (SCF) supermolecule computations, in which a decomposition of the total ΔE into its four corresponding components is done (N. Gresh, W. Stevens, and M. Krauss, J. Comp. Chem., 16, 843, 1995). For each complex, the evolution of each individual SMM energy component as a function of radial and in‐ and out‐of‐plane angular variations of the Zn2+ position reproduces with good accuracy the behavior of the corresponding SCF term. Computations performed subsequently on di‐ and oligoligated complexes of Zn2+ show that the SIBFA molecular mechanics (SMM) functionals, Epol and Ect, closely account for the nonadditive behaviors of the corresponding second‐order energy contributions determined from the ab initio SCF calculations on these complexes and their nonlinear dependence on the number of ligands. Thus, the total intermolecular interaction energies computed with this procedure reproduce, with good accuracy, the corresponding SCF ones without the need for additional, extraneous terms in the intermolecular potential of polyligated complexes of divalent cations. © 1995 by John Wiley & Sons, Inc.
A biphasic role of nuclear transcription factor (NF)‐κB in the islet β‐cell apoptosis induced by interleukin (IL)‐1β
Authors: Papaccio Gianpaolo , Graziano Antonio , d'Aquino Riccardo , Valiante Salvatore , Naro Fabio 
Published: December 2004

AbstractIL‐1β is an important mediator in the pathogenesis of type 1 diabetes both in vivo and in vitro and it has been shown to induce islet β‐cell apoptosis. Most of the IL‐1β effects seem to be mediated by NF‐κB transcription factor activation, but its role in the induction of islet β‐cell apoptosis has not yet been clarified. Taking advantage of the protease inhibitor TPCK (N‐tosyl‐L‐phenylalanine chloromethyl ketone), which specifically inhibits the nuclear transcription factor NF‐κB activation, we studied the role of NF‐κB in the rIL‐1β treated rat pancreatic islets. Our results show that TPCK blocked rIL‐1β‐mediated early increase of MnSOD activity and β‐cell defence/repair protein expression, suggesting a protective role for NF‐κB at the beginning of IL‐1β treatment; but, in a second phase, NF‐κB induces a sustained decrease of specific β‐cell proteins like insulin, GLUT‐2 and PDX‐1 with a concomitant increase of aspecific proteins and iNOS transcription. The appearance of iNOS expression correlates with increased levels of nitrite + nitrate levels and appearance of mitochondrial damage detected either at morphological and biochemical level. After 36 h of IL‐1β treatment islet β‐cells begin to undergo apoptosis. Since IL‐1β induction of apoptosis is completely prevented by TCPK treatment, this finding underscores the central role of NF‐κB in this process. Thus, our results clearly indicate that NF‐κB regulates MnSOD genes expression and MnSOD activity, which protects islet β‐cells by IL‐1β damage. Furthemore, when the IL‐1β stress impairs islet β‐cell function, NF‐κB activation regulates the entrance of islet β‐cell into the cell death program. © 2004 Wiley‐Liss, Inc.
Neuronal modulation of schwann cell glial fibrillary acidic protein (GFAP)
Authors: Mokuno K. , Kamholz J. , Behrman T. , Black C. , Sessa M. , Feinstein D. , Lee V. , Pleasure D. 
Published: December 2004

AbstractAdult rat sciatic nerves contain cytoskeletal peptides that resemble CNS glial fibrillary acidic protein (GFAP) in immunoreactivity and molecular weight. Immunohistological examination of teased nerve fascicles indicated that these peptides are expressed selectively by Schwann cells related to small axons. Radiolabelled mouse and rat CNS GFAP cDNA probes hybridized with a single, 2.7 kb RNA band in Northern blots prepared from total RNA from both rat sciatic nerve and rat brain. Sciatic nerve GFAP mRNA was detectable by this means in adult, 2 month, or 21 day postnatal rats, but not in 3, 6, or 10 day postnatal rats. Sciatic nerve transection caused a marked reduction in the level of GFAP mRNA in the axotomized distal stump. We conclude that Schwann cell synthesis of GFAP is developmentally regulated and that Schwann cells, unlike astroglia, require continued trophic input from small axons in order to express GFAP.
Gangliosides stimulate synthesis of prostaglandin E2 and prostacyclin in fetal rat brain hemispheres after episodes of global intrauterine ischemia
Authors: Yavin E. , Gil S. , Kunievsky B. , Harel S. 
Published: December 2004

AbstractThe ability of brain preparations from 20‐day‐old rat fetuses to synthesize prostanoids in vitro before and after interruption of the maternal‐fetal blood flow was examined using a radioimmunoassay technique. Synthesis of thromboxane B2(TxB; the stable thromboxane A2 metabolite) decreased with increasing restriction time; conversely, it was elevated with reperfusion. Synthesis of 6‐keto prostaglandin F1α(PGF; the stable prostacyclin metabolite) and prostaglandin E2 (PGE) prostanoids remained unchanged after 20 min restriction and through a 2 hr reperfusion period. Intraperitoneal administration of GM1 (45 mg/kg) into the pregnant rat, 3 hr before restriction, stimulated synthesis of PGE and reduced synthesis of TxB. A prostanoid vasoactive index (PVI), which reflects the relative proportion of the three prostanoids synthesized and asserts the vasoactive potential of the brain tissue, was established. A rise in this value was attained after intrafetal administration into the peritoneal cavity of either GM1, GM3, or isopropyl‐GM1 (AGF44) gangliosides, each given at 40μg dose in 5 μl volume, and N‐dichloroacetyl‐sphingosine (LIGA20; 15μg/5μl) ganglioside analog, 1 hr before restriction. The effect was primarily due to an increase in the capacity of fetal brain tissue to synthesize PGE and, to a lesser extent PGF, vasodilating prostanoids. The N‐methyl‐D‐aspartate (NMDA) receptor blocker MK801 (6.6 μg/μl) and the platelet activating factor (PAF) receptor antagonist BN52021 (0.1μmol/2μl), given by the same route, effectively raised by 60–80% the vasodilating potential of the brain tissue following ischemia. Based on the commonality seen with these chemically diverse anti‐ischemic agents, it is hypothesized that PGE and PGF elevation by gangliosides may be benefical rather than detrimental for the fetal ischemic brain. © 1993 Wiley‐Liss, Inc.
Interaction between CO and O
Authors: Kondratiev V. N. , Intezarova E. I. 
Published: January 2005

AbstractThe reaction between carbon monoxide and atomic oxygen was studied in a gas flow over a temperature range of 136 to 230°C at atmospheric pressure. The rate constant of this reaction, considered to be one for a second‐order reaction, was found to decrease with increasing temperature and to depend on the ratio of O2 to CO that was varied from 0.11 to 2.69. A conclusion was made that under the experimental conditions the reaction was third order
equation image
The rate constant of this reaction
equation image
was determined for a mixture of O2 and CO and it was found that the efficiency of O2 as particle M is four times that of CO.