bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations
Authors: Wang Bingze , Ford George P. 
Published: January 2005

AbstractAtomic charges derived from a recently described approach to the very rapid computation of AM1 electrostatic potentials (ESP) accurately parallel, but are ca. 20% smaller than, the corresponding HF/6‐31G* values. The dipole moments computed from the AM1 charges are virtually identical to those derived directly from the wave function and in rather better agreement with the experimental values than those computed using the HF/6‐31G* charges. Unlike other approaches to the semiempirical calculation of ESP‐derived charges, the present method also yields near HF/6‐31G* quality potentials close to the molecular periphery. For medium‐sized organic molecules (40‐100 basis functions), the method is approximately two orders of magnitude faster than those involving prior deorthogonalization of AM1 wave function and explicit computation of the full ESP integral matrix. © 1994 by John Wiley & Sons, Inc.
The structures of LiNC, NaNC, and KNC: Potential energy surface for the orbiting motion of the metal cation around the CN group
Authors: Dorigo Andrea , von Ragué Schleyer Paul , Hobza Pavel 
Published: January 2005

AbstractSets of XNC (X = Li, Na, and K) structures have been investigated using a variety of theoretical methods and basis sets. Two linear and a bridged structure correspond to an energy minimum for LiCN. For NaCN and KCN, the linear isocyanide is a minimum at most levels of theory but becomes a second‐order stationary point when correlated levels and large basis sets are used. Two transition structures are involved in the interconversion of the bridged form and each linear isomer. The isomerization of the bridged minimum to the linear XCN involves a substantial barrier in each case, so that the satellite motion of the metal is facile at one end but not at the other. Calculations with large basis sets and with electron correlation, fourth‐order Møller–Plesset theory for KNC, and quadratic configuration interaction [QCISD(T)] for LiNC and NaNC give qualitative and quantitative agreement with this experiment. The sodium and potassium cyanide prefer bridged forms, in contrast to the linear isocyanide LiNC. © 1994 by John Wiley & Sons, Inc.
Relativistic Dirac–Fock calculations for closed‐shell molecules
Authors: Pisani L. , Clementi E. 
Published: January 2005

AbstractA new code has been written to perform relativistic Dirac–Fock self‐consistent field (SCF) calculations on closed‐shell molecules of any symmetry. The choice of the basis set allows us to work at different levels of approximation depending on the precision required. Calculations on the H2Po molecule show that accurate results on specific problems like geometry optimization can be obtained by evaluating the two‐electron integrals on half the basis spinors. © 1994 by John Wiley & Sons, Inc.
Effect of charge on bond strength in hydrogenated amorphous silicon
Authors: Clare B. W. , Talukder G. , Jennings P. J. , Cornish J. C. L. , Hefter G. T. 
Published: January 2005

AbstractWe have studied the effect of excess charge on the bond strength in the silanes SiH4 and Si2H6 to assess whether charge trapping in a solid‐state lattice might promote the technologically important photodegradation of amorphous silicon alloys (the Staebler‐Wronski effect). The calculations indicate that both positive and negative charges reduce the strength of SiH and SiSi bonds considerably, to the point where they may be broken easily by visible or even infrared light. © 1994 by John Wiley & Sons, Inc.
Hash codes for the identification and classification of molecular structure elements
Authors: Ihlenfeldt Wolf Dietrich , Gasteiger Johann 
Published: January 2005

AbstractA set of algorithms is presented which establish the topological identity of atoms, bonds, molecules, and ensembles of molecules from a basic connection table. The computationally inexpensive result is a fixed‐length hash code which is suited for database applications and structure manipulation programs. The degree of differentiation between structural entities is adjusted easily for stereocenters, isotope labeling, atomic charges, and ionization locations or other properties. Special algorithms are presented which deal with problematic cases of uniform atomic environments. A number of practical applications demonstrate the usefulness of these hash codes. © 1994 by John Wiley & Sons, Inc.
New implementation of a program to calculate correlated band structures of polymers: An application to the band structure of polyparaphenylene (PPP)
Authors: Palmer Ian J. , Ladik Janos 
Published: January 2005

AbstractA new program has recently been implemented with the aim of extending quasi‐particle (QP) band structure calculations to polymers with larger unit cells. The theoretical background is briefly reviewed and the new algorithm described, which has been optimized for machines with vector processors. To illustrate the usefulness of this technique, calculations have been performed on polyparaphenylene (PPP) using a double‐zeta basis set. The calculated QP band gap between the valence and conduction bands is 2.3 eV, which compares favorably with the experimental value of 2.8 eV. The self‐consistent field (SCF) result with the same double‐zeta basis set is 8.7 eV. © 1994 by John Wiley & Sons, Inc.
Cluster analysis of molecular conformations
Authors: Shenkin Peter S. , McDonald D. Quentin 
Published: January 2005

AbstractWe describe a method for locating clusters of geometrically similar conformers in ensembles of chemical conformations. We first calculate the pairwise interconformational distance matrix in either torsional or Cartesian space and then use an agglomerative, single‐link clustering method to define a hierarchy of clusterings in the same space. Especially good clusterings are distinguished by high values of the separation ratio: the ratio of the shortest intercluster distance to the characteristic threshold distance defining the clustering. We also discuss other statistics. The method has been embodied in a program called XCluster, which can display the distance matrix, the hierarchy of clusterings, and the clustering statistics in a variety of formats. XCluster can also write out the clustered conformations for subsequent or simultaneous viewing with a molecular visualization program. We demonstrate the sorts of insight that this approach affords with examples obtained from conformational search and molecular dynamics procedures. © 1994 by John Wiley & Sons, Inc.
On the functional representation of bond energy functions
Authors: Dinur U. , Hagler A. T. 
Published: January 2005

AbstractAb initio calculations are used to test the ability of various representations to reproduce bond energies. It is found that expansion in 1/R, where R is the bond length, is remarkably efficient and is consistently better than the usual R expansion. A quadratic form in 1/R is better than a cubic representation in R and sometimes even as good as a quartic representation. A cubic function in 1/R is, in all cases studied, better performing than the quartic expansion in R. It is also found that parameters derived with the 1/R expansion are defined more sharply than those derived for the R expansion. It is suggested that the 1/R expansion may be computationally more efficient for simulations of large biomolecules and for constructions of reactive force fields than the standard bond functions. © 1994 by John Wiley & Sons, Inc.
The valence isomers of (CH)8 and (SiH)8: An ab initio MO study
Authors: Versteeg Uwe , Koch Wolfram 
Published: January 2005

AbstractThe 22 possible valence isomers of the (CH)8 and (SiH)8 systems have been studied by ab initio molecular orbital calculations at the MP2/6‐31G*//6‐31G* + ZPE level. Optimized geometries, relative energies, and, for some selected compounds, vibrational frequencies are reported. The systematic differences between the carbon and silicon compounds are analyzed. © 1994 by John Wiley & Sons, Inc.
Gaussian multipoles in practice: Electrostatic energies for intermolecular potentials
Authors: Wheatley Richard J. , Mitchell John B. O. 
Published: January 2005

AbstractA method is presented for calculating the total electrostatic interaction energies between molecules from ab initio monomer wave functions. This approach differs from existing methods, such as Stone's distributed multipole analysis (DMA), in including the short‐range penetration energy as well as the long‐range multipolar energy. The monomer charge densities are expressed as distributed series of atom‐centered functions which we call Gaussian multipoles; these are analogous to the distributed point multipoles used in DMA. Our procedure has been encoded in the GMUL program. Calculations have been performed on the formamide/formaldehyde complex, a model system for NH …︁ O hydrogen bonding in biological molecules, and also on guanidinium/benzene, modeling amino/aromatic interactions in proteins. We find that the penetration energy can be significant, especially in its contribution to the variation of the electrostatic energy with interaction geometry. A hybrid method, which uses Gaussian multipoles for short‐range atom pair interactions and point multipoles for long‐range ones, allows the electrostatic energies, including penetration, to be calculated at a much reduced cost. We also note that the penetration energy may provide the best route to an atom–atom anisotropic model for the exchange‐repulsion energy in intermolecular potentials. © 1994 by John Wiley & Sons, Inc.
Reversed stereochemical preference in binding of Ro 31‐8959 to HIV‐1 proteinase: A free energy perturbation analysis
Authors: Rao B. G. , Murcko M. A. 
Published: January 2005

AbstractRo 31‐8959 is a highly potent inhibitor of HIV‐1 proteinase in phase III clinical trials for treatment of AIDS. It is also the first subnanomolar inhibitor that demonstrated reversed stereochemical preference at the central hydroxyl group. Free energy perturbation calculations have been carried out to rationalize the preference for the R‐diastereomer by consideration of two models of the (weaker) S‐diastereomer. In the first model, the central hydroxyl group makes only one hydrogen bond with the active site aspartates, whereas the hydroxyl group in the second model makes at least three strong hydrogen bonds. Using the first model, the free energy difference in binding of Ro 31‐8959 and its S‐diastereomer is calculated to be 3.4 kcal/mol, which is in close agreement with the experimental value. Although the second model has a more favorable interaction with the active site aspartates compared to the first model, it has a higher energy N‐axial conformation at the decahydroisoquinoline group in P. We show here that the two contributions cancel each other and the two models of S‐diastereomer are predicted to have equivalent binding. The stereochemical preference in a hydroxyethylamine series of inhibitors appears to be affected by both intermolecular and intramolecular (conformational) energies. The binding data on the proline containing inhibitors are rationalized based on these results. © 1994 by John Wiley & Sons, Inc.
Stability of two‐dimensional crystalline aggregates of a protein studied by molecular dynamics
Authors: Higo Junichi , Yamaki Mariko , Hogyoku Michiru , Takahashi Takuya , Endo Shigeru , Nagayama Kuniaki 
Published: January 2005

AbstractTwo‐dimensional protein (ferritin) aggregates with a square lattice symmetry, which were formed within a thin liquid layer on a mercury surface, were studied by molecular dynamics (MD) simulation. For the simulation, the ferritin molecule was modeled by an assembly of 49 spheres, and the intermolecular interactions were given by simple formulae. During the simulation, molecules were confined within a layer, which corresponds to the thin liquid layer. An annealing MD simulation was done starting from a random molecular configuration within the layer, and aggregates with the square lattice symmetry were also obtained. To study the stability of aggregates, dissociation processes of the aggregates were analyzed using MD simulations at room temperature. Interactions between the nearest‐neighbor molecules were regarded as bonds. Mean bond energies and correlation coefficients between the bond energies were calculated from the MD trajectories. A decay profile according to the dissociation was obtained, yielding a dissociation rate constant. Buried bonds were stronger than peripheral bonds. The larger the aggregate size, the stronger the bond for each of the buried and peripheral bonds. A simple theoretical account, which is applicable to a general bonded network, was introduced to analyze the dynamics of the aggregates. © 1994 by John Wiley & Sons, Inc.
Application of a high‐performance, special‐purpose computer, GRAPE‐2A, to molecular dynamics
Authors: Higo Junichi , Endo Shigeru , Nagayama Kuniaki , Ito Tomoyoshi , Fukushige Toshiyuki , Ebisuzaki Toshikazu , Sugimoto Daiichiro , Miyagawa Hiroo , Kitamura Kunihiro , Makino Junichiro 
Published: January 2005

AbstractThe special‐purpose computer GRAPE‐2A accelerates the calculation of pairwise interactions in many‐body systems. This computer is a back‐end processor connected to a host computer through a Versa Module Europe (VME) bus. GRAPE‐2A receives coordinates and other physical data for particles from the host and then calculates the pairwise interactions. The host then integrates an equation of motion by using these interactions. We did molecular dynamics simulations for two systems of liquid water: System 1 (1000 molecules), and System 2 (1728 molecules). The time spent for one step of molecular dynamics was 3.9 s (System l), and 10.2 s (System 2). The larger the molecular system, the higher the performance. The speed of GRAPE‐2A did not depend on the formula describing the pairwise interaction. The cost performance was about 20 times better than that of the fastest workstations available today, and GRAPE‐2A cost only $22,000. © 1994 by John Wiley & Sons, Inc.
An algorithm for packing regular multistrand polypeptide structures by energy minimization
Authors: Gibson Kenneth D. , Scheraga Harold A. 
Published: January 2005

AbstractAn algorithm has been developed for packing polypeptide chains by energy minimization subject to regularity conditions, in which regularity is maintained without the addition of pseudoenergy terms by defining the energy as a function of appropriately chosen independent variables. The gradient of the energy with respect to the independent variables is calculated analytically. The speed and efficiency of convergence of the algorithm to a local energy minimum are comparable to those of existing algorithms for minimizing the energy of a single polypeptide chain. The algorithm has been used to reinvestigate the minimum‐energy regular structures of three‐stranded (L‐Ala)8, three‐stranded (L‐Val)6, five‐stranded (L‐Ile)6, and the regular and truncated three‐stranded (Gly‐L‐Pro‐L‐Pro)4 triple helices. Local minima with improved packing energies, but with essentially unchanged geometrical properties, were obtained in all cases. The algorithm was also used to reinvestigate the structures proposed previously for the I and II forms of crystalline silk fibroin. The silk II structure was reproduced with slightly improved packing and little other change. The orthorhombic silk I structure showed more change and considerably improved packing energy, but the new regular monoclinic silk I structure had considerably higher energy. The results support the structure proposed previously for silk II and the orthorhombic structure, but not the monoclinic structure proposed for silk I. © 1994 by John Wiley & Sons, Inc.
An application of the Miertus‐Scrocco‐Tomasi solvation model in molecular mechanics and dynamics simulations
Authors: Varnek A. A. , Wipff G. , Glebov A. S. , Feil D. 
Published: January 2005

AbstractThe point‐chart approximation of the Miertus‐Scrocco‐Tomasi solvation model (MST‐PC) based on a continuum representation of the solvent has been incorporated in force field calculations. Application in molecular mechanics (MM) involves conformational equilibria in solution: rotational isomers of ethylene glycol (I), 1,2‐difluoreothane (II), fluoroacetic acid (III), and representative conformers of macrocyclic receptors such as 18‐crown‐6 (IV), cryptand 2.2.2 (V), and t‐butyl‐calix[4]arenetetraamide (VI). Assessment of the MST‐PC results is based on the comparison with ab initio reactive field calculations (for I–III), with the continuum model of Still (W. C. Still et al., J. Am. Chem. Soc., 1990, 112, 6127) (for I–VI), and with average solute–solvent interaction energies obtained from molecular dynamics (MD) simulations with explicit solvent in water (I–VI) and in acetonitrile (IV–VI). It is demonstrated that the continuum solvent model qualitatively reproduces the trends in solvation energies in water. The few exceptions may be related to particular topological features of the solute. An improved discrete/continuum approach in which some first‐shell solvent molecules are considered as a part of the solute embedded in the dielectric continuum provides more realistic results, as is shown for VI in water. The MST‐PC model which mimics the solute–solvent electrostatic interaction only fails to reproduce conformationally dependent solvation energies in acetonitrile, in which the electrostatic contribution is relatively small compared to van der Waals interactions. Exploratory MD simulations within the continuum model in water are reported on urea and 18‐crown‐6. © 1995 by John Wiley & Sons, Inc.
Monte Carlo study of lipid membranes: Simulation of diparmitoylphosphatidylcholine bilayers in gel and liquid‐crystalline phases
Authors: Taga Tooru , Masuda Kazuhumi 
Published: January 2005

AbstractThe statistical properties of the bilayer membranes of diparmitoylphosphatidylcholine (DPPC) in the gel and liquid‐crystal phases were studied by Monte Carlo (MC) simulation using potential functions of the Lennard‐Jones, the simple Coulomb, and the bond torsion. The simulation was undertaken on a two‐dimensional periodic condition imposed on the bilayer model consisting of faithfully described molecules. The structure and ordering of the model bilayers accorded well with experiments, and the segment order parameters were in agreement with those of the nuclear magnetic resonance (NMR) experiments. The two kinds of lipid chains of DPPC do not equivalently behave in the bilayers, and chain 2 has lower ordering than chain 1. The order parameters of the first eight segments of chain 2 in the liquid‐crystal model are particularly small and are roughly constant. From electron density analysis, it has been observed that the liquid‐crystal bilayer has about one excess water molecule per one lipid molecule in comparison with the gel bilayer. The energy difference between the two bilayer models, taking account of the water contribution, is consistent with the latent heat of the phase transition. © 1995 by John Wiley & Sons, Inc.
A molecular mechanical model that reproduces the relative energies for chair and twist‐boat conformations of 1,3‐dioxanes
Authors: Howard Allison E. , Cieplak Piotr , Kollman Peter A. 
Published: January 2005

AbstractWe present molecular mechanics calculations on the conformational energies of several 2,2‐dimethyl‐trans‐4,6‐disubstituted‐1,3‐dioxanes. Previous studies by Rychnovsky et al.1 have suggested that the relative conformational energies of chair and twist‐boat forms of these 1,3‐dioxanes were poorly represented by the molecular mechanical models MM2* and MM3* (MacroModel2 implementations of MM2 and MM3) both when compared to experiment and to high‐level quantum mechanical calculations. We have studied these molecules with a molecular mechanical force field which features electrostatic‐potential‐based atomic charges. This model does an excellent job of reproducing the relative conformational energies of the highest level of theory (MP2/6‐31G*) applied to the problem. Furthermore, when empirically corrected using the MP2/6‐31G* relative conformational energies of the unsubstituted compound 2,2,4‐trimethyl‐1,3‐dioxane, the absolute energy differences calculated with this new model between the chair and twist‐boat conformers for five substituted compounds are within an average of 0.30 kcal/mol of the MP2/6‐31G* values. The correlation with experiment is also very good. One can, however, modify the initial molecular mechanical model with a single V1(OCOC) torsional potential and do an excellent job in reproducing the absolute conformational energies of the dioxanes as well, with an average error in conformational energies of 0.45 kcal/mol. This same torsional potential was independently developed by comparing ab initio and molecular mechanical energies of the molecule 1,1‐dimethoxymethane. Thus, we have succeeded in developing a general molecular mechanical model for 1,3‐dioxoalkanes. In addition, we have compared the standard MM2 and MM3 models with MM2* and MM3* (ref. 2) and have found some significant differences in relative conformational energies between MM2 and MM2*. MM2 has an improved correlation with the best ab initio data compared to MM2* but is still significantly worse than that found with lower‐level ab initio or AM1 semiempirical quantum mechanics or the new molecular mechanical model presented here. MM3 leads to conformational energies very similar to MM3*. Energy component analysis suggests that the single most important element in reproducing the conformational equilibrium is the electrostatic energy. This fact rationalizes the success of AMBER models, whose fundamental tenet is the accurate representation of quantum mechanically calculated molecular electrostatic effects. © 1995 by John Wiley & Sons, Inc.
An application of the reaction field theory to hydrated metal cations in the framework of the MNDO, AM1, and PM3 methods
Authors: Furuki Takao , Sakurai Minoru , Inoue Yoshio 
Published: January 2005

AbstractA reaction field theory, combined with the MNDO, AM1, and PM3 molecular orbital methods, was applied to hydration phenomena of metal cationic species. The first hydration shell was treated explicitly by using a supermolecular model, [M(H2O)n]m+, and its surrounding medium was described with a continuum dielectric. Hydration free energies were evaluated as a sum of the contributions from the electrostatic interaction with the bulk medium, the hydrated cluster formation, the cavity formation, and the vaporization of water molecules forming the cluster. As a whole, calculated hydration energies were in good agreement with the corresponding experimental data over various kinds of metal cationic species. © 1995 by John Wiley & Sons, Inc.