bluuebunny/crossref_metadata_2025 huggingface dataset:
A theoretical study of paths for decomposition and rearrangement of dihydroxycarbene
Authors: Feller David , Borden Weston Thatcher , Davidson Ernest R.
Published: January 2005

The transition states for fragmentation of dihydroxycarbene [C(OH)2] to H2 and CO2 and for the rearrangement of this carbene to formic acid were located by ab initio calculations. The relative energies of the transition states were determined at several levels of theory and the basis set dependence of the energies is discussed. At the best level of theory; using a basis set of double‐zeta quality augmented by polarization functions and with the inclusion of extensive CI, we found that the transition state for fragmentation was considerably higher in energy than that for rearrangement. This finding is at variance with the predictions of the Woodward‐‐Hoffmann rules because fragmentation represents an “allowed” reaction, whereas rearrangement is “forbidden.” In conformity with the Woodward–Hoffman rules, the transition state for rearrangement was found to be close in energy to H· + ·CO2H. The even higher energy of the transition state for concerted fragmentation to H2 and CO2 is attributed to the need for the latter fragment to remain substantially bent in order to permit H2 formation while maintaining a modicum of OH bonding. Difficulties in locating the transition state for concerted fragmentation are discussed and a new method for finding transition states is proposed.
The electrostatic potential of yeast tRNAPhe. II. The potentials of the phosphate groups in their various conformational states
Authors: Lavery Richard , De Oliveira Marcal , Pullman Bernard
Published: January 2005

The range of conformational states of the phosphate groups observed in the published crystal structure of tRNAPhe is used as the basis for theoretical studies on the effect of conformation on the electrostatic potentials of these moieties. Deductions concerning the influence of these effects on the potential of a complete tRNAPhe macromolecule are presented.
Reactions involving CO2, H2O, and NH3: The formation of (i) carbamic acid, (ii) urea, and (iii) carbonic acid
Authors: Buckingham A. D. , Handy N. C. , Rice J. E. , Somasundram K. , Dijkgraaf C.
Published: January 2005

A complete understanding of the synthesis of urea, (NH2)2CO, from NH3, CO2, and H2O remains an unsolved problem. It is considered that the formation of the intermediate ammonium carbamate (or the equivalent carbamic acid) takes place through the interaction of neutral species, and that this part of the synthesis is open to ab initio computations. Such calculations are reported on the formation of carbamic acid from NH3, CO2, and H2O. We have also investigated the formation of carbonic acid from CO2 and H2O showing that the six‐membered ring transition state is non‐planar, in contradiction with earlier reported calculations.
Ab initio determination of the proton affinities of small neutral and anionic molecules
Authors: Defrees D. J. , McLean A. D.
Published: January 2005

The proton affinity of a molecule in the gas phase is a fundamental measure of its basicity and is the factor controlling the course of many ion‐molecule reactions. In this article, ab initio molecular orbital theory at the MP4/6‐311 ++ G(3df, 3pd) level of theory is demonstrated to predict proton affinities (PA's) for small neutral and anionic bases to within 2 kcal mol−1. Furthermore, the errors are random, indicating that there are likely no systematic errors in either the experimental or theoretical PA's. Also, this level of theory is used to calibrate less sophisticated theoretical models which are suitable for larger molecules; the MP4/6‐311 ++ G(2d, 2p) and MP2/6‐311 ++ G(d, p) theoretical models should be particularly useful. A procedure for predicting the vibrational frequencies for anions is proposed and applied to CH3−, NH2−, OH−, and CN−.
An Efficient Method for using Molecular Symmetry. In Advance Selection of Zero Integrals
Authors: Kozmutza C. , Ozoróczy Zs.
Published: January 2005

The molecular symmetry has previously been used in an effective way for the reduction of the number of two‐electron integrals to be calculated. Here the method is further developed in such a way that the zero integrals due to the molecular symmetry can be easily selected in advance. It is pointed out, that this method, without using indices for the integrals does not need extra computational effort. The gain in computer time has been shown in the case of normal saturated hydrocarbons.
An empirical potential function for metal centers: Application to molecular mechanics calculations on metalloproteins
Authors: Vedani Angelo , Dobler Max , Dunitz Jack D.
Published: January 2005

At present, most molecular mechanics programs that model metalloproteins do not allow for specific geometric requirements at metal centers. An analysis of small‐molecule crystal structures containing four‐, five‐, and six‐coordinated zinc, retrieved from the Cambridge Structural Database (CSD), leads to a new metal‐center potential function for use in molecular mechanisc programs. This potential function includes as variables the metal‐ligand separations and the angles subtended at the metal and allows specifically for distortions from frequently occurring types of coordination geometries (e.g. tetrahedron square pyramid, trigonal bipyramid, and octahedron). The combination of such a metal‐center potential function and one for hydrogen bonds allowing for Ione‐pair directionality makes monopole electrostatic contributions to the force‐field energy superfluous, thus circumventing many problems associated with the assignment to the force‐field energy superfluous, thus circumventing many problems associated with the assignment of atomic apartial charges and a dielectric constant. The molecular mechanics program ‘YETI’, containing both types of potential functions, has been used to refine details of substrate binding of 16 complexes of human carbonic anhydrase II with small molecules. The stereochemistry of the refined complexes is in good agreement with data retrived from the CSD and hence allows realistic structure activity relationships.
Conformational analysis of the sixteen C(4)‐C(6) and C(4)‐C(8) linked dimers of (+)‐catechin and (−)‐epicatechin
Authors: Viswanadhan V. N. , Mattice Wayne L.
Published: January 2005

A conformational analysis has been performed for sixteen dimers of (+)‐catechin and/or (−)‐epicatechin using molecular mechanics (MM2). Monomer units are linked by 4α‐6, 4α‐8, 4β‐6, and 4β‐8 bonds. THe four possible combinations of (+)‐catechin and/or(−)‐epicatechin are used for each bonding pattern. The objectives are characterization of (1) the two rotational isomers at the bond between the two monomer units and (2) the conformations of the heterocyclic rings. There is a twofold rotation about the bond between monomer units. Differ4ences in the energies at the two minima range from a few tenths of a kcal/mol to several kcal/mol, depending on the dimer Heterocyclic rings occupy a range of conformations that can be described as half chairs with varying degrees of distoration toward C(2) or C(3) sofas. The more frequent distortion is toward the C(2) sofa. Interconversion between most of the heterocyclic ring conformations can be obtained by coordinated motion of C(2) and C(3), over a range of about 40 pm, with respect to the mean plane of the fused aromatic ring system.
Improving the flexible molecular fitting technique using distance matrices
Authors: Lejeune J. , Michel A. , Vercauteren D. P.
Published: January 2005

A new program for the molecular superposition of flexible molecules, IFMFIT (Improved or Interactive Flexible Molecular Fit), is presented. The essential new feature involves a complete revision of the representation of molecular structures making use of the briefly discussed Distance Matrix algorithm. A comparison is given between the input mode required by the original FMFIT program and that of our version as exemplified by the superposition of (R)‐chrysanthemic acid and (S)‐3‐methyl‐2‐(parachlorophenyl)‐butyric acid. This example demonstrates the superiority and the user‐interactive character made possible by our IFMFIT version.
Hydration structures and energetics of phospholipid
Authors: Kim Kwang S. , Clementi E.
Published: January 2005

Using previously reported ab initio potentials of the intermolecular interaction energies of phospholipid (PL), Lysophosphatidyl Ethanolamine, with one Na+ ion and one water molecule, we performed Monte Carlo simulations for PL‐water and PL‐Na+‐water systems. Water‐water and PL‐water interaction energetics of PL hydration sites are analyzed to understand, in a qualitative way, why the PL head part shows hydrophilicity and the tail part shows hydrophobicity. The interaction of Na+ with PL, as well as the interaction of water with PL, is visualized from the analysis of the hydration structures near PL, and the radial distribution functions are analyzed for selected hydration sites. The PL molecule shows much stronger interaction with Na+ than with water. The Na+ ion is likely to be strongly bound to PO, even to the extent of being trapped, whereas, for water, there exist two strong binding regions near NH and PO. Three water molecules near NH are much more strongly bound than four water molecules near the double‐bonded oxygens of PO. The hydrogens of CH2 adjacent to NH show somewhat strong hydrophilicity, while the hydrogens of CH2 adjacent to PO does not show such characteristics. The CH2 groups at the PL tail part give repulsive interactions with water molecules, showing hydrophobicity. Water molecules near the PL tail are stabilized only by water‐water interactions.
Centrifugal distortions in molecules: An ab initio approach with application to ozone
Authors: Lohr Lawrence L. , Helman A. J.
Published: January 2005

Our procedure for employing analytical gradients of ab initio potential energy hypersurfaces in the description of centrifugally distorted molecules is applied for the first time to an asymmetric top, namely ozone. Both single determinantal (HF/6‐31G*) and analytically fitted multiconfigurational self‐consistent field surfaces were utilized. The focus of the HF/6‐31G* study is upon the centrifugal distortion pathway. Quartic centrifugal spectroscopic coefficients are obtained in both cases and are in reasonable agreement with experiment.
Chemical applications of topology and group theory. 23. A comparison of graph‐theoretical and extended Hückel methods for study of bonding in octahedral and icosahedral boranes
Authors: King R. B.
Published: January 2005

The graph‐theory derived model for the bonding topology in the globally delocalized polyhedral boranes B6H62− and B12H122− is evaluated by comparison of the energies of the core molecular orbitals with those obtained by the 1962 LCAO‐MO extended Hückel calculations of Hoffmann and Lipscomb. Of particular interest is how well the complete graphs K6 and K12 used in the graph‐theory derived model approximate the bonding topologies of the unique internal orbitals (radial orbitals) of the octahedron and icosahedron, respectively. In the case of the B6H62− octahedron the single positive eigenvalue of the K6 graph corresponds to the results from the extended Hückel calculations. In addition, the parameters from the latter calculations indicate a ratio of 0.625 for the overlap of the unique internal orbitals of the trans atom pairs relative to cis atom pairs as compared with unity implied by an unweighted K6 graph. In the case of the B12H122− icosahedron the graph‐theory derived model is far less satisfactory since the single positive eigenvalue of the K12 graph disagrees with the four bonding core molecular orbitals (an A1g and three triply degenerate T1u molecular orbitals) found by the extended Hückel calculations after removing the effect of the mixing of core and surface bonding orbitals corresponding to the same irreducible representations. However, this core‐surface orbital mixing raises the energy of the triply degenerate T1u core molecular orbitals to antibonding levels so that the graph‐theory derived model fortuitiously gives correct skeletal electron counts for the regular icosahedron despite this fundamental error.
Computational studies of 1,2‐dithiete and dithioglyoxal
Authors: Goddard John D.
Published: January 2005

Ab initio calculations are reported on the energies, geometries, vibrational frequencies, and ionization potentials of the H2C2S2 isomers: 1,2‐dithiete, cis‐dithioglyoxal, and trans‐dithioglyoxal. In contrast to most earlier computations, the results of this work indicate that 1,2‐dithiete and cis‐dithioglyoxal lie close in energy (within 3 kcal/mol) with the dithial more stable. Trans‐dithioglyoxal is found to be 4.1 kcal/mol more stable than the cis isomer and faces a barrier to internal rotation of 5.5 kcal/mol. The predicted rotational constants for 1,2‐dithiete agree within ∼0.05 GHz with the experimentally observed values thus lending credence to the predictions for cis‐dithioglyoxal (Ae 14.30683, Be 2.46324, Ce 2.10143 GHz). Vibrational frequencies are given as potential aids to the identification of these molecules. 6‐31G* ΔSCF calculations predict that at low energies (8 to 13 eV) the photoelectron spectra of 1,2‐dithiete, cis‐dithioglyoxal and trans‐dithioglyoxal should be similar.
Discrete models of growth and dynamical percolation in chemistry
Authors: Fraser Simon J.
Published: January 2005

Space‐time lattice (cellular automaton) models of pattern formation and growth are described. Suitable local rules for automation evolution represent the spreading of wave fronts of activity in an excitable medium. A random distribution of seeds produces expanding rings that fuse and are annihilated. The seeding density, pA, is used as a scaling parameter to give unique, reduced dynamics in an arbitrary dimension d. For d = 2, in this (continuum) picture, the rings fuse globally (percolate) at a critical instant, t̂c = 0.45. For the unscaled time evolution, dynamical percolation is examined in the pA × t plane. A swath of these percolating states is found. On the “explosion” boundary of this swath the percolation cluster just forms; on the “implosion” boundary it breaks up. Using a small‐sample method the fractal dimension of the critical (boundary) cluster is estimated to be 1.9 (±0.01). Also percolation for continuously emitting seeds, which produce “discs” of activity, is related to ring evolution.
The application of strictly localized geminals to the description of chemical bonds
Authors: Poirier Raymond A. , Surján Péter R.
Published: January 2005

A theory is developed in which closed‐shell molecules are viewed as systems of weakly interacting chemical bonds. Composite‐particle creation operators obtained by an appropriate quasiparticle transformation are used to create the wave function of two‐electron bonds. These quasiparticles are bosons, since they are composed of two electrons, but the total many‐electron wave function is properly antisymmetric. The internal structure of the quasi‐Bose‐particles is affected by inductive interbond interactions. Delocalization and dispersion interactions between different bonds are neglected, thus the approach corresponds to a first‐order many‐body PT (Perturbation Theory) with a correlated, but fully localized, reference state. The whole formalism is developed ab initio. The nonorthogonality problem is handled by a biorthogonal formulation. To illustrate the effectiveness of the model, numerical calculations are reported.
Quasiperiodization in classical hyperchaos
Authors: Rössler O. E. , Hoffmann M.
Published: January 2005

A 1D gas with maximal chaos in the sense of Sinai is considered. An idea originally proposed by Gibbs (that particle indistinguishability imposes a well‐defined symmetry having nontrivial quantitative implications) is investigated in the light of this example. A new quantitative implication of the Gibbs paradox, quasiperiodization, is found to apply to the present system.
Towards a quantum chemical software package utilizing transferable fragments as molecular building blocks
Authors: Náray‐Szabó Gábor , Kramer György , Nagy Péter , Kugler Sándor
Published: January 2005

Computer programs have been developed or are under development for the IBM personal computer that enable their users to get information on atomic charges, electrostatic potentials, conformational and other properties of molecular systems containing H, C, N, O, F, Si, P, S, or Cl atoms. The zero‐order wavefunction is constructed of strictly localized molecular orbitals with fixed atomic orbital coefficients. The wave function can be refined by optimizing these coefficients, i.e., considering inductive effects via a coupled set of 2 × 2 secular equations within the CNDO/2 approximation. Delocalization and exchange effects are accounted for by expanding the wavefunction on a basis of the aforementioned strictly localized orbitals, instead of conventional atomic orbitals, and solving the corresponding SCF equations. Our method has been applied to the study of large systems. We calculated the electrostatic field of the complex of β‐trypsin and basic pancreatic trypsin inhibitor and it has been found that strong field regions more or less coincide with hydration sites. A further potential application of protein electrostatic fields is in NMR spectroscopy. We found a linear correlation between CαH or backbone NH proton chemical shifts and the protein field at the site of the corresponding proton. At last, we propose a simple method to mimic the bulk around atomic clusters modeling crystalline and amorphous silicon. Based on this method we found a linear correlation between atomic net charges and bond angle distortions in silicon clusters with 35 atoms.
Towards a valence‐orbital/bond‐orbital description of biochemical H‐bonds from ab initio calculations
Authors: Zuccarello Felice , Re Giuseppe Del
Published: January 2005

We have studied the system NH3…H+…HNCH‐CHCH2, which is a model for an enzymatic site characterized by an important pi‐electron contribution, with the aim of contributing to the molecular orbital theory of H‐bridge formation and proton transfer. Ab initio canonical orbitals from STO‐3G and 4.31G bases have been determined for various geometrical configurations, and analyzed in terms of Mulliken's Modified Valence Atomic Orbitals obtained by suitable contraction. Also, the orbital correlation diagram has been obtained and discussed. At least two sigma MO's can be considered specific of the H‐bond: they involve the expected hybrids giving rise to stereoelectronic effects associated with the lone pairs of the two heavy atoms. Population analysis suggests that the bridge hydrogen changes its population very little during its motion along the bridge, although its in situ atomic orbital does not change: this means that it acts essentially as a relay center in charge transfer between the two moieties of the H‐bonded complex. As expected on intuitive grounds, charge transfer involves essentially the sigma cores.
Application of SINDO1 to sulphur compounds
Authors: Jug Karl , Iffert Rüdiger
Published: January 2005

SINDO1 calculations are presented for ground state geometries, heats of formation, ionization potentials and dipole moments. These calculations are based on a new parametrization of SINDO1 for second‐row elements which features inclusion of 3d orbitals and zero point energies. The comparison shows an improvement over MNDO, especially for hypervalent sulphur compounds.
Systematic drug receptor mapping: A new approach to the analysis of conformational energy calculations of flexible molecules with application to dopaminergic and adrenergic agonists
Authors: Sanathanan Lilly , Danaher Elizabeth , Kim Ki‐Hwan , Martin Yvonne
Published: January 2005

The computer program PRODIS is used to find low energy conformations of flexible molecules by searching the potential energy surface(s) of one or more torsion angles via rigid rotation. The n‐dimensional grid of energy versus torsion angles is then converted to a Boltzman probability distribution, with the probability being represented not as a function of torsion angle, but rather a distance between two atoms. These atoms are chosen by comparison with a known, active analogue in which certain atoms have previously been determined as requirements for drug activity. PRODIS produces a list of low energy conformations, their corresponding interatomic distances and the Boltzman probability for each distance ±0.125, as well as the total probability for each conformation. The user also specifies a target interatomic distance and range (usually derived from a more rigid analogue) for which PRODIS lists all conformations and their Boltzman probability that meet this distance.
Molecular orbital calculations on solvents and other small molecules: Correlation between electronic and molecular properties ν, αMOL, π*, and β.
Authors: Lewis David F.V.
Published: January 2005

Molecular orbital calculation by the MINDO/3 method are reported for 50 compounds used as solvents in chemical reactions. Relationships between various parameters of electronic structure and molecular properties such as dipole moment, polarizability and Taft solvent parameters are presented. Comparison between experimental values of π* and calculated values is given.
Benzene, aromatic rings, van der Waals molecules, and crystals of aromatic molecules in molecular mechanics (MM3)
Authors: Allinger Norman L. , Lii Jenn‐Huei
Published: January 2005

Benzene has been studied with the MM3 force field, first as a monomer, then as a van der Waals dimer, then in the crystal. The non‐bonded aromatic portion of the MM3 force field has been derived to fit reasonably well the known properties for the above. The force field includes dipoles of 0.6 and 0.9 D for CH and CC bonds, respectively. The benzene dimer is calculated to have a lower energy when perpendicular, than when eclipsed face to face. The crystal of benzene has a herringbone pattern with correct cell constants and heat of sublimation, while hexamethylbenzene as the dimer and in the crystal has a skewed‐stack of pancakes type structure, as observed.
An investigation of the relative stabilities of the isomers of CF2N2: Comparison of ab initio and MNDO calculations
Authors: Glidewell Christopher , Higgins Derek , Thomson Colin
Published: January 2005

Ab initio SCF calculations at the HF/3‐21G level and semi‐empirical MNDO calculations have been used to locate the stationary points on the CF2N2 energy surface. Perfluorodiazomethane is predicted to be most stable isomer, but perfluorodiazirine is predicted to lie only ca 41 kJ higher in energy at the SCF level. There are significant differences between the ab initio and MNDO results for the ordering of some of the isomers. Frequency calculations give results in good agreement with the limited experimental data on these molecules.
Determination of the water geometry in violuric acid monohydrate with a Monte Carlo simulation
Authors: Onuchic J. N. , Corongiu G.
Published: January 2005

The positions and orientations of water molecules in violuric acid crystals have been determined with the Metropolis Monte Carlo method. The interaction potentials between water and violuric acid needed in the simulation have been developed using ab initio calculations corrected for the basis set superposition error with the C.P. technique and fitted to atom‐atom pairwise potentials. The agreement between experimental data and simulation results is good, proving that the interaction potentials can be used with confidence.
Intermediate water structures in solution of Nα‐acetyl‐N‐methylphenylalaninamide
Authors: Kim Seungmoak , Yoon Chang No , Jhon Mu Shik
Published: January 2005

Intermediate 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

A 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

The 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

The 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

In 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

A 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

YETI, 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

A 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

Formulas 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

In 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.
Bivariate interpolation for experimental designs
Authors: Silver G. L.
Published: January 2005

Two new methods of bivariate interpolation suitable for experimental designs are summarized. The methods use experimental data obtained in usual manner. The programs are short and rapid and are often more accurate on test functions than the standard method.
Orbital electronegativity and analytical representation of atom valence state energy
Authors: Labanowski Jan K. , Dammkoehler Richard A. , Motoc Ioan
Published: January 2005

An 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

We 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

The 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

A 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

The 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

A 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

We 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

The 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

Using 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

Extended 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

A 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

The 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.