bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new method for the calculation of atomic and local hardness
Authors: Baumer Luca , Sala Giordano , Sello Guido 
Published: January 2005

AbstractThe relationships between atomic hardness, atomic electronegativity, and electronic energy are considered and emphasized. A new method for calculating atomic hardness is described. The concept of local hardness is quantified through the calculation of a new variable named alfahardness. Atomic hardness and alfahardness are used for the calculation of both the mean molecular and local properties. The results obtained are discussed and a comparison made with the analogous quantities presented by Pearson. An algorithm has been realized and transformed into a computer routine for use within a CAOS program.
Pepto: An expert system for automatic peak assignment of two‐dimensional nuclear magnetic resonance spectra of proteins
Authors: Catasti Paolo , Carrara Enrico , Nicolini Claudio 
Published: January 2005

AbstractTwo‐dimensional Nuclear Magnetic Resonance (2DFTNMR) is presently the most powerful tool to determine protein structures in solution. Peak assignment (an interpretation of the two‐dimensional spectra that leads to the individuation of pairs of Hydrogen atoms that are involved in an NOE peak) is a cornerstone of such use of 2DFTNMR. Manual peak assignment of a protein often requires months of work by a specialized equipe. An automation of this task could speed up the protein study process, or alternatively allow to study previously unmanageable proteins. This article describes PEPTO, an expert system for the interpretation of sets of 2DFTNMR spectra on proteins. The present version of the program deals with spectra obtained from NOESY and COSY experiments. Tests of PEPTO on simulated spectra of five proteins with known assignments are also described and dicussed.
Combined application of pair potentials and the MM2 force field for the modeling of ionophores
Authors: Badertscher Martin , Musso Stefano , Welti Martin , Pretsch Ernö , Maruizumi Takuya , Ha Tae‐kyu 
Published: January 2005

AbstractComplexes of alkali and alkaline earth cations with organic compounds are modeled by describing ionligand interaction energies with pair potentials and intraligand as well as interligand energies with the MM2 potential. New pair potentials for the interaction of Li+, Na+, K+, Mg2+, and Ca2+ ions are derived on the basis of 30,000 ab initio interaction energy values with 70 selected model ligand molecules. Various problems of the combination of these two basically different potentials are discussed. An application for the K+ complex of 18‐crown‐6 is presented. For more flexible ligands the introduction of three‐body correction terms of the pair potentials seems necessary.
Molecular mechanics (MM3) calculations on conjugated hydrocarbons
Authors: Allinger Norman L. , Li Fanbing , Yan Liqun , Tai Julia C. 
Published: January 2005

AbstractThe MM3 molecular mechanics program has been extended to conjugated systems. A VESCF method is applied to the pi‐system to calculate bond orders, from which various stretching and torsional parameters are obtained. The procedure gives somewhat better results than the analogous MM2 calculations. It has been applied to a study of 81 compounds of aromatic and other conjugated hydrocarbons, as well as 45 alkenes and unconjugated polyenes. The structures calculated are generally in good agreement with experiment, and the heats of formation of these compounds can be calculated with a rms value of 0.62 kcal/mol, which may be compared with the average experimental error of 0.61 kcal/mol. In addition, vibrational frequencies for five representative conjugated model structures are calculated, with an rms value of 46 cm−1, and from these, other properties such as entropy can be calculated.
Monte Carlo simulations of liquid alkyl ethers with the OPLS potential functions
Authors: Briggs James M. , Matsui Tooru , Jorgensen William L. 
Published: January 2005

AbstractIntermolecular potential functions have been developed for use in computer simulations of alkyl ethers. The simple OPLS model was adopted and parameterized to yield good descriptions of bimolecular and ion‐molecule complexes as well as to reproduce experimental thermodynamic properties of liquid ethers. The principal testing featured Monte Carlo statistical mechanics simulations for liquid dimethyl ether (DME), ethyl methyl ether (EME), diethyl ether (DEE), and tetrahydrofuran (THF). Average errors of 1–3% are obtained for the computed densities and heats of vaporization including results for THF at pressures up to 5000 atm. The torsional motion about the central CO bonds in EME and DEE was included in the simulations using rotational potential functions fit to results of molecular mechanics (MM2) calculations. The liquid‐state environment is found to have negligible effect on the conformational equilibria.
Partial charges by multipole constraint. Application to the amino acids
Authors: Gruschus James M. , Kuki Atsuo 
Published: January 2005

AbstractAtom‐centered partial charges which exactly reproduce the lowest several multipoles of a molecule's charge distribution can be obtained in a straightforward and convenient manner from the output of existing electronic structure calculations. The multipole constraint method is demonstrated by a computation of partial charges for the twenty common amino acids. The electron density employed here, derived from a semiempirical MNDO calculation, incorporates Slater‐type orbitals which imbue it with the exponential fall‐off vital to electronic tunneling calculations. In addition, a procedure based on these charges is described which divides the original electron density into two components, a large component with a simple electrostatic potential, and a much smaller residual whose several lowest multipoles vanish.
Correlation of the acidity of substituted phenols, anilines, and benzoic acids calculated by MNDO, AM1, and PM3 with Hammett‐type substituent constants
Authors: Karaman Rafik , Huang Jun‐Tsu Luke , Fry James L. 
Published: January 2005

AbstractHeats of formation and net atomic charges of some 120 structures involving substituted phenols, anilines, and benzoic acids and the corresponding anions were calculated by MNDO, AM1, and PM3 semiempirical methods. The gas phase acidities of substituted phenols and anilines and the net atomic charges on the anionic heteroatoms of the corresponding anions have been successfully correlated with σ− constants. Moreover, good correlations with σ were found for the charges on the acidic hydrogens of substituted phenols and anilines. In contrast, the gas phase acidities of substituted benzoic acids and the charges on the anionic oxygens of the corresponding anions are better correlated with Taft σ° constants. Comparisons of these results with experimental data and ab initio theoretical calculations indicate that AM1 and PM3 methods are much better than MNDO in predicting the acidity of aromatic compounds.
Theoretical analysis of the electronic spectrum of GeH4 from ab initio CI calculations
Authors: Sanz Javier Fernändez , Dargelos Alain 
Published: January 2005

AbstractAb initio CI calculations using pseudopotentials to describe germanium inner electrons are carried out on the low‐lying excited singlet states (T2) of GeH4. A theoretical analysis of these states in terms of Mulliken population of Rydberg orbitals for each state and oscillator strengths allow us to reinterpret its experimental Vacuum UV electronic spectrum.
Pseudopotential calculations for methyl compounds of zinc and magnesium
Authors: Kaupp M. , Stoll H. , Preuss H. 
Published: January 2005

AbstractPseudopotentials and valence basis sets to be used in calculations for organometallic compounds of zinc and magnesium have been tested in calculations for the M(CH3)n (M = Zn, Mg; n = 1,2) molecules. Valence correlation effects are treated at the SDCI and CEPA levels. The capability of a polarization potential on zinc to account for the valence shell contracting effect of core valence correlation is studied. Properties considered are geometries, force constants, Mulliken populations, ionization potentials, atomization, and binding energies. Differences in bonding between the two dimethyl compounds are discussed.
GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set
Authors: Pascual‐Ahuir Juan Luis , Silla Estanislao 
Published: January 2005

AbstractThe algorithm used by the program GEPOL to compute the Molecular Surface (MS), as defined by Richards, is presented in detail. GEPOL starts like other algorithms from a set of spheres with van der Waals radii, centered on the atoms or group of atoms of the molecule. GEPOL computes the MS by first searching the spaces inaccessible to the solvent and consequently filling them with a new set of spheres. Here we study the behavior of the method with its parameters, presenting several examples of application.
Molecular mechanics study of myelin basic protein peptide 87‐118: Some local energy minima
Authors: Gilliom Richard D. , Stoner Gerald L. 
Published: January 2005

AbstractMyelin basic protein (MBP) is the major extrinsic protein of the myelin sheath in the central nervous system. It is this protein that is destroyed in such demyelinating diseases as multiple sclerosis. We have examined the predicted structures of one segment of MBP using the molecular mechanics program ECEPP83 developed by Scheraga and co‐workers as modified by Chuman, Momany, and Schafer. We have focused upon a segment, 87‐118, containing the Pro‐Pro‐Pro sequence (residues 100–102), which has been predicted from standard algorithms to exist in a hairpin loop connecting anti‐parallel beta‐strands. Several local energy minima have been found and reported. Tripoline sequences are not rare in proteins, but their structure and function is still uncertain.
An algorithm for the simultaneous superposition of a structural series
Authors: Kearsley Simon K. 
Published: January 2005

AbstractA procedure is delineated for finding the optimal superposition of a series of chemical structures. Quaternions are used to represent the absolute orientation of the structures–rotations of the structures need never be carried out explicitly. The Rational Function Optimization method is used to minimize a simultaneous superposition residual similar to the one given by Gerber and Müller. The robustness of the method is illustrated by comparing a series of conformations of a polyene carotenoid.
Automated conformational analysis: Directed conformational search using the A* algorithm
Authors: Leach Andrew R. , Prout Keith 
Published: January 2005

AbstractA common requirement in conformational analysis is the identification of a molecule's lowest energy conformations. The application of the A* algorithm to this problem is examined. The algorithm uses heuristic information about the problem domain to direct the search and has been implemented in a system for performing automated conformational analysis. The method is detailed and sample results presented. Some limitations of the approach are identified.
A novel decomposition of torsional potentials into pairwise interactions: A study of energy second derivatives
Authors: Dinur U. , Hagler A. T. 
Published: January 2005

AbstractA general method of analyzing intramolecular torsional potentials in terms of energy second derivatives that couple the rotating atoms is presented. The method offers a rigorous decomposition of the total torsional potential into pairwise (dihedral) interactions and enables one to derive nonbonded torsional interactions between 1–4 atoms as well as between more distant atoms and sites. The method is demonstrated on ethane, propane and acetaldehyde. It is shown that the 1–4 H…H dihedral potentials in ethane and propane are very similar, thereby supporting the notion of transferable force field potential functions. However, the dihedral potentials that are obtained differ from 1–4 potentials that are used in current force fields. Intramolecular three body effects are clearly seen in this method and are found to be relatively large for the dihedral interactions, although in the one case studied (propane) the overall effect on the methyl‐methyl interaction is negligible due to cancellation of terms. The analysis explicitly shows that the barrier in acetaldehyde is due mainly to the dihedral H…H interaction.
Structural effects of fluorine substitution in proteins
Authors: Gregory D. H. , Gerig J. T. 
Published: January 2005

AbstractThe consequences of substitution of fluorine for the para hydrogen of a phenylalanine residue in ribonuclease‐S were investigated by conformational energy calculations using the AMBER force field. Both the fluorine‐containing protein and the corresponding nonfluorinated material were subjected to conformational adjustment through energy minimization and the minimum energy structures so defined were compared. Fluorine substitution leads to small alterations in many atomic positions in the protein, with adjustments at at sites more than 0.5 nm from the fluorine appearing to be somewhat larger than those within the immediate vicinity of the fluorine. Several atoms proximate to the fluorine atom were observed to move toward the fluorine while others in the same vicinity move away. The greater bulk of the fluorine atom and the strongly different electronic properties of fluorine compared to hydrogen thus appear to be insufficient to cause a consistent, unidirectional change in nearest‐neighbor interactions upon introduction of a fluorine atom into a protein structure. Virtually all changes in atomic positions that are predicted by these calculations would be barely detectable by a crystallographic study with a resolution of 0.2 nm.
Molecular silverware. I. General solutions to excluded volume constrained problems
Authors: Blanco Mario 
Published: January 2005

AbstractGeneral mathematical solutions to excluded volume constrained problems in computational chemistry are reported. The solutions have been used to create a new family of molecular modeling algorithms to facilitate the study of molecular interactions in condensed phases. The new algorithms, collectively known as Molecular Silverware, are for the most part interactive and designed for packing, solvating, and sampling molecules embedded in simple or complex topological environments. Multifolded, disconnected, or porous molecular structures are permitted. Molecular Silverware assists the preparation of Monte Carlo and molecular dynamics simulations at a small fraction of the total simulation time. Primary targets for applications include the study of molecular recognition mechanisms and the selective binding of DNA, RNA, peptides, saccharides and other biopolymers in solution as well as the prediction of phase separation behavior and physical properties of non‐crystalline condensed phases such as bulk polymers, polymer blends, organic liquids, membranes, micelles, gels, crosslinked networks, glasses, and amorphous heterogeneous catalysts. As a result of this new approach to excluded volume constraints, the computer simulation of noncrystalline condensed phases is no longer hampered by the lack of a general and efficient method for the creation and configurational sampling of small and large molecular assemblies at high densities.
Comments on the characteristic polynomial of a graph
Authors: Balasubramanian K. 
Published: January 2005

AbstractSeveral unique advantages of the Le Verrier–Fadeev–Frame method for the characteristic polynomials of graphs over the method proposed by Zivković recently based on the Givens–Householder method are described. It is shown that the Givens–Householder method proposed by Zivković, by itself fails for directed graphs, signed graphs, and complex nonhermetian graphs requiring extensive modifications to the Householder algorithm through the double + random shift QR procedure requiring more computations than claimed. Furthermore, the QR procedure does not always converge and requires random shifts. To the contrary, it is shown that the Le Verrier–Fadeev–Frame method does not require any such modifications or random shifts and takes less total CPU times when both algorithms are run using vector processors. Hence it is demonstrated that the Le Verrier–Frame algorithm is efficient and superior in its universal and direct applicability to all graphs requiring no further modifications (directed, signed, and complex).
On a proposed radiation‐induced polaronic hole in silicon dioxide
Authors: Rao P. S. , McEachern R. J. , Weil J. A. 
Published: January 2005

AbstractAb‐initio self‐consistent‐field molecular‐orbital (SCF MO) Hartree–Fock (HF) calculations using the STO‐3G, 6‐31G, and 6‐31G* basis sets, were performed to model quasi‐tetrahedral silicon species in silicon dioxide. Mostly nine‐atom clusters, [Si(OH)4]qt, with charge number qt = 0 or + 1, were studied. The positions of the Si and O atoms were varied to achieve minimum total energies, while the protons were held fixed in the O‐(neighboring)Si direction to simulate the rigid crystal surroundings. The α‐quartz‐type local symmetry C2 was found to be retained for the neutral cluster, but not for the ionic one. The unrestricted HF calculations indicate that the latter paramagnetic centre, (qt = +1), has its spin population almost entirely on one short‐bonded oxygen ion bonded weakly to its neighboring Si, and is quite high in energy (9.55 eV with 6‐31G) compared to the diamagnetic centre (qt = 0). The ionization energy is much higher than the self‐trapping potential of the polaronic hole, a fact which may account for the failure so far to observe a [SiO4]+1 center in quartz by means of continuous‐wave electron paramagnetic resonance spectroscopy. Calculations on the [SiO4]+1 center agree well with ultraviolet spectra, and with the [hole portion of a] proposed radiation‐induced exciton in quartz. The hole in [Si(OH)4]+1 can be shifted from a short‐bonded to a long‐bonded oxygen to give the excited state [Si(OH)4]es+1. Conclusions reached with the nine‐atom clusters were confirmed by a series of calculations on the extended model [Si(OSiH3)4]qt. Comparisons with the known isoelectronic species [AlO4]0 were carried out.
Free energy difference calculations by thermodynamic integration: Difficulties in obtaining a precise value
Authors: Mitchell Michael J. , McCammon J. Andrew 
Published: January 2005

AbstractFree energy difference calculations have been performed by the “slow growth” method of thermodynamic integration of the AMBER 3.0 molecular dynamics program for the mutation of a conformationally restricted threonine dipeptide, N‐acetyl threonyl‐N‐methylamide, to the corresponding alanyl dipeptide. By varying the total simulation length, it has been determined that precise free energy values are obtained only for simulations of greater than 100 ps total simulation time length. By varying the starting configurations for simulations of the same length, it has been determined that averaging the free energies obtained from shorter simulations may not give precise answers. Possible reasons for this behavior are discussed.
OPKINE, a multipurpose program for kinetics
Authors: Pla F. Perez , Baeza J. J. Baeza , Ramos G. Ramis , Palou J. 
Published: January 2005

AbstractThe program OPKINE is presented for the study of reaction mechanisms and multicomponent analysis in dynamic conditions. This program is written in FORTRAN‐77 for IBM 30/90 and VAX 8300 computers, and permits the simultaneous evaluation of both rate constants and initial reagent concentrations or, alternatively, rate constants and sensitivities. Up to 20 kinetic curves, with up to 400 points each, can be treated to evaluate up to 40 parameters. Integration of the system of differential equations is performed by means of the Runge–Kutta–Fehlberg method. OPKINE is provided with the Simplex, and modified versions of the Davidon–Fletcher–Powell and Gauss–Newton–Marquardt optimization methods. A Monte Carlo procedure to search for the seeds is also available. Simulated experiments have been used to check the performances of the program. Complex kinetic mechanisms and mixtures of a large number of analytes can be managed with good results.
Incorporating solvent and ion screening into molecular dynamics using the finite‐difference Poisson–Boltzmann method
Authors: Sharp Kim 
Published: January 2005

AbstractThe finite difference method for solving the Poisson–Boltzmann equation is used to calculate the reaction field acting on a macromolecular solute due to the surrounding water and ions. Comparisons with analytical test cases indicate that the solvation forces can be calculated rapidly and accurately with this method. These forces act to move charged solute atoms towards the solvent where they are better solvated, and to screen interactions between charges. A way of combining such calculations with conventional molecular dynamics force fields is proposed which requires little modification of existing molecular dynamics programs. Simulations on the alanine dipeptide show that solvent forces affect the conformational dynamics by reducing the preference for internal H‐bonding forms, increasing theR‐alpha helix preference and reducing transition barriers. These solvent effects are similar to previous explicit solvent simulations, but require little more computation than vacuum simulations. The method should scale up with little increase in computational cost to larger molecules such as proteins and nucleic acids.
Chemical shift bond derivatives for molecules containing first‐row atoms
Authors: Chesnut D. B. , Wright D. W. 
Published: January 2005

AbstractThe primary and secondary first and second derivatives of the NMR isotropic chemical shift with respect to bond length modification have been calculated in the gauge invariant atomic orbital (GIAO) perturbed Hartree–Fock approach for some 177 first‐row nuclei in 63 molecules using the mixed basis heavy:6–311G(d)/hydrogen:4–31. The shift derivative with respect to multiple bond length changes correlates linearly with the shift itself while changes involving single bonds behave differently. Agreement between experimental derivatives and those calculated theoretically is good but the calculations show that second derivatives as well as both types of secondary effects cannot always be neglected. The correlation between the shift derivative and the isotropic shift indicates an exponential variation of the chemical shift with bond length near the vicinity of the equilibrium structure for multiple bonds.
MRD‐CI potential surfaces using balanced basis sets. VI. Correlation of bond order with bond function composition for first‐row diatomic molecules
Authors: Barclay V. J. , Wright James S. 
Published: January 2005

AbstractThis article presents theoretical calculations on bond energies for the first‐row diatomics C2, CN, CO, CF, N2, NO, NF, O2, FO, and F2, which vary in bond order from one to three. The atomic‐centered basis functions are systematically augmented with bond functions (BFs), which range in composition from (sp) to 2(spd), to determine the basis set which yields a dissociation energy closest to the experimental De. A strong correlation is found to exist between the bond order and the number of BFs required in the optimum basis set. Based on these results, we are able to predict the optimum composition of the BF basis which should be added to a DZP‐quality AO basis set for a case in which only the bond order is known. These optimized BF basis sets are shown in the accompanying article to give more accurate potential curves than larger basis sets without bond functions.