bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational properties and homolytic bond cleavage of organic peroxides. I. An empirical approach based upon molecular mechanics and ab initio calculations
Authors: Benassi Rois , Folli Ugo , Sbardellati Silvia , Taddei Ferdinando 
Published: January 2005

AbstractThe conformational features of a large number of hydroperoxides ROOH and peroxides ROOR′, where R and R′ are alkyl groups of different and increasing size and phenyl rings, including ortho substituted derivatives, were obtained from molecular mechanics calculations by employing a standard package. For the molecules of small molecular size, comparison was carried out with the results of ab initio calculations. Heats of formation were also obtained from molecular mechanics for hydroperoxides and peroxides: The values are, in general, overestimated. For the molecules containing the CF3 group, the calculated values are subject to large errors and heats of formation were obtained from ab initio total energies in the “atom equivalents” scheme. To estimate the homolytic dissociation energies of the different bonds in the peroxide molecules, heats of formation of R·, ·OR, and ·OOR radicals were employed and several of them had to be calculated. Different approaches were employed—molecular mechanics calculations, ab initio energies within the atom equivalent and isodesmic reaction schemes, and Benson's group additivity rule; values consistent within the different calculation methods were chosen for estimating dissociation energies. The bond dissociation energies indicate different trends in these molecules as a function of the nature of the R and R′ groups and the possible electronic effects operating in these molecules are discussed. © 1993 John Wiley & Sons, Inc.
Comparison of a posteriori and a priori BSSE correction schemes for SCF intermolecular energies
Authors: Valiron Pierre , Vibók Ágnes , Mayer István 
Published: January 2005

AbstractA systematic SCF study has been undertaken to compare the conventional a posteriori Boys–Bernardi BSSE correction scheme with our recent CHA/F method in which BSSE is excluded in a priori manner. Potential curves have been obtained for nine simple hydrogen‐bonded systems by using nine different basis sets for each. It is concluded that the difference between the a posteriori BB and the a priori CHA schemes diminishes much faster when the basis set improves than BSSE disappears from the uncorrected SCF results. This fact gives an additional confidence in the CHA results, permitting one to draw the explicit conclusion that, at the SCF level of theory, the a priori CHA/F scheme can be considered the ultimate solution of the BSSE problem for weakly bonded systems. © 1993 John Wiley & Sons, Inc.
Ab initio calculations on phosphorus compounds. II. Effects of disubstitution on ligand apicophilicity in phosphoranes
Authors: Wang Peng , Zhang Yala , Glaser Rainer , Streitwieser Andrew , Schleyer Paul von R. 
Published: January 2005

AbstractGeometry optimizations at the HF/3‐21G(*) and HF/6‐31G* levels of ab initio theory have been carried out for various isomers of model disubstituted phosphoranes PH3XY(X, YOH, CH3, NH2, and SH). Reasonable agreement was obtained between the optimized geometries and available crystal structure data for analogous compounds. The isomers were further characterized by frequency calculations. The MP2/6‐31G*//6‐31G* + ZPE energy data reveal that the interactions between the ligands are relatively small (0–4 kcal mol−1) for the most stable conformations of the isomers. Hence, for these conformations the apicophilicities (based upon monosubstituted phosphoranes) are approximately additive. The less stable PH3XY conformations are in general transition states or higher‐order saddle points, and their interligand interactions are larger in magnitude (up to 10 kcal mol−1); the results with these conformations suggest that apicophilicities may not be as additive for some highly substituted phosphoranes. © 1993 John Wiley & Sons, Inc.
Application of explicitly correlated Gaussian functions for calculations of the ground state of the beryllium atom
Authors: Schwegler Eric , Kozlowski Pawel M. , Adamowicz Ludwik 
Published: January 2005

AbstractThe electronic energy of atoms and molecules may be evaluated accurately by the use of wave functions where the interelectronic distances are explicitly present. In particular, explicitly correlated Gaussian‐type functions make these types of calculations feasible and computationally tractable even for more extended systems. The resulting multielectron integrals may be reduced to standard one‐ and two‐electron integrals that are readily evaluated. Initial calculations have been made for the Be atom where all four electrons were correlated at the same time. The preliminary results show that accurate results may be obtained. © 1993 John Wiley & Sons, Inc.
Ab initio copper–water interaction potential for the simulation of aqueous solutions
Authors: Cordeiro M. Natália D.S. , Gomes José A.N.F. 
Published: January 2005

AbstractA new ab initio effective two‐body potential that aims at mimicking the average copper–water interaction energy of the first solvation shell was developed. This new potential, together with the MCY water–water potential and a three‐body ion–water–water induction potential, is tested in simulations of gas‐phase clusters [Cu2+(H2O)20] and diluted solutions [Cu2+(H2O)200] at T = 298 K. The results of simulations with conventional ab initio pair potentials, with and without three‐body induction corrections, are also presented. The different types of copper–water interaction potentials are evaluated comparatively and the efficiency of the newly proposed effective pair potential is discussed. © 1993 John Wiley & Sons, Inc.
Molecular mechanics calculations (MM3) on sulfones
Authors: Allinger Norman L. , Fan Yi 
Published: January 2005

AbstractThe structures of several sulfones, including dimethyl sulfone, methyl ethyl sulfone, methyl vinyl sulfone, and diphenyl sulfone, have been fit with the MM3 force field to existing experimental data from electron diffraction and microwave spectroscopy. The vibrational spectra have also been fit for six of these compounds. The torsional parameters for the aliphatic sulfones were fit to ab initio 6‐31G data. Heats of formation were also fit. © 1993 John Wiley & Sons, Inc.
Calculation of hydrophobic interactions from molecular dynamics, surface areas, and experimental hydrocarbon solubilities
Authors: Hermann Robert B. 
Published: January 2005

AbstractUsing experimental solubilities and partial pressures for hydrocarbon solution in water and molecular dynamics calculations of hydrocarbon water interaction energies, hydrocarbon–water cavity potentials are obtained and then plotted vs. accessible surface area. The data used is mainly for aliphatic hydrocarbons, but benzene is included. Molecular dynamics calculations of pairs of hydrocarbon molecules together with the cavity potential curve are then used to obtain hydrophobic interaction free energies between the hydrocarbon pairs. While the cavity potential change is related to a change in surface area for hydrocarbon systems, the hydrocarbon–water interaction energy is not, so that the hydrophobic binding energy is not. The results are in agreement with previous results by a different method (R.B. Hermann, In Seventh Jerusalem Symposium on Quantum Pharmacology, E. Bergman and B. Pullman, Eds., D. Reidel, Dordrecht, 1974, p. 441) in that there is little or no solvent‐induced binding free energy between small hydrocarbon molecules in a dilute aqueous solution. It is proposed that the cavity potential vs. accessible surface area curve obtained here can be used together with OPLS parameters to calculate both hydrocarbon–water solvation free energies and hydrophobic interactions. © 1993 John Wiley & Sons, Inc.
A molecular mechanics study of alkyl peroxides
Authors: Chen Kuohsiang , Allinger Norman L. 
Published: January 2005

AbstractStudies have been carried out on alkyl peroxides with MM3 that have led to a parameter set that allows the calculation of geometries, energies, vibrational frequencies, and heats of formation for alkyl hydroperoxides (ROOH) and dialkyl peroxides (R1OOR2). The results obtained are in agreement with the available experimental and theoretical data. A similar, although less good, parameter set has been developed for MM2. © 1993 John Wiley & Sons, Inc.
Linear combination of Lanczos vectors: A storage‐efficient algorithm for sparse matrix eigenvector computations
Authors: Koslowski T. , Von Niessen W. 
Published: January 2005

AbstractWe present a storage‐efficient and robust algorithm for the computation of eigenvectors of large sparse symmetrical matrices using a Lanczos scheme. The algorithm is based upon a linear combination of Lanczos vectors (LCLV) with a variable iteration depth. A simple method is given to determine the iteration depth before the eigenvector computation is performed. Test calculations are reported for tight‐binding models of ordered and disordered 2‐D systems. The algorithm turns out to be reliable if an eigenvector residual less than 10−4 is required. We report benchmarks for various computers. Possible fields of application are discussed. © 1993 John Wiley & Sons, Inc.
Implementation of the direct SCF and RPA methods on loosely coupled networks of workstations
Authors: Feyereisen Martin W. , Kendall Rick A. , Nichols Jeff , Dame David , Golab Joseph T. 
Published: January 2005

AbstractThe use of a cluster of workstations as an alternative supercomputer resource is demonstrated using the ab initio direct SCF and RPA code DISCO. DISCO was implemented using several different mechanisms to achieve the requisite parallelization. The various parallel software mechanisms are characterized based upon several different criteria, including portability, ease of use, and relative efficiency. The application of direct SCF and RPA techniques to study the static polarizability of paranitroaniline is described. © 1993 John Wiley & Sons, Inc.
Theoretical investigations on thallium halides: Relativistic and electron correlation effects in T1X and T1X3 compounds (XF, C1, Br, and I)
Authors: Schwerdtfeger Peter , Ischtwan Josef 
Published: January 2005

AbstractRelativistic and electron correlation effects in thallium halides TlX and TlX3 (XF, Cl, Br, and I) are investigated by extensive ab initio configuration interaction calculations. Spin–orbit coupling is included at the Hartree–Fock level for the diatomic TlBr and TlI. At the best level of treatment of electron correlation (quadratic configuration interaction), the calculated molecular properties are in good agreement with experimental results, i.e., for the diatomic thallium halides deviations from experimental values are <0.06 Å for bond distances, <0.14 mdyn/Å for force constants, <35 kJ/mol for dissociation energies, and <0.3 D for dipole moments. The convergence of the Møller–Plesset series up to the fourth order is discussed. Two alternative structures of TlI3 are compared. At the Møller–Plesset level of theory, the trigonal planar structure with thallium in the oxidation state + 3 is the preferred gas phase arrangement compared with the bent arrangement containing a linear I unit and thallium in the oxidation state + 1, the difference being ca. 95 kJ/mol. Vibrational frequencies are predicted for all trigonal planar thallium(III) halides. © 1993 John Wiley & Sons, Inc.
Cumulative and discrete similarity analysis of electrostatic potentials and fields
Authors: Petke J.D. 
Published: January 2005

AbstractA new index suitable for computing molecular similarity based upon the similarity of molecular properties such as electrostatic potentials or electrostatic fields is presented in two forms. For one form of the present index, general conditions are established for which a linear measure of similarity is obtained. An illustrative example is provided in which the electrostatic field and electrostatic potential of guanine obtained from different wave functions are compared. © 1993 John Wiley & Sons, Inc.
Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides
Authors: Sokalski W.A. , Keller D.A. , Ornstein R.L. , Rein R. 
Published: January 2005

AbstractThe defects in atomic monopole models of molecular charge distribution have been analyzed for several model‐blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off‐center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N‐acetyl, N′‐methylamide‐blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed. © 1993 John Wiley & Sons, Inc.
AMBER force‐field parameters for guanosine triphosphate and its imido and methylene analogs
Authors: Cannon John F. 
Published: January 2005

AbstractParameters were derived for guanosine triphosphate (GTP) and GTP analogs suitable for the AMBER force field. Electrostatically derived net atomic charges and force parameters were extracted from MNDO semiempirical calculations. The later parameters came from fitting MNDO and AMBER atom–atom forces in a manner that is extensible to other compounds that lack sufficient vibrational spectral data. The geometric parameters for these compounds were obtained from model compounds in the Cambridge crystallographic data base. Dynamic simulations of Na4 GTP and Na2 Mg GTP of 140 and 100 ps, respectively, indicated a strong preference for a syn C2′ exo conformation in solution. © 1993 John Wiley & Sons, Inc.
Ab initio study of hydrogen bonding in the phenol–water system
Authors: Feller David , Feyereisen Martin W. 
Published: January 2005

AbstractThree hydrogen‐bonded minima on the phenol‐water, C6H5OH—H2O, potential energy surface were located with 3–21G and 6–31G** basis sets at both Hartree–Fock and MP2 levels of theory. MP2 binding energies were computed using large “correlation consistent” basis sets that included extra diffuse functions on all atoms. An estimate of the effect of expanding the basis set to the triple‐zeta level (multiple f functions on carbon and oxygen and multiple d functions on hydrogen) was derived from calculations on a related prototype system. The best estimates of the electronic binding energies for the three minima are –7.8, –5.0, and –2.0 kcal/mol. The consequences of uncertainties in the geometries and limitations in the level of correlation recovery are analyzed. It is suggested that our best estimates will likely underestimate the complete basis set, full CI values by 0.1–0.3 kcal/mol. Vibrational normal modes were determined for all three minima, including an MP2/6–31G** analysis for the most strongly bound complex. Computational strategies for larger phenol–water complexes are discussed. © John Wiley & Sons, Inc.
New method for the derivation of net atomic charges from the electrostatic potential
Authors: Su Zhengwei 
Published: January 2005

AbstractNet atomic charges are derived from a least‐squares fitting to electrostatic potentials at atomic sites. The method treats atoms in the molecule as having spherically averaged Hartree–Fock densities, the atomic densities overlapping with one another. The method has the advantage of best reproducing the electrostatic potentials at the atomic nuclei and avoiding the arbitrariness in choosing the points used in the fitting. We have written a FORTRAN program, CHELPN92 (Z. Su, Chemistry Department, SUNY at Buffalo, Buffalo, NY, 1992), based on the method and applied it to deuterated benzene, l‐alanine, d,l‐histidine, 2‐methyl‐4‐nitroaniline, and deuterated pyridinium‐1‐dicyanomethylide using the molecular geometry and electrostatic potentials from analysis of accurate X‐ray diffraction data. The derived charges are used to calculate the molecular dipole moments. While the charges from this method are in general significantly different from those from the kappa refinement [P. Coppens, T.N. Guru Row, P. Leung, E.D. Stevens, P.J. Becker, and Y.W. Yang, Acta Cryst. A, 35, 63 (1979)], the dipole moments obtained with the new method agree well with those from the kappa refinement. © John Wiley & Sons, Inc.
Characterization of force fields for lipid molecules: Applications to crystal structures
Authors: Williams Donald E. , Stouch Terry R. 
Published: January 2005

AbstractThe nonbonded portion of a force field for lecithins was characterized by application to the study of the crystal packing geometry and energetics of eight different molecules. The molecules were either lecithin fragments or chosen to isolate particular intermolecular features to test the accuracy of the force field specifically for those interactions. In particular, the hydrocarbon interactions, hydrogen bonding, electrostatics, and phosphate interactions were critiqued. The results support previous findings that indicated that this force field is reasonably accurate for lecithins. For all molecules, a minimum was found near the experimentally determined crystal structure. Using D‐glucitol as an example, it is shown that the structural effect of hydrogen bonding is better represented by a nonelectrostatic force‐field model than by a purely electrostatic model. Results obtained with glycerylphosphocholine and four smaller organic phosphate molecules suggest that further study of nonbonded interactions of phosphate groups is needed. © John Wiley & Sons, Inc.
Ab initio models for multiple‐hydrogen exchange: Comparison of cyclic four‐ and six‐center systems
Authors: Heidrich Dietmar , Van Eikema Hommes Nicolaas J. R. , Von Ragué Schleyer Paul 
Published: January 2005

AbstractHigh‐level ab initio calculations {QCISD(T)/6‐311 +G**//MP2(fu)/6‐31 +G**, with corrections for higher polarization [evaluated at MP2/6‐311 +G(3df,2p)] and ΔZPE//MP2(fu)/6‐31 +G**, i.e., comparable to Gaussian‐2 theory} indicate concerted mechanisms for double‐ and triple‐hydrogen exchange reactions in HF and HCl dimers and trimers, in mixed dimers and trimers containing one NH3, and in mixed dimers of HF, HCl, and NH3 with formic acid. All these reactions proceed via cyclic four‐ or six‐center transition structures, the latter being generally more favorable. Calculated activation barriers (ΔHd̊ at 0 K, kcal/mol) are 42.3 for (HF)2, 20.3 for (HF)3, 41.2 for (HCl)2, 25.6 for (HCl)3, 36.0 for NH3‐HF, 10.6 for NH3(HF)2, 19.9 for NH3‐HCl, 2.3 for NH3(HCl)2, 9.7 for HCO2H‐HF, 7.0 for HCO2H‐HCl, and 11.3, for HCO2H‐NH3. The barriers are lower for the more ionic systems and when more ion pair character is present. © John Wiley & Sons, Inc.
Ab initio SCF and Møller—plesset studies on hexafluorides of selenium and tellurium
Authors: Klobukowski Mariusz 
Published: January 2005

AbstractSCF and Møller–Plesset calculations were done for the systems AB6 (TeF6 and SeF6) and AB6E (TeF and SeF) to determine their relative stabilities and geometric structures. The SCF calculations show that both TeF (as expected) and SeF (despite a small central atom) possess nonoctahedral shapes. However, at the Møller–Plesset level only the TeF2−6 ion, studied with a large valence basis set, retains nonoctahedral geometry. The calculated structural parameters of the ion in C3v symmetry (the bond lengths are 2.212 and 1.975 Å and the bond angles are 104.9 and 83.4 °) differ considerably from the octahedral values (2.101 Å and 90.0°), yet the corresponding total energy is only about 1 kcal/mol smaller. The results show significant dependence of the computational predictions on the basis sets used and indicate the need to include electron correlation effects in the studies devoted to establishing the stereochemical activity of the lone electron pair. © John Wiley & Sons, Inc.
Partitioning the motion in molecular dynamics simulations into characteristic modes of motion
Authors: Dauber‐Osguthorpe Pnina , Osguthorpe David J. 
Published: January 2005

AbstractMolecular dynamics (MD) simulations result in a comprehensive description of molecular motion. However, to gain insight into the dynamic behavior of molecules it is important to be able to identify different types of motions and characterize them. We have developed a novel technique aimed at characterizing the motion of the system using digital signal processing techniques. The amplitudes and phases of the Fourier transform of the atomic fluctuations are used to define the characteristic modes of motion in the MD trajectory. This yields a pictorial description of the oscillatory motions in a manor analogous to normal‐mode (NM) analysis. The validity of this method has been tested on small molecules such as water, acetamide, and a blocked polyalanine in a helical conformation. The NMs obtained by diagonalizing the mass‐weighted second derivative matrix were combined to generate “NM trajectories” that served as well‐characterized test cases. Distinct characteristic modes can be extracted from both NM and MD trajectories. The modes extracted from the NM trajectories were identical to the original NMs. The modes extracted from the MD trajectories were in most cases highly correlated to the corresponding NM. However, intermixing of some of the modes occurred, particularly when conformational changes took place. This technique is flexible and can be applied to the molecular system as a whole or to a subset of atoms of interest. Fourier transform calculations are fast and therefore the analysis stage is not demanding in computational resources. Anharmonicity is included explicitly in the simulations and solvent can be included as well. © John Wiley & Sons, Inc.
Comparison of two force fields by molecular dynamics simulations of glucose crystals: Effect of using ewald sums
Authors: Kouwijzer M.L.C.E. , Van Eijck B.P. , Kroes S.J. , Kroon J. 
Published: January 2005

AbstractTo compare the GROMOS force field with one designed by Ha et al., molecular dynamics simulations of α‐D‐glucose anhydrate and monohydrate crystals were performed. Also, the long‐range interactions were calculated both with a cutoff approximation and with Ewald summations. The results are compared with results obtained experimentally by neutron and X‐ray diffraction. The force‐field parameters had been optimized with the cutoff approximation; this apparently led to worse results when the Ewald summations were used. However, in all simulations the symmetry was roughly preserved and the mean atomic coordinates and thermal parameters, bond angles, and dihedrals without hydrogen atoms were rather well reproduced. The dihedrals with hydrogen atoms exhibited conformational transitions, which resulted in a disordered hydrogen bonding scheme. In general, the GROMOS force field performed better than the Ha force field. © John Wiley & Sons, Inc.
Modeling of magic water clusters (H2O)20 and (H2O)21H+ with the PM3 quantum‐mechanical method
Authors: Jurema Marcus W. , Kirschner Karl N. , Shields George C. 
Published: January 2005

AbstractThe PM3 quantum‐mechanical method is able to model the magic water clusters (H2O)20 and (H2O)21H+. Results indicate that the H3O+ ion is tightly bound within the (H2O)20 cluster by multiple hydrogen bonds, causing deformation to the symmetric (H2O)20 pentagonal dodecahedron structure. The structures, energetics, and hydrogen bond patterns of six local minima (H2O)21H+ clusters are presented. © John Wiley & Sons, Inc.