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  • 1
    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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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 6
    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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  • 7
    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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  • 8
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 9
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 10
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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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  • 11
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 12
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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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  • 13
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 14
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    Journal of Computational Chemistry 17 (1996), S. 954-961 
    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 density or sum of states for a collection of independent oscillators, free rotors, and one-dimensional hindered rotors is obtained with good accuracy by numerical inversion of the corresponding total partition function by the method of steepest descents. The hindered-rotor partition functions are used in both classical and quantum forms, the latter in the approximation proposed by Truhlar [J. Comput. Chem., 12, 266 (1991)]. The numerical inversion compares well with analytical results obtained in a simple artificial case and also with an exact count of states in a large ethane-like system. Inversion of the hindered-rotor classical partition function is shown to lead to a somewhat different energy dependence of the sum or density of states, relative to the quantum counterpart, which is considered to be a more realistic representation. The routines presented are simple and fast enough to be of use in microcanonical rate calculations. © 1996 by John Wiley & Sons, Inc.
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  • 15
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    Journal of Computational Chemistry 17 (1996), S. 1520-1531 
    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 report theoretical calculations of ion extraction selectivity by ionophores, based on molecular dynamics simulations coupled with the free energy perturbation technique. This method is applied to the Calix[4]-bis-crown6 (L) ionophore, which displays remarkable selectivity for Cs+ over Na+ extraction from an aqueous to a chloroform phase. Using a thermodynamic cycle, we model the cation extraction selectivity of L from water to chloroform and calculate a peak for Cs+, in agreement with the experiment. This high Cs+ ionophoricity is accounted for mostly by differential solvation effects, with standard 1-6-12 pairwise potentials without need of “special π interactions” with the ionophore. The effect of a picrate (Pic-) counterion on structures and selectivities is investigated. Finally, we report simulations on the L ionophore free and on the LCs+ and LCs+Pic- complexes at the water/chloroform interface. We find that all these species are “adsorbed” at the interface like surfactants instead of diffusing spontaneously to the organic phase. © 1996 by John Wiley & Sons, Inc.
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  • 16
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    Journal of Computational Chemistry 17 (1996), S. 1559-1563 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Scattering matrices in an adiabatic basis were calculated for a model two-state atomic collision using a simple modification (normalization of the wave function) of the Fox - Goodwin three-point recurrence relation. Unlike the previous application of this method to scattering the present algorithm was able to precisely calculate the scattering matrix not only at low collision energies (eV), but also at high energies (keV). An analysis of the convergence of the modified Fox - Goodwin algorithm is also discussed for several angular momenta and for several energies where the results were compared to the renormalized Numerov method. © 1996 by John Wiley & Sons, Inc.
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  • 17
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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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  • 18
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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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  • 19
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    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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  • 20
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    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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  • 21
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    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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  • 22
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    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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  • 23
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    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
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    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
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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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    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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    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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    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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    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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    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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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
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    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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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A density matrix evolution method [H. J. C. Berendsen and J. Mavri, J. Phys. Chem., 97, 13464 (1993)] to simulate the dynamics of quantum systems embedded in a classical environment is applied to study the inelastic collisions of a classical particle with a five-level quantum harmonic oscillator. We improved the numerical performance by rewriting the Liouville-von Neumann equation in the interaction representation and so eliminated the frequencies of the unperturbed oscillator. Furthermore, replacement of the fixed time step fourth-order Runge-Kutta integrator with an adaptive step size control fourth-order Runge-Kutta resulted in significantly lower computational effort at the same desired accuracy. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996) 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
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    Topics: Chemistry and Pharmacology , Computer Science
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  • 34
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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: 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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  • 35
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    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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    Journal of Computational Chemistry 17 (1996), S. 976-991 
    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 presents a fast adaptive method for the computation of long-range electrostatic interactions in computer simulations of polyelectrolyte DNA. Classically, the computation of electrostatic energy involves a direct summation of all pairwise in teractions due to the charged phosphate groups in the molecule. This results in an N-body interaction problem with an asymptotic time complexity of O(N2) which is computationally very expensive and limits the number of phosphate groups that can be used in computer simulations of polyelectrolyte DNA to at most several hundred. We describe an effort to speed up computer simulations of polyelectrolyte DNA with the use of a fast adaptive hierarchical algorithm for the computation of electrostatic energy (i.e., modified Debye-Hückel energy). The asymptotic time complexity is reduced to O(N) with the implementation of the fast hierarchical algorithm on serial computers. This is achieved by grouping phosphate groups into an adaptive hierarchical data structure and computing the interactions between groups using low order multipole and Taylor series expansions expressed in Cartesian coordinates. We first examine the accuracy and speed enhancements of the fast hierarchical method in the computation of the electrostatic energy of circular DNA at zero and high salt concentrations. The fast hierarchical method is further tested in a one-step Monte Carlo (MC) simulated annealing algorithm for closed circular supercoiled DNA. In all cases, we observe order of magnitude reductions in the computation time with negligible loss of numerical accuracy in the electrostatic energy computation. © 1996 by John Wiley & Sons, Inc.
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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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    Journal of Computational Chemistry 17 (1996), S. 1056-1067 
    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 applied the spectral-representation technique developed by Katsuki and Huzinaga as a model potential in calculating the electronic structure of Cu clusters. The characteristics of this potential were closely investigated in Cu and Cu2. For Cu, Cu2, Cu5, Cu9, and Cu13, we performed all-electron ab initio self-consistent field calculations and model-potential calculations where 3p, 3d, and 4s electrons, and 3d and 4s electrons are treated as valence electrons. The ionization potentials (IPs) given by the all-electron calculations were 6.26, 5.55, 4.52, 4.02, and 4.08 eV for Cu, Cu2, Cu5, Cu9, and Cu13, respectively. The IPs given by the model-potential calculations were 6.25, 5.56, 4.62, 4.09, and 4.23 eV for the 3p-, 3d-, and 4s-valence electrons, and 6.26, 5.68, 4.71, 4.07, and 4.19 eV for the 3d- and 4s-valence electrons. The IPs given by the model-potential calculations agree well with those of the all-electron calculations. We also performed model-potential calculations where only the 4s electrons were treated as valence electrons. The calculated IPs were 6.47, 5.98, 5.38, 4.63, and 4.88 eV for Cu, Cu2, Cu5, Cu9, and Cu13, respectively. These are ca. 0.8 eV higher than the IPs by the all-electron calculation for the larger clusters of Cu5, Cu9, and Cu13. The higher IPs originate from the expulsion of the 3d electrons from the valence electrons. We also performed model-potential calculations with 4s electrons for Cu74. The calculated IP is 4.61 eV, which is estimated to be 0.8 eV larger than that obtained by the all-electron calculation. The IPs with correlation corrections are 7.7, 7.4, 6.3, 5.8, 5.9, and 5.6 eV for Cu, Cu2, Cu5, Cu9, Cu13, and Cu74, respectively. Experimental values are 7.73, 7.37, 6.30, 5.37, 5.67, and 5.26 eV. The agreement between the two is fairly good. The electron affinities are also discussed. © 1996 by John Wiley & Sons, Inc.
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    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.
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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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    Journal of Computational Chemistry 17 (1996), S. 1156-1162 
    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 describe a new method to simulate confined fluids in equilibrium with a bulk. The equilibrium is first located at a low density, where conventional methods relying upon real or virtual particle exchanges are reliable. Thereafter, the chemical potential of the fluid is increased by the same amount in both systems using a variation of a recently developed free energy difference method in an isobaric (isotension) ensemble. The method, illustrated here for a simple fluid in a planar slit, is shown to be reliable up to high densities. As the method does not rely upon particle exchanges it is ideally suited to the simulation of equilibria in complex fluids, e.g., molecular liquids and polymers. © 1996 by John Wiley & Sons, Inc.
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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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    Journal of Computational Chemistry 17 (1996), S. 358-366 
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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 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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    Journal of Computational Chemistry 17 (1996), S. 396-408 
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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: 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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    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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    Journal of Computational Chemistry 17 (1996), S. 1541-1548 
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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: Molecular dynamics simulations have been carried out on the cyclopentane molecule using a diagonal force field and the results compared with both experiment and a recent study which used the MM3 force field [W. Cui, F. Li, and N. L. Allinger, J. Am. Chem. Soc., 115, 2943 (1993)]. The current simulation resulted in an RMS pseudorotational velocity of 1036 deg/ps, compared to the model estimated value of 400 deg/ps and the MM3 result of 1700 deg/ps. The pseudorotation amplitude was calculated to be 0.46 ± 0.02 Å, compared to the experimental value of 0.48 Å and the MM3 value of 0.5 ± 0.03 Å. The two distinct average C(SINGLE BOND)H bond lengths seen for the axial and equatorial conformations in the MM3 simulation were not observed. The energy barrier to passing through the planar conformation was calculated at 4.7 kcal/mol as compared to the experimental value of 5.2 kcal/mol and the MM3 value of 4.2 kcal/mol. During the simulation, the angle bending term dominated the potential energy, followed by the torsion energy, as was seen with MM3. The third largest energy term was the bond stretching, followed by the van der Waals interaction, the reverse of what was seen with MM3. The effects of carrying out the simulation under conditions of constant energy versus constant temperature are discussed. © 1996 by John Wiley & Sons, Inc.
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  • 47
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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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  • 48
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    Journal of Computational Chemistry 17 (1996), S. 1587-1597 
    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 recently proposed molecular dynamics method for estimating binding free energies is applied to the complexation of two charged benzamidine inhibitors with trypsin. The difficulties with calculations of absolute binding energies for charged molecules, associated with long-range electrostatic contributions, are discussed and it is shown how to deal with these effectively. In particular, energetic effects caused by the trunction of dipole-dipole interactions in the medium surrounding the charged ligand are examined and found to be significant. Calculations of the absolute binding energy for benzamidine using the free energy perturbation approach are also reported. These simulations illustrate the typical problems associated with annihilation transformations of molecules bound inside proteins. © 1996 by John Wiley & Sons, Inc.
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  • 49
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    Journal of Computational Chemistry 17 (1996), S. 1633-1644 
    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 convenient computational approach for the calculation of the p Kas of ionizable groups in a protein is described. The method uses detailed models of the charges in both the neutral and ionized form of each ionizable group. A full derivation of the theoretical framework is presented, as are details of its implementation in the UHBD program. Application to four proteins whose crystal structures are known shows that the detailed charge model improves agreement with experimentally determined pKas when a low protein dielectric constant is assumed, relative to the results with a simpler single-site ionization model. It is also found that use of the detailed charge model increases the sensitivity of the computed pKas to the details of proton placement. © 1996 by John Wiley & Sons, Inc.
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  • 50
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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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  • 51
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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 and rotational decoupling approximations are tested in three-dimensional Fermi Golden Rule calculations on energies, lifetimes, and product state distributions of the vibrationally predissociating atom - diatom van der Waals complexes. The validity of approximate separations of diatom vibration, decoupling of stretching and bending intermolecular motions, and rotational infinite order sudden approximation for product scattering is characterized by comparison with the results of accurate calculations on the Ne ··· Cl2, Ne ··· ICl, and He ··· ICl systems. The most accurate approximate schemes are recommended. © 1996 by John Wiley & Sons, Inc.
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  • 52
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    Journal of Computational Chemistry 18 (1997), S. 139-149 
    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 program for automatic resonance assignment of nuclear magnetic resonance (NMR) spectra of proteins, GARANT (General Algorithm for Resonance Assignment), is introduced. Three principal elements used in this approach are: (a) representation of resonance assignments as an optimal match of two graphs describing, respectively, peaks expected from combined knowledge of the primary structure and the magnetization transfer pathways in the spectra used, and experimentally observed peaks; (b) a scoring scheme able to distinguish between correct and incorrect resonance assignments; and (c) combination of an evolutionary algorithm with a local optimization routine. The score that evaluates the match of expected peaks to observed peaks relies on the agreement of the information available about these peaks, most prominently, but not exclusively, the chemical shifts. Tests show that the combination of an evolutionary algorithm and a local optimization routine yields results that are clearly superior to those obtained when using either of the two techniques separately in the search for the correct assignments. GARANT is laid out for assignment problems involving peaks observed in two- and three-dimensional homonuclear and heteronuclear NMR spectra of proteins. © 1997 by John Wiley & Sons, Inc.
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  • 53
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    Journal of Computational Chemistry 18 (1997), S. 159-168 
    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 parallel implementation of the computation of RHF energy second derivatives with respect to the nuclear coordinates is described. The algorithm and organization of the code are described in detail on the most computationally demanding steps with special emphasis on the integral transformation code. Key features of the proposed algorithm are its large degree of concurrency, limited interprocessor communication, and critical memory needs distributed over the processors. The cpu times and computer and network resources used are reported and discussed for a few examples. © 1997 by John Wiley & Sons, Inc.
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  • 54
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    Journal of Computational Chemistry 18 (1997), S. 198-210 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: All four possible Diels-Alder reactions between 2H-phosphole and phosphaethene were examined at various theoretical levels, including HF, MP4SDQ, CCSD(T), and CASSCF. MP2/6-31G* geometry optimizations could not be employed since the potential energy surface is qualitatively incorrect at this level of theory, due to the inherent underestimation of the activation energies (ameliorated at higher-order MP or coupled-cluster levels). Solvent effects were examined employing the Onsager, polarized continuum, and isodensity and surface polarized continuum models. At MP4SDQ/6-31G*//HF/6-31G* these reactions are exothermic by 34-38 kcal mol-1 and have very low activation energies, 5-7 kcal mol-1. The P—P/C—C regioisomer products are lower in energy than the C—P isomers and, within each pair, the exo isomer is lower in energy. At low computational levels the smallest activation energy is for the reaction leading to the C—P endo product. Larger basis sets, electron correlation, and solvent favor the transition state leading to the experimentally observed P—P/C—P endo isomer. The dimerization of phosphole is, therefore, kinetically controlled. Based on geometric and electron density analysis, the reactions are concerted and synchronous. © 1997 by John Wiley & Sons, Inc.
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  • 55
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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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  • 56
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    Journal of Computational Chemistry 17 (1996), S. 1085-1098 
    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 introduce a general and versatile MS Windows application for solving the spherically symmetric diffusion problem, involving up to two coupled spherically symmetric Smoluchowski equations. The application is based on a modular, configurable, user-friendly graphical interface, in which input parameters are introduced through a graphical representation of the system of partial differential equations and output attributes can be obtained graphically during propagation.The numerical algorithm consists of finite differencing in space and Chebyshev propagation in time; it includes an implementation of virtual gridding, which enhances the accuracy of calculating boundary conditions and steep potentials. The program has b een checked against a wide collection of analytical solutions and applied to an experimentally open problem in excited-state proton-transfer to solvent. © 1996 by John Wiley & Sons, Inc.
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  • 57
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    Journal of Computational Chemistry 17 (1996), S. 1099-1107 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Structures of the H3O+-OH ion pair surrounded by up to three water molecules have been studied. Since the ion-pair structure is always above the corresponding neutral water structure, a constrained geometry optimization is needed. The energy difference between the ion-pair structure and the neutral water structure is studied as a function of the number of surrounding water molecules. The effect of the surrounding water solvent is also studied by placing the model system in a spherical cavity in a dielectric medium. The main results are that the energy difference stabilizes at 10-20 kcal/mol for the larger clusters and that an effect indicating a mechanism for charge separation can be noticed on the geometries of these clusters. Results obtained using gradient-corrected density-functional theory are compared to a configuration interaction treatment using a scaling procedure of the correlation energy. © 1996 by John Wiley & Sons, Inc.
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  • 58
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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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  • 59
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    Journal of Computational Chemistry 17 (1996), S. 669-694 
    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 MM4 force field has been extended to alkenes. It retains most of the formalism and computational schemes that were present in MM3. Several additional cross-terms have been added in MM4 that were not present in MM3, mainly to improve vibrational frequencies but also to improve structures and energies. About 100 molecules have been examined, many in multiple conformations. Geometries are fit for the most part to within the following ranges: 0.004 Å for bond lengths, 1° for bond angles, 4° for torsion angles, and 0.5% for moments of inertia (r2). Conformational energy differences/barriers are generally fit to within 0.5 kcal/mol unless they are very large. The vibrational frequency rms error for 7 alkenes is 25 cm-1. © 1996 by John Wiley & Sons, Inc.
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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
    Topics: Chemistry and Pharmacology , Computer Science
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  • 61
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    Journal of Computational Chemistry 18 (1997), S. 9-19 
    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 G2 search of the triplet [H4, Si, P]+ potential energy surface (PES) was carried out, along with a study of a number of mechanisms for the reaction of the P+ (3P) ion with silane. The most stable isomer, which corresponds to the species resulting from transferring three hydrogen atoms from the silicon to the phosphorus atom, lies 67.3 kcal/mol below the reactants' level. The P+—SiH4 ion-molecule complex also has remarkable stability, 20.4 kcal/mol. Bond properties were calculated and are discussed for all the stable species found on the PES. Various exothermic reaction paths were also fully characterized. The abstractions of a hydrogen molecule and a hydrogen atom, yielding species with P—Si bonds, have comparable kinetic hindrance, although release of molecular hydrogen was found to be more exothermic. Finally, hydrogen and/or charge transfer reactions between P+ (3P) and silane are also discussed. © 1997 by John Wiley & Sons, Inc.
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  • 62
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    Journal of Computational Chemistry 18 (1997), S. 449-462 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Four commonly used molecular mechanics force fields, CHARMM22, OPLS, CVFF, and GROMOS87, are compared for their ability to reproduce experimental free energies of hydration (ΔGhydr) from molecular dynamics (MD) simulations for a set of small nonpolar and polar organic molecules: propane, cyclopropane, dimethylether, and acetone. ΔGhydr values were calculated by multiconfiguration thermodynamic integration for each of the different force fields with three different sets of partial atomic charges: full charges from an electrostatic potential fit (ESP), and ESP charges scaled by 0.8 and 0.6. All force fields, except for GROMOS87, give reasonable results for ΔGhydr · if partial atomic charges of appropriate magnitude are assigned. For GROMOS87, the agreement with experiment for hydrocarbons (propane and ethane) was improved considerably by modifying the repulsive part of the carbon-water oxygen Lennard-Jones potential. The small molecules studied are related to the chemical moieties constituting camphor (C10Hl6O). By invoking force-field transferability, we calculated the ΔGhydr for camphor. With the modified GROMOS force field, a ΔGhydr within 4 kJ/mol of the experimental value of -14.8 kJ/mol was obtained. Camphor is one of the largest molecules for which an absolute hydration free energy has been calculated by molecular simulation. The accuracy and reliability of the thermodynamic integration calculations were analyzed in detail and we found that, for ΔGhydr calculations for the set of small molecules in aqueous solution, molecular dynamics simulations of 0.8-1.0 ns in length give an upper statistical error bound of 1.5 kJ/mol, whereas shorter simulations of 0.25 nm in length given an upper statistical error bound of 3.5 kJ/mol. © 1997 by John Wiley & Sons, Inc.
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  • 63
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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: We describe the implementation of the cell multipole method (CMM) in a complete molecular dynamics (MD) simulation program (MPSim) for massively parallel supercomputers. Tests are made of how the program scales with size (linearly) and with number of CPUs (nearly linearly) in applications involving up to 107 particles and up to 500 CPUs. Applications include estimating the surface tension of Ar and calculating the structure of rhinovirus 14 without requiring icosahedral symmetry. © 1997 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
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  • 65
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    Journal of Computational Chemistry 17 (1996), S. 1296-1308 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Comparative molecular field analysis (CoMFA) is a three-dimensional quantitative structure-activity relationship (3D-QSAR) method which correlates precalculated fields surrounding a set of molecules with some target property. Among others, the electrostatic fields are commonly used. These are usually generated by calculating the Coulomb potential between a probe and the molecules bearing atom-centered point charges. The present study was performed in order to investigate up to which extent different methods to calculate electrostatic potentials can influence the results of a CoMFA. Therefore, a variety of charge calculation methods was applied to a data set consisting of 37 ligands of the benzodiazepine receptor inverse agonist-antagonist active site. These methods included Gasteiger-Marsili, semiempirical (MNDO, AM1, and PM3), and ab initio (HF/STO-3G, HF/3-21G*, and HF/6-31G*) charges. Semiempirical as well as ab initio electron populations were derived both from the Mulliken population analysis (MPA) or from fitting the charges to the molecular electrostatic potential (ESPFIT charges). In addition, the molecular electrostatic potentials (MEPs) resulting from ab initio calculations were mapped directly onto the CoMFA grid. With regard to the cross-validated r2 values (r2cv) of the resulting QSAR models, the ESPFIT-derived potentials yielded generally higher r2cv values than those resulting from MPA charges. For example, at the HF/3-21G* level the r2cv rose from 0.61 (MPA-derived potentials) to 0.76 (ESPFIT fields). The MEPs mapped directly onto the CoMFA grid were not superior to the corresponding ESPFIT-derived potentials. Semiempirical ESPFIT charges appeared to be of similar quality compared with ab initio ESPFIT electron populations in the CoMFAs. When no scaling between the steric and electrostatic descriptor matrices was applied, the electrostatic contributions were influenced to a high degree by the magnitude of the corresponding field values. © 1996 by John Wiley & Sons, Inc.
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    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.
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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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    Journal of Computational Chemistry 18 (1997), S. 712-721 
    ISSN: 0192-8651
    Keywords: molecular mechanics ; neolignans ; conformational analysis ; environment effect ; active conformation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational analysis of 20 neolignans was performed to determine the most probable conformer that may fit the receptor. The molecular mechanics method (MM2) was employed to construct conformational maps in both a vacuum and a biological environment. Boltzmann's distribution among several local minima was calculated. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 712-721, 1997
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    Journal of Computational Chemistry 18 (1997), S. 723-743 
    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 Monte Carlo docking procedure that combines random displacements of the substrate and protein side chains with minimization of the enzyme - substrate complex is described and applied to finding the binding mode of the blocked tetrapeptide N-acetyl-Leu-Pro-Phe-methylamide to the FK506 binding protein (FKBP). The tetrapeptide, an analog of the preferred FKBP substrate, and the FKBP binding site are flexible during the docking procedure. The twisted-imide transition-state form of the substrate is used during docking. The enzyme charges are scaled individually to account for solvent screening of specific binding site residues during the Monte Carlo sampling. To evaluate the relative binding free energies of the resulting structures, a rapid method for calculating polar and nonpolar solvation effects is introduced. Accurate electrostatic solute - solvent energies are calculated by solving the finite-difference linearized Poisson - Boltzmann equation; nonpolar contributions to the stability of the different conformers are estimated by the free energy of cavity formation, which is obtained from the molecular surface, and the solute - solvent van der Waals energy, which is calculated with a continuum approach. In the conformation of the enzyme - substrate complex with the lowest free energy, the tetrapeptide is bound as a type VIa proline turn with solvent accessible ends to permit longer polypeptide chains to act as substrates. Except for the imide carbonyl, which is involved in polar interactions with aromatic side chains of the FKBP binding site, all of the seven potential hydrogen bond donors or acceptors of the tetrapeptide are satisfied. The FKBP binding site has a similar conformation in the substrate complex as in the FKBP-FK506 cocrystal structure, except for the predicted reorientation of the Tyr 82 hydroxyl, which plays an important role in substrate binding. The present model for the FKBP - substrate complex is in agreement with the recently determined crystal structure of a cyclic peptide - FK506 hybrid bound to FKBP and supports the structure obtained previously by iterative model building. In addition, it is consistent with the observed effects of FKBP point mutations on the enzyme activity. The approach described here should be useful, in general, for the prediction of the structure of a molecule in solution or as part of a complex. It provides for the effective sampling of conformational space and for the inclusion of solvent effects. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 796-811 
    ISSN: 0192-8651
    Keywords: DNA ; normal mode ; flexibility ; modeling ; DNA bending ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Normal mode calculations for two alternating sequence dodecamers in A, B, and Z conformations have been performed in dihedral angle space extended to endocyclic valence angles to account for sugar ring flexibility. Normal modes are analyzed in terms of helicoidal and backbone parameter variations with special attention being paid to global deformations of the double helix such as bending, twisting, or stretching. Results show that the allomorphic form of DNA has the largest influence on the flexibility of the sugar-phosphate backbone. Amplitudes of these vibrations follow the order: B 〉 Z 〉 A. In contrast, the amplitudes of helicoidal parameter variations are much more dependent on the base sequence. Global deformations of the double helix occur with characteristic times in the range of 1 to 10 ps and can be of mixed character, the strongest bending mode being at the same the time strongest stretching mode. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 796-811, 1997
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  • 71
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    Journal of Computational Chemistry 18 (1997), S. 381-392 
    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 the results of simulations of the structures and optical absorption spectra of Na atoms in solid and liquid Ar at its triple point, and in critical-point Ar fluid. The spectral simulations combine a classical Monte Carlo scheme for generating thermally accessible ground state configurations, along with a first-order perturbation theory treatment of the interactions between the excited Na*(3p 2P) atom and the surrounding Ar perturbers [Boatz and Fajardo, J. Chem. Phys., 101, 3472 (1994)]. These simulations predict a “triplet” (i.e., three peaks) absorption lineshape for Na atoms in solid and liquid Ar at its triple point, and an asymmetrical, blue degraded absorption band for Na atoms in critical Ar fluid. We also note and discuss the similarities between the simulated Na/Ar(1) lineshape and an experimental Li/Ar/Xe mixed host matrix spectrum, and the similarities between the simulated spectrum of Na atoms in critical point Ar fluid, and an experimental Li/H2 matrix absorption spectrum. © 1997 by John Wiley & Sons, Inc.
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  • 72
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    Journal of Computational Chemistry 18 (1997), S. 403-415 
    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 has been developed for minimizing the energy of a polypeptide with rigid geometry while keeping all disulfide loops closed exactly. Exact closure of disulfide loops implies that some dihedral angles become implicit functions of the remaining dihedral angles in the polypeptide; the efficacy of the method is related to the manner in which the implicitly defined dihedral angles are chosen. The method has been used to find minimum-energy conformations of bovine pancreatic trypsin inhibitor, ribonuclease A, crambin, the defensin HNP3 dimer, and ω-conotoxin. For the first two proteins, the starting conformations for energy minimization had been derived previously from crystal structures using pseudopotentials to keep the disulfide loops almost closed. Starting conformations for the remaining three proteins were derived from their crystal or NMR structures by similar procedures. In all cases, the energy-minimized structures had a significantly and, in some cases, substantially, lower energy than the starting structures. The RMS deviations between the exactly closed energy- minimized structures and the crystal or NMR structures from which they were derived ranged from 0.9 Å to 1.9 Å, suggesting that the computed structures can serve as “regularized” native structures for these proteins. The energy of a ribonuclease derivative lacking the 65-72 disulfide bridge was minimized using the procedure; the result showed that this derivative has a low-energy structure with a conformation very close to that of native ribonuclease, and is consistent with its postulated role in the folding of ribonuclease. These results offer strong support for the validity of the rigid-geometry model in the studies of the conformational energy of proteins. © 1997 by John Wiley & Sons, Inc.
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  • 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: A computational scheme is presented which combines quantum mechanical ab initio techniques with methods using analytical potential functions. The scheme is designed for use in structure optimizations and is also applicable to molecular dynamics simulations. The implementation covers both molecular and periodic systems. The problem of the link atoms is solved by a subtraction scheme which is easily implemented for any combination of methods. As a first application dense and microporous silica polymorphs are studied. The Hartree-Fock method is combined with both a force field and an ion pair shell model potential. Comparison is made with lattice energy minimizations which use the force field or the shell model potential alone as well as with free cluster optimizations and optimizations in which the outer part of the cluster is kept fixed. © 1997 by John Wiley & Sons, Inc.
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  • 74
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    Journal of Computational Chemistry 18 (1997), S. 489-500 
    ISSN: 0192-8651
    Keywords: benzofuroxan ; ortho-dinitrosobenzene ; nitrosobenzene ; vibrational spectra ; tautomerism ; density functional theory (DFT) ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular rearrangement of benzofuroxan was studied by comparing calculated and experimental IR spectra, the latter taken before and during the reaction. All calculations were performed at the B3-LYP/6-31G(d) density functional level with a further refinement of the computed force constants done by applying the scaled quantum mechanical force field (SQM) technique. Complete assignments for the IR spectra of benzofuroxan and nitrosobenzene are given. The agreement between computed and experimental spectra is excellent, but in benzofuroxan these spectra are very different from previously calculated data. The conformation of the ortho-dinitrosobenzene intermediate of this tautomeric reaction was identified by modeling a composite IR spectrum of four possible components. It shows good agreement with an experimental spectrum that was obtained after photolysing benzofuroxan in Xe matrix. Knowing the conformation of the intermediate provides insight into the reaction mechanism and allows inferences for the thermal reaction, which could not be clarified conclusively by energetic considerations only. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 489-500, 1997
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  • 75
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    Journal of Computational Chemistry 18 (1997), S. 533-551 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Allyl cation geometries optimized using an extended version of MMP2, newly parameterized for localized and delocalized classical cations, compare favorably with those obtained at the MP2(full) /6-31G* level. Hence, the force field should provide good starting structures for ab initio calculations. The π-electron densities obtained by these two very different methods are quite similar. The relative energies of various isomers at MP4/6-31G*//MP2(full)/6-31G* are reproduced well by the force-field calculations. The heats of formation calculated by MMP2, as well as those predicted from the ab initio data, agree with experimentally determined values. The force-field method provides interpretive capabilities. Energy differences between isomers can be separated into electronic and steric contributions, reasonable estimates of resonance energies are given, and nonbonded resonance energies in delocalized cations can be evaluated. The stabilizing 1-3 π-interactions in allyl cations are quite significant, but are reduced by alkyl groups hyperconjugatively and sterically. © 1997 by John Wiley & Sons, Inc.
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  • 76
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    Journal of Computational Chemistry 18 (1997), S. 569-583 
    ISSN: 0192-8651
    Keywords: fast multigrid boundary element method ; macromolecular electrostatic calculations ; poisson equation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A fast multigrid boundary element (MBE) method for solving the Poisson equation for macromolecular electrostatic calculations in a solvent is developed. To convert the integral equation of the BE method into a numerical linear equation of low dimensions, the MBE method uses an adaptive tesselation of the molecular surface by BEs with nonregular size. The size of the BEs increases in three successive levels as the uniformity of the electrostatic field on the molecular surface increases. The MBE method provides a high degree of consistency, good accuracy, and stability when the sizes of the BEs are varied. The computational complexity of the unrestricted MBE method scales as O(Nat), where Nat is the number of atoms in the macromolecule. The MBE method is ideally suited for parallel computations and for an integrated algorithm for calculations of solvation free energy and free energy of ionization, which are coupled with the conformation of a solute molecule. The current version of the 3-level MBE method is used to calculate the free energy of transfer from a vacuum to an aqueous solution and the free energy of the equilibrium state of ionization of a 17-residue peptide in a given conformation at a given pH in ∼ 400 s of CPU time on one node of the IBM SP2 supercomputer. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 569-583, 1997
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  • 77
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    Journal of Computational Chemistry 18 (1997), S. 584-593 
    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 homomolecular differential bond separation reaction may be defined as the difference between the conventional bond separation reactions involving the unsaturated system and its saturated counterpart. Such a reaction is homomolecular in that the basic molecular structures involved are the same on both sides of the reaction. The type of homodesmotic reaction that also conserves structure in this way may be termed a homomolecular homodesmotic reaction. Both types of homomolecular reactions are readily related to hydrogenation reactions and, more importantly, to each other. Δ B(n), the energy of the homomolecular differential bond separation reaction involving a system with n double bonds, and H(n), the corresponding homomolecular homodesmotic reaction, are related by: $$\Delta B(n)-H(n)= n \cdot (h(1)-h(e))$$ where h(1) and h(e) are the hydrogenation energies of the system's monoene and of ethylene, respectively. Both types of reactions yield measures of cyclic conjugation energies that for certain classifications of molecules are simply related to each other. Consideration of extra conjugation in the monoenes allows a ready interpretation of those cases in which a simple classification is not obtained. Ab initio calculations illustrating these effects have been carried out on a variety of molecules including many five- and six-membered ring systems using second order Møller-Plesset and density functional approaches. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1857-1862 
    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 describe novel lookup tables for the rapid calculation of interatomic interactions. The tables have nonuniform distributions of bin widths tailored to minimize numerical error and maximize computational speed. Since interaction energies are precalculated, computer time requirements are essentially independent of the form of the potential function used. In test calculations using the AMBER force field and an internal coordinate Monte Carlo algorithm, the lookup table runs 15% faster than direct calculation of nonbonded interactions. The method is more advantageous for more complicated energy functions. As an example of a more complicated potential function, we have tested a pairwise approximation to accessible surface area. In this case, the use of the lookup table results in a speedup of a factor of two. The method is straightforward to implement and should be widely applicable. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1848-1856 
    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 ring chain tautomerism of benzofurazan-1-oxide (benzofuroxan) has been reinvestigated using ab initio as well as nonlocal density functional theory. The failure in predicting energies and geometries of this reaction by wave functions at the Hartree-Fock or even at the MP2 level could be overcome by using the nonlocal three-parameter hybrid exchange correlation functional of Becke and Lee, Young, and Parr (B3-LYP). Two possible reaction paths via ortho-dinitrosobenzene have been studied, considering both ground and transition states. At the B3-LYP level of theory, both mechanisms show very similar activation energies which are in excellent agreement with experimental results. Solvent effects, simulated by a self-consistent reaction field (SCRF) model, cause alternations in the preferred mechanism as well as in the most stable intermediates. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 490-519 
    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 introduces MMFF94, the initial published version of the Merck molecular force field (MMFF). It describes the objectives set for MMFF, the form it takes, and the range of systems to which it applies. This study also outlines the methodology employed in parameterizing MMFF94 and summarizes its performance in reproducing computational and experimental data. Though similar to MM3 in some respects, MMFF94 differs in ways intended to facilitate application to condensed-phase processes in molecular-dynamics simulations. Indeed, MMFF94 seeks to achieve MM3-like accuracy for small molecules in a combined “organic/protein” force field that is equally applicable to proteins and other systems of biological significance. A second distinguishing feature is that the core portion of MMFF94 has primarily been derived from high-quality computational data - ca. 500 molecular structures optimized at the HF/6-31G* level, 475 structures optimized at the MP2/6-31G* level, 380 MP2/6-31G* structures evaluated at a defined approximation to the MP4SDQ/TZP level, and 1450 structures partly derived from MP2/6-31G* geometries and evaluated at the MP2/TZP level. A third distinguishing feature is that MMFF94 has been parameterized for a wide variety of chemical systems of interest to organic and medicial chemists, including many that feature frequently occurring combinations of functional groups for which little, if any, useful experimental data are available. The methodology used in parameterizing MMFF94 represents a fourth distinguishing feature. Rather than using the common “functional group” approach, nearly all MMFF parameters have been determined in a mutually consistent fashion from the full set of available computational data. MMFF94 reproduces the computational data used in its parameterization very well. In addition, MMFF94 reproduces experimental bond lengths (0.014 Å root mean square [rms]), bond angles (1.2° rms), vibrational frequencies (61 cm-1 rms), conformational energies (0.38 kcal/mol/rms), and rotational barriers (0.39 kcal/mol rms) very nearly as well as does MM3 for comparable systems. MMFF94 also describes intermolecular interactions in hydrogen-bonded systems in a way that closely parallels that given by the highly regarded OPLS force field. © 1996 John Wiley & Sons, Inc.
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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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  • 82
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    Journal of Computational Chemistry 17 (1996) 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
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    Topics: Chemistry and Pharmacology , Computer Science
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  • 83
    ISSN: 0192-8651
    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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    Journal of Computational Chemistry 18 (1997), S. 1-8 
    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 polarizable continuum model of Miertus et al. was implemented in the semiempirical molecular orbital method SINDO1. A fast and precise method for the calculation of solvation energies is achieved based on isodensity surfaces for the cavity surface and on approximated electrostatic potentials. The calculated solvation energies in water agree well with experimental and other calculated data. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 28-44 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Force-field calculations are reported for large delocalized cations. The results for the geometries, heats of formation, and π-electron densities agree well with MP2(full)/6-31G* ab initio calculations. Both methods give similar results for the distortion of the carbon skeletons of unsubstituted cations by hyperconjugating methyl groups. Because of the SCF treatment of π-interactions, the MMP2 force-field technique enables calculations of resonance energies in delocalized cations. The additional resonance stabilization produced by extending conjugation is directly related to the π-charge on the carbon at which a vinyl group is substituted. The good agreement of MMP2 results for nonbonded resonance effects in large delocalized cationic π-systems with ab initio data suggests that MMP2 can be used to study the influence of these interactions in cationic π-systems too large to be calculated by correlated ab initio methods. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 45-55 
    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 optimization using natural internal coordinates was applied for transition metal complexes. The original definitions were extended here for the skeletal degrees of freedom which are related to the translational and rotational displacements of the ηn-bonded ligands. We suggest definitions for skeletal coordinates of ηn-bonded small unsaturated rings and chains. The performance of geometry optimizations using the suggested coordinates were tested on various conformers of 14 complexes. Consideration was given to alternative representations of the skeletal internal coordinates, and the performance of optimization is compared. Using the skeletal internal coordinates presented here, most transition metal complexes were optimized between 10 and 20 geometry optimization cycles in spite of the usually poor starting geometry and crude approximation for the Hessian. We also optimized the geometry of some complexes in Cartesian coordinates using the Hessian from a parametrized redundant force field. We found that it took between two and three times as many iterations to reach convergence in Cartesian coordinates than using natural internal coordinates. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 80-85 
    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 generating a full backbone protein structure from the coordinates of α-carbons, is presented. The method extracts information from known protein structures to generate statistical positions for the reconstructed atoms. Tests on a set of proteins structures show the algorithm to be of comparable accuracy to existing procedures. However, the basic advantage of the presented method is its simplicity and speed. In a test run, the present program is shown to be much faster than existing database searching algorithms, and reconstructs about 8000 residues per second. Thus, it may be included as an independent procedure in protein folding algorithms to rapidly generate approximate coordinates of backbone atoms. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 115-125 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown that the molecular surface and the accessible surface lead to exactly the same results when calculating solvation free energies and transfer free energies, from methods using the surface tension as a parameter if the exact geometric curvature is used with the accessible surface. However, the use of the exact curvature is not necessarily the best approach chemically. Other modifications, including an approximate curvature improves the approach. Such modifications are difficult to include in methods in which the molecular surface rather than the accessible surface is used to calculate solvent effects. A modification of a Gaussian curvature term is necessary if dissociation is to be accounted for properly. The inclusion of a Gaussian curvature term, in addition to the usual mean curvature term, reconciles the difference in magnitude of the microscopic and macroscopic surface tension in the case of the accessible surface area. © 1997 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 five energetically lowest minima on the potential energy surface of N-acetyl-N′-methylalaninamide were optimized at the Becke3LYP/DZd level of theory to compare these density functional theory results with the literature findings at restricted Hartree-Fock/3-21G. While the relative energies are very similar, the amide moiety is predicted to be much more flexible at Becke3LYP/DZd. As a consequence, the three minima that favor a nonplanar amide group differ by up to 14° in their φ and ψ values between the two levels. To compare the change in the density functional NMR chemical shifts with respect to φ and ψ with experimental results, Becke3LYP/DZd was employed to optimize a structure for N-acetyl-N′-methylalaninamide at each 30° interval on the (φ, ψ) surface in the regions that correspond to the α helix and the β-pleated sheet and at each 60° interval elsewhere. The corresponding NMR chemical shielding surface was computed with the density functional program deMon. The resultant NMR chemical shielding surfaces for N and Cβ are in good agreement with the experiment, while the change in the NMR chemical shielding of C′ and Cα cannot be described only in terms of φ and ψ. The chemical shifts for those atoms also depend on the nonplanarity of the amide moiety. We evaluated this dependence for N-methylacetamide as a model system. Estimates of the parameters derived from N-methyl-acetamide allowed the NMR-shielding surfaces of C′ and Cα to be corrected for the nonplanar nitrogen influence. Although the effect is less pronounced with lower level theoretical geometries, due to the smaller degree of pyramidalization of the amide nitrogen, the (φ, ψ) NMR chemical shielding surfaces will need to be corrected. The agreement with the experiment was much better for the corrected surface of C′ when the nitrogen in the α helix had a nonplanar environment. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 211-220 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Test particle calculations are employed to derive van der Waals parameters for methane. It is shown that it is possible to derive these parameters completely based on ab initio calculations. The newly derived parameters are tested in molecular dynamics calculations of liquid methane and the results are compared with the results of existing force fields. It is shown that the newly derived parameters perform better in the prediction of the density, the heat of vaporization, and the self-diffusion coefficient of methane. Scaling of the parameters to account for systematic errors in the employed ab initio method does not generally improve the parameters with respect to the properties calculated. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 221-239 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Empirical force field parameters for nicotinamide (NIC+) and 1,4-dihydronicotinamide (NICH) were developed for use in modeling of the coenzymes nicotinamide adenine dinucleotide (NAD+) and NAD hydride (NADH). The parametrization follows the methodology used in the development of the CHARMM22 all-hydrogen parameters for proteins, nucleic acids, and lipids. Parametrization of inorganic phosphate for use in adenosine di- and triphosphates (e.g., ADP and ATP) is also presented. While high level ab initio data, such as conformational energies, dipole moments, interactions with water, and vibrational frequencies, were adequately reproduced by the developed parameters, strong emphasis was placed on the successful reproduction of experimental geometries and crystal data. Results for molecular dynamics crystal simulations were in good agreement with available crystallographic data.Simulations of NAD+ in the enzyme alcohol dehydrogenase compared quite favorably with experimental geometries and protein matrix interactions. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 260-267 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown that the claims that density functional theory (DFT) can handle orbitally degenerate states are ungrounded. The constraint search formulation of DFT allows one to determine a set of densities and eigenvalues for the degenerate term that, however, are neither observables, nor can they be used to solve the system of coupled equations for the nuclear motions to obtain observables, as in the wave function presentation. A striking example of the failure of the existing versions of DFT to describe degenerate states is provided by the Berry phase problem: the strong dependence of the results on the phase properties of the electronic wave function that are smeared out in the density formulation. The solution of the Jahn-Teller E-e problem illustrates these statements. For nondegenerate states with the full wave function taken in the adiabatic approximation as a product of the electronic and nuclear parts, the formulation of DFT is rigorous if and only if the dependence of the electronic wave function on nuclear coordinates is ignored. This lowers the accuracy of the results, in general, and may lead to erroneous presentation as in the case of molecular systems in strong magnetic fields. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 290-299 
    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 development of a crystal indexing computer program using interplanar angles and lattice spacings is very useful, particularly in nanocrystal research by transmission electron microscopy. However, the indexing involves a large number of possible variables, which prohibits the use of simple mathematical techniques. This article is concerned with an application of a combinatorial optimization technique using the simulated annealing algorithm for solving the crystal indexing problem where traditional descent optimization cannot be used. We show that the program can unambiguously identify the Miller indices using a set of interplanar angles even for crystals with low symmetry elements. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 313-322 
    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 the theory and implementation of a new approach for studying solvent effects. The electronic structure of the solute, calculated at the ab initio level, is obtained in the presence of the surrounding medium. We employ a mean field theory in which the solvent response is described by means of point charges chosen in such a way that they reproduce the average value of the solvent electrostatic potential calculated from molecular dynamics data. In this way, the complete solvent potential can be introduced into the solute Hamiltonian without making use of a one-center multiple expansion of the solute-solvent potential. In the proposed method, only one quantum calculation has to be performed and a great number of configurations can easily be included making the calculation statistically significant. We show that, despite the large fluctuations in the solute charge distribution induced by the solvent, the proposed mean field theory adequately reproduces the energetics and properties of formamide and water molecules in aqueous solution. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 368-380 
    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 potential energy model is developed to study the intramolecular proton transfer in the enol form of acetylacetone. It makes use of the empirical valence bond approach developed by Warshel to combine standard molecular mechanics potentials for the reactant and product states to reproduce the interconversion between these two states. Most parameters have been fitted to reproduce the key features of an ab initio potential surface obtained from 4-31G* Hartree-Fock calculations. The partial charges have been fitted to reproduce the electrostatic potential surface of 6-31G* Hartree-Fock wave functions, subject to total charge and symmetry constraints, using a fitting procedure based on generalized inverses. The resulting potential energy function reproduces the features most important for proton transfer simulations, while being several orders of magnitude faster in evaluation time than ab initio energy calculations. © 1997 by John Wiley & Sons, Inc.
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  • 96
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    Journal of Computational Chemistry 18 (1997), S. 393-402 
    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 thermal effect of a reaction makes the temperature inside the reaction system deviate from a prescribed heating program. To take into account the effect of such temperature deviations on kinetic evaluations, a computational method applicable to an arbitrary variation in temperature has been developed. The method combines the isoconversional principle of evaluating the activation energy with numerical integration of the equation, dα/dt = k[T(t)]f(α), over the actual variation of the temperature with the time, T(t). Details of the numerical algorithm are reported. A model example has been used to verify the reliability of this method as compared to an analogous method which does not account for the deviations of the temperature from a prescribed program. The method has been tested for tolerance for noise in the temperature. © 1997 by John Wiley & Sons, Inc.
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  • 97
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    Journal of Computational Chemistry 18 (1997), S. 430-448 
    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 massively parallel version of the configuration interaction (CI) section of the COLUMBUS multireference singles and doubles CI (MRCISD) program system is described. In an extension of our previous parallelization work, which was based on message passing, the global array (GA) toolkit has now been used. For each process, these tools permit asynchronous and efficient access to logical blocks of 1- and 2-dimensional (2-D) arrays physically distributed over the memory of all processors. The GAs are available on most of the major parallel computer systems enabling very convenient portability of our parallel program code. To demonstrate the features of the parallel COLUMBUS CI code, benchmark calculations on selected MRCI and SRCI test cases are reported for the CRAY T3D, Intel Paragon, and IBM SP2. Excellent scaling with the number of processors up to 256 processors (CRAY T3D) was observed. The CI section of a 19 million configuration MRCISD calculation was carried out within 20 min wall clock time on 256 processors of a CRAY T3D. Computations with 38 million configurations were performed recently; calculations up to about 100 million configurations seem possible within the near future. © 1997 by John Wiley & Sons, Inc.
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  • 98
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    Journal of Computational Chemistry 18 (1997), S. 478-488 
    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 implementation of parallel molecular dynamics techniques is discussed in the context of the simulation of single-site anisotropic potentials. We describe the use of both replicated data and domain decomposition approaches to molecular dynamics and present results for systems of up to 65536 Gay-Berne molecules on a range of parallel computers (Transtech i860/XP Paramid, Intel iPSC/860 Hypercube, Cray T3D). We find that excellent parallel speed-ups are possible for both techniques, with the domain decomposition method found to be the most efficient for the largest systems studied. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 522-532 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Interaction energies are a function of the molecular charge distribution. In previous work, we found that the set of atomic partial charges giving the best agreement with experimental vacuum dipole moments were from density functional theory calculations using an extended basis set. Extension of such computations to larger molecules requires an atomic partial charge calculation beyond present computational resources. A solution to this problem is the calculation of atomic partial charges for segments of the molecule and reassociation of such fragments to yield partial charges for the entire molecule. Various partitions and reassociation methods for five molecules relevant to HIV-1 protease inhibitors are examined. A useful method of reassociation is introduced in which atomic partial charges for a large molecule are computed by fitting to the combined electrostatic potential calculated from the fragment partial charges. As expected, the best sites for partitions are shown to be carbon - carbon rather than carbon - nitrogen bonds. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 562-568 
    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 number of cluster models used to study the interaction of NH3 and NH-4 with the Bronsted sites of the acidic zeolite, chabazite, are assessed by comparison with the results from full periodic Hartree-Fock calculations. Corrections to bare cluster models to take account of the electrostatic environment due to the periodic zeolite are found to agree well with periodic calculations, and appear to be more successful than a more sophisticated embedding procedure. © 1997 by John Wiley & Sons, Inc.
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