bluuebunny/crossref_metadata_2025_split 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

AbstractThe 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

AbstractThe 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

AbstractA 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

AbstractThe 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

AbstractThe 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

AbstractAt 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

AbstractA 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

AbstractA 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

AbstractUsing 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

AbstractOur 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

AbstractThe 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

AbstractAb 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

AbstractSpace‐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

AbstractA 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

AbstractA 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

AbstractComputer 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

AbstractWe 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

AbstractSINDO1 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

AbstractThe 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

AbstractMolecular 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

AbstractBenzene 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

AbstractAb 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

AbstractThe 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.