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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 74-86 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A possible application of a novel double-iterated Kalman filter (DIKF) as an algorithm for molecular structure determination is investigated in this work. Unlike traditional optimization algorithms, the DIKF does not exploit experimental nuclear magnetic resonance (NMR) constraints in a penalty function to be minimized but used them to filter the atomic coordinates. Furthermore, it is a nonlinear Bayesian estimator able to handle the uncertainty in the experimental data and in the computed structures, represented as covariance matrices. The algorithm presented applies all constraints simultaneously, in contrast with DIKF algorithms for structure determination found in literature, which apply the constraints one at a time. The performances of both paradigms are tested and compared with those obtained by a commonly used optimization algorithm (based on the conjugate gradient method). Besides providing estimates of the conformational uncertainty directly in the final covariance matrix, DIKF algorithms appear to generate structures with a better stereochemistry and be able to work with realistically imprecise constraints, while time performances are strongly affected by the heavy matricial calculations they require. © 1996 by John Wiley & Sons, Inc.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 156-166 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structural stabilities of endo and exo conformations of retronecine and heliotridine molecules were analyzed using different ab initio, semiempirical, and molecular mechanics methods. All electron and pseudopotential ab initio calculations at the Hartree-Fock level of theory with 6-31G* and CEP-31G* basis sets provided structures in excellent agreement with available experimental results obtained from X-ray crystal structure and 1H-NMR (nuclear magnetic resonance) studies in D2O solutions. The exo conformations showed a greater stability for both molecules. The most significant difference between the calculations was found in the ring planarity of heliotridine, whose distortion was associated with the interaction between the O(11)H group and the C(1)-C(2) double bond as well as with a hydrogen bond between O(11)H and N(4). The discrepancy between pseudopotential and all-electron optimized geometries was reduced after inclusion of the innermost electrons of C(1), C(2), and N(4) in the core potential calculation. The MNDO, AM1, and PM3 semiempirical results showed poor agreement with experimental data. The five-membered rings were observed to be planar for AM1 and MNDO calculations. The PM3 calculations for exo-retronecine showed a greater stability than the endo conformer, in agreement with ab initio results. A good agreement was observed between MM3 and ab initio geometries, with small differences probably due to hydrogen bonds. While exo-retronecine was calculated to be more stable than the endo conformer, the MM3 calculations suggested that endo-heliotridine was slightly more stable than the exo form. © 1996 by John Wiley & Sons, Inc.
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 4
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 5
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 385-385 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 6
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 806-820 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The self-consistent reaction field (SCRF) method proposed by Miertus, Scrocco, and Tomasi (MST) was extended to solutions of neutral solutes in CCl4. A detailed parametrization of the solute/solvent interface and of the “hardness” atomic parameters determining the van der Waals interactions was performed from comparison with experimental data and Monte Carlo simulations. The parametrization was carried out at both ab initio (6-31G*) and semiempirical (MNDO, AM1, PM3) levels. The MST/SCRF optimized versions provide accurate estimates of the free energy of solvation in CCl4 for the series of molecules studied. Furthermore, a precise description of the solvent effect on different chemical processes in CCl4 solution supports the reliability of the parametrization. © 1996 by John Wiley & Sons, Inc.
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  • 7
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 940-953 
    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 multiparameter multistep relaxation (MPMSR) method, a routine within a new suite of parameterization programs entitled parameter analysis and refinement toolkit system (PARTS), was developed to assist in the development of molecular mechanics (MM3 and MM2) force field parameters and represents an ongoing effort in our laboratories to generate more accurate force fields in shorter times. In contrast to other computerized parameterization approaches, this method simulates intuition guided trial-and-error and has been used successfully within our laboratories to develop MM2 and MM3 force fields. The primary aim of this approach is to minimize human inspection time and effort, with simultaneous improvement in the efficiency and accuracy of the parameterization process. In an effort to validate the generality of the MPMSR method, a well parameterized data set of phosphine derivatives was reexamined. With the identical set of training molecules used in the original MM3 phosphine parameterization and with minimal human intervention, MPMSR shortened the process from several months to approximately five days. Although the previous phosphine force field is well parameterized, the newly generated MPMSR set of parameters has achieved an overall better fit to the experimentally observed data and ab initio calculations. © 1996 by John Wiley & Sons, Inc.
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  • 8
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 992-1001 
    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 four-index transformation has a high ratio of data transfer to computation making it a potential “bottleneck” for parallel correlation energy determination. We present formulas for the communication times on different parallel architectures for an algorithm that is primarily designed for distributed-memory machines. We also implemented the algorithm on two shared-memory parallel computers, the Encore Multimax and the Alliant FX-8, and measured wall clock times for several problem sizes and processor configurations. © 1996 by 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. 1013-1024 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Although no crystal structures of mixed-chain phosphatidylcholines with unsaturated sn-2 acyl chains exist, the force field method in conjunction with the experimentally determined structure of saturated identical-chain phosphatidylcholine can be applied to simulate molecular structure for mixed-chain phosphatidylcholines. In this study, the packing models of mixed-chain 1-palmitoyl-2-linoleoyl-phosphatidylcholines in bilayers at temperatures below the gel-liquid crystalline phase transition temperature or T 〈 Tm are simulated by using Allinger's MM3(92) force field. Our results indicate that the unsaturated sn-2 acyl chains of the mixed-chain lipid can fold into two energy-minimized topologies: the crankshaftlike and the U-shaped motifs. The folded region in the crankshiftlike sn-2 acyl chain is characterized by a sequence s- Δs+s+Δs-, and the U-shaped chain arises from the characteristic sequence s-Δs+s-Δs+, where s± denotes the ± skew conformation and Δ the cis carbon-carbon double bond. These modeled structures of 1-palmitoyl-2-linoleoyl-phosphatidylcholines in the bilayer at T 〈 Tm should not be regarded as highly rigid structures, since torsion angles of carbon-carbon bonds associated with sequences s Δs+s+Δs and s Δs+s-Δ s+ can fluctuate somewhat without appreciably affecting the steric energy of the corresponding lipid bilayer. © 1996 by John Wiley & Sons, Inc.
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  • 10
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    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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  • 11
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1068-1084 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics (MD) simulations of α-D-maltose (maltose) in vacuo and with explicit inclusion of water were performed using the GROMOS force field that was modified to include a potential energy term for the exo-anomeric effect. Different simulation temperatures, the influence of the size of the water box, and carbohydrate-specific force field parameter values were evaluated with respect to sampling efficiency and average conformations. First, maltose was surrounded by 500 water molecules and simulated for 750 ps. Furthermore, three 500-ps MD simulations in vacuo were run to identify the effect of solvation on the location of the preferred conformation and on the flexibility of the molecule. Inclusion of water leads to a change of the preferred conformation from φ/ψ1 ≅ -20°/-17° in vacuo to -40°/-31° in aqueous solution. The explicit incorporation of water molecules into the simulation gave rise to only short-lived hydrogen bond interactions. In particular, a hydrogen bond found in vacuo from OH3 of the reducing glucose to O2′ of the nonreducing glucose was rarely present when water was included in the simulation. In vacuo the conformational freedom of the glycosidic linkage and the hydroxymethyl and hydroxyl groups were strongly reduced due to intramolecular hydrogen bonds. Two 200-ps MD runs with inclusion of 137 water molecules at temperatures of 350 and 400 K showed the expected increase of the transitions between the rotamers of the hydroxymethyl groups. An equilibrium for the conformation of the glycosidic linkage was only reached when raising the temperature parameter of the MD simulation further to 600 K. However, at this temperature inversions of the pyranose ring were already observed within a 1-ns MD simulation. Parametrization of GROMOS to include the exo-anomeric effect proved to be necessary because the previously published force field has no provisions to account for the exo-anomeric effect, as revealed by two MD simulations in water and in vacuo that indicated a significant population at positive φ angles. Using dimethoxymethane as a model for the O-glycosidic linkage, the empirical potential function for the rotation about the C1(SINGLE BOND)O1 bond was adjusted to represent the potential calculated by STO 6-31G* ab initio calculations. MD simulations using the adjusted force field revealed a reduced population with positive φ values. A separate parametrization of the potential for the reducing hydroxyl group of saccharides resulted in a better description of the conformation, as well as increased stability of the integration algorithm. Finally, the existing GROMOS force field was supplemented by an additional gauche potential. Its effect on the conformation of the hydroxymethyl groups was evaluated by a 500-ps MD simulation in water. © 1996 by John Wiley & Sons, Inc.
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  • 12
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We investigated the convergence behavior of potential of mean force (PMF) calculations using free energy perturbation (FEP), thermodynamic integration (TI), and “slow growth” (SG) techniques. The critical comparison of these alternative approaches is illustrated by the study of three different systems: two tagged argon atoms in a periodic box of argon, two methane molecules, and two benzene molecules maintained in a “T-shaped” conformation, both dimers embedded in a periodic box of water. The complete PMF simulations were carried out considering several protocols, in which the number of intermediate “λ” states, together with the amount of sampling per individual state, were varied. In most cases, as much as 1 ns of molecular dynamics (MD) sampling was used to derive each free energy profile. For the different systems examined, we find that FEP and TI unquestionably constitute robust computational methods leading to results of comparable accuracy. We also show that proper convergence of the free energy calculations, and further quantitative interpretation of the PMFs, requires total simulation times much higher than has been hitherto estimated. In some circumstances, the free energy profiles derived from FEP calculations tend to be slightly poorer than those obtained with TI, as a probable consequence of the greater sensitivity of FEP to the window spacing δλ. In the context of TI, and to a lesser extent FEP, simulations, it appears preferable to employ a limited number of “λ” points of the integrand involving extensive sampling, rather than numerous points with fewer samplings. Finally, we note that, at least in the case of nonpolar interactions, PMFs of reasonable quality can be generated using SG, and at a substantially lower cost than with either FEP or TI. © 1996 by John Wiley & Sons, Inc.
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  • 13
    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 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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  • 14
    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 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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  • 15
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1309-1317 
    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 and density functional (DFT) calculations were performed on radical cations with the formula HXCO+· (X = H, F, and CI) and their isomers XCOH+·. Hartree-Fock, Møller-Plesset at second order (MP2), and quadratic configuration interaction including singles and doubles (QCISD) methods were employed for geometry optimizations at the ab initio level. Becke's 1988 and three-parameter exchange potentials, together with Vosko-Wilk-Nusair (VWN) and Lee-Yang-Paar (LYP) correlation potentials (BVWN, BLYP, and B3LYP) were used for the DFT calculations. HF and MPn isomerization energies are severely in error, mostly due to a bad description of the XHCO+· cation radicals at the Hartree-Fock level, leading to oscillatory behavior of the perturbation series. QCISD methods, at least, are needed to obtain accurate results at the conventional ab initio level, even using large extended basis sets. B3LYP results are most similar to QCISD results for the isomerization energies of the three cation radicals. Parent neutral species are also described to a high degree of accuracy. B3LYP methods are faster than QCISD (and as exact as them) for all the cases studied here. MP2 methods, although giving incorrect results, are faster than B3LYP up to about 80 basis functions. For larger problems, B3LYP methods are faster. The best theoretical results obtained indicate that fluoro- and chloroformaldehyde cation radicals are less stable than their hydroxyfluoro- and hydroxychloromethylene isomers, the reverse situation than for the formaldehyde cation radical. The best values found in this article for the isomerization energy of XHCO+· are -26 ± 2 kJ/mol (X = H), +37 ± 2 kJ/mol (X = F), and +28 ± 2 kJ/mol (X = CI). Ionization energies of 10.9, 12.3, and 11.4 eV are predicted for the XHCO species (X = H, F, CI). © 1996 by John Wiley & Sons, Inc.
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  • 16
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1344-1351 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new procedure to solve the Poisson-Boltzmann equation is proposed and shown to be efficient. The electrostatic potential due to the reaction field is calculated directly. Self-interactions among the charges are completely eliminated. Therefore, the reference calculation to cancel out the self-energy is not needed. © 1996 by John Wiley & Sons, Inc.
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  • 17
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    Journal of Computational Chemistry 17 (1996), S. 49-56 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A redundant internal coordinate system for optimizing molecular geometries is constructed from all bonds, all valence angles between bonded atoms, and all dihedral angles between bonded atoms. Redundancies are removed by using the generalized inverse of the G matrix; constraints can be added by using an appropriate projector. For minimizations, redundant internal coordinates provide substantial improvements in optimization efficiency over Cartesian and nonredundant internal coordinates, especially for flexible and polycyclic systems. Transition structure searches are also improved when redundant coordinates are used and when the initial steps are guided by the quadratic synchronous transit approach. © 1996 by John Wiley & Sons, Inc.
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  • 18
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    Journal of Computational Chemistry 17 (1996), S. 57-73 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present analytical expressions for the first derivatives of area and other geometrical quantities of polygonal tesserae defined on molecular surfaces. This is a necessary step in the calculation of free energy derivatives with respect to nuclear coordinates for molecular solutes, in the framework of the polarizable continuum method. An application to solute-solvent dispersion energy derivatives is presented. © 1996 by John Wiley & Sons, Inc.
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  • 19
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    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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  • 20
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We discuss issues in developing scalable parallel algorithms and focus on the distribution, as opposed to the replication, of key data structures. Replication of large data structures limits the maximum calculation size by imposing a low ratio of processors to memory. Only applications which distribute both data and computation across processors are truly scalable. The use of shared data structures that may be independently accessed by each process even in a distributed memory environment greatly simplifies development and provides a significant performance enhancement. We describe tools we have developed to support this programming paradigm. These tools are used to develop a highly efficient and scalable algorithm to perform self-consistent field calculations on molecular systems. A simple and classical strip-mining algorithm suffices to achieve an efficient and scalable Fock matrix construction in which all matrices are fully distributed. By strip mining over atoms, we also exploit all available sparsity and pave the way to adopting more sophisticated methods for summation of the Coulomb and exchange interactions. © 1996 by John Wiley & Sons, Inc.
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  • 21
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    Journal of Computational Chemistry 17 (1996), S. 1571-1586 
    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 role for electronic structure databases in assisting users of quantum chemistry applications select better model parameters is discussed in light of experiences gained from a software prototype known as the Computational Chemistry Input Assistant (CCIA). It is argued that the ready availability of information pertaining to the applications and theoretical models can substantially increase the likelihood of novice users obtaining the desired accuracy from their calculations while simultaneously making better use of computer resources. Expert users, who find themselves contemplating studies in new areas of research, may also benefit from the proposed tools. For maximum impact, this assistance should be provided while users are actively engaged in preparing calculations. © 1996 by John Wiley & Sons, Inc.
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  • 22
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    Journal of Computational Chemistry 17 (1996), S. ii 
    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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  • 23
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The redox capacities of 5-hydroxy-1,4-naphthaquinone (VI), 5-8-dihydroxy-1,4-naphthaquinone (VII), and 5,8-dihydroxy-1,4-naphthaquinone imine (VIII) as model systems for the pharmacophore of aclacinomycin A, adriamycin/daunomycin, and 5-iminodaunomycin (5IDN), respectively, along with 1,4-naphthaquinone (V), 1,4-benzoquinone (IV), and 1,4-benzoquinone imine (IX), have been investigated by the AM1 semiempirical method. The reduction activation of the parent (Q) model systems to their various redox states [quinone radical anion (Q-2), semiquinone (QH·), semiquinone anion (QH-), and hydroquinone (QH2)], the redox capacities of the redox states, and the intermolecular electron self-exchange processes between the redox states and electron transfer reactions from the redox states to molecular oxygen have been examined using reaction enthalpies, adiabatic ionization potentials and electron affinities, and absolute and adiabatic electronegativities. Keto - enol transformations and the effects of solvation and H bonding on keto-enol tautomers of VI and of the hydroquinones of VI and VIII have also been assessed. The results indicate that the reactivity of VIII, relative to that of VII, may not be diminished. VI, however, appears to be less reactive than VII, and this suggests clues for the reduced toxicities of aclacinomycin A. Overall, the results suggest that the experimentally observed reduced cardiotoxic effects of 5IDN may be explained by changes in electron configuration and/or electron density and in geometry, such as changes in planarity that accompany enol to keto transformations in the reduction by product of 5IDN (Bird et al.7) - that is, between the hydroquinone (II) of naphthacenedione (I) and naphthacenone (III). Moreover, the results suggest that the two-electron reduction product, Q-2, of the drugs can be the reductant that produces reactive dioxygen species, such as O2-· and HO2·, via electron transfer to molecular oxygen as opposed to QH· and QH2, which have been postulated to be responsible for electron transfer. This possibly new role for Q-2 may be important in cardioxicity, particularly in aprotic and/or hydrophobic media. © 1996 by John Wiley & Sons, Inc.
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  • 24
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    Journal of Computational Chemistry 17 (1996), S. 1645-1652 
    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 developed, general computer program that performs vibrational self-consistent field (VSCF) calculations for large molecules is described. The program, which we refer to as VSCF―95, requires as its only input a force field in mass-scaled normal coordinates. Currently, it is limited to a maximum of 200 normal modes, and the force field is limited to coupling terms involving a maximum of six normal modes, with a maximum order of six in any normal mode. As output the program returns VSCF energies for specified quantum states. We illustrate the code with two new applications. The first is to HCO, for which we use a full sixth-order force field. The second is to a model of the fullerene, C60, for which we have calculated a 75,731-term force field, which includes all anharmonic terms up to fifth order, and all two-mode coupling terms up to fourth order. © 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
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 26
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular geometries were fully optimized for AlCl3, AlCl-4, Al2Cl6, Al2Cl-7, AlF3, AlF-4, Al2F6, Al-2F7, BCl3, BCl-4, B2Cl6, B2Cl-7, BF3, BF-4, B2F6, and B2F-7, as well as a few mixed halogen species, at the Hartree-Fock (HF) level, using basis sets from STO-3G to 6-311 + G(d). In some cases geometries were also optimized at the MP2 level. Where possible, the computed geometries were compared to known structures from electron or X-ray diffraction. The agreement between these was quite good for the neutral species, and somewhat poorer for the anions. Vibrational frequencies were calculated for all species at the HF level with the largest basis set. The geometries were characterized as minima or transition structures. Various formation reaction enthalpies were calculated; these compare well with known values. More extensive calculations on the BF3/BF-4 system indicate the structures and enthalpies are nearly converged with respect to basis set size and level of correlation treatment. The previously unknown species B2Cl-7 is predicted to be energetically stable on the basis of the calculations. Some features of the 11B NMR spectra of room temperature melts consisting of mixtures of boron trichloride with 1-methyl-3-ethylimidazolium chloride are presented. These features suggest that these melts may contain small amounts of B2Cl-7 as an intermediate in an exchange reaction. © 1996 by John Wiley & Sons, Inc.
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  • 27
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    Journal of Computational Chemistry 17 (1996), S. 1712-1725 
    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 essential biological functions are controlled by proteins that bind to specific sequences in genomic DNA. In this article we present a simplified model for analyzing DNA-protein interactions mediated exclusively by hydrogen bonds. Based on this model, an optimized algorithm for geometric pattern recognition was developed. The large number of local energy minima are efficiently screened by using a geometric approach to pattern matching based on a square-well potential. The second part of the algorithm represents a closed form solution for minimization based on a quadratic potential. A Monte Carlo method applied to a modified Lennard-Jones potential is used as a third step to rank DNA sequences in terms of pattern matching. Using protein structures derived from four DNA-protein complexes with three-dimensional coordinates established by X-ray diffraction analysis, all possible DNA sequences to which these proteins could bind were ranked in terms of binding energies. The algorithm predicts the correct DNA sequence when at least two hydrogen bonds per base pair are involved in binding to the protein, providing a partial solution to the three-dimensional docking problem. This study lays a framework for future refinements of the algorithm in which the number of assumptions made in the present analysis are reduced. © 1996 by John Wiley & Sons, Inc.
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  • 28
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    Journal of Computational Chemistry 17 (1996), S. 1757-1770 
    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 study investigates the differences between the predictions of various properties of rigid and flexible simple point charge water models at supercritical conditions. Molecular dynamics simulations were conducted for supercritical water in a temperature range of 773-1073 K and densities in the range 115-659 kg/m3. We present thermodynamic data, pair correlation functions, self-diffusivity, power spectra, dielectric constants, and variaous measures of hydrogen bonding at different state conditions. The flexible water model performs better in predicting the pressures along the supercritical isotherms simulated. Agreement between experimental and calculated dielectric constants is superior for the flexible water model, particularly at high densities. The flexible model exhibits a greater degree of hydrogen bonding and more persistent hydrogen bonds than does the rigid model. The structural features of supercritical water at high densities are identical for the two water models. At low densities, however, the flexible potential exhibits pair correlation functions with enhanced peaks. Inclusion of flexibility in the potential model does not result in a significant shift in the position of the rotational/librational peak in the power spectrum. The self-diffusivities obtained from the simulations are within the accuracy of the experimental values for both the rigid and flexible models. On balance the inclusion of flexibility improves agreement with the properties of real supercritical water while incurring little or no additional computational burden. © 1996 by John Wiley & Sons, Inc.
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  • 29
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    Journal of Computational Chemistry 17 (1996), S. 1804-1819 
    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 behavior of 2-trifluoromethylphenol was investigated by means of theoretical calculations. Four characteristic structures have been found on the potential energy hypersurface of the compound: anti form (local minimum), in which the hydroxy hydrogen points away from the trifluoromethyl group; and three syn forms (the hydrogen points towards the trifluoromethyl group), with different trifluoromethyl torsions (global minimum, one low and another one high lying saddle-point). The geometry of these conformers were optimized by ab initio calculations using 6-31G** basis set. The effects of electron correlation were investigated by MP2 and various DFT methods. To investigate the intramolecular interaction in the syn forms, the electron density distribution was calculated at the MP2 level of theory. In the structure corresponding to the global minimum at the MP2/6-31G** level a bond critical point was found in Bader's sense between the hydroxy hydrogen and a fluorine of the trifluoromethyl group indicating hydrogen bonding interaction. The length of the hydrogen bond, 1.98 Å, corresponds to medium strength interaction. The O(SINGLE BOND)H bond is slightly twisted and the C(SINGLE BOND)F bond, interacting with it, is considerably twisted out of the plane of the benzene ring to the same side of the ring. The most pronounced geometrical consequence of the hydrogen bond is the 0.02-Å lengthening of the C(SINGLE BOND)F bond participating in its formation. All the other geometrical changes in 2-trifluoromethylphenol, as compared with trifluoromethylbenzene and phenol, are also consistent with the phenomenon of resonance-assisted hydrogen bonding. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1783-1803 
    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 computer model has been developed to simulate the adsorption of proteins onto charged surfaces displaying an electric double layer. Coadsorption of ions onto the surface is included by means of explicit ions. Only electrostatic interactions are considered. Monte Carlo simulations in the canonical ensemble of the enzyme cutinase and 15 variants (modeled from the X-ray tertiary structure of the wild-type) were performed. Adsorption free energies for all variants were calculated by the thermodynamic integration method. Distributions of the electric moment and the vector pointing toward the protein active site and parallel to its central β-sheet were determined to elucidate the mean orientation of the protein with respect to the surface as a function of its distance from the surface. It was found that the free energy of adsorption varied linearly with the total charge of the protein, while the electric moment (dipole moment) had a second-order but significant effect. Though an increase of the electric moment generally resulted in a slightly increased affinity of the protein for the surface, close to the surface the mean force acting on the protein clearly varied linearly with the strength of the electric moment, such that a clear correlation between the latter and the protein orientation with respect to the surface could be established. Wild-type cutinase displayed the highest affinity for the charged surface amongst all proteins having the same total charge, even though it did not have the largest electric moment. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 587-615 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article describes the parameterization and performance of MMFF94 for conformational energies, rotational barriers, and equilibrium torsion angles. It describes the derivation of the torsion parameters from high-quality computational data and characterizes MMFF94's ability to reproduce both computational and experimental data, the latter particularly in relation to MM3. The computational data included: (i) ∼ 250 comparisons of conformational energy based on “MP4SDQ/TZP” calculations (triple-zeta plus polarization calculations at a defined approximation to the highly correlated MP4SDQ level) at MP2/6-31G* geometries; and (ii) ∼ 1200 MP2/TZP comparisons of “torsion profile” structures at geometries derived from MP2/6-31G* geometries. The torsion parameters were derived in restrained least-squares fits that used the complete set of available computational data, thereby ensuring that a fully optimal set of parameters would be obtained. The final parameters reproduce the “MP4SDQ/TZP” and MP2/TZP computational data with root mean square (rms) deviations of 0.31 and 0.50 kcal/mol, respectively. In addition, MMFF94 reproduces a set of 37 experimental gas-phase and solution conformational energies, enthalpies, and free energies with a rms deviation of 0.38 kcal/mol; for comparison, the “MP4SDQ/TZP” calculations and MM3 each gives a rms deviation of 0.37 kcal/mol. Furthermore, MMFF94 reproduces 28 experimentally determined rotational barriers with a rms deviation of 0.39 kcal/mol. Given the diverse nature of the experimental conformational energies and rotational barriers and the clear indications of experimental error in some cases, the MMFF94 results appear excellent. Nevertheless, MMFF94 encounters somewhat greater difficulty in handling multifunctional compounds that place highly polar functional groups in close proximity, probably because it, like other commonly used force fields, too greatly simplifies the description of electrostatic interactions. Some suggestions for enhancements to MMFF94's functional form are discussed. © 1996 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 642-668 
    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 force field has been developed for alkanes and cycloalkanes, excluding small rings, to improve the calculation of vibrational frequencies, rotational barriers, and numerous relatively small errors that were observed to result from the use of the MM3 force field. © 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: The hyperconjugative result of bond stretching in alkenes has been studied with MM4. A low-temperature crystallographic study of 1,2-diarylindane[a]indane has been carried out, together with ab initio (MP2/6-31G*) calculations on model systems. The results are well reproduced with a force field designed to explicitly include hyperconjugation (MM4), and they show beyond doubt that hyperconjugative bond elongations exist both in theory and by experiment. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 878-887 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The frequency distributions of internal dynamics of a protein are calculated in solution using normal mode analysis. Our test case is bovine pancreatic trypsin inhibitor, consisting of 58 amino acid residues. Each water molecule surrounding the protein is treated as an internally rigid body that can move with the vibrating protein. The water molecules are redistributed around the protein, as dictated by the potential energy. It is shown that water molecules around the protein are essential for the protein to keep its tertiary structure close to the X-ray structure. The density of states calculated in this model is shifted toward high frequencies when compared with results previously obtained with a model in which the water molecules were not allowed to move with the protein. This shift toward high-frequency states originates from the stronger interactions of water molecules with the sidechain atoms in the protein. The present model is computationally demanding. So the previous (frozen water) model is suggested to be a reasonable approximation for expressing internal dynamics of a protein in solution. © 1996 by John Wiley & Sons, Inc.
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    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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  • 36
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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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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have used molecular modeling to investigate the enantioselective separation of the monoterpene α-pinene on permethylated β-cyclodextrin and on α-cyclodextrin and the enantioselective separation of three cyclohexanetriol derivatives on permethylated β-cyclodextrin. Using the Consistent Valence Force Field (CVFF) from Insight/Discover, we have carried out systematic rigid-body docking grid searches on each of the optical antipodes of the organic guest molecules interacting with the cyclodextrins, followed by minimizations of the low-energy docked structures. A statistical mechanical analysis of the minimized energies yields data that agree in four out of five cases with the experimental elution order of enantiomers. The computed energies of the rigid-body docking before minimizations do not agree with the experimental results, suggesting that a conformational induced fit of the cyclodextrins upon binding of the organic guests may be involved in the mechanism of the chiral recognition. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 970-975 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new fast and accurate algorithm for numerical calculation of the van der Waals and solvent accessible surface areas based on the sorted table of cosines is described. This algorithm does not depend upon the particular distribution of the points on the sphere surface, and thus allows use of the most accurate points distribution available. Direct comparisons (on the same computer) with other known fast algorithms are performed. The comparisons show that this algorithm is the fastest when accurate calculation of the van der Waals surface is required and is at least as fast as the fastest competitor algorithm for the evaluation of the solvent accessible surface area. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1002-1012 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Calculations of loop segments in bovine pancreatic trypsin inhibitor starting from random conformations are more efficient, reproducible, and reliable due to several program enhancements. Monte Carlo simulated annealing (MCSA) calculations of a five-residue α-helix N-terminus segment (H5) and β-strand segment (B5) in this study are compared to the corresponding loop calculations in our previous study. Characteristics of the calculations are: the lowest final total energy conformations (LECs) are within 5 kcal/mol; the average backbone deviations of the computed segments from the native X-ray conformations are 0.43 ± 0.15 Å for H5 and 0.68 ± 0.20 Å for B5; and all the native backbone-backbone hydrogen bonds (H bonds) are present in the best LECs. Compared to the previous study, the H5 and B5 calculations are about 3 and 24 times more efficient, respectively. In the analysis of the best H5 simulated annealing run, backbone-backbone H bonds appear between RT = 4 and 70 kcal/mol, where RT is the Boltzmann temperature factor. H bonds that involve side chains appear in the RT = 1-10 kcal/mol range. Program enhancements implemented are varying main chain versus side chain dihedral angle selection rate, varying φ/ψ and χ1/χ2 dihedral angles in pairs, the use of main chain and side chain rotamer libraries, and varying the location of the segment origin. © 1996 by John Wiley & Sons, Inc.
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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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    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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    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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    Journal of Computational Chemistry 17 (1996), S. 1152-1155 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for refining high order numerical integration schemes is described. Particular focus is on integration schemes over the unit sphere with octahedral symmetry. The method is powerful enough that new integration schemes can be found from rough intuitive guesses. New schemes up to order 59 are presented. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1132-1141 
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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 formulae is developed for the derivatives of torsion angle energy terms and is introduced into the program CHARMM. These formulae, which are based on derivatives of the torsion angle itself, avoid the singularities introduced by use of the derivatives of the torsion angle cosine. The potential energy can include any differentiable function of the torsion angle and there is no need for a special treatment for cases where planar conformations are not extrema. The resulting code is simpler than the original version and yields correct derivatives in all practical situations. Because the minimum of the torsion energy can be at any angle, the functionality of the existing energy routines is generalized. © 1996 by John Wiley & Sons, Inc.
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Journal of Computational Chemistry 17 (1996), S. 1171-1182 
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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: In a continuing effort to provide the computational community with a reference work comparing all of the available conformer searching methods, we have exposed the standard set of small molecules to two commonly used stochastic searching techniques. Advantages and limitations of these methods are discussed. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1197-1216 
    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 suggested that multivariate methods such as principal component analysis (PCA) are useful tools in the analysis of large data sets from quantum chemical computations of reaction pathways. The potential of this methodology is investigated through an examination of the details of a medium-sized reaction: the Ziegler-Natta ethylene insertion reaction. Furthermore, PCA is used to compare two reaction pathways for the electrophilic addition of hydrochloric acid to propene. In both instances, the reaction pathways are determined at the Hartree-Fock level using the intrinsic reaction coordinate approach. The analyses are carried out on various kinds of descriptors, including geometry parameters, Mulliken charges, and overlap populations, and their relative efficiencies in terms of PCA modeling of the reactions are assessed. The results show that it may be necessary to combine analyses based on different descriptors and to analyze subsections of the reaction path separately in order to obtain both high resolution and interpretability. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1258-1268 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The distribution of molecular electrostatic potential (MEP) on a surface is a common model used to describe simultaneously steric properties (e.g., size, shape) and reactive properties (e.g., electro- and nucleophilic positions) of a molecule. In this work, we analyze some relations between these two properties. In particular, we explore the possible definition of an optimum fused-sphere molecular surface from properties of the MEP distribution. With this goal, we study how several statistical descriptors of the two-dimensional MEP distribution change upon shrinking or enlarging a van der Waals surface. We find that some of the descriptors exhibit critical points in terms of a scaling factor. We use this property to define effective atomic radii. In particular, we find that a reasonable molecular envelope is defined as the surface having the lowest (i.e., most negative) average negative MEP, with the largest possible dispersion about the mean. We discuss the resulting atomic radii and compare them with others in the literature derived from only steric considerations. The present results expand the scope of fused-sphere surfaces for modeling microscopic or structural molecular properties. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996), S. 1269-1275 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present here a new iterative technique for reliable estimation of multidimensional free energy and potential of mean force (PMF) values by computer simulation. This method is an extension of the weighted histogram analysis method [S. Kumar et al., J. Comput. Chem., 13, 1011, (1992)]. We have tested the technique by generating free-energy-based Ramachandran plots and by computing the PMF values for end-to-end distances for several polypeptides using the ECEPP/2 and AMBER force fields. © 1996 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 17 (1996) 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 51
    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 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 18 (1997), S. 552-561 
    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 algorithm for four-index transformation and MP2 energy evaluation, for distributed memory parallel (MIMD) machines is presented. The underlying serial algorithm for the present parallel effort is the four-index transform. The scheme works through parallelization over AO integrals and, therefore, spreads the O(n3) memory requirement across the processors, reducing it to O(n2). In this sense, the scheme superimposes a shared memory architecture onto the distributed memory setup. A detailed analysis of the algorithm is presented for networks with 4, 6, 8, 10, and 12 processors employing a smaller test case of 86 contractions. Model direct MP2 calculations for systems of sizes ranging from 160 to 238 basis functions are reported for 11- and 22-processor networks. A gain of at least 40% and above is observed for the larger systems. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 601-608 
    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 MOLFDIR package of programs is used to perform fully relativistic all-electron Dirac-Fock and Dirac-Fock-Breit calculations for the the XeFn (n = 1, 2, 4, 6) molecules assuming experimental symmetries. The Xe-F bound length for XeF2, XeF4, and XeF6 is optimized and the total ground-state energies are reported. The variation of the relativistic energy and the Breit correction with the internuclear distance is plotted. The role of relativistic corrections in the proper prediction of the Xe-F distance and the dissociation energy of the molecule is discussed. The problem of the reduction of the number of scalar two-electron integrals is studied. Our results illustrate the possibilities, difficulties, and limitations of the finite basis Dirac-Fock calculations for polyatomic molecules of different symmetries. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 660-676 
    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 calculated Madelung energies and Madelung forces of the electrostatic interaction for nine crystal structures are reported. The method of direct summation with two different shifted-force potentials is compared to the Ewald summation. There is a considerable difference in the convergence of the energy and the force for the two shifted-force potentials regarding the cutoff radius. The convergence depends not only on the potential itself, but also on the crystal structure. One of the shifted-force potentials used is implemented in the CHARMM force field. The energy calculated with this potential shows a good convergence for small cutoff radii. With the other shifted-force potential, the force shows a better convergence for small cutoff radii. The number of pair interactions for obtaining the Madelung limit using the Ewald summation and the direct summation of a shifted-force potential is also reported. For complex structures like zeolites, the number of relevant pair interactions is smaller using the direct summation of a shifted-force potential. For simple structures such as cesium chloride, the number of significant pair interactions is smaller using the Ewald summation. © 1997 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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  • 58
    ISSN: 0192-8651
    Keywords: parallel computation ; SCF NMR chemical shifts ; GIAO ; pseudodiagonalization ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We implemented our gauge-including atomic orbital (GIAO) NMR chemical shielding program on a workstation cluster, using the parallel virtual machine (PVM) message-passing system. On a modest number of nodes, we achieved close to linear speedup. This program is characterized by several novel features. It uses the new integral program of Wolinski that calculates integrals in vectorized batches, increases efficiency, and simplifies parallelization. The self-consistent field (SCF) step includes a multi-Fock algorithm, i.e., the simultaneous calculation of several Fock matrices with the same integral set, increasing the efficiency of the direct SCF procedure. The SCF diagonalization step, which is difficult to parallelize, has been replaced by pseudodiagonalization. The latter, widely used in semiempirical programs, becomes important in ab initio type calculations above a certain size, because the ultimate scaling of the diagonalization step is steeper than that of integral computation. Examples of the calculation of the NMR shieldings in large systems at the SCF level are shown. Parallelization of the density functional code is underway. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 816-825, 1997
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    Journal of Computational Chemistry 18 (1997), S. 277-289 
    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, complementarity, is developed for conformational search of macrocyclic molecules. The algorithm scans a large number of candidate conformations and energy-minimizes only the promising ones. These candidates can be generated by two operators that construct new conformations from known minima. The candidates have similar bonded-interaction energy as the known minima and possibly lower nonbonded interaction energy. This algorithm is 9 to 11 times faster than the existing methods when tested on two large rings, cycloheptadecane and rifamycin SV. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 323-329 
    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 the application of the adaptive simulated annealing (ASA) method as a global optimization approach to biomolecular structure determination, using the ECEPP/2 (empirical conformation energy program for peptides) potential energy form. As applied to Met-enkephalin, our optimization results in a conformation that is in agreement with other studies. In addition, a dominant right-handed α-helical conformation is predicted for a 14-residue poly (L-alanine) model peptide in a limited search range. These results show that ASA is an efficient and robust algorithm for conformational analysis. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 343-350 
    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 problem of how to calculate the electrostatic interactions between molecules and a solvent is a very important one in theoretical chemistry and biophysics. One of the more commonly used methods has been to represent the solvent by a dielectric continuum and then to solve the Poisson (or the Poisson-Boltzmann) equation for the potential due to the charge distribution of the solute. The solution of the equation has, up to now, been largely carried out using finite-difference grid-based methods. In this article, we investigate the use of an alternative method, based on a basis set expansion of the potential. The choice of basis functions, the representation of the dielectric function and the accuracy that can be obtained are discussed and illustrated by example calculations on small molecules. © 1997 by John Wiley & Sons, Inc.
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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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    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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    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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    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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    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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    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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    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 18 (1997), S. 617-628 
    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 importance of the inclusion of the Madelung potential in cluster models of ionic surfaces is the subject of this work. We have determined Hartree-Fock all electron wave functions for a series of MgO clusters with and without a large array of surrounding point charges (PC) chosen to reproduce the Madelung potential. The phenomena investigated include: the reactivity of surface oxygens toward CO2, atomic hydrogen, and H+; the geometry and adsorption energy of water and the vibrational shift of CO adsorbed at Mg2+ sites; the electronic structure and the hyperfine coupling constants of oxygen vacancies, the paramagnetic Fs+ centers. While some clusters give results which are virtually independent of the presence of the PCs, other clusters, typically of small size, give physically incorrect results when the PCs are not included. The embedding of the cluster in PCs guarantees a similar response for clusters of different size, at variance with the bare clusters, where the long range coulombic interactions are not included. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 609-616 
    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 [3 + 2] cycloaddition reaction of phosphaacetylene with diazomethane was investigated by means of high level ab initio calculations. It was deduced that the aromatic diazaphosphole is formed via a nonaromatic intermediate. The regiospecificity of the reaction is thus determined by the energy difference between the two transition states that lead to the two possible regioisomeric intermediates. Of the transition states in the concerted pathways, the one leading to the regioisomer with two PC bonds (3) was found to be more stable at all the levels of theory investigated, including coupled-cluster singles doubles (CCSD)(T)/6-311 + G*//Møller-Plessett(MP)2/6-311 + G* (+ basis set superposition, BSSE, correction). The energy difference between the two transition states, however, is always less than 2 kcal/mol. When the free energies in the two reactions are calculated by use of the harmonic frequencies, the energy separation between the two transition structures remains practically unchanged. The free energy of activation ΔG† was 21 kcal/mol at the CCSD(T)/6-311 + G* level of theory and use of the MP2/6-31 + G* frequencies. At the MP2 level, a rather stable complex is obtained in the initial phase of the reaction. However, the stability of the complexes decreases at the CCSD(T) level, and application of the BSSE correction results in unstable complexes. © 1997 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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  • 76
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
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    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 
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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: 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 
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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: 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 
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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 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 
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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 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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    Journal of Computational Chemistry 18 (1997), S. 393-402 
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
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    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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    Journal of Computational Chemistry 18 (1997), S. 430-448 
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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 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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    Journal of Computational Chemistry 18 (1997), S. 1750-1759 
    ISSN: 0192-8651
    Keywords: Langevin dynamics ; Monte Carlo ; Poisson-Boltzmann equation ; alanine dipeptide ; continuum solvent ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We apply a combination of stochastic dynamics and Monte Carlo methods (MC/SD) to alanine dipeptide, with solvation forces derived from a Poisson-Boltzmann model supplemented with apolar terms. Our purpose is to study the effects of the model parameters, such as the friction constant and the size of the electrostatic finite difference grid, on the rate of conformational sampling and on the accuracy of the resulting free energy map. For dialanine, a converged Ramachandran map is produced in significantly less time than what is required by stochastic dynamics or Monte Carlo alone. MC/SD is also shown to be faster, per timestep, than explicit methods.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1750-1759, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1785-1791 
    ISSN: 0192-8651
    Keywords: multiple time steps ; r-RESPA ; Verlet method ; molecular dynamics ; fast multipole method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Numerical experiments are performed on a 36,000-atom protein-DNA-water simulation to ascertain the effectiveness of two devices for reducing the time spent computing long-range electrostatics interactions. It is shown for Verlet-I/r-RESPA multiple time stepping, which is based on approximating long-range forces as widely separated impulses, that a long time step of 5 fs results in a dramatic energy drift and that this is reduced by using an even larger long time step. It is also shown that the use of as many as six terms in a fast multipole algorithm approximation to long-range electrostatics still fails to prevent significant energy drift even though four digits of accuracy is obtained.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1785-1791, 1997
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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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    Journal of Computational Chemistry 18 (1997), S. 594-599 
    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 is presented for the location of the global minimum of a multiple minima problem. It begins with a series of randomly placed probes in phase space, and then uses an iterative Gaussian redistribution of the worst probes into better regions of phase space until all probes converge to a single point. The method quickly converges, does not require derivatives, and is resistant to becoming trapped in local minima. Comparison of this algorithm with others using a standard test suite demonstrates that the number of function calls has been decreased conservatively by a factor of about three with the same degree of accuracy. A sample problem of a system of seven Lennard-Jones particles is presented as a concrete example. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 638-645 
    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 new method is described to superimpose molecules using a crystallographic Fourier transform approach. Superimposed molecules, among other purposes, serve as a basis for three-dimensional (3D) QSAR analyses in drug design and therefore an objective and reproducible method of molecule alignment is of major importance. Fourier data are generated for hypothetical crystals of cubic symmetry for the compounds under consideration. A Patterson-density-based similarity index is used to optimize rotational alignment of the molecules. After optimization of rotational orientation, an electron density derived similarity index is used to further optimize overlap of electron density as a function of translation of the molecules. Both similarity indices are maximized by a simple optimization routine, thus enabling automated superposition. The use of Fourier space offers several advantages. First, rotational and translational parameters can be optimized separately, thus providing a small parameter space. Second, a limited number of data already provide an adequate, continuous description of the electron (or Patterson) density distribution. Third, crystallography provides simple methods to calculate the Fourier transforms that are needed. The resolution of the Patterson (electron) density representation used for superposition can be varied in a straightforward manner. Results are shown for the superposition of two antiviral agents, 2rs1 and 2r04; the dihydrofolate reductase ligands, methotrexate and dihydrofolate; and a set of three ε-thrombin inhibitors. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 677-693 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Charge distributions of a protonated and unprotonated Schiff base model compound are determined using different quantum chemical methods. After fitting the model molecule onto the protonated retinal Schiff base in Bacteriorhodopsin, electrostatic interaction energies between the model molecule and protein are calculated. Interaction energies as well as the calculated pK1/2 values of the model molecule are shown to depend considerably on the chosen charge distribution. Electrostatic potential derived partial charges determined at different ab initio levels reveal interaction energies between the model molecule and nearby residues such as ARG-82, ASP-85, and ASP-212, which are relatively method independent. Consequently, such charge distributions also result in pK1/2 values for the model molecule that are very similar. Larger deviations in the electrostatic interaction energies, however, are found in the case of charge distributions derived according to the Mulliken population analysis. Nevertheless, some sets of Mulliken derived partial charges predicted pK1/2 values for the model molecule that are close to those determined with electrostatic potential derived partial charges. This agreement, however, is only achieved because the individual errors of the contributing terms are approximately compensated. The use of the extended atom model is shown to be problematic. Although potential derived charges can correctly describe electrostatic interaction energies, they fail to predict pK1/2 values. On the basis of the present investigation a new set of partial charges for the protonated and unprotonated retinal Schiff base is proposed to be used in molecular dynamics simulations and electrostatics calculations. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 702-711 
    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 typical shallowness of the potential surfaces of weakly bound clusters implies sizable ground-state vibrational excursions in the weak modes, a feature often complicated by considerable anharmonicity. The difficulties of vibrational analysis are exacerbated as the number of weak modes increases with the number of molecules in a cluster. Quantum Monte Carlo (QMC) approaches offer a general suitability to the problem of vibrational dynamics of weakly bound clusters in that they can fully account for anharmonicity and large amplitude motions. We report on the effectiveness and convergence behavior of diffusion quantum Monte Carlo for both energies and the key spectroscopic values of vibrationally averaged rotational constants. QMC involves recurring evaluations of the interaction potential, and we show how property-based, two-and three-body potentials (e.g., those involving intrinsic molecular tensor properties) may be carefully linked to the QMC propagation steps. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 1211-1221 
    ISSN: 0192-8651
    Keywords: force fields ; medium-sized heterocycles ; transannular interaction ; drug design ; molecular modeling ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Medium-sized nitrogen-containing heterocycles have considerable potential as structurally novel templates for new medicinal agents. In order to evaluate this potential and to investigate their binding to various target receptors, satisfactory modeling of the properties of such compounds with force-field based computational methods is required, especially the conformations accessible to the molecules at and around their global minimum conformation. This is currently only possible with selected force fields for compounds that show a special intramolecular interaction such as the transannular interaction between a basic nitrogen atom and a carbonyl carbon atom. This article substantiates this claim and discusses two approaches to modify the commercially available CFF91 force field. The different approaches are discussed and assessed by their performance in reproducing the conformation in the crystal for a series of known model compounds. In summary, very good agreement with the experimental structure is achieved. The modified force fields are then used to investigate a potentially bioactive lead compound. The lead compound is predicted to be able to mimic the shape of a fused-ring compound with biological activity. © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1211-1221
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    Journal of Computational Chemistry 18 (1997), S. 1245-1252 
    ISSN: 0192-8651
    Keywords: hydrogen bonding ; α-helix stability ; energetics ; protein folding ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The intramolecular helix backbone 〉C(DOUBLE BOND)O---H - N〈 hydrogen bonding energies in poly(L-alanine) α helices have been estimated both in vacuum and in an aqueous environment using the parameter sets of five of the most commonly used force fields for modeling biomolecules, namely AMBER, CHARMM, ECEPP, GROMOS, and OPLS. The relative capabilities of these force fields in describing the H-bonding interactions with different dielectric continuum models have been assessed. A modified Hingerty-Lavery function is proposed for the treatment of electrostatic interactions of biomolecules in an aqueous environment. The helix backbone H-bonding energies predicted by this function (∼-1 kcal/mol) correspond closely with the experiment. © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1245-1252
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    Journal of Computational Chemistry 18 (1997), S. 1282-1294 
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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: Diabatic ordering of the normal model of a reaction complex along the reaction path has several advantages with regard to adiabatic ordering. The method is based on rotations of the vibrational normal modes at one point, s, of the reaction path to maximize overlap with the vibrational modes at a neighboring point. Global rotations precede the rotations of degenerate modes so that changes in the direction of the reaction path and changes in the force constant matrix, which represent the two major effects for changes in mode ordering, can be separated. Overlap criteria identify resolved and unresolved avoided crossings of normal modes of the same symmetry. Diabatic mode ordering (DMO) can be used to resolve the latter by reducing the step size, thus guaranteeing correct ordering of normal modes in dependence of s. DMO is generally applicable to properties of the reaction complex that depend on s such as normal mode frequencies, orbital energies, the energy of excited states, etc. Additional applications are possible using a generalized reaction path vector, which may describe the change in atom masses, geometrical parameters, and/or the force constant matrix. In this way, the vibrational spectra of isotopomers can be investigated or the vibrational frequencies of different molecules correlated. © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1282-1294, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1327-1327 
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1329-1343 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a method for the direct generation of the lists of strings, suited for integral-driven full-CI (FCI) algorithms. This method generates the string lists each time they are used, and hence sensibly reduces the memory requirements, compared to our previous method that precalculates the lists. It was also extended to permit a truncation of the string space, according to the level of excitation.   © 1997 by John Wiley & Sons, Inc.   J Comput Chem 18: 1329-1343, 1997
    Additional Material: 2 Ill.
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  • 97
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1354-1364 
    ISSN: 0192-8651
    Keywords: molecular dynamics of polymers ; internal coordinate molecular dynamics ; constraint dynamics ; molecular dynamics in torsion angle space ; implicit leapfrog integrator ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conventional molecular dynamics simulations of macromolecules require long computational times because the most interesting motions are very slow compared to the fast oscillations of bond lengths and bond angles that limit the integration time step. Simulation of dynamics in the space of internal coordinates, that is, with bond lengths, bond angles, and torsions as independent variables, gives a theoretical possibility of eliminating all uninteresting fast degrees of freedom from the system. This article presents a new method for internal coordinate molecular dynamics simulations of macromolecules. Equations of motion are derived that are applicable to branched chain molecules with any number of internal degrees of freedom. Equations use the canonical variables and they are much simpler than existing analogs. In the numerical tests the internal coordinate dynamics are compared with the traditional Cartesian coordinate molecular dynamics in simulations of a 56 residue globular protein. For the first time it was possible to compare the two alternative methods on identical molecular models in conventional quality tests. It is shown that the traditional and internal coordinate dynamics require the same time step size for the same accuracy and that in the standard geometry approximation of amino acids, that is, with fixed bond lengths, bond angles, and rigid aromatic groups, the characteristic step size is 4 fs, which is 2 times higher than with fixed bond lengths only. The step size can be increased up to 11 fs when rotation of hydrogen atoms is suppressed.   © 1997 by John Wiley & Sons, Inc.   J Comput Chem 18: 1354-1364, 1997
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  • 98
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 60-70 
    ISSN: 0192-8651
    Keywords: molecular-dynamics minimization ; conformational search ; water cluster ; Lennard-Jones clusters ; Coulombic clusters ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new conformational search method, molecular dynamics-minimization (MDM), is proposed, which combines a molecular dynamics sampling strategy with energy minimizations in the search for low-energy molecular structures. This new method is applied to the search for low energy configurations of clusters of coulombic charges on a unit sphere, Lennard-Jones clusters, and water clusters. The MDM method is shown to be efficient in finding the lowest energy configurations of these clusters. A closer comparison of MDM with alternative conformational search methods on Lennard-Jones clusters shows that, although MDM is not as efficient as the Monte Carlo-minimization method in locating the global energy minima, it is more efficient than the diffusion equation method and the method of minimization from randomly generated structures. Given the versatility of the molecular dynamics sampling strategy in comparison to Monte Carlo in treating molecular complexes or molecules in explicit solution, one anticipates that the MDM method could be profitably applied to conformational search problems where the number of degrees of freedom is much greater.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 60-70, 1998
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  • 99
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 94-101 
    ISSN: 0192-8651
    Keywords: Dunham method ; rovibrational energy levels ; rovibrational Schrödinger equation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A numerical algorithm of the Dunham method for the solution of the rovibrational Schrödinger equation is proposed. It uses a new quasi-Hermitian method of constructing the optimal approximate polynomial for the tabularly defined potential curve of a diatomic molecule obtained from an ab initio calculation. In this method the optimal polynomial approximates the potential curve and its derivatives, but it uses only information about the potential curve for its construction. This property of the new method arises from analysis of a spectral representation of the optimal polynomial to determine how well it approximates the potential curve and its derivatives. Appropriate derivatives of the potential curve, needed in the Dunham method, are calculated by recurrence relations. Comparison with the finite-difference method shows that the precision of both methods is similar, while the Dunham method is hundreds of times faster.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 94-101, 1998
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  • 100
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. vii 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: No abstract.
    Additional Material: 1 Ill.
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