bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intermediate water structures in solution of Nα‐acetyl‐N‐methylphenylalaninamide
Authors: Kim Seungmoak , Yoon Chang No , Jhon Mu Shik 
Published: January 2005

AbstractIntermediate water structures in a solution of Nα‐acetyl‐N‐methylphenylalaninamide[Phe(amide)2] were investigated by the energy minimization method. The results show that ninety‐eight water molecules hydrate Phe(amide)2 and several kinds of cyclic structures are observed. The distribution of water molecules around Phe(amide)2 agrees with the results of molecular dynamics and monte carlo studies. The distribution of cyclic structures shows that the six‐membered ones are distributed mainly at the outside of the first hydration shell.
Effect of the substituents on the conformational behavior of five‐membered rings: Application to the cis‐ and trans‐2,5‐dimethoxytetrahydrofuran
Authors: Diez Ernesto , Palma Jesús , San‐Fabián Jesús , Guilleme Joaquin , Esteban Angel L. , Galache Maria P. 
Published: January 2005

AbstractA model is proposed which assumes that the pseudorotational potential in five‐membered rings is given by the combination of contributions from the unsubstituted ring, from the individual substituents and from interactions between pairs of substituents. The application of this model to the potentials calculated by the MM2 force field for the cis and trans‐2,5‐dimethoxytetrahydrofuran shows that the contributions from the individual substituents explain the main features of the potentials of these disubstituted rings. The pseudorotational analysis from vicinal proton spin‐spin coupling constants 3JHH confirms the realibility of the MM2 potentials.
On velocity scaling in molecular dynamics simulations
Authors: Hermansson Kersti , Lie George C. , Clementi Enrico 
Published: January 2005

AbstractThe effect of scaling the molecular velocities to a fixed total energy in molecular dynamics simulations within the (N,V,E) ensemble has been investigated. The effect of using different time steps is also discussed. It is found that, even for small time steps, velocity scaling has a substantial influence on the resulting molecular trajectories, velocities, and forces. Furthermore, velocity rescaling and larger time step seem to have an additive effect on the calculated trajectories, but not on the average thermodynamic properties, such as temperature, pressure, and energy.
Computer generation of characteristic polynomials of edge‐weighted graphs, heterographs, and directed graphs
Authors: Balasubramanian K. 
Published: January 2005

AbstractThe computer code developed previously (K. Balasubramanian, J. Computational Chem., 5, 387 (1984)) for the characteristic polynomials of ordinary (nonweighted) graphs is extended in this investigation to edge‐weighted graphs, heterographs (vertex‐weighted), graphs with loops, directed graphs, and signed graphs. This extension leads to a number of important applications of this code to several areas such as chemical kinetics, statistical mechanics, quantum chemistry of polymers, and unsaturated systems containing heteroatoms which include bond alternation. The characteristic polynomials of several edgeweighted graphs which may represent conjugated systems with bond alternations, heterographs (molecules with heteroatoms), directed graphs (chemical reaction network), and signed graphs and lattices are obtained for the first time.
A novel approach to the use of graph theory in structure–activity relationship studies. Application to the qualitative evaluation of mutagenicity in a series of nonfused ring aromatic compounds
Authors: Klopman Gilles , Raychaudhury Chandan 
Published: January 2005

AbstractIn this article we describe a novel approach to the application of graph theory in structure–activity relationship studies. An information–theoretical topological index for the vertices of a molecular graph has been used for the qualitative evaluation of the mutagenic activity of a series of nonfused ring aromatic compounds. The use of a vertex index contrasts with the conventional approach of using a topological index for the entire molecule. The idea is to identify regions, or substructures in the molecules (molecular graphs) which may be used to determine certain biological activity of chemical compounds. The results obtained in this paper indicate that the present approach is capable of classifying the mutagenic activity of the compounds under consideration and may find useful application in structure–activity relationship studies of diverse bioactive compounds.
Charge calculations in molecular mechanics. V. Silicon compounds and π bonding
Authors: Abraham Raymond J. , Grant Guy H. 
Published: January 2005

AbstractA previously published scheme for the calculation of partial atomic charges has been extended to include silicon, and has been parameterized for a range of SiX bonds (XC,H,O,F,Cl,Br). For the silicon–halogen and silicon–oxygen bonds, a comparison is made between charges calculated with and without the inclusion of π‐bonding. An extensive data set consisting of experimental geometries and dipole moments for the silicon compounds considered is presented and this leads to the selection of standard SiX bond lengths. The calculated dipole moments for the above compounds are in good agreement with those obtained experimentally only when the π charges are included. A comparison has also been made between the partial charges from this scheme and those obtained from computational methods using the Mulliken population analysis. There is considerable disagreement between the methods. Finally, the implications of the charges and structural data are considered in terms of application to zeolite systems.
YETI: An interactive molecular mechanics program for small‐molecule protein complexes
Authors: Vedani Angelo 
Published: January 2005

AbstractYETI, an interactive molecular mechanics program for drug‐design applications on small‐molecule protein complexes, is described. To model short‐range interactions in better agreement with experimental data, its force‐field energy expression includes directional potential functions for H‐bonds, salt linkages, and metal ligand interactions. The program works on an internal coordinate concept and uses a conjugate‐gradient minimizer. YETI is available for distribution through the author. The program has been used to model details of small‐molecule binding to the enzyme human carbonic anhydrase I. The impact of the directional potential functions on the geometry of H‐bonds and metal‐ligand interactions is discussed.
Pattern recognition in the prediction of protein structure. I. Tripeptide conformational probabilities calculated from the amino acid sequence
Authors: Lambert Millard H. , Scheraga Harold A. 
Published: January 2005

AbstractA procedure that uses pattern recognition techniques to compute tripeptide conformational probabilities is described. The procedure differs in several respects from the many “secondary structure” prediction algorithms that have been published over the last 20 years. First, the procedure classifies tripeptides into 64 different conformational types, rather than just α, β and coil, as is commonly done. Thus, the procedure can attempt to predict regions of irregular structure. Second, the procedure uses the methods of pattern recognition, which are powerful but conceptually simple. In this approach, amino acid properties are used to map peptide sequences into a multivariate property space. Particular tripeptide conformations tend to map to particular regions of the property space. These regions are represented by multivariate gaussian distributions, where the parameters of the distributions are determined from tripeptides in the protein X‐ray data bank. Finally, rather than making simple predictions, the procedure computes probabilities. Tripeptide conformational probabilities are calculated in the multivariate property space using the gaussian distributions. In a prediction, the procedure might find that a particular tripeptide in a protein has a 36% chance of being in the ααα conformation, a 17% chance of being ααϵ, a 14% chance of being ααα*, etc. The α‐helical conformation is thus the most probable, but, in predicting the structure of the protein, a search algorithm should also consider some of the other possibilities. The values of the probability provide a rational basis for selecting from among the possible conformations. The second article of this series describes a procedure that uses the probabilities to direct a search through the conformational space of a protein. The third article of the series describes a procedure that generates actual three‐dimensional structures, and minimizes their energies. The three articles together describe a complete procedure, termed “pattern recognition‐based importance‐sampling minimization” (PRISM), for predicting protein structure from amino acid sequence.
Analytical energy derivatives and normal modes in force fields employing lone‐pair pseudoatoms
Authors: Waldman Marvin , Masek Brian B. 
Published: January 2005

AbstractFormulas are derived for analytical first and second energy derivatives with respect to nuclear coordinates in molecular mechanics force fields employing lone‐pair pseudoatoms. These derivatives may further be used for the calculation of normal modes and vibrational frequencies while properly accounting for the presence of pseudoatoms. The equations are applied using the MM2 force field to calculate the vibrational spectrum of methanol to illustrate the applicability of the method. The results are compared to both experiment and a numerical approximation in which small masses are assigned to the lone‐pair pseudoatoms.
Molecular symmetry and ab initio calculations. I. Symmetry‐matrix and symmetry‐supermatrix
Authors: Cao Xiaoping 
Published: January 2005

AbstractIn this article the matrix elements can be grouped into classes by means of the molecular symmetry. By introducing the concepts of symmetry‐matrix and symmetry‐supermatrix and determining their operation rules, the storage of the supermatrix can be asymptotically reduced by a factor of ca. g2 (g is the order of the molecular symmetry group) and the calculation of Fock matrix during each SCF cycle can be reduced proportionally. Besides, by using the DIIS method combined with the symmetry‐matrices, the convergence behavior for highly symmetric molecules can be improved.
Orbital electronegativity and analytical representation of atom valence state energy
Authors: Labanowski Jan K. , Dammkoehler Richard A. , Motoc Ioan 
Published: January 2005

AbstractAn analytical representation of atom valence state energy (E(nj), j = 1,…︁4; E(nj) is a nonlinear function of orbital occupancy numbers nj) is proposed and explicitly derived for HAr; the values of electronegativity calculated based on E(nj) agree within truncation error with those of Hinze and Jaffe. However, in our representation, orbital electronegativity χ and hardness parameters η of a given orbital always include nonlinear contributions from other orbitals, hence accounting for their influence on χ and η. An atomic charge calculation procedure based on E(nj) is also described and shown to perform well.
High temperature annealed molecular dynamics simulations as a tool for conformational sampling. Application to the bicyclic “222” cryptand
Authors: Auffinger P. , Wipff G. 
Published: January 2005

AbstractWe have performed “High Temperature Annealed Molecular Dynamics Simulations” (HTAMDS) on the bicyclic 222 cryptand, and on model M+/222 cryptates with different representations of M+. The analysis of four sets of 500 structures allows assessment of the ability of HTAMDS to: (1) interconvert experimentally known conformers starting from one of them, (2) locate the energy minima, (3) generate new conformers of low energy, and (4) account for the average structure observed on the NMR time scale. In view of the ionophoric behavior of 222, structures are also analyzed in terms of the “in/out” orientation of the binding sites. It is found that simulations on the free molecule, although widely sampling the conformational space, do not give structures adequate for cation inclusion. They generate however the lowest energy structure known experimentally and other new closely related ones. Inclusion of the substrate in the simulation (either as a purely electrostatic “driver,” or as a charged sphere) is required to generate conformations found in several complexes. These results suggest that in the field of drug design, conformation of drugs suitable for binding to a given receptor may not be found when the simulations are performed on the isolated drug or substrate.
A comparison of the IGLO and LORG methods for the calculations of nuclear magnetic shieldings
Authors: Facelli Julio C. , Grant David M. , Bouman Thomas D. , Hansen Aage E. 
Published: January 2005

AbstractThe individual gauge for localized orbitals (IGLO) and localized orbital/local origin (LORG) methods for the calculation of chemical shieldings are compared from their theoretical and computational viewpoints. A detailed analysis of the fluorine α‐substituent effect in a series of fluoromethanes is given in terms of the IGLO and LORG bond contributions. The performance of both methods is discussed for molecular systems of fairly different sizes.
Calculation of the nonlinear optical properties of molecules
Authors: Kurtz Henry A. , Stewart James J. P. , Dieter Kenneth M. 
Published: January 2005

AbstractA finite‐field method for the calculation of polarizabilities and hyperpolarizabilities is developed based on both an energy expansion and a dipole moment expansion. This procedure is implemented in the MOPAC semiempirical program. Values and components of the dipole moment (μ), polarizability (α), first hyperpolarizability (β), and second hyperpolarizability (γ) are calculated as an extension of the usual MOPAC run. Applications to benzene and substituted benzenes are shown as test cases utilizing both MNDO and AM1 Hamiltonians.
Evaluation of a finite multipole expansion technique for the computation of electrostatic potentials of dibenzo‐p‐dioxins and related systems
Authors: Murray Jane S. , Grice M. Edward , Politzer Peter , Rabinowitz James R. 
Published: January 2005

AbstractThe electrostatic potential V(r) that the nuclei and electrons of a molecule create in the surrounding space is well established as a guide in the study of molecular reactivity, and particularly, of biological recognition processes. Its rigorous computation is, however, very demanding of computer time for large molecules, such as those of interest in recognition interactions. We have accordingly investigated the use of an approximate finite multicenter multipole expansion technique to determine its applicability for producing reliable electrostatic potentials of dibenzo‐p‐dioxins and related molecules, with significantly reduced amounts of computer time, at distances of interest in recognition studies. A comparative analysis of the potentials of three dibenzo‐p‐dioxins and a substituted naphthalene molecule computed using both the multipole expansion technique and Gaussian 82 at the STO‐5G level has been carried out. Overall we find that regions of negative and positive V(r) at 1.75 Å above the molecular plane are very well reproduced by the multipole expansion technique, with up to a 20‐fold improvement in computer time.
Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops
Authors: Dudek Michael J. , Scheraga Harold A. 
Published: January 2005

AbstractA procedure has been developed for global energy minimization of surface loops of proteins in the presence of a fixed core. The ECEPP potential function has been modified to allow more accurate representations of hydrogen bond interactions and intrinsic torsional energies. A computationally efficient representation of hydration free energy has been introduced. A local minimization procedure has been developed that uses a cutoff distance, minimization with respect to subsets of degrees of freedom, analytical second derivatives, and distance constraints between rigid segments to achieve efficiency in applications to surface loops. Efficient procedures have been developed for deforming segments of the initial backbone structure and for removing overlaps. Global energy minimization of a surface loop is accomplished by generating a sequence (or a trajectory) of local minima, the component steps of which are generated by searching collections of local minima obtained by deforming seven‐residue segments of the surface loop. The search at each component step consists of the following calculations: (1) A large collection of backbone structures is generated by deforming a seven‐residue segment of the initial backbone structure. (2) A collection of low‐energy backbone structures is generated by applying local energy minimization to the resulting collection of backbone structures (interactions involving side chains that will be searched in this component step are not included in the energy). (3) One low‐energy side‐chain structure is generated for each of the resulting low‐energy backbone structures. (4) A collection of low‐energy local minima is generated by applying local energy minimization to the resulting collection of structures. (5) The local minimum with the lowest energy is retained as the next point of the trajectory. Applications of our global search procedure to surface segments of bovine pancreatic trypsin inhibitor (BPTI) and bovine trypsin suggest that component‐step searches are reasonably complete. The computational efficiency of component‐step searches is such that trajectories consisting of about 10 component steps are feasible using an FPS‐5200 array processor. Our procedure for global energy minimization of surface loops is being used to identify and correct problems with the potential function and to calculate protein structure using a combination of sequence homology and global energy minimization.
Use of parallel processing in the study of protein. Ligand binding
Authors: Goodfellow Julia M. , Jones Douglas M. , Laskowski Roman A. , Moss David S. , Saqi Mansoor , Thanki Narmada , Westlake Richard 
Published: January 2005

AbstractWe have undertaken an energy minimization study of the binding of a small ligand, water, to amino acid side‐chains. These calculations have been performed on a Meiko Computing surface containing a small number of transputers and on a larger transputer array installed at Edinburgh University. The aim of this study is twofold. First, we wished to compare these potential energy maps for a given side‐chain as a function of the local secondary structure and also of the neighboring residue types. Secondly, the energy maps are found to be in good agreement with experimental distributions on the binding of water molecules to amino acid side‐chains. The use of our in‐house Meiko computing surface increases the speed of these calculations by a factor of about 25 over a VAX 11/750. With larger arrays of transputers, such as that at Edinburgh “concurrent” Supercomputer Project, we achieve increases in speed of over 200 such that these energy maps can be calculated at interactive speeds.
On the use of series to integrate rate equations
Authors: Poland Douglas 
Published: January 2005

AbstractThe coefficients in power series, in the variable time, describing coupled nonlinear chemical reactions are easily obtained from a recursion relation. Since these series have a limited radius of convergence they are not very useful as such. If the series are inverted to give time as a function of the appropriate power of a progress variable, the new series converge over the entire time course of the reaction. If, further, the long‐time asymptotic behavior, obtained from the linearized kinetic equations, is used, one can obtain a series expansion for a function that describes the correct short‐time behavior. This function can be estimated very well using truncated series. The method works well for consecutive nonlinear reactions where the progress variables are monotonic functions of time; this includes many cases where the concentrations of intermediate species go through a maximum as the reaction progresses.
Free energy calculation of a soft sphere solid using an adaptive, importance sampling Monte Carlo algorithm
Authors: Kulver Robert 
Published: January 2005

AbstractUsing an adaptive, importance sampling Monte Carlo algorithm, the free energy and equation of state of a soft sphere solid are calculated. The Monte Carlo integration technique to be described is unlike standard methods in that it can evaluate directly the partition function and consequently the free energy of a solid. The results for a soft sphere solid are compared with data obtained from a thermodynamic integration method due to Hoover et al.7 The equation of state obtained from Monte Carlo integration is in agreement with Hoover's method while the free energy calculations compare favorably only at densities greater than that of the freezing transition.
Extended basis sets for the transition metals yttrium through cadmium
Authors: Hansen Lillian M. , Marynick Dennis S. 
Published: January 2005

AbstractExtended Slater basis sets were developed for the transition metals yttrium through cadmium. Gaussian expansions of these basis sets are extremely useful for ab initio methods which employ six Cartesian Gaussians for the description of the d orbitals. The s‐type function generated from the symmetric combination of the x2, y2, and z2 Cartesian Gaussians is used to describe the 4s region, thereby reducing the overall number of functions for molecular calculations and reducing the redundancy in the basis set.
Comments on a comparison of AM1 with the recently developed PM3 method
Authors: Dewar Michael J. S. , Healy Eamonn F. , Holder Andrew J. , Yuan Yate‐Ching 
Published: January 2005

AbstractA reparameterized version (PM3) of AM1 has recently been reported and the results for several hundred molecules compared with those from AM1 itself. The comparison implied that PM3 represents a significant improvement over the earlier treatment. The apparently poor performance of AM1 is, however, due to the inclusion of “AM1 results” for elements (A1,P,S) for which AM1 parameters were unavailable. If these are omitted, PM3 is seen to be only marginally better than AM1. Since this conclusion refers only to a specific set of stable molecules, it is not clear whether even this small improvement will apply to other species or studies of reactions. It is in any case insufficient to justify the confusion caused by the release of the new treatment.
AM1 molecular orbital studies of the structures, conformations, protonation energies, and electronic properties of triazine dihydrofolate reductase inhibitors
Authors: Welsh William J. 
Published: January 2005

AbstractThe structural, conformational, and electronic properties of three triazine antifolates were determined by AM1 molecular orbital calculations, and the results were compared with other theoretical studies and with X‐ray crystallographic studies of these and similar triazines both in the crystalline state and as complexes bound to dihydrofolate reductase. Calculated protonation energies confirm crystal structure data indicating N‐protonation analogous to that reported for MTX in similar environments. Overall, the calculated structural and conformational properties are in good agreement with X‐ray crystallographic results for these and similar triazines as found in the crystalline state and in enzymebound ternary complexes. However, for one triazine AM1 predicts a conformation with the bulky aromatic substituent twisted about 60° away from coplanarity with the triazine ring, in contrast to the nearly coplanar conformation found in the crystalline state. Intermolecular interactions favoring the coplanar conformation may thus be operative in the crystalline environment. The unique conformational preferences and greater conformation flexibility of triazines in general and of this triazine in particular may provide a key to understanding their biological activity.