bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ab initio study of the proton affinities of some heteroatomic rings: Imidazole, oxazole, and thiazole
Authors: Kabir Shahrzad , Sapse Anne‐Marie 
Published: January 2005

AbstractThe proton affinities of imidazole, oxazole, and thiazole rings, relevant to the binding of lexitropsins that contain these rings to the minor groove of DNA, are calculated using ab initio (Hartree–Fock) calculations. It is found that the proton affinities decrease in the order imidazole, oxazole, thiazole and that a methyl group substituent increases the proton affinity of imidazole, while a peptidic group decreases it.
A Monte Carlo simulation of free energy relationships for the electron transfer reaction between Fe+ and Fe2+ in water
Authors: González‐Lafont Angels , Lluch José M. , Oliva Antonio , Bertrán Juan 
Published: January 2005

AbstractA free energy barrier ΔF≠ = 174.2 kJ/mol for the self‐exchange electron transfer reaction model Fe+/Fe2+ in water has been calculated by combining Monte Carlo simulations and the statistical perturbation theory. We have shown that, even for those electron transfer reactions that present a very high free energy barrier of activation, the free energy curve behaves parabolically versus the reaction coordinate, which justifies the quadratic expression for the activation free energy done by Marcus.
Sixty‐atom carbon cages
Authors: Liu X. , Klein D. J. , Seitz W. A. , Schmalz T. G. 
Published: January 2005

AbstractThe enumeration of all 60‐atom carbon cages associated to trivalent polyhedra with five‐and six‐sided faces is addressed. This isomer problem is computationally solved to give 1790 cages, with a further resolution into subclasses of cages with differing numbers p of abutting pairs of pentagonal faces. The individual cages are generated, and then there are computed various graph‐theoretic invariants, including Hückel MO energies, HOMO‐LUMO gaps, Kekulé structure counts, and conjugated‐circuit counts. Associated properties as a function of p are reported and found to be in concert with earlier qualitative arguments. It is found that the most stable of these cages is the unqiue p = 0 Buckminsterfullerene structure.
Conformational sampling and ensemble generation by molecular dynamics simulations: 18‐Crown‐6 as a test case
Authors: Sun Yaxiong , Kollman Peter A. 
Published: January 2005

AbstractUsing the crown ether 18‐crown‐6 as a test system, molecular dynamics has been evaluated as a technique for conformational searching and thermodynamic ensemble generation. By running a series of 200 ps and 2 ns simulations, an “optimum” temperature range for conformational searching, i.e., the temperature at which one finds the largest number of low energy structures, was demonstrated to be dependent on the time interval at which one examines the structure. By considering conformational degeneracy and entropy with the rigid rotor harmonic oscillator approximation we have been able to demonstrate that the ensemble generated approaches thermodynamic equilibrium in about 6 ns of simulation. To our knowledge this is the first time this has been demonstrated for a complex organic molecule and it highlights the power and usefulness of molecular dynamics as a method for thermodynamic ensemble generation and conformational searching.
Conformational analysis of trehalose disaccharides and analogues using MM3
Authors: Dowd Michael K. , Reilly Peter J. , French Alfred D. 
Published: January 2005

AbstractEnergy surfaces for the relative orientations of the pyranosyl rings of α,α‐, α,β‐, and β,β‐trehalose and analogues were generated with MM3. Sixteen starting conformations of the rotatable side groups of α,β‐trehalose were considered, while only 10 conformations were needed for α,α‐ and β,β‐trehalose because of molecular symmetry. Energies were calculated at 20° increments of the two torsional angles of the glycosidic linkage, but otherwise the molecules were fully relaxed. The structure at the overall minimum for α,α‐trehalose agrees well with that found in crystal structures, and also agrees with interpretations of NMR and optical rotation data. The energy surfaces for the three trehaloses differ greatly from each other, but are each similar to those for the corresponding three 2‐(6‐methyltetrahydropyran‐2‐yloxy)6‐methyltetrahydropyrans. This suggests that linkage type (axial or equatorial) is more important than exocyclic substituents in determining trehalose conformations. A comparison with surfaces from the corresponding 5a‐carba trehalose analogues illustrates that the exo‐anomeric effect is important in determining disaccharide conformation.
Basis set and correlation energy dependence of geometry and harmonic frequencies of difluoroethane, CHF2CH3
Authors: Speis Martin , Buss Volker 
Published: January 2005

AbstractOptimum geometries and harmonic frequencies calculated at the Hartree–Fock and the MP2 level are reported for the fluorohydrocarbon CHF2CH3; basis sets employed range from STO‐3G to 6‐311G**. The significantly shortened CC distance of 1.50 Å is reproduced already with the simplest split‐valence basis set; the CF distance of 1.36 Å on the other hand needs MP2 correction at least at the double‐ζ or 6‐311G* level. Symmetry coordinates defined in terms of internal coordinates are in qualitative agreement with available experimental evidence. Even the best basis set yields frequencies that differ from experimental (anharmonic) values by up to 200 cm−1 indicating the well‐known necessity of including higher‐order force constants if quantitative agreement with experiment is to be achieved.
A concurrent algorithm for parallel calculation of eigenvalues and eigenvectors of real symmetric matrices
Authors: Carbo Ramon , Molino Lluís , Calabuig Blanca 
Published: January 2005

AbstractElementary Jacobi Rotations are used as the basic tools to obtain eigenvalues and eigenvectors of arbitrary real symmetric matrices. The proposed algorithm has a complete concurrent structure, that is: every eigenvalue‐eigenvector pair can be obtained in any order and in an independent way from the rest. Examples based on diagonally dominant real symmetric matrices are given.
Calculated structures and relative stabilities of furoxan, some 1,2‐dinitrosoethylenes and other isomers
Authors: Seminario Jorge M. , Concha Monica C. , Politzer Peter 
Published: January 2005

AbstractThe structures and relative stabilities of furoxan and some of its isomers, e.g., the 1,2‐dinitrosoethylenes, have been determined by means of ab initio Hartee–Fock and Møller–Plesset calculations. Geometries were optimized at the HF/3‐21G, HF/6‐31G* and MP2/6‐31G* levels, and subsequently used for computing MP2/6‐31G*, MP3/6‐31G*, and MP4/6‐31G* energies. The results are markedly affected by the inclusion of electronic correlation, which renders three of the isomers unstable. It also emphasizes the importance of a zwitterionic contribution to the structure of furoxan, which promotes ring‐opening through a cis 1,2‐dinitrosoethylene intermediate/transition state that has an MP4/6‐31G*//MP2/6‐31G* energy that is 31.6 kcal/mol above furoxan.
Davydov soliton dynamics: Initial state, boundary conditions, and numerical procedure
Authors: Förner Wolfgang 
Published: January 2005

AbstractThe performance of a Runge‐Kutta method of fourth order in dynamic simulations within Davydov's so‐called |D2〉 state ansatz is studied by comparison with analytical solutions available for two special cases. Further, the Runge–Kutta method is compared with the one‐step procedure used by Su and Schrieffer. A detailed analysis of the structure and energetics of Davydov solitons is given. The differences in the dynamics between open chain ends and periodic boundary conditions are also discussed. The properties of the soliton detector plot introduced by Lomdahl and Kerr are studied. Finally, three widely used initial states for Davydov soliton dynamics are compared.
Floating functions satisfying the hellmann—feynman theorem: Single floating scheme
Authors: Hirao K. , Mogi K. 
Published: January 2005

AbstractThe electrostatic calculation for molecules using approximated variational wave functions leads to well known difficulties connected with the application of the Hellmann‐Feynman (HF) theorem. This is due to the basis set inadequacies in the underlying calculations. This defect can easily be remedied by floating functions, whose centers are optimized in space. We can keep almost everything of the traditional wave function with a nuclear‐fixed basis set, but we apply single floating to ensure the HF theorem. Then, one can obtain a wave function obeying the HF theorem. This provides a great conceptual simplification and may lead to practical advantages. The single floating scheme, which retains one expansion center per nucleus, is successfully applied to a series of small molecules using SCF and CASSCF wave functions with sufficiently polarized basis sets.
Comparison of ab initio, semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems
Authors: Ferguson David M. , Gould Ian R. , Glauser William A. , Schroeder Stefan , Kollman Peter A. 
Published: January 2005

AbstractThe potential energy surfaces of four cyclic alkanes have been examined using molecular mechanics, semiempirical, and ab initio methods to determine if they produce mutually consistent results and investigate the source of any errors between the methods. The C5  C8 cyclic alkanes were chosen since these structures present a finite set of conformations and transition‐state geometries and are still within the computational time and memory limits of the quantum mechanical approaches. We also examined several conformations of 1,2‐dideoxyribose to determine the effect of heteroatoms on the results for the 5‐membered ring. The molecular mechanics and ab initio calculations are consistent in the relative energies and geometries determined for the conformers of all ring systems. While the semiempirical calculations yielded geometries consistent with the other methods (except for 5‐membered rings), the relative energies often deviated substantially. A decomposition analysis of the semiempirical and molecular mechanics energies revealed that the disparities are mainly due to errors in the 1‐center energies of the semiempirical calculations. The 2‐center bonding and nonbonding energies followed reasonable trends for the conformers. The core‐repulsion function, however, is suspected of producing anomalies. A minimum in the attractive Gaussian of this term at 2.1 Å for HH interactions partly explains the propensity of the 5‐membered rings to optimize to near planarity (decreasing 1,2‐diaxial hydrogen distances to 2.3 Å) and the underestimation of the relative energy of the boat structure of cyclohexane.
Locally implicit solution of a reaction‐diffusion system with stiff kinetics
Authors: Vasquez Desiderio A. 
Published: January 2005

AbstractThe Tyson‐Fife reaction‐diffusion equations are solved numerically using a locally implicit approach. Since the variables evolve at very different time scales, the resulting system of equations is stiff. The reaction term is responsible for the stiffness and the time step is increased by using an implicit method. The diffusion operator is evaluated explicitly and the system of implicit nonlinear equations is decoupled. The method is particularly useful for parameter values in which the equations are very stiff, such as the values obtained directly from the experimental reaction rate constants. Previous efforts modified the parameters on the equations to avoid stiffness. The equations then become a simplified model of excitable media and, for those cases, the locally implicit method gives a faster although less accurate solution. Nevertheless, since the modified equations no longer represent a particular chemical system an accurate solution is not as important. The algorithm is applied to observe the transition from simple motion to compound motion of a spiral tip.
Artificial redox enzymes. II. A computational chemistry study1
Authors: Tong Weida , Ye Hongping , Rong Ding , D'Souza Valerian T. 
Published: January 2005

AbstractA computational chemistry study of the artificial redox enzyme synthesized by covalently attaching flavin to cyclodextrins explains some of its properties. Calculations indicate that the flavin moiety covalently attached to cyclodextrin is not within the cavity of cyclodextrin. This result is consistent with the UV‐vis spectrum of the artificial enzyme. The calculations also indicate hydrogen bonds formed between the carbonyl groups of the catalytic functionality and the hydroxyl groups of cyclodextrin play a role in their most stable conformation. This explains the observed overall stability of these artificial enzymes compared to riboflavin. Electrostatic energies and solvation energies play a major role in the stability of the hosts and the orientation of guests included within the artificial enzymes. The rates of oxidation of various thiols catalyzed by the artificial enzyme can be explained by the relative distances between the sulfur atom of the substrates and C(4a) of the flavin moiety.
Conformational preferences for hydroxyl groups in substituted tetrahydropyrans
Authors: Zheng Ya‐Jun , Le Grand Scott M. , Merz Kenneth M. 
Published: January 2005

AbstractQuantum mechanical (ab initio and semiempirical) and force field calculations are reported for representative torsion potentials in several tetrahydropyran derivatives. The overall agreement between the various methods is quite good except that the AMBER torsion profiles are sensitive to the choice of atomic point charges. Using electrostatic potential (ESP) derived atomic point charges determined with the STO‐3G basis set we find that AMBER is able to match the best quantum mechanical results quite well. However, when the point charges are derived using the 6‐31G* basis set we find that scaling the intramolecular electrostatic nonbond interactions is necessary. AM1 does not work very well for these compounds when compared to the ab initio methods and, therefore, should only be used in cases when ab initio calculations would be prohibitive. Based upon our results we feel that any force field that makes use of 6‐31G* ESP derived atomic point charges will need to scale intramolecular interactions. Implications of scaling intramolecular interactions to the development of force fields based on 6‐31G* ESP derived atomic point charges are discussed. © 1992 by John Wiley & Sons, Inc.
Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3‐methylindole
Authors: Westbrook John D. , Levy Ronald M. , Krogh‐Jespersen Karsten 
Published: January 2005

AbstractProcedures have been developed to generate molecular electrostatic potentials based on correlated wave function from ab initio or semiempirical electronic structure programs. A new algorithm for point‐wise sampling of the potential is described and used to obtain partial atomic charges via a linear, least squares fit between classical and quantum mechanical electrostatic potentials. The proposed sampling algorithm is efficient and promises to introduce less rotational variance in the potential derived partial charges than algorithms applied previously. Electrostatic potentials and fitted atomic charges from ab initio (HF/6–31G* and MP2/6‐31G*) and semiempirical (INDO/S; HF, SECI, and SDCI) wave functions are presented for the electronic ground (S0) and excited (1Lb, 1La) states of 3‐methylindole. © 1992 by John Wiley & Sons, Inc.
Rapid estimation of charge distribution. II. Heteroatoms
Authors: Houser John J. , Klopman Gilles 
Published: January 2005

AbstractA rapid method for estimating CNDO charges in large data bases using a reparameterized Del Re method has been described previously. In this article the method is extended to saturated compounds containing B, N, O, F, Si, P, S, and Cl. Good results are obtained by forcing the Del Re δo parameter for each element to be linearly related to its Pauling electronegativity, but with the slopes and intercepts being different for second‐ and third‐row elements. With a test set of 17 compounds and 71 atoms, the CNDO charge was reproduced with an average deviation of ±0.03. The largest deviations, up to ±0.2, were observed for carbons having multiple F or Cl substituents and for sterically hindered atoms. © 1992 by John Wiley & Sons, Inc.
Molecular dynamics on a distributed‐memory multiprocessor
Authors: Lin S.L. , Mellor‐Crummey J. , Pettitt B.M. , Phillips G.N. 
Published: January 2005

AbstractDynamics simulations of molecular systems are notoriously computationally intensive. Using parallel computers for these simulations is important for reducing their turnaround time. In this article we describe a parallelization of the simulation program CHARMM for the Intel iPSC/860, a distributed memory multiprocessor. In the parallelization, the computational work is partitioned among the processors for core calculations including the calculation of forces, the integration of equations of motion, the correction of atomic coordinates by constraint, and the generation and update of data structures used to compute nonbonded interactions. Processors coordinate their activity using synchronous communication to exchange data values. Key data structures used are partitioned among the processors in nearly equal pieces, reducing the memory requirement per node and making it possible to simulate larger molecular systems. We examine the effectiveness of the parallelization in the context of a case study of a realistic molecular system. While effective speedup was achieved for many of the dynamics calculations, other calculations fared less well due to growing communication costs for exchanging data among processors. The strategies we used are applicable to parallelization of similar molecular mechanics and dynamics programs for distributed memory multiprocessors. © 1992 by John Wiley & Sons, Inc.
Analysis of the gas‐phase addition of water to formaldehyde: A semiempirical and ab initio study of bifunctional catalysis by H2O
Authors: Ventura Oscar N. , CoitiñO Elena L. , Lledós Agustí , Bertran Juan 
Published: January 2005

AbstractSemiempirical AM1, MNDO‐PM3, and MNDO/M, as well as ab initio Hartree–Fock and Möller–Plesset calculations using the 4‐31G, 6‐31G(d,p), and 6‐31 +G(d,p) basis sets have been done on the water‐assisted addition of water to formaldehyde. ab initio methods predict a reduction of 30% of the bimolecular ΔG0,‡ (from 48 to 33 kcal/mol) when an ancillary water molecule is used as catalyst. AM1 and MNDO‐PM3 predict anticatalysis instead; ΔG0,‡ for the termolecular addition is larger than the one for the bimolecular reaction. MNDO/M predicts a modest decrease, from 42 to 39 kcal/mol. We conclude that, as predicted by the ab initio calculations, there is a bifunctional catalysis caused by the ancillary water. Two of the semiempirical methods are qualitatively (and all of them quatitatively) in disagreement with this conclusion. © 1992 by John Wiley & Sons, Inc.
Ab Initio investigation of the structures and stabilities of CH2N2, CHFN2, and CF2N2 isomers: Important consequences of MP2 optimizations
Authors: Boldyrev Alexander I. , Schleyer Paul v. R. , Higgins D. , Thomson Colin , Kramarenko Sofia S. 
Published: January 2005

AbstractAb initio calculations of the potential energy surfaces of CH2N2, CHFN2, and CF2N2 at MP4SDTQ/6‐31G*//MP2(full)/6‐31G* reveal several surprising features. While diazomethane is more stable than diazirine, only the three‐membered ring forms of the fluorine‐substituted isomers are known experimentally. We find fluorodiazomethane and difluorodiazomethane not to be viable species: They have no barriers toward exothermic dissociation into N2 and CHF or CF2, respectively. In contrast, the three‐membered ring isomers, fluorodiazirine and difluorodiazirine, have high barriers toward dissociation despite being high in energy. Diazomethane bends easily; a nonplanar Cs minimum is found at MP2(full)/6‐31G* but C2v symmetry is preferred at QCISD/6‐31G*. © 1992 by John Wiley & Sons, Inc.
General expression for the density dependence of the mori coefficients
Authors: Morales Juan J. , Nuevo María J. 
Published: January 2005

AbstractThe particular expression that relates the first Mori coefficients of the solvent particles with the solute particles as a function of their masses m1 and m2 is generalized to the case of the solute particle also having a different volume. The resulting density relationship, in terms of the mass factor M(m2) and coupling constants CD, is also valid for the second Mori coefficients and for two‐ and three‐dimensional system. © 1992 by John Wiley & Sons, Inc.
Study of hydrogen bonding interactions relevant to biomolecular structure and function
Authors: Zheng Ya‐Jun , Merz Kenneth M. 
Published: January 2005

AbstractAb initio molecular orbital calculations were used to study hydrogen bonding interactions and interatomic distances of a number of hydrogen bonded complexes that are germane to biomolecular structure and function. The calculations were carried out at the STO‐3G, 3‐21G, 6‐31G*, and MP2/6‐31G* levels (geometries were fully optimized at each level). For anionic species, 6‐31 + G* and MP2/6‐31 + G* were also used. In some cases, more sophisticated calculations were also carried out. Whenever possible, the corresponding enthalpy, entropy, and free energy of complexation were calculated. The agreement with the limited quantity of experimental data is good. For comparison, we also carried out semiempirical molecular orbital calculations. In general, AM1 and PM3 give lower interaction enthalpies than the best ab initio results. With regard to structural results, AM1 tends to favor bifurcated structures for OH‐O and NHO types of hydrogen bonds, but not for hydrogen bonds involving O‐HS and S‐HO, where the usual hydrogen bond patterns are observed. Overall, AM1 geometries are in general in poor agreement with ab initio structural results. On the other hand, PM3 gives geometries similar to the ab initio ones. Hence, from the structural point of view PM3 does show some improvement over AM1. Finally, insights into the formation of cyclic or open formate–water hydrogen bonded complexes are presented. © 1992 by John Wiley & Sons, Inc.
Molecular dynamics simulation of a poly(oxyethylene) chain dissolved in benzene
Authors: Depner M. , Schürmann B.L. 
Published: January 2005

AbstractMolecular dynamics simulations of pure benzene and a poly(oxyethylene) chain in benzene are performed. The simulation of pure benzene is found to agree excellently with previous simulations despite using a different force field. A comparison is made between the results of simulations of the poly(oxyethylene) chain in benzene and in water and of stochastic simulations with respect to mean torsional angles, trans/gauche fractions, and transition rates. Characteristic deviations are found for the simulation in water and explained by specific atomic interactions, while there is satisfactory agreement with a stochastic simulation based upon the simple Langevin equation using a friction coefficient of 1 ps−1. The characteristic ratio of poly(oxyethylene) in benzene is calculated on the basis of the rotational isomeric state model. © 1992 by John Wiley & Sons, Inc.
An electron repulsion integral compression algorithm
Authors: Fülscher Markus P. , Widmark Per‐Olof 
Published: January 2005

AbstractA data compression algorithm for packing/unpacking floating point numbers is presented. The method has been used to compress large volumes of data commonly generated in ab initio quantum mechanical calculations. To retain an accuracy of 10−6 Hartree on the final energy, the required file space needed is approximately half its original size whereas the CPU time required to solve the Hartree–Fock self‐consistent field equations increases with 30–60%. © 1993 John Wiley & Sons, Inc.