摘要:

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

ISSN:0192-8651    

DOI:10.1002/jcc.540141102

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractComputer methods for analytic surface calculations of molecular systems suffer from numerical instabilities and are CPU time consuming. In this article, we present proposals toward the solution of both problems. Singularities arise when nearly collinear triples of neighboring atoms or multiple vertices are encountered during the calculation. Topological decisions in analytic surface calculation algorithms (accessibility of vertices and arcs) are based upon the comparison of distances or angles. If two such numbers are nearly equal, then currently used computer programs may not resolve this ambiguity correctly and can subsequently fail. In this article, modifications in the analytic surface calculation algorithm are described that recognize singularities automatically and treat them appropriately without restarting parts of the computation. The computing time required to execute these alterations is minimal. The basic modification consists in defining an accuracy limit within which two values may be assumed as equal. The search algorithm has been reformulated to reduce the computational effort. A new set of formulas makes it possible to avoid mostly the extraction of square roots. Tests for small‐and medium‐sized intersection circles and for pairs of vertices with small vertex height help recognize fully buried circles and vertex pairs at an early stage. The new program can compute the complete topology of the surface and accessible surface area of the protein crambin in 1.50–4.29 s (on a single R3000 processor of an SGI 4D/480) depending on the compactness of the conformation where the limits correspond to the fully extended or fully folded chain, respectively. The algorithm, implemented in a computer program, will be made available on request. © John Wiley&Son

ISSN:0192-8651    

DOI:10.1002/jcc.540141103

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractTo compare the GROMOS force field with one designed by Ha et al., molecular dynamics simulations of α‐D‐glucose anhydrate and monohydrate crystals were performed. Also, the long‐range interactions were calculated both with a cutoff approximation and with Ewald summations. The results are compared with results obtained experimentally by neutron and X‐ray diffraction. The force‐field parameters had been optimized with the cutoff approximation; this apparently led to worse results when the Ewald summations were used. However, in all simulations the symmetry was roughly preserved and the mean atomic coordinates and thermal parameters, bond angles, and dihedrals without hydrogen atoms were rather well reproduced. The dihedrals with hydrogen atoms exhibited conformational transitions, which resulted in a disordered hydrogen bonding scheme. In general, the GROMOS force field performed better than the Ha force field. © John Wile

ISSN:0192-8651    

DOI:10.1002/jcc.540141104

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe quantification of surface roughness of globular proteins and synthetical macromolecules in the globular state is discussed using the concept offractality. TheHausdorff dimensionas a measure for local and global fractality of surfaces is applied. To calculate the Hausdorff dimension of any surface at a high level of accuracy, a new algorithm is presented that is based on a triangulated solvent‐accessible molecular surface. It can be demonstrated that protein surfaces (as calculated on the basis of experimentally determined structures) as well as surfaces of globular polyethylene (PE) conformers (calculated on the basis of structural information basing on extensive Monte Carlo and molecular dynamics simulations) in fact show self‐similarity within a reasonable yardstick range, at least in a global statistical sense. The same is true for parts of a protein surface provided that these regions are not too small. The concept of self‐similarity breaks down when individual surface points are considered. The results obtained for the fractal dimension of PE surfaces (average fractal dimensionD= 2.23) lead to the conclusion that protein surfaces probably do not exhibit a unique and specific degree of geometrical complexity (or surface roughness) characterized by a fractal dimension of approximatelyD= 2.2 as was argued in the past. It is clear that the concept of self‐similarity is helpful for the classification of surface roughness of large molecules, but it seems questionable whether this concept is useful for the identification of active sites or other questions related to the field of molecular recognition. © John Wiley&S

ISSN:0192-8651    

DOI:10.1002/jcc.540141105

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractLithium parameters have been optimized for Stewart's standard PM3 method. The average deviation of the heats of formation calculated for 18 reference compounds is 6.2 kcal/mol from the experimental or high‐levelab initiodata; the average deviation with Li/MNDO is 18.9 kcal/mol. The average error in bond lengths is also reduced by a factor of two to three. Ionization potentials and dipole moments are reproduced with comparable accuracy than Li/MNDO. However, the mean deviation for the heats of formation of both methods increases when being applied to other systems, especially to small inorgnic molecules. The applicability of the new parameter set is demonstrated further for various compounds not included in the reference set, for the calculation of the activation barriers of several lithiation reactions, as well as for the estimation of oligomerization energies of methyl lithium (including the tetramer). Li/PM3 gives reliable results even for large dimeric complexes, like [{4‐(CH3CR)C5H4N}Li]2, containing TMEDA or THF as coligands and reproduces the haptotropic interaction between Li+and π‐systems (e.g., in benzyl lithium) as well as the relative energies and structural features of compounds with “hypervalent” atoms (e.g., in lithiated sulfones). © John Wile

ISSN:0192-8651    

DOI:10.1002/jcc.540141106

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe limiting factor to account for the increased rate of intramolecular reactions between functional groups as opposed to their intermolecular counterparts can and has been explained both by proximity effects and by activation energy. Neither explanation has emerged as the single most important reason in all or even the majority of cases studied. We have therefore reexamined the spatiotemporal hypothesis of Menger and the transition‐state energy approach of Houk on a consistent set of compounds subjected to the Barton oxidation or related reactions in an effort to more clearly define the reasons for the proximity effect. For the 26 structures studied, neither hypothesis provides a consistent, quantitative explanation although the transitionstate energy hypothesis offered the most promise. © John Wiley&Sons, I

ISSN:0192-8651    

DOI:10.1002/jcc.540141107

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe problem of the representation of the RKR (or IPA) diatomic potential by a simple analytic function is considered. This old problem has for a fairly good solution the Coxon‐Hajigeorgiou functionU(x) =D[1 ‐ exp‐fn(x)]2withfn(x) = Σ m= 1namxm. The problem of the determination of the disposable parametersa1…an[in order thatU(r)fits the given RKR potential] is reduced to that of a set of linear equations inamwhere a standard least‐squares technique is used. The application to several states (ground or excited) of several molecules shows that a fairly “good” fit is obtained forn∼ 10, even for the stateXOg—I2bounded by 109 vibrational levels, for which the RKR potential is defined by the coordinates of 219 points. It is shown that the percentage deviation |U(r)RKR‐U(r)| throughout the range ofrvalues is about 0.04% forXΣLi2, 0.0005% forXΣHCl, 0.06% forXOgI2, and 0.05% forBOuI2(as examples). This approach shows the same success for deep and shallow potentials. The comparison of the computedEv(vibrational energy) andBv(rotational constant) with their corresponding experimental values shows that a good agreement is reached even for high vibrational levels close to the diss

ISSN:0192-8651    

DOI:10.1002/jcc.540141108

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

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

ISSN:0192-8651    

DOI:10.1002/jcc.540141109

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractWe apply a recently developed method, the multicanonical algorithm, to the problem of tertiary structure prediction of peptides and proteins. As a simple example to test the effectiveness of the algorithm, metenkephalin is studied and the ergodicity problem, or multiple‐minima problem, is shown to be overcome by this algorithm. The lowest‐energy conformation obtained agrees with that determined by other efficient methods such as Monte Carlo simulated annealing. The superiority of the present method to simulated annealing lies in the fact that the relationship to the canonical ensemble remains exactly controlled. Once the multicanonical parameters are determined, only one simulation run is necessary to obtain the lowest‐energy conformation and further the results of this one run can be used to calculate various thermodynamic quantities at any temperature. The latter point is demonstrated by the calculation of the average potential energy and specific heat as functions of temperature. © John Wiley&Son

ISSN:0192-8651    

DOI:10.1002/jcc.540141110

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractModifications are made to a previously published algorithm for constrained optimization in Cartesian coordinates (J. Comp. Chem.,13, 240, 1992) to incorporate both fixed and dummy atoms. Standard distance and angle constraints can now be specified with respect to dummy atoms, greatly extending the range of constraints that can be handled. Fixed atoms can be eliminated from the optimization space and so there is no need to calculate their gradients resulting in potentially significant savings of CPU time inab initiocomputations. Several examples illustrate the range and versatility of the modified algorithm. © John Wiley&Sons, Inc

ISSN:0192-8651    

DOI:10.1002/jcc.540141111

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY