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  • 1995-1999  (294)
  • 1920-1924
  • 1996  (294)
  • Theoretical, Physical and Computational Chemistry  (294)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 58 (1996), S. 637-643 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple procedure is presented for obtaining the standard Young tableaux for the representation [(N/2) + S,(N/2) - S] of the permutation group ℒN for an N-electron system in spin state S directly from the spin branching diagram. We redefine the coordinate axes of the branching diagram to obtain a graph in terms of the partitions of the two-rowed Young diagram and define walks in this graph which yield directly the first rows of the allowed standard Young tableaux spanning a given representation when suitable weights have been assigned to the nodes in the graph. The allowed states are in a lexically ordered form and permit going easily from an index to an array and vice versa. © 1996 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 58 (1996), S. 645-655 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The development of the idea of a chemical bond is traced from Frankland to Heitler and London and beyond with emphasis on how electrons came to be considered essential to explaining the bond. © 1996 John Wiley & Sons, Inc.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 58 (1996), S. 657-670 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Starting with knowledge of the internal energy of a polyatomic system as a multidimensional function of the coordinates of the component atoms - the effective potential surface, one can explore the topography of this surface to find its stationary points and topology. Clusters are particularly effective vehicles for developing the methods of doing this, although it is essentially as easy to study small molecules as it is clusters, if the corresponding surfaces are already known. If the system is small enough, all the minima, the relevant saddles, and the corresponding reaction paths can be found; if the system is larger, then only statistical sampling methods can be applied. Such explorations can be used as efficient ways to test the physical plausibility of potential surfaces, e.g., to determine whether a surface developed to describe spectra is valid enough globally to be used for scattering studies. With the readily manageable potentials such as that composed of the sum of pairwise Morse interactions, it is now straightforward to explore how the form of the basic pair interactions affects the multidimensional topography of the surface. For systems of many particles, it is beginning to seem feasible to infer from topographical properties of the surface the extent to which a system undergoing cooling is either glass-forming or “focusing,” in the sense of going to a single structure or a small set of related structures. © 1996 John Wiley & Sons, Inc.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 58 (1996), S. 707-715 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of different isodesmic and homodesmic reactions defining strain energies in 3-membered rings are described and discussed. One isodesmic and one homodesmic reaction are applied numerically with the purpose of estimating strain in heterosiliranes including second-row and third-row heteroatoms. All molecules involved are optimized using SCF/6-31G**, and energies are calculated using MP2/6-31G**//SCF/6-31G** calculations. The results are discussed with reference to limitations of the chosen models. © 1996 John Wiley & Sons, Inc.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 58 (1996), S. 699-706 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We investigate the phenomenon of bond alternation in ring molecules of the type (CH)2n, which occurs due to the Peierls instability. We prove that the energy-minimizing configuration of bond lengths always has period two when n is odd. When n is even, a new instability may destroy the periodicity two as long as n is not too large. We also analyze the corresponding problem for the Heisenberg antiferromagnetic “spin-Peierls” system and prove that instabilities other than period two never occur there. © 1996 John Wiley & Sons, Inc.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 58 (1996), S. 717-731 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a scheme that - within certain approximations - connects the single-particle energies of defect-induced localized orbitals in quasi-one-dimensional systems to the band structures of related periodic structures. The mathematical foundations for the scheme are based on a transfer-matrix formulation of the Schrödinger equation. In contrast to most earlier approaches based on transfer matrices, the present formulation is directly related to parameter-free methods for electronic-structure calculations with more or less well-converged basis sets. Thereby, the transfer matrices get a dimension that in the general case is larger than two and it is, in addition, shown that a complete description of the system requires the introduction of a complementary set of matrices. However, in the ultimate formulation of the scheme, neither set of matrices needs to be defined. The scheme is illustrated through three examples, for which the band structures of the periodic structures have been obtained using a first-principles, density-functional, full-potential LMTO method for helical polymers. The three examples include trans-polyacetylene and polycarbonitrile as examples of conjugated polymers as well as the hydrogen-bonded polymer hydrogen fluoride. In both cases, we study solitonic defects. As the last example, we study selenium helices with special emphasis on defects involving local distortions of the dihedral angle. We finally discuss the approximations and limitations of the approach and will give some simple estimates of their implications. © 1996 John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1-18 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Potential derived (PD) atomic charges, obtained by fitting to molecular electrostatic potentials, are widely used in molecular modeling and simulation calculations. These charges are known to depend on the sample of points chosen for the fit, on the particular point selection algorithm, on molecular translations and rotations in many instances, and even on molecular conformation. Following a critique of currently available methods, a novel point selection scheme is described which results in a highly isotropic array of points located on a series of fused-sphere van der Waals surfaces. The pattern of points is based on tesselations of the icosahedron, and these are discussed in some detail along with their connection with virus morphology, geodesic domes, and symmetric fullerene structures. Using methanol as a test case, it is shown that the new method leads to PD charges which are independent of translation and display minimal rotational dependence, and are hence far better suited to the determination of PD charges from electrostatic potentials obtained from both theory and experimental X-ray diffraction data. The conformation dependence of the newly derived PD charges for alanyl dipeptide is found to be substantially less than obtained earlier by Williams [Biopolymers 29, 1367 (1990)]. © 1996 by John Wiley & Sons, Inc.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 19-29 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A theoretical model to investigate chemical processes in solution is described. It is based on the use of a coupled density functional/molecular mechanics Hamiltonian. The most interesting feature of the method is that it allows a detailed study of the solute's electronic distribution and of its fluctuations. We present the results for isothermal-isobaric constant-NPT Monte Carlo simulation of a water molecule in liquid water. The quantum subsystem is described using a double-zeta quality basis set with polarization orbitals and nonlocal exchange-correlation corrections. The classical system is constituted by 128 classical TIP3P or Simple Point Charge (SPC) water molecules. The atom-atom radial distribution functions present a good agreement with the experimental curves. Differences with respect to the classical simulation are discussed. The instantaneous and the averaged polarization of the quantum molecule are also analyzed. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 30-41 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum chemical calculations of potentially superacidic neutral Brönsted acids were carried out using the PM3 method. It was shown that the PM3 method can be used to predict the gas phase acidities of acidic compounds only if empirical corrections are made. A strong acidifying effect is predicted for a new family of compounds in which an sp2 oxygen is substituted by an (DOUBLE BOND) NSO2CF3 group. So, for example, such replacement is expected to result in acid strengthening by 47.5 kcal/mol in the case of CH3CHO and by 22.7 kcal/mol in the case of CF3SO2OH. The acidities of such compounds are predicted to be increased further (nonadditively) by stepwise replacements of (DOUBLE BOND) O by (DOUBLE BOND) NSO2CF3. The geometries of known superacidic systems were reproduced quite well by PM3 method. The geometries of several superacidic systems were analyzed. © 1996 by John Wiley & Sons, Inc.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 42-48 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The relative stability of the 3A2, 1A2, and 1A1 states of phenylnitrene is evaluated by means of ab initio calculations followed by difference-dedicated configuration interaction (DDCI). This approach is based on effective Hamiltonian theory at a low order of perturbation to select rationally the determinants which contribute to the energy difference. The CI space built on this criterion is then treated variationally. The method allows a considerable reduction of the CI space compared with a complete CAS*SDCI calculation (where CAS stands for complete active space). Depending on the concerned energy difference, different model spaces may be chosen, as illustrated in the 3A2 → 1A2 and the 3A2 → 1A1 transitions in phenylnitrene. Since the CI space may reach considerable dimensions, a direct CI algorithm for selected CI spaces, the SCIEL algorithm, has been used to perform the calculations. The results are in excellent agreement with previous calculations and with available experimental data. © 1996 by John Wiley & Sons, Inc.
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  • 11
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 57-73 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present analytical expressions for the first derivatives of area and other geometrical quantities of polygonal tesserae defined on molecular surfaces. This is a necessary step in the calculation of free energy derivatives with respect to nuclear coordinates for molecular solutes, in the framework of the polarizable continuum method. An application to solute-solvent dispersion energy derivatives is presented. © 1996 by John Wiley & Sons, Inc.
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  • 12
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 49-56 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A redundant internal coordinate system for optimizing molecular geometries is constructed from all bonds, all valence angles between bonded atoms, and all dihedral angles between bonded atoms. Redundancies are removed by using the generalized inverse of the G matrix; constraints can be added by using an appropriate projector. For minimizations, redundant internal coordinates provide substantial improvements in optimization efficiency over Cartesian and nonredundant internal coordinates, especially for flexible and polycyclic systems. Transition structure searches are also improved when redundant coordinates are used and when the initial steps are guided by the quadratic synchronous transit approach. © 1996 by John Wiley & Sons, Inc.
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  • 13
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 74-86 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A possible application of a novel double-iterated Kalman filter (DIKF) as an algorithm for molecular structure determination is investigated in this work. Unlike traditional optimization algorithms, the DIKF does not exploit experimental nuclear magnetic resonance (NMR) constraints in a penalty function to be minimized but used them to filter the atomic coordinates. Furthermore, it is a nonlinear Bayesian estimator able to handle the uncertainty in the experimental data and in the computed structures, represented as covariance matrices. The algorithm presented applies all constraints simultaneously, in contrast with DIKF algorithms for structure determination found in literature, which apply the constraints one at a time. The performances of both paradigms are tested and compared with those obtained by a commonly used optimization algorithm (based on the conjugate gradient method). Besides providing estimates of the conformational uncertainty directly in the final covariance matrix, DIKF algorithms appear to generate structures with a better stereochemistry and be able to work with realistically imprecise constraints, while time performances are strongly affected by the heavy matricial calculations they require. © 1996 by John Wiley & Sons, Inc.
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  • 14
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 87-108 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A semiempirical treatment of electrostatic potentials and partial charges is presented. These are the basic components needed for the evaluation of electrostatic interaction energies in combined quantum mechanical and molecular mechanical approaches. The procedure to compute electrostatic potentials uses AM1 and MNDO wave functions and is based on one previously suggested by Ford and Wang. It retains the NDDO approximation and is thus both easy to implement and computationally efficient. Partial atomic charges are derived from a semiempirical charge equilibration model, which is based on the principle of electronegativity equalization. Large sets of ab initio restricted Hartee-Fock (RHF/6-31G*) reference data have been used to calibrate the semiempirical models. Applying the final parameters (C, H, N, O), the ab initio electrostatic potentials are reproduced with an average accuracy of 20% (AM1) and 25% (MNDO), respectively, and the ab initio potential derived charges normally to within 0.1 e. In most cases our parameterized models are more accurate than the much more expensive quasi ab initio techniques, which employ deorthogonalized semiempirical wave functions and have generally been preferred in previous applications. © 1996 John Wiley & Sons, Inc.
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  • 15
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996) 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 16
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several parallel algorithms for Fock matrix construction are described. The algorithms calculate only the unique integrals, distribute the Fock and density matrices over the processors of a massively parallel computer, use blocking techniques to construct the distributed data structures, and use clustering techniques on each processor to maximize data reuse. Algorithms based on both square and row-blocked distributions of the Fock and density matrices are described and evaluated. Variants of the algorithms are discussed that use either triple-sort or canonical ordering of integrals, and dynamic or static task clustering schemes. The algorithms are shown to adapt to screening, with communication volume scaling down with computation costs. Modeling techniques are used to characterize algorithm performance. Given the characteristics of existing massively parallel computers, all the algorithms are shown to be highly efficient for problems of moderate size. The algorithms using the row-blocked data distribution are the most efficient. © 1996 by John Wiley & Sons, Inc.
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  • 17
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We discuss issues in developing scalable parallel algorithms and focus on the distribution, as opposed to the replication, of key data structures. Replication of large data structures limits the maximum calculation size by imposing a low ratio of processors to memory. Only applications which distribute both data and computation across processors are truly scalable. The use of shared data structures that may be independently accessed by each process even in a distributed memory environment greatly simplifies development and provides a significant performance enhancement. We describe tools we have developed to support this programming paradigm. These tools are used to develop a highly efficient and scalable algorithm to perform self-consistent field calculations on molecular systems. A simple and classical strip-mining algorithm suffices to achieve an efficient and scalable Fock matrix construction in which all matrices are fully distributed. By strip mining over atoms, we also exploit all available sparsity and pave the way to adopting more sophisticated methods for summation of the Coulomb and exchange interactions. © 1996 by John Wiley & Sons, Inc.
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  • 18
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 133-147 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational space of 1,2-ethanediol is studied on the basis of ab initio and semiempirical calculations. All possible conformers are treated. The relative energies of the conformers are systematically studied using various basis sets up to 6-311 + G(3df, 3pd) in order to perform calculations as accurate as possible within a reasonable amount of computer time. Electron correlation is included using Møller-Plesset perturbation theory. We propose two methods to evaluate the basis set superposition error associated with the intramolecular hydrogen bond appearing in some of the conformers. The results of semiempirical calculations are compared with these ab initio calculations. © 1996 by John Wiley & Sons, Inc.
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  • 19
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A parameterized self-consistent reaction field model allowing computation of the total free energy of hydration of organic molecules at the ab initio level is presented. The approach uses electrostatic plus polarization energies calculated with the help of a continuum model. The remaining solvation free energy terms are obtained by a simple formula based on atomic parameters and atomic accessible surface areas (ASAs), which are determined with the ASA analytical algorithm. Analytical derivatives of the atomic surfaces areas have been implemented. The atomic parameters have been obtained by a linear regression fit of the calculated and experimental free energies of solution in water for a set of 35 molecules, leading to a standard deviation of 0.75 kcal/mol. Effects of nonelectrostatic terms on solute geometries, association energies, and activation barriers are illustrated. © 1996 by John Wiley & Sons, Inc.
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  • 20
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 178-184 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A configuration interaction (CI) method in restricted CI (RCI) space obtained by imposing inequality-type restrictions on the occupancies of groups of molecular orbitals (MOs) was studied. The direct CI approach in such space was analyzed, and some recommendations concerning practical implementation of the RCI method are given. The corresponding program has been written in FORTRAN 77 for an IBM 486 DX personal computer and has been used for electronic structure calculations on transition metal complexes using a valence MO basis with the INDO approximation. © 1996 by John Wiley & Sons, Inc.
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  • 21
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 156-166 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structural stabilities of endo and exo conformations of retronecine and heliotridine molecules were analyzed using different ab initio, semiempirical, and molecular mechanics methods. All electron and pseudopotential ab initio calculations at the Hartree-Fock level of theory with 6-31G* and CEP-31G* basis sets provided structures in excellent agreement with available experimental results obtained from X-ray crystal structure and 1H-NMR (nuclear magnetic resonance) studies in D2O solutions. The exo conformations showed a greater stability for both molecules. The most significant difference between the calculations was found in the ring planarity of heliotridine, whose distortion was associated with the interaction between the O(11)H group and the C(1)-C(2) double bond as well as with a hydrogen bond between O(11)H and N(4). The discrepancy between pseudopotential and all-electron optimized geometries was reduced after inclusion of the innermost electrons of C(1), C(2), and N(4) in the core potential calculation. The MNDO, AM1, and PM3 semiempirical results showed poor agreement with experimental data. The five-membered rings were observed to be planar for AM1 and MNDO calculations. The PM3 calculations for exo-retronecine showed a greater stability than the endo conformer, in agreement with ab initio results. A good agreement was observed between MM3 and ab initio geometries, with small differences probably due to hydrogen bonds. While exo-retronecine was calculated to be more stable than the endo conformer, the MM3 calculations suggested that endo-heliotridine was slightly more stable than the exo form. © 1996 by John Wiley & Sons, Inc.
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  • 22
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 167-177 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Factorial design and principal component analyses are applied to CH3F infrared frequencies and intensities calculated from ab initio wave functions. In the factorial analysis, the quantitative effects of changing from a 6-31G to a 6-311G basis, of including polarization and diffuse orbitals, and of correcting for electron correlation using the second-order Møller-Plesset procedure are determined for all frequencies and intensities. The most significant main effect observed for the frequencies corresponds to the shift from Hartree-Fock to MP2 calculations, which tends to lower all frequency values by approximately 100 cm-1. For the intensities, the main effects are larger for the CF stretching and the CH3 asymmetric stretching modes. Interaction effects between two or more of the four factors are found to be of minor importance, except for the interaction between correlation and polarization. The principal component analysis indicates that wave functions with polarization and diffuse orbitals at the second-order Møller-Plesset level provide the best estimates for the harmonic frequencies, but not for the intensities. For the frequencies, the first principal component distinguishes between MP2 and Hartree-Fock calculations, while the second component separates the wave functions with polarization orbitals from those without these orbitals. For the intensities, the separation is similar but less well defined. This analysis also shows that wave function optimization to calculate accurate intensities is more difficult than an optimization for frequencies. © 1996 by John Wiley & Sons, Inc.
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  • 23
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 185-190 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new ab initio reaction field model has been applied to the calculation of the change in free energy of ionization on going from the gas phase to dimethylsulfoxide solution for a series of weak organic acids. In most cases, the observed change in free energy is reproduced within the experimental uncertainty of the gas phase experimental data. © 1996 by John Wiley & Sons, Inc.
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  • 24
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 191-203 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The rotational symmetry boundary condition proposed by Cagin et al. [J. Comp. Chem., 12, 627 (1991)] is implemented in the molecular dynamics simulation program, APRICOT, to make simulations of icosahedrally symmetrical capsids practical. The principle of the rotational symmetry boundary condition is strictly formulated with a new algorithm to track each atom by protomer and cell number. Further, the 60 cells and the 60 protomers of a capsid are treated as elements of the point group I. This treatment is necessary to determine the protomer numbers of atoms and to define indicators of atom pairs named relative protomer numbers. A method designated border residue flags is also introduced to further accelerate neighbor atom pair list generation. The method as we have implemented it is so fast that it was possible, using inexpensive workstations, to perform a 60-ps molecular dynamics simulation on an entire structure of a rhinoviral capsid including a 71-Å-thick shell of water molecules. This work is the first molecular dynamics simulation of an entire capsid under rotational symmetry boundary conditions. The structure of the capsid is well conserved during the simulation. Because conventional periodic boundary conditions are not applicable to rotational symmetries, it has been difficult, until this study, to perform calculations on macromolecules in crystallographic or noncrystallographic symmetries that are composed of rotational symmetries and linear translation. Therefore, our development is expected to provide a powerful tool for studies of macromolecules in such symmetries. The merits, limitations, and possibilities for further elaboration of this development are discussed. © 1996 by John Wiley & Sons, Inc.
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  • 25
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 226-237 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: New effective potentials acting between pairs of residues in proteins are proposed based on statistics of average distances and standard deviations between Cα atoms of residues in protein tertiary structures. Gaussian functions are adopted as analytical forms of the potentials. A protein structure is modeled as a chain molecule with a fixed bond length connecting particles approximating the effects of amino acid residues. The potentials derived in this study are used for conformational sampling of trypsin inhibitor from bovine pancreas. Sampling is done with the Monte Carlo simulated annealing method. Sampled conformations can be classified into a few groups or structural classes, and one of these classes contains structures relatively close (with 7.8-8.7 Å root mean square [rms] deviation) to the X-ray structure. The native structure exhibits relatively low energy. These results denote a rather smooth landscape of the present potential energy surfaces. One class of classified structures contains nativelike structures, which suggests that the native structure can be predicted by further refinement of structures in this class. We discuss other properties and the effectiveness of the present potentials for description of protein structures. © 1996 by John Wiley & Sons, Inc.
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  • 26
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The redox capacities of 5-hydroxy-1,4-naphthaquinone (VI), 5-8-dihydroxy-1,4-naphthaquinone (VII), and 5,8-dihydroxy-1,4-naphthaquinone imine (VIII) as model systems for the pharmacophore of aclacinomycin A, adriamycin/daunomycin, and 5-iminodaunomycin (5IDN), respectively, along with 1,4-naphthaquinone (V), 1,4-benzoquinone (IV), and 1,4-benzoquinone imine (IX), have been investigated by the AM1 semiempirical method. The reduction activation of the parent (Q) model systems to their various redox states [quinone radical anion (Q-2), semiquinone (QH·), semiquinone anion (QH-), and hydroquinone (QH2)], the redox capacities of the redox states, and the intermolecular electron self-exchange processes between the redox states and electron transfer reactions from the redox states to molecular oxygen have been examined using reaction enthalpies, adiabatic ionization potentials and electron affinities, and absolute and adiabatic electronegativities. Keto - enol transformations and the effects of solvation and H bonding on keto-enol tautomers of VI and of the hydroquinones of VI and VIII have also been assessed. The results indicate that the reactivity of VIII, relative to that of VII, may not be diminished. VI, however, appears to be less reactive than VII, and this suggests clues for the reduced toxicities of aclacinomycin A. Overall, the results suggest that the experimentally observed reduced cardiotoxic effects of 5IDN may be explained by changes in electron configuration and/or electron density and in geometry, such as changes in planarity that accompany enol to keto transformations in the reduction by product of 5IDN (Bird et al.7) - that is, between the hydroquinone (II) of naphthacenedione (I) and naphthacenone (III). Moreover, the results suggest that the two-electron reduction product, Q-2, of the drugs can be the reductant that produces reactive dioxygen species, such as O2-· and HO2·, via electron transfer to molecular oxygen as opposed to QH· and QH2, which have been postulated to be responsible for electron transfer. This possibly new role for Q-2 may be important in cardioxicity, particularly in aprotic and/or hydrophobic media. © 1996 by John Wiley & Sons, Inc.
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  • 27
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    Journal of Computational Chemistry 17 (1996) 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 28
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    Journal of Computational Chemistry 17 (1996), S. 238-249 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Metropolis Monte Carlo method has been developed for studying the effects of dielectric constant and counterion charge density and distribution on the energetics of formation and equilibria of the regular arrays or domain structures formed by bacteria l lipopolysaccharides. The method utilizes a regular triangular prism primitive as a reductive structural representation of each lipopolysaccharide anchor (lipid A molecule). Charges for the two phosphate groups are localized at one apex and midway along the opposite side of the regular triangular top face of each prism. The counterions are not localized but are represented as a fine cloud of charge modeled by distributing the total charge over a fine two-dimensional cubic lattice. The six alkyl chains of the lipid A molecule are aligned along the long axes of the prism and are contained by its faces. All prisms are confined to the same plane but are allowed to translate within the plane and to rotate about axes perpendicular to the plane. The potential energy function contains an electrostatic term and a van der Waals term. A discontinuous dielectric is used to separate the aqueous and hydrophobic areas of the system. Trial moves involve both a rotational and a translational operation. The configurations predicted by this method are consistent with the crystal morphologies which have been observed for lipopolysaccharides. This analysis readily allows the evaluation of thermodynamic properties, such as heat capacity, entropy, and energy. The root mean square average separation of units was also calculated as a function of iteration number. © 1996 by John Wiley & Sons, Inc.
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  • 29
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    Journal of Computational Chemistry 17 (1996), S. 267-272 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Davidson's method is widely used for finding the lowest eigenvalues of large matrices. Recently, mathematicians have shown that Davidson's derivation could be improved. They have corrected the derivation yielding a new iteration method. In this article this new method is adapted for realistic MRCI and MRCEPA calculations. Results show that the new method converges significantly faster in H2O and O2 with moderately elongated bonds than Davidson's original method. The new method offers new insights into the rate of convergence of Davidson's original method. © 1996 by John Wiley & Sons, Inc.
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  • 30
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    Journal of Computational Chemistry 17 (1996), S. 250-265 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a comparison between two different approaches to parallelizing the grand canonical Monte Carlo simulation technique (GCMC) for classical fluids: a spatial decomposition and a time decomposition. The spatial decomposition relies on the fact that for short-ranged fluids, such as the cut and shifted Lennard-Jones potential used in this work, atoms separated by a greater distance than the reach of the potential act independently, and thus different processors can work concurrently in regions of the same system which are sufficiently far apart. The time decomposition is an exactly parallel approach which employs simultaneous (GCMC) simulations, one per processor, identical in every respect except the initial random number seed, with the thermodynamic output variables averaged across all processors. While scaling characteristics for the spatial decomposition are presented for 8-1024 processor systems, the comparison between the two decompositions is limited to the 8-128 processor range due to the warm-up time and memory imitations of the time decomposition. Using a combination of speed and statistical efficiency, the two algorithms are compared at two different state points. While the time decomposition reaches a given value of standard error in the system's potential energy more quickly than the spatial decomposition for both densities, the warm-up time demands of the time decomposition quickly become insurmountable as the system size increases. © 1996 by John Wiley & Sons, Inc.
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  • 31
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    Journal of Computational Chemistry 17 (1996), S. 289-297 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In spite of much work on path-following methods, a solid mathematical foundation (especially convergence conditions and their practical measures) are lacking in most cases. In our previous articles the general theory of a new global searching procedure, the dynamically defined reaction path (DDRP) method, its rigorous mathematical formulation, the algorithm, a practical computation program, and some applications to abstract mathematical functions and simple chemical examples have been presented. In this article we give a short theoretical description and some practical criteria and measures for the convergence of the method and illustrate the principles and uses by numerical mathematical and chemical examples. © 1996 by John Wiley & Sons, Inc.
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  • 32
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    Journal of Computational Chemistry 17 (1996), S. 273-288 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Free energies of solvation of phenylimidazole inhibitors of cytochrome P450cam were determined using (1) free energy simulation, (2) AMSOL-SM2 semiempirical methods, and (3) Poisson-Boltzmann methods. The goals of this study were threefold: (1) to compare the results obtained from the three different methods, (2) to investigate the effect of inclusion of intraperturbed group interactions on free energy simulation estimates of solvation free energy differences, and (3) to investigate to what extent differences in free energies of solvation among three of these inhibitors could account for observed differences in their enzyme binding free energies. In general, relative solvation free energies obtained from the free energy simulations and AMSOL-SM2 methods give comparable results (i.e., the same rank ordering and similar quantitative results, differing significantly from results obtained using Poisson-Boltzmann methods). The free energy simulation studies suggest that the neglect of intraperturbed group interactions had little effect on rank order of free energies of solvation of the polar phenylimidazoles. The relative desolvation free energies of the three inhibitors of P450cam - 1-phenylimidazole (1-PI), 2-phenylimidazole (2-PI), and 4-phenylimidazole (4-PI) - with known enzyme bound X-ray structures parallel that of their known binding affinities and could account for most of the differences in the free energies of binding of these three inhibitors to P450cam. The origin of the difference of the free energies of solution of these three inhibitors is primarily the additional interaction between solvent and N(SINGLE BOND)H group in the imidazole ring of 2- and 4-phenylimidazole that is absent in the 1-phenylimidazole isomer. This hypothesis is substantiated by a second comparison of the relative solvation free energies of 4-phenylimidazole with its methylated derivative, 3-methyl-4-phenylimidazole, also lacking an N(SINGLE BOND)H group. © 1996 by John Wiley & Sons, Inc.
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  • 33
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    Journal of Computational Chemistry 17 (1996), S. 306-312 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The infrared absorption spectra of hydrogenated amorphous silicon alloys have been simulated using MOPAC. The calculated spectra compare well with those obtained experimentally. Simulation studies have also been carried out on the effect of contamination of hydrogenated amorphous silicon by common atmospheric contaminants: oxygen and nitrogen. These studies provide a basis for the study of diffusion and reconstruction of amorphous silicon alloys during annealing and photodegradation. This article indicates that infrared spectroscopy, combined with molecular modeling, could be used to study the molecular mechanisms associated with the photodegradation of amorphous silicon alloys. © 1996 by John Wiley & Sons, Inc.
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  • 34
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    Journal of Computational Chemistry 17 (1996), S. 298-305 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Transition states for the Diels-Alder reactions of 2,3-diaza-1,3-butadiene with ethylene, formaldehyde, formaldimine, cis- and trans- diazene, and nitrosyl hydride were located by ab initio molecular orbital calculations. The bond orders of the new forming bonds have been used to determine the asynchronicity of the reactions. Ab initio calculations show that the energy barrier for the hetero-Diels-Alder reactions is relatively high. The highest energy barrier of 34.76 kcal/mol calculated at the MP4/6-31G*//MP2/6-31G* level was found for the exo-cis-diazene addition to 2,3-diaza-1,3-butadiene. In all cases, when two diastereomeric transition structures are possible, the one with the endo hydrogen, exo lone pair was predicted to have a lower activation barrier. This behavior can be explained by the n-π and n-n loan pair repulsion interaction between the dienophile and diene heteroatoms in the corresponding transition state. The barrier is higher for those reactions which in the transition state have more lone electron pairs. Also, the barrier is higher when the lone pairs are endo oriented than when they are exo oriented in the transition state. © 1996 by John Wiley & Sons, Inc.
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  • 35
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    Journal of Computational Chemistry 17 (1996), S. 313-325 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article a procedure for generating starting orbitals for generalized valence bond (GVB) calculations is presented. This is achieved by selecting orbitals which correspond to specific bonds or electron pairs. These orbitals can be identified from the localized molecular orbitals, for both occupied and virtual orbitals, which are obtained through a unitary transformation of the Hartree-Fock canonical molecular orbitals using the Boys's localization method. A scheme has also been implemented which achieves optimum convergence of the pairwise orbital optimization. An object-oriented GVB program is developed which automatically generates reliable initial GVB orbitals, leading to proper and fast convergence. © 1996 by John Wiley & Sons, Inc.
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  • 36
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    Journal of Computational Chemistry 17 (1996), S. 338-349 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: More than a dozen stationary points on the potential energy surface for the 1:1 glycine zwitterion - water complex have been investigated at Hartree-Fock or MP2 levels of theory with basis sets ranging from split valence (4-31G) to split valence plus polarization and diffuse function (6-31 + + G**) quality. Only one true minimum (GLYZWM, C1 symmetry) could be located on the potential energy surface. GLYZWM features a bridged water molecule acting as both a hydrogen bond acceptor and donor with the NH3- and CO2- units of the glycine zwitterion. The total hydrogen bond energy in GLYZWM is computed as 16 kcal/mol (MP2/6-31 ++ G** // 6-31 ++ G**, including corrections for basis set superpositions errors). The computed vibrational frequencies and normal mode forms of the GLYZWM complex resemble in many cases experimental assignments made for the glycine zwitterion in bulk water on the basis of Raman spectroscopy. © 1996 by John Wiley & Sons, Inc.
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  • 37
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    Journal of Computational Chemistry 17 (1996), S. 326-337 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Short-range molecular dynamics simulations of molecular systems are commonly parallelized by replicated-data methods, in which each processor stores a copy of all atom positions. This enables computation of bonded 2-, 3-, and 4-body forces within the molecular topology to be partitioned among processors straightforwardly. A drawback to such methods is that the interprocessor communication scales as N (the number of atoms) independent of P (the number of processors). Thus, their parallel efficiency falls off rapidly when large numbers of processors are used. In this article a new parallel method for simulating macromolecular or small-molecule systems is presented, called force-decomposition. Its memory and communication costs scale as N/√P, allowing larger problems to be run faster on greater numbers of processors. Like replicated-data techniques, and in contrast to spatial-decomposition approaches, the new method can be simply load balanced and performs well even for irregular simulation geometries. The implementation of the algorithm in a prototypical macromolecular simulation code ParBond is also discussed. On a 1024-processor Intel Paragon, ParBond runs a standard benchmark simulation of solvated myoglobin with a parallel efficiency of 61% and at 40 times the speed of a vectorized version of CHARMM running on a single Cray Y-MP processor. © 1996 by John Wiley & Sons, Inc.
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  • 38
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    Journal of Computational Chemistry 17 (1996), S. 350-357 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A full account of how to calculate the electrostatic binding energy using the finite difference solution to the linearized Poisson-Boltzmann equation (FDPB) for protein-ligand systems is described. The following tests show that the statistical and systematic errors due to discrete grid representation of molecular shape and charges amount to about 1% and 5% of calculated binding energy difference, respectively. The greater accuracy results from a three-stage error cancellation: first in ΔGs, then ΔΔGds, and finally ΔΔGele. We conclude in this study that the intrinsic error of FDPB is mostly canceled in computing binding energy differences. Among the parameters examined, the partial charge, dielectric constant, and radius of solvent can influence the calculated results most. © 1996 by John Wiley & Sons, Inc.
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  • 39
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    Journal of Computational Chemistry 17 (1996), S. 358-366 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The use of a multipolar decomposition of the far electrostatic potential for the purposes of molecular field similarity comparison between structurally different molecules has been impractical because the multipolar decomposition depends on the center of expansion. That center of expansion is essentially arbitrary, which renders the multipolar coefficients to be a nonunique characterization of the field. This article provides the definition of a center of expansion at which the multipolar decomposition is unique. For the first time, it is possible to use multipolar decomposition to characterize molecular fields beyond the first term, which is invariant under translation of the center of expansion. Calculations are performed for two structurally distinct types of HIV-1 inhibitors, three non-nucleoside reverse transcriptase inhibitors, and three phospholipids using these unique multipolar descriptors. Differences and similarities in the calculated values of these descriptors will be shown to parallel the differences and similarities of molecular charge distributions. © 1996 by John Wiley & Sons, Inc.
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  • 40
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    Journal of Computational Chemistry 17 (1996) 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 41
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    Journal of Computational Chemistry 17 (1996), S. 386-395 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A combined ab initio quantum mechanical and molecular mechanical (AI-QM/MM) potential for use in molecular modeling and simulation has been described. In this article, we summarize a procedure for deriving the empirical parameters embedded in a combined QM/MM model and suggest a set of Lennard-Jones parameters for the combined ab initio 3-21G and MM OPLS-TIP3P (AI-3/MM) potential. Interaction energies and geometrical parameters predicted with the AI-3/MM model for over 80 hydrogen-bonded complexes of organic compounds with water were found to be in good accord with ab initio 6-31G(d) results. We anticipate that the AI-3/MM potential should be reasonable for use in condensed phase simulations. © 1996 by John Wiley & Sons, Inc.
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  • 42
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    Journal of Computational Chemistry 17 (1996), S. 367-383 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The present work examines the conditioning of the least-squares matrix for obtaining potential derived charges and presents a modification of the CHELP method for fitting atomic charges to electrostatic potentials. Results from singular value decompositions (SVDs) of the least-squares matrices show that, in general, the least-squares matrix for this fitting problem will be rank deficient. Thus, statistically valid charges cannot be assigned to all the atoms in a given molecule. We find also that, contrary to popular notions, increasing the point density of the fit has little or no influence on the rank of the problem. Improvement in the rank can best be achieved by selecting points closer to the molecular surface. Basis set has, as expected, no effect on the number of charges that can be assigned. Finally, a well-defined, computationally efficient algorithm (CHELP-SVD) is presented for determining the rank of the least-squares matrix in potential-derived charge fitting schemes, selecting the appropriate subset of atoms to which charges can be assigned based on that rank estimate, and then refitting the selected set of charges. © 1996 by John Wiley & Sons, Inc.
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  • 43
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    Journal of Computational Chemistry 17 (1996), S. 396-408 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformations and rotational barriers in a series of conjugated primary and tertiary amides have been analyzed by a modified MM2(91) force field, which treats the amide nitrogen as part of the conjugated system by redefining the atom type for the nitrogen. Ab initio molecular orbital calculations at the MP2/6-31G* level have been performed on the stable conformers and transition structures of acrylamide and β-trans-aminoacrylamide. The results have been used, with published experimental and computational data, to generate parameters for the MM2 force field. The force field has been applied to various conjugated amides, such as reduced nicotinamide adenine dinucleotide (NADH) and NAD+ analogues, nicotinamide, urea, vinylogous urea derivatives, and nucleic acid bases. The fundamental difference between primary and tertiary conjugated amides with respect to both conformation and barrier is highlighted. © 1996 by John Wiley & Sons, Inc.
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  • 44
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    Journal of Computational Chemistry 17 (1996), S. 409-417 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have developed a molecular modeling procedure to determine the relative configuration of a chiral molecule from nuclear magnetic resonance (NMR) data. Our procedure uses constrained molecular mechanics, and the constraints are interproton distances derived from the experimental nuclear Overhauser enhancement (NOE) data. The main feature is a period of high-temperature dynamics in which frequent inversions occur at most chiral sites. This allows the distance constraints to guide the molecule into configurations consistent with the NOE data. For molecules with complex ring systems, high-temperature dynamics alone may fail to invert certain chiral centers with sufficient frequency. We have countered this by allowing as an option additional inversions of selected chiral centers. The procedure tested successfully on organic molecules of known stereochemistry, with 5 to 17 chiral centers, provided that the number of available constraints was at least twice the number of chiral centers. The procedure is tolerant of large errors in the estimated interproton distances and is reasonably rapid. For a series of sugars, the time required increases less than quadratically with the number of atoms. © 1996 by John Wiley & Sons, Inc.
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  • 45
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    Journal of Computational Chemistry 17 (1996), S. 418-428 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An extended dynamic programming algorithm is presented that is applicable to the fragment assembly phase of the site mapping fragment assembly approach to peptide docking. After constructing a free energy map of the receptor using each of the amino acids in the peptides to be docked, we apply the algorithm to two systems: HIV-1 protease complexed with a synthetic hexameric inhibitor, and MHC HLA-A2 complexed with a nonameric peptide. The all atom root mean square deviation between the predicted and crystal structures was 1.7 and 2.0 Å, respectively. While these results are reasonable considering the relatively coarse level of mapping, the more important result is that the structures are probably very close to the best obtainable by an exhaustive search through the entire data map, and yet are obtained with a reduction of 3-5 orders of magnitude in the number of computations. We also outline a prescription for an iterative procedure which finds the global minimum with increasing confidence. © 1996 by John Wiley & Sons, Inc.
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  • 46
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    Journal of Computational Chemistry 17 (1996), S. 429-449 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several commonly used molecular mechanics force fields have been tested for accuracy in conformational energy calculations. Differences in performance between the force fields are discussed for different classes of structures. MMFF93 and force fields based on the MM2 or MM3 functional form are found to perform significantly better than other force fields in the test, with average conformational energy errors around 0.5 kcal/mol. CFF91 also reaches this accuracy for the subset in which fully determined parameters are used, but it doubles the overall error due to use of estimated parameters. Harmonic force fields generally have average errors exceeding 1 kcal/mol. Factors influencing accuracy are identified and discussed. © 1996 by John Wiley & Son s, Inc.
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  • 47
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    Journal of Computational Chemistry 17 (1996), S. 450-468 
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new set of force field parameters for carbohydrates is reported. The parameter set is based on the CHARMM22 force field of Karplus and co-workers. The parameterization is based on newly performed high-level ab initio calculations [MP2/6-311 + G (2d, 2p)/ /6-31G**] of fragment molecules. A good agreement of the modified force field and ab initio data is achieved, which is demonstrated with a variety of molecules. © 1996 by John Wiley & Sons, Inc.
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  • 48
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    Journal of Computational Chemistry 17 (1996) 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 49
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    Journal of Computational Chemistry 17 (1996), S. 469-475 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parallel computing seems to be the solution for molecular dynamics of large atomic systems, such as proteins in water environments, but the simulation time critically depends on the processor allocation strategy. A study of the optimal processor allocation based on a space decomposition algorithm for single instruction multiple data flow mesh computers is presented. A particular effort has been made to identify the best criterion according to which the atoms can be allocated to the processors using a spatial decomposition approach. The computing time depends on the granularity of the space decomposition among processing elements and on the ratio between the computation power of processing elements and the communication speed of the interprocessor network. © 1996 by John Wiley & Sons, Inc.
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  • 50
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    Journal of Computational Chemistry 17 (1996), S. 385-385 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 51
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    Journal of Computational Chemistry 17 (1996), S. 476-488 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The extended simulated annealing process (ESAP) is a useful method for modeling the partial structure of proteins [J. Higo et al., Biopolymers, 32, 33 (1992)]. In ESAP, a protein molecule is divided into two parts: small, flexible fragments constituting the concerned partial structure, and the remaining part, for which the structure is kept rigid during the simulation. We have improved the program of ESAP so that it can be adapted to general macromolecules. Any sidechain on the rigid part can be set to rotate. Soft repulsion between van der Waals spheres is introduced to avoid conformational trapping into local minima. This improved program was tested for modeling structural changes caused by eight kinds of amino acid mutation at the 86th residue in T4 lysozyme. For each mutant we obtained a model structure that was close to the X-ray structure. The root mean square (rms) deviations from the X-ray structure were 0.3 to 0.8 Å for all heavy atoms and about 0.2 Å for the main-chain atoms. We also modeled the structure of an Ile mutant, for which the X-ray structure has not yet been reported. ESAP can be used to model structural changes due to a single residue mutation in proteins. © 1996 by John Wiley & Sons, Inc.
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  • 52
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    Journal of Computational Chemistry 17 (1996), S. 757-766 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital theory and density functional theory calculations have been carried out on dimethoxymethane as a model for the anomeric effect. We optimized various conformations of dimethoxymethane using Gaussian 92 at the MP2/6-311 + + G**, MP2/DZP + Diffuse, MP2/6-31G**, and Becke3LYP/6-31G** levels of theory. These methods were evaluated based on their performance in reproducing structures and energies of dimethoxymethane when compared to experiment. This study also examined the structure and energy of dimethoxymethane as a function of dihedral angles for examining the anomeric effect at the MP2/6-31G** and Becke3LYP/6-31G** levels of theory. These calculations are qualitatively consistent with the anomeric effect observations in carbohydrates and with earlier calculations. Quantitative comparisons with earlier results reveal that dimethoxymethane has lower total energies, smaller rotational barriers, and shorter bond lengths than was previously determined. The Becke3LYP calculations were also compared to the MP2 results. The density functional theory findings show that the minimum energy structures correspond well with experimental and MP2 data. The total and relative energies from molecular orbital theory and density functional theory vary to some extent. Contour plots of the relative energies of dimethoxymethane were evaluated and compared to a relative energy contour plot determined by MM3. The contour plots were similar, showing slightly larger changes in energies for the MP2 results than for the Becke3LYP results, which in turn were slightly larger than the MM3 results. Density functional theory calculations are an excellent alternative method of calculation due to increased speed and reliable accuracy of the density functional calculations. These results will serve as a benchmark for modelling the anomeric effect in carbohydrates. © 1996 John Wiley & Sons, Inc.
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  • 53
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    Journal of Computational Chemistry 17 (1996), S. 767-780 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular geometries of the 1-chloro-, 1-fluoro-, 1-methyl-, and 1-hydrogenosilatranes were fully optimized by the restricted Hartree-Fock (HF) method supplemented with 3-21G, 3-21G(d), 6-31G(d), and CEP-31G(d) basis sets; by MP2 calculations using 6-31G(d) and CEP-31G(d) basis sets; and by GGA-DFT calculations using 6-31G(d5) basis set with the aim of locating the positions of the local minima on the energy hypersurface. The HF/6-31G(d) calculations predict long (〉254 pm) and the MP2/CEP calculations predicted short (∼225 pm) equilibrium Si(SINGLE BOND)N distances. The present GGA-DFT calculations reproduce the available gas phase experimental Si(SINGLE BOND)N distances correctly. The solid phase experimental results predict that the Si(SINGLE BOND)N distance is shorter in 1-chlorosilatrane than in 1-fluorosilatrane. In this respect the HF results show a strong basis set dependence, the MP2/CEP results contradict the experiment, and the GGA-DFT results in electrolytic medium agree with the experiment. The latter calculations predict that 1-chlorosilatrane is more polarizable than 1-fluorosilatrane and also support a general Si(SINGLE BOND)N distance shortening trend for silatranes during the transition from gas phase to polar liquid or solid phase. The calculations predict that the ethoxy links of the silatrane skeleton are flexible. Consequently, it is difficult to measure experimentally the related bond lengths and bond and torsion angles. This is the probable origin of the surprisingly large differences for the experimental structural parameters. On the basis of experimental analogies, ab initio calculations, and density functional theory (DFT) calculations, a gas phase equilibrium (re) geometry is predicted for 1-chlorosilatrane. The semiempirical methods predict a so-called exo minimum (at above 310 pm Si(SINGLE BOND)N distance); however, the ab initio and GGA-DFT calculations suggest that this form is nonexistent. The GGA-DFT geometry optima were characterized by frequency analysis. © 1996 by John Wiley & Sons, Inc.
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  • 54
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    Journal of Computational Chemistry 17 (1996), S. 781-789 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The equilibrium geometries and transition states for interconversion of the CSiH2 isomers in the singlet electronic ground state are optimized at the MP2 and CCSD(T) levels of theory using a TZ2P basis set. The heats of formation, vibrational frequencies, infrared intensities, and rotational constants are also predicted. There are three energy minima on the CSiH2 potential energy surface. Energy calculations at CCSD(T)/TZ2P(fd) + ZPE predict that the global energy minimum is silavinylidene (1), which is 34.1 kcal mol-1 lower in energy than trans-bent silaacetylene (2) and 84.1 kcal mol-1 more stable than the vinylidene isomer (3). The barrier for rearrangement 2→1 is calculated at the same level of theory to be 5.1 kcal mol-1, while for the rearrangement 3→2 a barrier of 2.7 kcal mol-1 is predicted. The natural bond orbital (NBO) population scheme indicates a clear polarization of the C(SINGLE BOND)Si bonds toward the carbon end. A significant ionic contribution to the C(SINGLE BOND)Si bonds of 1 and 2 is suggested by the NBO analysis. The C(SINGLE BOND)Si bond length of trans-bent silaacetylene (2) is longer than previously calculated [1.665 Å at CCSD(T)/TZ2P)]. The calculated carbon-silicon bond length of 2 is in the middle between the C(SINGLE BOND)Si double bond length of 1 (1.721 Å) and the C(SINGLE BOND)Si triple bond of the linear form HCSiH (4), which is 1.604 Å. Structure 4 is a higher-order saddle point on the potential energy surface. © 1996 by John Wiley & Sons, Inc.
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  • 55
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    Journal of Computational Chemistry 17 (1996), S. 790-805 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A simple method for evaluating the molecular electrostatic potential (MEP) map without self-consistent field molecular orbital (SCF-MO) calculation is extended, and the parameters for amino acids, peptides, and proteins are determined. In this method, the electrostatic potentials due to electrons in the valence shells are calculated by a set of simple empirical functions at various origins, and those due to the core electrons and nuclei by point charge approximation. For application of the method to amino acids, peptides, and proteins, the functions for the σ and π bonds and lone-pair electrons involved in these species were determined, and the MEP maps calculated by the empirical functions were compared with those calculated by an ab initio method. It is shown that the method reproduces correctly the shape of ab initio MEP map even for the repulsive MEP region. The method is shown to be very useful for rapid evaluation of reliable MEPs for large biological molecules. © 1996 by John Wiley & Sons, Inc.
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  • 56
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    Journal of Computational Chemistry 17 (1996), S. 806-820 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The self-consistent reaction field (SCRF) method proposed by Miertus, Scrocco, and Tomasi (MST) was extended to solutions of neutral solutes in CCl4. A detailed parametrization of the solute/solvent interface and of the “hardness” atomic parameters determining the van der Waals interactions was performed from comparison with experimental data and Monte Carlo simulations. The parametrization was carried out at both ab initio (6-31G*) and semiempirical (MNDO, AM1, PM3) levels. The MST/SCRF optimized versions provide accurate estimates of the free energy of solvation in CCl4 for the series of molecules studied. Furthermore, a precise description of the solvent effect on different chemical processes in CCl4 solution supports the reliability of the parametrization. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 821-834 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Multidimensional conformational analysis (MDCA) predicted the existence of nine stable backbone conformations (αL, αD, βL, γL, γD, δL, δD, εL, and εD) on the 2D-Ramachandran map, E = E(φ, ψ), for a single amino acid diamide (HCONH-CHR-CONH2). The potential energy hypersurfaces (E = E[φ, ψ, χ1, χ2]) of For-L-Ser-NH2 associated with the αL-, bgr;L-, γL-, δL-, and εL-type stable backbone orientations are investigated in this article. An appropriate number of side-chain rotamers is associated with each of the backbone conformers. In the case of serine, where R = -CH2OH, the two sidechain torsional angles (χ1, χ2) should lead to 3 * 3 = 9 different sidechain orientations according to MDCA. For certain backbone structures, some of the sidechain conformations were nonexistent. © 1996 by John Wiley & Sons, Inc.
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  • 58
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    Journal of Computational Chemistry 17 (1996), S. 835-840 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structures of two isomers, difluorodisulfane (FSSF) and thiothionylfluoride(SSF2), and the corresponding transition structure were generated with density functional theory (DFT) methods. Three groups of DFT methods were used: local(Local Spin Density Approximation, LSDA), nonlocal (local with gradient corrections; BLYP and BP86), and hybrid methods that include a mixture of Hartree-Fock (HF) exchange with nonlocal correlation (Becke3BLYP, Becke3P86). An extended basis set [6-311 + + G(3df)] was used for all calculations, although satisfactory results can be obtained with the 6-311G(d) basis set. The geometries obtained were compared with both restricted Hartree-Fock (RHF) calculated and experimentally obtained values. The energy outcome and the activation barrier for the isomerization were evaluated. It was determined that excellent geometries can be obtained with the Becke3B86 hybrid method, whereas for reasonable energies MP2 single-point calculations on these geometries are necessary. © 1996 by John Wiley & Sons, Inc.
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  • 59
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    Journal of Computational Chemistry 17 (1996), S. 841-850 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MP2/6-31G* interaction energies were calculated for more than 80 geometries of stacked cytosine dimer. Diffuse polarization functions were used to properly cover the dispersion energy. The results of ab initio calculations were compared with those obtained from three electrostatic empirical potential models, constructed as the sum of a Lennard-Jones potential (covering dispersion and repulsion contributions) and the electrostatic term. Point charges and point multipoles of the electrostatic term were also obtained at the MP2/6-31G* level of theory. The point charge MEP model (atomic charges derived from molecular electrostatic potential) satisfactorily reproduced the ab initio data. Addition of π-charges localized below and above the cytosine plane did not affect the calculated energies. The model employing the distributed multipole analysis gave worse agreement with the ab initio data than the MEP approach. The MP2 MEP charges were also derived using larger sets of atomic orbitals: cc-pVDZ, 6-311 + G(2d, p), and aug-cc-pVDZ. Differences between interaction energies calculated using these three sets of point charges and the MP2/6-31G* charges were smaller than 0.8 kcal/mol. The correlated ab initio calculations were also compared with the density functional theory (DFT) method. DFT calculations well reproduced the electrostatic part of interaction energy. They also covered some nonelectrostatic short-range effects which were not reproduced by the empirical potentials. The DFT method does not include the dispersion energy. This energy, approximated by an empirical term, was therefore added to the DFT interaction energy. The resulting interaction energy exhibited an artifact secondary minimum for a 3.9-4.0 vertical separation of bases. This defect is inherent in the DFT functionals, because it is not observed for the Hartree-Fock + dispersion interaction energy.© 1996 John Wiley & Sons, Inc.
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  • 60
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    Journal of Computational Chemistry 17 (1996), S. 851-863 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The concepts of symmetry-matrix and symmetry-supermatrix introduced in article I[J. Comput. Chem., 10, 957 (1989)] can be generalized to the Dirac-Fock method. By using the semidirect product decomposition of Oh and the linear vector space theory, the irreducible representation basis of Oh for any molecular system (Oh or its subgroups) can be deduced analytically in the nonorthonormal Cartesian Gaussian basis. This method is extended to discuss the double-valued representations of Oh* in the complex Cartesian Gaussian spinor basis. In the double-valued irreducible representation basis of D2*, the matrix of kinetic operator c(OVERLINE)σ(/OVERLINE)·(OVERLINE)p(/OVELINE) in the Dirac-Fock equation can be reduced into a real symmetric and can be grouped into classes under the operations in D3d. Therefore, the symmetry-matrix and symmetry-supermatrix can also be used in the Dirac-Fock method to reduce the storage of two electron integrals and calculations of Fock matrix during iterations by a factor of ca. g2 (g is the order of the molecular symmetry group). In addition, a method to deal with the nonorthonormal space is presented. © 1996 by John Wiley & Sons, Inc.
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  • 61
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    Journal of Computational Chemistry 17 (1996), S. 878-887 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The frequency distributions of internal dynamics of a protein are calculated in solution using normal mode analysis. Our test case is bovine pancreatic trypsin inhibitor, consisting of 58 amino acid residues. Each water molecule surrounding the protein is treated as an internally rigid body that can move with the vibrating protein. The water molecules are redistributed around the protein, as dictated by the potential energy. It is shown that water molecules around the protein are essential for the protein to keep its tertiary structure close to the X-ray structure. The density of states calculated in this model is shifted toward high frequencies when compared with results previously obtained with a model in which the water molecules were not allowed to move with the protein. This shift toward high-frequency states originates from the stronger interactions of water molecules with the sidechain atoms in the protein. The present model is computationally demanding. So the previous (frozen water) model is suggested to be a reasonable approximation for expressing internal dynamics of a protein in solution. © 1996 by John Wiley & Sons, Inc.
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  • 62
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    Journal of Computational Chemistry 17 (1996), S. 864-877 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: At present, there are two widely used approaches for computing molecular hydration and electrostatic effects within the continuum approximation: the finite difference method, in which the electric potential is directly computed on a cubic grid, and the induced polarization charge or boundary element method, in which an induced charge distribution is first computed on the molecular surface and in which solvation effects are then calculated by reference to the reaction field arising from this induced surface charge. While the induced surface charge approach has a number of advantages over finite differences, especially in the computation of hydration forces and solvent stabilization, the applications of this technique have been largely restricted to small molecules. This is primarily due to the very large system of equations that results when the surface of a macromolecule is discretized into elements small enough to ensure an acceptable level of numerical accuracy within the continuum model. This article describes a new algorithm for implementing boundary element calculations within the continuum model. The essence of our approach is only to compute explicitly those interactions between surface elements that are relatively close together and to approximate long-range interactions by grid-based multipole expansion. The resulting system of equations has a relatively sparse coefficient matrix and requires disk storage that increases linearly with molecular surface area. The technique has numerous applications in the analysis of solvation effects in large molecules, especially in the area of conformational analysis, where it is critical to accurately estimate the global hydration energy for the entire structure. © 1996 by John Wiley & Sons, Inc.
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  • 63
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    Journal of Computational Chemistry 17 (1996), S. 888-904 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A comparison is made between geometry optimization in Cartesian coordinates, in Z-matrix coordinates, and in natural internal coordinates for the location of transition states. In contrast to the situation with minima, where all three coordinate systems are of comparable efficiency if a reliable estimate of the Hessian matrix is available at the starting geometry, results for 25 different transition states covering a wide range of structural types demonstrate that in practice Z-matrix coordinates are generally superior. For Cartesian coordinates, the commonly used Hessian update schemes are unable to guarantee preservation of the necessary transition state eigenvalue structure, while current algorithms for generating natural internal coordinates may have difficulty handling the distorted geometries associated with transition states. The widely used Eigenvector Following (EF) algorithm is shown to be extremely efficient for optimizing transition states. © 1996 by John Wiley & Sons, Inc.
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  • 64
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    Journal of Computational Chemistry 17 (1996) 
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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    Journal of Computational Chemistry 17 (1996), S. 905-909 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital theory has been used to study the mechanism of the formation of C3H3+ from the reaction of CH3+ with acetylene. The highest level geometry optimizations and frequencies were computed at MP2-FC/6-31G**; single point energies of all the critical structures were computed to the MP4-FC/6-31G**//MP2-FC/6-31G** theory level. One of the three alternative transition structures leading to the formation of C3H3+ gives the cyclopropenyl cation and the other two the propargyl cation. The proportions of C3H2D+ and C3HD2+ obtained when CD3+ reacts with acetylene, and the composite nature of the metastable peak observed for the[C3H5]+→[C3H3]++ H2 fragmentation are explained by assuming a different degree of deuterium scrambling depending on the energy of the system. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1152-1155 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for refining high order numerical integration schemes is described. Particular focus is on integration schemes over the unit sphere with octahedral symmetry. The method is powerful enough that new integration schemes can be found from rough intuitive guesses. New schemes up to order 59 are presented. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1132-1141 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new set of formulae is developed for the derivatives of torsion angle energy terms and is introduced into the program CHARMM. These formulae, which are based on derivatives of the torsion angle itself, avoid the singularities introduced by use of the derivatives of the torsion angle cosine. The potential energy can include any differentiable function of the torsion angle and there is no need for a special treatment for cases where planar conformations are not extrema. The resulting code is simpler than the original version and yields correct derivatives in all practical situations. Because the minimum of the torsion energy can be at any angle, the functionality of the existing energy routines is generalized. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1142-1151 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present results from the application of two conformational searching methods: genetic algorithms (GA) and direct search methods for finding low energy conformations of organic molecules. GAs are in a class of biologically motivated optimization methods that evolve a population of individuals in which individuals who are more “fit” have a higher probability of surviving into subsequent generations. The parallel direct search method (PDS) is a type of pattern search method that uses an adaptive grid to search for minima. Both methods found energies equal to or lower than the energy of the relaxed crystal structure in all cases, at a relatively small cost in CPU time. We suggest that either method would be a good candidate to find 3-D conformations in a large scale screening application. © 1996 by John Wiley & Sons, Inc.
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  • 69
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    Journal of Computational Chemistry 17 (1996), S. 1163-1170 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry optimizations for several conformations of tri-, tetra-, and pentacyclosiloxane (H2SiO)n (n = 3, 4, and 5) were carried out, and the relative stabilities were compared at the Hartree-Fock (HF) and second order perturbation theory (MP2) levels of theory using the 6-31G* and 6-311G(d, p) basis sets. At the highest levels of theory, the only minimum for n = 4 (D4) occurs at the highly symmetric D4h structure. In contrast, several, nearly isoenergetic, minima are found on the D5 surface. These have C1, C2, Cs, and D5h symmetries. While the C1 structure has the lowest MP2/6-311G(d, p) energy, this species is predicted to be highly fluxional, and the distribution of isomers is dependent on temperature. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996) 
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 71
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    Journal of Computational Chemistry 17 (1996), S. 1171-1182 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In a continuing effort to provide the computational community with a reference work comparing all of the available conformer searching methods, we have exposed the standard set of small molecules to two commonly used stochastic searching techniques. Advantages and limitations of these methods are discussed. © 1996 by John Wiley & Sons, Inc.
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The configurational isomers of 1,4-bis[2-(3,4,5-trimethoxyphenyl)ethenyl]benzene have been investigated by ab initio and MOPAC-AM1 semiempirical methods. The calculations were guided by and compared with single crystal X-ray results of the trans, trans-isomer (taken from the literature) and of the cis,cis-isomer (reported here). Using 4-21G-based ab initio calculations, free state geometries, deviations from coplanarity, and barriers to rotation of the central and peripheral rings were evaluated. Such barriers were also enumerated for the solid state of the cis,cis- and trans,trans-isomers. A single-molecule cluster surrounded by point charges sufficed to rationalize observed solid state properties in the trans,trans-isomer, including the quasi-free rotation of the central ring. A multimolecule cluster, however, was required to rationalize the restricted rotation of the rings in the cis,cis-isomer. MOPAC-AM1 methods were used to calculate geometries and energies of rotameric forms on the singlet photoisomerization path cis,cis → cis,trans → trans,trans. Finally, UV absorption wavelengths and oscillator strengths were calculated and the electronic structure of the states discussed. © 1996 by John Wiley & Sons, Inc.
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  • 73
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    Journal of Computational Chemistry 17 (1996), S. 1318-1327 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Analytical second derivatives of the energy are derived and efficiently implemented for semiempirical MNDO-type methods including AM1, PM3, and MNDO/d. A new algorithm for the simultaneous solution of several CPHF equations is proposed in which the amount of memory required is independent of the number of iterations. The analytical approach is faster than the numerical approach typically by a factor of 5 and exhibits a reliable convergence over a wide range of molecules. The asymptotic memory and secondary storage requirements of the reported procedure can be as low as O(N2) without significant degradation of the performance. © 1996 by John Wiley & Sons, Inc.
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  • 74
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    Journal of Computational Chemistry 17 (1996), S. 1344-1351 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new procedure to solve the Poisson-Boltzmann equation is proposed and shown to be efficient. The electrostatic potential due to the reaction field is calculated directly. Self-interactions among the charges are completely eliminated. Therefore, the reference calculation to cancel out the self-energy is not needed. © 1996 by John Wiley & Sons, Inc.
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  • 75
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    Journal of Computational Chemistry 17 (1996), S. 1352-1358 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new algorithm for quantitative assessment of similarity between two atoms in molecules is presented. Both the atomic similarity index and its derivatives with respect to the three Euler angles that describe the mutual orientation of the atoms under comparison are computed efficiently by taking advantage of the recently developed analytical representations for atomic zero-flux surfaces. The use of such representations makes it possible to substantially enhance the accuracy of the computed similarity indices without increasing the cost of their evaluation. Numerical tests involving oxygen atoms in several carbonyl compounds demonstrate the ability of the new algorithm to discern small changes in atomic similarity that are brought about by second-neighbor effects. Comparisons among hydrogen atoms in the acrolein molecule reveal the usefulness of the similarity index in detection and quantification of the effects of steric interactions on atomic shapes. © 1996 by John Wiley & Sons, Inc.
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  • 76
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    Journal of Computational Chemistry 17 (1996), S. 1385-1386 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: No abstract.
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  • 77
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    Journal of Computational Chemistry 17 (1996), S. 1395-1405 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations have been carried out on s-trans-N-vinylmethyleneammonium, pyridinium, and related compounds to obtain rotational barriers, structures, and vibrational frequencies. The restricted Hartree-Fock (RHF) level of theory with 6-31G** basis set was used for these calculations. In addition, the MM2(91) and MM3(94) force fields have been parameterized to calculate these positively charged nitrogen-containing compounds. A bond order term was incorporated in the force field to reproduce accurately the rotational barriers of s-trans-N-vinylmethyleneammonium and related compounds. Molecular mechanics geometries and vibrational frequencies compare well with those calculated by ab initio methods. © 1996 by John Wiley & Sons, Inc.
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  • 78
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    Journal of Computational Chemistry 17 (1996), S. 1431-1443 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Locally dense basis sets using the mixed 6-311G(d, p)/3-21G basis can be used to reproduce total energies and correlation energies after empirical adjustment to 2-4 kcal/mol for a variety of small and medium size molecules containing hydrog en, carbon, and oxygen. Post-Hartree\-Fock methods can be calculated faster by this method by factors of 2-3, in general, and higher in the presence of high molecular symmetry; density functional approaches take longer and are impractical in the locally dense basis set approach. It is shown that the correlation energy in two of the better characterized density functional approaches is generally significantly larger than that of the post-Hartree-Fock treatments studied here and appears to be insensitive to the basis set employed. © 1996 by John Wiley & Sons, Inc.
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  • 79
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    Journal of Computational Chemistry 17 (1996) 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 80
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    Journal of Computational Chemistry 17 (1996), S. 1444-1452 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Semiempirical molecular orbital theory has been used to study the effects of solvation by acetonitrile on the Stevens rearrangement of methylammonium formylmethylide to 2-aminopropanal. Three methods of solvation have been used to investigate both the electrostatic and specific solvent-solute effects of solvation: a supermolecule calculation involving the complete geometry optimization of up to six solvent molecules about the solute, the conductor-like screening model (COSMO) polarizable continuum method which allows for geometry optimization of the solute in a solvent defined by its dielectric constant, and a hybrid method in which up to five solvent molecules are incorporated inside the solute cavity and complete geometry optimization of the complex is carried out within the polarizable continuum. A comparison of the calculated geometries, rearrangement activation energies, and enthalpies of solvation from these approaches is presented, and the explicit versus bulk solvation effects are discussed. The overall effect of all methods for incorporating solvation effects is that the radical pair pathway is perferred over the concerted mechanism. © 1996 by John Wiley & Sons, Inc.
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  • 81
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    Journal of Computational Chemistry 17 (1996), S. 1481-1495 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A combined ab initio SCF supermolecule and molecular mechanics investigation is carried out on the binding energetics of the divalent cations Mg2+, Ca2+, Zn2+, and Cd2+ to a series of the most common ligand functional groups found in biomolecules. The SCF binding energy components are resolved using the restricted variational space method.1 The results show that the SIBFA molecular mechanics (SMM) procedure2 reproduces the ab initio binding energies and total energy variations as a function of intermolecular variables. The model also reproduces the selectivity energetics for exchange reactions. Thus, the SMM procedure can be used without reparametrization to describe the coordination energetics of complex molecules including those subject to coordination changes. The energetic properties of divalent cation-hexahydrate complexes are compared as examples of a complete, realistic coordination system. The hexahydrates exhibit strong nonadditive effects typical of dication coordination. Nevertheless, these energetics are satisfactorily reproduced by the SMM procedure. © 1996 John Wiley & Sons, Inc.
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  • 82
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    Journal of Computational Chemistry 17 (1996), S. 1532-1540 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The previously reported 2Ag, 2A1g, and 2Bg states of ionized ethane are characterized at several levels of theory. The diborane-like 2Ag state, which gives rise to the observed ESR spectrum, is predicted by SCF and CCD calculations not to exist in a separate minimum from the 2A1g state formed by ionization of the C(SINGLE BOND)C bond. However, as reported by Lunell and Huang, second-order Moller-Plesset theory places the 2Ag lowest, provided polarization functions are included on carbon. QCISD theory predicts that both A states correspond to potential energy minima, but places the long-bond 2A1g state lower, at least with moderately large basis sets. F orbitals on carbon stabilize the diborane structure more than the long-bond one. When a potential energy surface is generated for a series of fixed C(SINGLE BOND)C bond lengths by optimizing all variables except for the C(SINGLE BOND)C bond length with MP2 theory and calculating the energy with QCISD(T), the 2Ag state is predicted to be the lowest energy state with the 2A1g state 1.83 kJ/mol above it. The two A states are predicted to be separated by a barrier 2.79 kJ/mol above the lower state. This barrier is above the zero-point energy in the C(SINGLE BOND)C stretch for the lower state but below the ZPE for this stretch in the upper state, which is therefore predicted not to exist as a stable species. A single quantum of vibrational excitation in the low frequency C(SINGLE BOND)C stretch is predicted to yield an ion with a poorly defined C(SINGLE BOND)C bond length. The highest levels of theory employed give poor agreement with the experimental hyperfine coupling constants. The discrepancy could either be due to neglect of vibrational effects, to poor inherent accuracy of the calculation, as one author has concluded, or to compression of the ion by the matrix as suggested by another. The 2Bg state is found to be higher in energy than the A states at all theoretical levels and is predicted to have a large (160.2-177.4 G) hyperfine coupling from four hydrogens. The transition state for simultaneous exchange of two hydrogen atoms between the carbons by a diborane structure is predicted to lie above the lowest energy fragmentation threshold, in agreement with experiment. © 1996 by John Wiley & Sons, Inc.
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  • 83
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    Journal of Computational Chemistry 17 (1996), S. 1549-1558 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An approximate method for calculating the exposed volume of the hydration shell (VHS) about an atom, the Reduced Radius Independent Gaussian Sphere (RRIGS) approximation, is presented. A key ingredient in this method is the use of reduced van der Waals radii so that the error of including only double overlap terms (and omitting multiple overlap terms) in calculating the VHS is balanced by a reduction in the magnitude of the double overlap terms. Also, the double overlap is modeled with a gaussian function. The RRIGS approximate calculation of the VHS is shown to be very accurate (the rms deviation of the VHS of each atom in avian pancreatic polypeptide and bovine pancreatic trypsin inhibitor was 14.0 and 15.8 Å3, respectively, out of a range of values between 0 and 600 Å3). The RRIGS approximation is used to develop a potential function to represent the free energy of solvation for proteins. The pairwise gaussian form of the potential enables it to be incorporated into a gaussian representation of ECEPP (Empirical Conformational Energy Program for Peptides) for use in the Diffusion Equation Method (DEM) of global optimization. Inclusion of the effects of hydration by means of this potential is shown to require less than twice the computational time needed for computing the ECEPP conformational potential energy alone; this makes inclusion of solvent computationally feasible. Furthermore, this gaussian hydration potential function and its derivatives are continuous, so that it may be readily minimized. The combined potential of ECEPP/3 plus hydration is shown to require fewer energy evaluations per local minimization than ECEPP/3 alone for two small peptides. © 1996 by John Wiley & Sons, Inc.
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  • 84
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    Journal of Computational Chemistry 17 (1996) 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 85
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    Journal of Computational Chemistry 17 (1996), S. 520-552 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article defines the parameterization and performance of MMFF94 for intermolecular interactions. It specifies the novel “buffered” functional forms used for treating van der Waals (vdW) and electrostatic interactions, and describes the use of : (1) high quality ab initio data to parameterize vdW interactions involving aliphatic hydrogens; and (2) HF/6-31G* calculations on hydrogen-bonded complexes to parameterize nonbonded interactions in polar systems. Comparisons show that appropriate trends in the HF/6-31G* data are well reproduced by MMFF94 and that intermolecular interaction energies and geometries closely parallel those given by the highly regarded OPLS force field. A proper balance between solvent-solvent, solvent-solute, and solute-solute interactions, critically important for prospective success in aqueous simulations, thus appears to be attained. Comparison of MMFF94, OPLS, CHELPG electrostatic potential fit, QEq, Gasteiger, and Abraham charges for 20 small molecules and ions also shows the close correspondence between MMFF94 and OPLS. As do OPLS and all current, widely used force fields, MMFF94 employs “effective pair potentials” which incorporate in an averaged way the increases in polarity which occur in high dielectric media. Some limitations of this approach are discussed and suggestions for possible enhancements to MMFF94's functional form are noted. © 1996 John Wiley & Sons, Inc.
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  • 86
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    Journal of Computational Chemistry 17 (1996), S. 553-586 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article describes the parameterization and performance of MMFF94 for molecular geometries and deformations. It defines the form used for the valence-coordinate terms that represent variations in bond lengths and angles, and it describes the derivation of quadratic force constants from HF/6-31G* data and the derivation of reference bond lengths and angles from fits to MP2/6-31G*-optimized geometries. Comparisons offered show that MMFF94 accurately reproduces the computational data used in its parameterization and demonstrate that its derivation from such data simultaneously confers the ability to reproduce experiment. In particular, MMFF94 reproduces experimentally determined bond lengths and angles for 30 organic molecules with root mean square (rms) deviations of 0.014 Å and 1.2°, respectively. MM3 reproduces bond angles to the same accuracy, but reproduces experimental bond lengths more accurately, in part because it was fit directly to thermally averaged experimental bond lengths; MMFF94, in contrast, was fit to (usually shorter) energy-minimum values, as is proper for an anharmonic force field intended for use in molecular-dynamics simulations. The comparisons also show that UFF and a recent version of CHARMm (QUANTA 3.3 parameterization) are less accurate for molecular geometries than either MMFF94 or MM3. For vibrational frequencies, MMFF94 and MM3 give comparable overall rms deviations versus experiment of 61 cm-1 and 57 cm-1, respectively, for 15 small, mostly organic molecules. In a number of instances, MM3's derivation employed observed frequencies that differ substantially - by nearly 400 cm-1 in one case - from other published frequencies which had themselves been confirmed theoretically by good-quality ab initio calculations. Overall, the comparisons to experimental geometries and vibrational frequencies demonstrate that MMFF94 achieves MM3-like accuracy for organic systems for which MM3 has been parameterized. Because MMFF94 is derived mainly from computational data, however, it has been possible to parameterize MMFF94 with equal rigor for a wide variety of additional systems for which little or no useful experimental data exist. Equally good performance can be expected for such systems. © John Wiley & Sons, Inc.
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  • 87
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    Journal of Computational Chemistry 17 (1996), S. 587-615 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article describes the parameterization and performance of MMFF94 for conformational energies, rotational barriers, and equilibrium torsion angles. It describes the derivation of the torsion parameters from high-quality computational data and characterizes MMFF94's ability to reproduce both computational and experimental data, the latter particularly in relation to MM3. The computational data included: (i) ∼ 250 comparisons of conformational energy based on “MP4SDQ/TZP” calculations (triple-zeta plus polarization calculations at a defined approximation to the highly correlated MP4SDQ level) at MP2/6-31G* geometries; and (ii) ∼ 1200 MP2/TZP comparisons of “torsion profile” structures at geometries derived from MP2/6-31G* geometries. The torsion parameters were derived in restrained least-squares fits that used the complete set of available computational data, thereby ensuring that a fully optimal set of parameters would be obtained. The final parameters reproduce the “MP4SDQ/TZP” and MP2/TZP computational data with root mean square (rms) deviations of 0.31 and 0.50 kcal/mol, respectively. In addition, MMFF94 reproduces a set of 37 experimental gas-phase and solution conformational energies, enthalpies, and free energies with a rms deviation of 0.38 kcal/mol; for comparison, the “MP4SDQ/TZP” calculations and MM3 each gives a rms deviation of 0.37 kcal/mol. Furthermore, MMFF94 reproduces 28 experimentally determined rotational barriers with a rms deviation of 0.39 kcal/mol. Given the diverse nature of the experimental conformational energies and rotational barriers and the clear indications of experimental error in some cases, the MMFF94 results appear excellent. Nevertheless, MMFF94 encounters somewhat greater difficulty in handling multifunctional compounds that place highly polar functional groups in close proximity, probably because it, like other commonly used force fields, too greatly simplifies the description of electrostatic interactions. Some suggestions for enhancements to MMFF94's functional form are discussed. © 1996 John Wiley & Sons, Inc.
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  • 88
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Vibrational frequencies for 11 alkenes and 8 conjugated hydrocarbons have been analyzed with MM4. The root mean square (rms) difference between the experimental and MM4 values is 25 cm-1 for seven alkenes and 31 cm-1 for eight conjugated hydrocarbons, compared to MM3 rms differences of 38 cm-1 for alkenes and 52 cm-1 for conjugated hydrocarbons. New MM4 cross-terms which primarily affect vibrational frequencies include bend-torsion-bend, improper torsion-torsion-improper torsion, and stretch-stretch, which improve in-plane bending, out-of-plane bending, and stretching frequencies, respectively. The stretching force parameter for conjugated bonds has been changed to vary quadratically with bond order (instead of linearly, as in MM3). The addition of a V4 term to the torsional potential for alkenes and conjugated hydrocarbons helps improve torsional frequencies. The torsion-torsion cross-term increases out-of-plane bending frequencies in conjugated hydrocarbons. This overall improvement in the vibrational frequencies does not result in any sacrifice in the accuracy of other quantities calculated by MM4. © 1996 by John Wiley & Sons, Inc.
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  • 89
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The hyperconjugative result of bond stretching in alkenes has been studied with MM4. A low-temperature crystallographic study of 1,2-diarylindane[a]indane has been carried out, together with ab initio (MP2/6-31G*) calculations on model systems. The results are well reproduced with a force field designed to explicitly include hyperconjugation (MM4), and they show beyond doubt that hyperconjugative bond elongations exist both in theory and by experiment. © 1996 by John Wiley & Sons, Inc.
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  • 90
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    Journal of Computational Chemistry 17 (1996), S. 489-489 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 91
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    Journal of Computational Chemistry 17 (1996), S. 910-917 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The computational algorithm that works in the coordinate space of dihedral angles(i.e., bond lengths and bond angles are kept fixed and only rotatable dihedral angles are treated as independent variables) is extended to deal with the pseudorotational m otion of furanose rings by introducing a variable of pseudorotation. Then, this algorithm is applied to a distance geometry calculation that generates three-dimensional (3D) structures that are consistent with given constraints of interatomic distances. This method efficiently generates 3D structures of an RNA hairpin loop which satisfy a set of experimental NMR data. © 1996 by John Wiley & Sons, Inc.
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  • 92
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    Journal of Computational Chemistry 17 (1996), S. 970-975 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new fast and accurate algorithm for numerical calculation of the van der Waals and solvent accessible surface areas based on the sorted table of cosines is described. This algorithm does not depend upon the particular distribution of the points on the sphere surface, and thus allows use of the most accurate points distribution available. Direct comparisons (on the same computer) with other known fast algorithms are performed. The comparisons show that this algorithm is the fastest when accurate calculation of the van der Waals surface is required and is at least as fast as the fastest competitor algorithm for the evaluation of the solvent accessible surface area. © 1996 by John Wiley & Sons, Inc.
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  • 93
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    Journal of Computational Chemistry 17 (1996), S. 1025-1032 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Energy calculations based on lattice models of protein chains are always approximate, because any such a model distorts distances between chain links and, consequently, the energies of interaction between them. The energetic errors of lattice models are examined here for 15 proteins of different sizes and types of secondary structure, for lattice spacings ranging from 0.25 to 2.5 Å. The lattice models are derived using previously described algorithms which insure a minimal root mean square (rms) deviation from the off-lattice structure for any given lattice-protein orientation. For each protein structure we computed a set of different lattice models with virtually equal rms deviations, and then compared their energies. Energy calculations were based on the pairwise potentials. We found that the energies of lattice models follows a normal distribution with a nonnegligible dispersion, even at a fine lattice spacing of 0.25 Å. For any lattice model of a protein, the lattice spacing must be 1.0 Å or less in order to be able to distinguish energetically between the folded and extended states. However, when an ensemble of lattice models is considered, this distinction can be made for lattice spacing up to 2.0 Å. We conclude that to attain a better approximation of the protein lattice model energies, one must adjust potentials to the lattice spacing. © 1996 by John Wiley & Sons, Inc.
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  • 94
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    Journal of Computational Chemistry 17 (1996), S. 1033-1055 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for describing a polypeptide chain based on an electrostatic multipole representation is introduced. The main features of the description are outlined. Appropriate energy functions for nonbonded interactions are developed. The full atomic representation may be retrieved from the electrostatic multipole representation at any point in a calculation. The multipole description and the energy functions are tested by calculation of steric maps for different amino acid side-chain groups. The ability to calculate energetically stable structures is demonstrated by energy conformation maps and the results of energy calculations in optimal secondary structural elements. Results from dynamics simulations of helical chains of polyglycine, polyalanine, polyvaline, and a 21-residue helix obtained from the crystal structure of sperm whale myoglobin are included to demonstrate the efficiency of the algorithm. It is demonstrated that this description of the polypeptide chain is both simple and complete and will allow for the rapid simulation of chain dynamics without loss of essential information about the chain. © 1996 by John Wiley & Sons, Inc.
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  • 95
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    Journal of Computational Chemistry 17 (1996), S. 1068-1084 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics (MD) simulations of α-D-maltose (maltose) in vacuo and with explicit inclusion of water were performed using the GROMOS force field that was modified to include a potential energy term for the exo-anomeric effect. Different simulation temperatures, the influence of the size of the water box, and carbohydrate-specific force field parameter values were evaluated with respect to sampling efficiency and average conformations. First, maltose was surrounded by 500 water molecules and simulated for 750 ps. Furthermore, three 500-ps MD simulations in vacuo were run to identify the effect of solvation on the location of the preferred conformation and on the flexibility of the molecule. Inclusion of water leads to a change of the preferred conformation from φ/ψ1 ≅ -20°/-17° in vacuo to -40°/-31° in aqueous solution. The explicit incorporation of water molecules into the simulation gave rise to only short-lived hydrogen bond interactions. In particular, a hydrogen bond found in vacuo from OH3 of the reducing glucose to O2′ of the nonreducing glucose was rarely present when water was included in the simulation. In vacuo the conformational freedom of the glycosidic linkage and the hydroxymethyl and hydroxyl groups were strongly reduced due to intramolecular hydrogen bonds. Two 200-ps MD runs with inclusion of 137 water molecules at temperatures of 350 and 400 K showed the expected increase of the transitions between the rotamers of the hydroxymethyl groups. An equilibrium for the conformation of the glycosidic linkage was only reached when raising the temperature parameter of the MD simulation further to 600 K. However, at this temperature inversions of the pyranose ring were already observed within a 1-ns MD simulation. Parametrization of GROMOS to include the exo-anomeric effect proved to be necessary because the previously published force field has no provisions to account for the exo-anomeric effect, as revealed by two MD simulations in water and in vacuo that indicated a significant population at positive φ angles. Using dimethoxymethane as a model for the O-glycosidic linkage, the empirical potential function for the rotation about the C1(SINGLE BOND)O1 bond was adjusted to represent the potential calculated by STO 6-31G* ab initio calculations. MD simulations using the adjusted force field revealed a reduced population with positive φ values. A separate parametrization of the potential for the reducing hydroxyl group of saccharides resulted in a better description of the conformation, as well as increased stability of the integration algorithm. Finally, the existing GROMOS force field was supplemented by an additional gauche potential. Its effect on the conformation of the hydroxymethyl groups was evaluated by a 500-ps MD simulation in water. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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  • 96
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1108-1111 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In the research of electron transfer (ET) reactions, the theoretical calculation of the ET matrix element VBA is of special importance. Some examples in which the two electron-localized states have a zero overlap were found. Thus, a new procedure for VBA calculation was developed and applied to the investigation of the donor-acceptor 90° oriented ET reactions. This procedure, which is a supplement necessary to the recently developed approach suitable for a nonorthogonal case, was derived in detail. To check the rationality of the zero value of VBA in the reaction O2O-2 → O-2O2, the angle dependence of SBA and VBA between two electron-localized states was calculated. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 97
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We investigated the convergence behavior of potential of mean force (PMF) calculations using free energy perturbation (FEP), thermodynamic integration (TI), and “slow growth” (SG) techniques. The critical comparison of these alternative approaches is illustrated by the study of three different systems: two tagged argon atoms in a periodic box of argon, two methane molecules, and two benzene molecules maintained in a “T-shaped” conformation, both dimers embedded in a periodic box of water. The complete PMF simulations were carried out considering several protocols, in which the number of intermediate “λ” states, together with the amount of sampling per individual state, were varied. In most cases, as much as 1 ns of molecular dynamics (MD) sampling was used to derive each free energy profile. For the different systems examined, we find that FEP and TI unquestionably constitute robust computational methods leading to results of comparable accuracy. We also show that proper convergence of the free energy calculations, and further quantitative interpretation of the PMFs, requires total simulation times much higher than has been hitherto estimated. In some circumstances, the free energy profiles derived from FEP calculations tend to be slightly poorer than those obtained with TI, as a probable consequence of the greater sensitivity of FEP to the window spacing δλ. In the context of TI, and to a lesser extent FEP, simulations, it appears preferable to employ a limited number of “λ” points of the integrand involving extensive sampling, rather than numerous points with fewer samplings. Finally, we note that, at least in the case of nonpolar interactions, PMFs of reasonable quality can be generated using SG, and at a substantially lower cost than with either FEP or TI. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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  • 98
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1269-1275 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present here a new iterative technique for reliable estimation of multidimensional free energy and potential of mean force (PMF) values by computer simulation. This method is an extension of the weighted histogram analysis method [S. Kumar et al., J. Comput. Chem., 13, 1011, (1992)]. We have tested the technique by generating free-energy-based Ramachandran plots and by computing the PMF values for end-to-end distances for several polypeptides using the ECEPP/2 and AMBER force fields. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 99
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1258-1268 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The distribution of molecular electrostatic potential (MEP) on a surface is a common model used to describe simultaneously steric properties (e.g., size, shape) and reactive properties (e.g., electro- and nucleophilic positions) of a molecule. In this work, we analyze some relations between these two properties. In particular, we explore the possible definition of an optimum fused-sphere molecular surface from properties of the MEP distribution. With this goal, we study how several statistical descriptors of the two-dimensional MEP distribution change upon shrinking or enlarging a van der Waals surface. We find that some of the descriptors exhibit critical points in terms of a scaling factor. We use this property to define effective atomic radii. In particular, we find that a reasonable molecular envelope is defined as the surface having the lowest (i.e., most negative) average negative MEP, with the largest possible dispersion about the mean. We discuss the resulting atomic radii and compare them with others in the literature derived from only steric considerations. The present results expand the scope of fused-sphere surfaces for modeling microscopic or structural molecular properties. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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  • 100
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1339-1343 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The integrated intensity of vibrational transitions depends on the magnitude of the derivatives of the dipole with respect to nuclear motion. These derivatives are usually obtained by time-consuming ab initio calculations. In this paper we apply a long-range model, based on distributed schemes for describing the charge densities and polarizabilities of molecules, to the prediction of dipole derivatives and infrared intensities for the N2 … HF complex. The results are found to agree qualitatively with full ab initio self-consistent field calculations. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 2 Tab.
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