摘要:

AbstractA common problem in the solution of the Poisson–Boltzmann equation using finite difference methods is the self‐energy of the system, also known as the grid energy. Because atoms are typically modeled as a point charge, the infinite self‐energy of a point charge is likewise modeled. In this article, a simple, alternate treatment of atomic charge is described where each atom is represented as a sphere of uniform charge. Unlike the point charge model, this method converges as the grid spacing is reduced. The uniform charge model generates the same electrostatic field outside the atoms. In addition, the use of fine grids reduces the variations in the potential due to variations in the position of atoms relative to the grid. Calculations of Born ion solvation energies, small‐molecule solvation energies, and the electrostatic field of superoxide dismutase are used to demonstrate that this method yields the same results as the point charge model. © John Wiley&S

ISSN:0192-8651    

DOI:10.1002/jcc.540141202

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractA set of simple models of hydrogenated amorphous silicon (a‐Si:H) consisting of hypothetical silane molecules with diamond or similar lattices was studied by the semiempirical AM1 method. Densities of states and infrared spectra were calculated for the silane molecules and similar molecules with dangling bonds disorder, and with boron or phosphorus substitution to simulate doping. Some examples are presented, and a comparison is made with experimental properties of a‐Si:H. It is proposed to use these models in a study of the Staebler–Wronski photodegradation of a‐Si:H and other aspects of amorphous silicon technology. © John Wiley&S

ISSN:0192-8651    

DOI:10.1002/jcc.540141203

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe recently developed parallel coupled‐cluster algorithm of Rendell, Lee, and Lindh [Chem. Phys. Lett.,194, 84 (1992)] is extended to allow four‐indexed quantities containing one or two indices in the virtual orbital space to be stored across the global memory of distributed‐memory parallel processors. Quantities such as the double‐excitation amplitudes can now be distributed over multiple nodes, with blocks of data retrieved from remote nodes by the use of interrupt handlers. As an application of the new code, we have investigated the potential energy surface of the 2‐hydroxypyridine/2‐pyridone tautomers. Using large basis sets, the structure of each tautomer and the transition state connecting the two minima has been determined at the SCF level. The relative energy difference and the activation energy were then redetermined using the MP2, CCSD, and CCSD(T) methods. All calculations have been performed on Intel distributed‐memory supercomputers. The largest coupled‐cluster calculations contained over 2 million double‐excitation amplitudes. © Jo

ISSN:0192-8651    

DOI:10.1002/jcc.540141204

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe restricted SCF (single‐configuration SCF) and MCSCF (multiconfiguration SCF) calculations are performed to compute the ground‐state electric dipole moments of four pairs of diatomic molecules—(1) CO and BF; (2) SiO and AlF; (3) CS and BCl; and (4) SiS and AlCl—at a number of internuclear distances on both sides of the equilibrium position. Near Hartree–Fock accuracy is obtained in the SCF calculations. All eight molecules have a range of internuclear distance in which electric dipole moments are of the polarity ofA−B+. The shapes of computed electric dipole moment functions are discussed in the language of the molecular orbital method and in relationship to electronegativities of atoms. The present study gives us deeper understanding of electron transfer inside molecules and consequently of the apparent contradiction between electronegativity and the dipole polarity of some molecules. © John Wil

ISSN:0192-8651    

DOI:10.1002/jcc.540141205

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractPipecolic acid derivatives have proven to be effective P′1groups in a series of highly potent inhibitors of the enzyme HIV protease. One such inhibitor, Ro 31‐8959, contains the saturated bicyclic ring system decahydroisoquinoline (DIQ) in the P′1position. The binding orientation of Ro 31‐8959 is known from X‐ray crystallography. However, the bound conformation of theS‐hydroxy diastereomer has not been studied, and for this molecule there are at least two different possible binding conformations. Specifically, theN‐alkyl substituents may be equatorial or axial and the 3‐carboxamide may be rotated into several different orientations. To gain a better understanding of the relative energies of these various conformations,ab initiomolecular orbital calculations have been carried out on a series of pipecolic acid and DIQ derivatives. The results indicate that the lowest‐energyN‐equatorial rotamer is always at least 3 kcal/mol more stable than the lowest‐energyN‐axial rotamer. The presence of the second ring, as in the DIQ system, considerably raises the equatorial–axial difference to nearly 7 kcal/mol. Also, the preferred rotation angle of the amide group is different for theN‐equatorial andN‐axial cases. When the molecular dynamics‐averaged conformation of the boundS‐hydroxy inhibitor is considered, the energy difference between theN‐equatorial andN‐axial conformers drops to 4–5 kcal/mol. The preferred amide rotations in these systems are compared to those found in proline‐containing peptides. Finally, some observations are made with respect to the large conformational energy penalty necessary for b

ISSN:0192-8651    

DOI:10.1002/jcc.540141206

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractAn algorithm is introduced that tests whether a proposed elementary reaction can be realized within a specified number of cleavages and formations of covalent bonds. This is related to the problem of computing the minimum chemical distance of a given stoichiometry, but differs from it in important ways that are exploited in the algorithm design. One application of the algorithm is as a filter in MECHEM—a computer aid for the elucidation of reaction pathways. In that application, reaction steps implying more changes to covalent bonds than a given threshold are ruled implausible, and in practice such tests need to be carried out many thousands of times. Future applications of the algorithm can be expected because the question addressed is a fundamental one: What elementary reactions can occur? © 1993 by John Wiley&Sons, I

ISSN:0192-8651    

DOI:10.1002/jcc.540141207

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractA method for the estimation of pKafrom empirically calculated atomic charges has been developed and tested on a diverse set of organic oxyacids. The approach involves a comparison of the atomic charges calculated for both the acid and the negative ion that is formed after loss of the acidic proton. These charges have been used in conjunction with the familiar concepts of induction and resonance to develop an accurate formula to predict pKa. Results for a set of 135 compounds, including alcohols, phenols, and carboxylic acids, yielded a fit of pKawithr= 0.993 and an rms error of 0.455. © John Wiley&Sons, Inc

ISSN:0192-8651    

DOI:10.1002/jcc.540141208

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe total energies per unit cell of both the undistorted and the Peierls‐distorted polyacene polymers are computed from the respective HF/6‐311G** and MP2/6‐311G** finite‐cluster data using 40 different extrapolation schemes. The benchmark calculations, which aim at assessing the efficiency of extrapolation methods, clearly show that the best procedure for obtaining rapidly converging bulk properties should involve computation of the energy differences, followed by rational extrapolation techniques such Wynn'spalgorithm or its iteration, both with the interpolation pointsxn= (n+ 1)2, and closely related extrapolation methods, or Wynn's ε algorithm and its close relative, Aitken's iterated Δ2algorithm. © John Wiley

ISSN:0192-8651    

DOI:10.1002/jcc.540141209

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe net atomic charge parameters for halogen atoms and the atoms in aromatic molecules have been determined by the modified partial equalization of orbital electronegativity method. The same parameters are used for the halogen atoms both in aromatic and nonaromatic systems. The calculated dipole moments of haloalkanes agree well with experiment, but those of the halogenated aromatic molecules do not reproduce the experimental values as well as those of the haloalkanes; in particular, the computed dipole moments for monohalogenated benzenes are all lower than the experimental values because of the influence of the lonepair electrons on the halogens. Within the limitations of an atom‐centered point‐charge approximation, our calculated dipole moments, both for haloalkanes and halogented aromatic molecules, agree well with experimental values. © John Wiley&Sons,

ISSN:0192-8651    

DOI:10.1002/jcc.540141210

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractBy using the dynamically defined reaction path (DDRP) method and starting from various initial polygons, the intrinsic reaction coordinate (IRC) of the H2+ H → H + H2reaction has been calculated. The numerical stability of the method is illustrated by the evolution phases of the reaction path. Techniques and experiences on the parameter choice and effects of the parameter values on the stability and computer time consumption are discussed. © John Wiley&Sons, I

ISSN:0192-8651    

DOI:10.1002/jcc.540141211

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY