摘要:

AbstractAn algorithm for the rapid analytical determination of the accessible surface areas of solute molecules is described. The accessible surface areas as well as the derivatives with respect to the Cartesian coordinates of the atoms are computed by a program called “MSEED,” which is based in part on Connolly's analytical formulas for determining surface area. Comparisons of the CPU time required for MSEED, Connolly's numerical algorithm DOT, and a program for surface area determination (ANA) based on Connolly's analytical algorithm, are presented. MSEED is shown to be as much as 70 times faster than ANA and up to 11 times faster than DOT for several proteins. The greater speed of MSEED is achieved partially because nonproductive computation of the surface areas ofinternalatoms is avoided. A sample minimization of an energy function, which included a term for hydration, was carried out on MET‐enkephalin using MSEED to compute the solvent‐accessible surface area and its derivatives. The potential employed was ECEPP/2 plus an empirical potential for solvation based on the solvent‐accessible surface area of the peptide. The CPU time required for 150 steps of minimization with the potential that included solvation was approximately twice as great as the CPU time required for 150 steps of minimization with the ECEPP/2 poten

ISSN:0192-8651    

DOI:10.1002/jcc.540130102

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractA six‐term auxiliary integral expression for the two‐electron Gaussian integral is derived on the basis of the Chebyshev polynomial approximation instead of the seven‐term Taylor expansion. This expression and the related recurrence formula enable us to perform a high‐speed calculation on a vector processing c

ISSN:0192-8651    

DOI:10.1002/jcc.540130103

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractAn overall adsorption quantity for a heterogeneous solid is usually expressed by an integral equation, which contains a distribution function that describes heterogeneous properties of this solid. The calculation of this distribution function is an ill‐posed problem. The current article shows that the difficulties arising from the ill‐posed nature of an adsorption equation can be overcome with the regularization method. This work presents general principles of regularization for solving the ill‐posed problems without detailed mathematical considerations. The application of the regularization method to calculate a distribution function from any overall adsorption functions is illustrated with both simulated and experimental adsorption isot

ISSN:0192-8651    

DOI:10.1002/jcc.540130104

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractUsing the crown ether 18‐crown‐6 as a test system, molecular dynamics has been evaluated as a technique for conformational searching and thermodynamic ensemble generation. By running a series of 200 ps and 2 ns simulations, an “optimum” temperature range for conformational searching, i.e., the temperature at which one finds the largest number of low energy structures, was demonstrated to be dependent on the time interval at which one examines the structure. By considering conformational degeneracy and entropy with the rigid rotor harmonic oscillator approximation we have been able to demonstrate that the ensemble generated approaches thermodynamic equilibrium in about 6 ns of simulation. To our knowledge this is the first time this has been demonstrated for a complex organic molecule and it highlights the power and usefulness of molecular dynamics as a method for thermodynamic ensemble generation and conformational se

ISSN:0192-8651    

DOI:10.1002/jcc.540130105

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractDistance geometry and molecular dynamics simulation techniques were compared in their ability to search the conformational potential energy surface of β‐cyclodextrin. Structures generated by the DISGEO program were minimized using three different atomic point charge sets. Some of these structures were used as starting points for molecular dynamics simulationin vacuoat 298K. The distance geometry results showed that the global features of the conformational potential energy surface were generally independent of the point charge set. The distance geometry technique was able to find structures of lower energy than those obtained by direct minimization of the X‐ray or neutron diffraction structures. However, the molecular dynamics simulation technique was consistently able to find structures of lower energy than those generated by distance geometry. Root mean square fit of the trajectory structures to the starting structure showed that the simulation allowed the molecule to explore regions of the potential energy surface in the neighborhood of the starting structure. Both the distance geometry and molecular dynamics simulation techniques showed that β‐cyclodextrin can adopt a wide range of conformations in the gas phase and that these conformations are much less symmetrical than the crystalline st

ISSN:0192-8651    

DOI:10.1002/jcc.540130106

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractThe application of molecular mechanics methods for the study of structures has become a standard approach to conformational analysis. The MM2 force field has been extended to include imines. In general, a diverse group of aliphatic and aromatic imine structures can now be treated. The rotational energy profiles and barriers to N‐substituted imines about theCsp2Csp2single bonds adjacent to CN functional group were calculated viaab initioMO theory. Information obtained from the quantum mechanical calculations at the 3‐21G, 6‐31G*, and MP4/6‐31G* //6‐31G* levels was used both to study the phenomena involved and to parameterize MM2. Thesyn‐antiisomerization was also studied, and the mechanistic pathways have been evaluated. In cases where the comparison with experimental data can be made, the agre

ISSN:0192-8651    

DOI:10.1002/jcc.540130107

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractWe used Brownian dynamics simulations of substrate O 2−encounters with the enzyme bovine erythrocyte Cu, Zn superoxide dismutase (SOD) to study the effects of multiple charge modifications in the enzyme on the kinetics of its diffusion‐controlled reaction. When the charges of two or three residues were changed, the calculated rate consant relative to that for the unmodified enzyme was usually found to be the product of relative rate constants for the enzymes with the corresponding single‐site changes. This “multiplicativity” rule may be useful in the design of enzymes that operate with diffusion‐controlled kinetics. Residues that deviate from the general rule are found in the active site channel of SOD, and the origin of these deviations

ISSN:0192-8651    

DOI:10.1002/jcc.540130108

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractThe ability of approximate Density Functional Theory to calculate molecular electron affinities has been probed by a series of calculations on the hydrides CH3, NH2, OH, and HC2as well as the multibonded species CN, BO, N3, OCN, and NO2. The simple Hartree–Fock Slater scheme lacks dynamic correlations and underestimates on the average the adiabatic electron affinities (EAad) by 0.7 eV. A considerable improvement is obtained by the Local Density Approximation (LDA) in which dynamic correlation is included. Values from LDA calculation underestimate, on the average, the adiabatic electron affinities by 0.4 eV. The best agreement with experiment is obtained by the LDA/NL scheme in which a nonlocal correction recently proposed by Becke is added to the LDA energy expression. The LDA/NL method underestimatesEAadby 0.2 eV. It is concluded that the LDA/NL method affordsEAad's in as good agreement with experiment asab initiotechniques in which electron correlation is taken into account by extensive configuration interaction. A full geometry optimization has been carried out on the nine neutral sample molecules as well as the corresponding anion

ISSN:0192-8651    

DOI:10.1002/jcc.540130109

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractAn algorithm for the calculation of local and global curvatures of molecular surfaces is presented. The analysis is based on a surface representation as a set of points in 3‐D space (“dotted surface” representation). The surface data are used to subdivide the surfac into domains with different curvatures. All domains are characterized by a reference point with a corresponding curvature profile specifiying the topological properties in its neighborhood. The curvature profiles provide a method for a systematic comparison of the shapes of different molecules. Such a strategy is important for the treatment of molecular recognition problems. The enzyme‐inhibitor complex trypsin/BPTI was chosen to demonstrate the scopes of the

ISSN:0192-8651    

DOI:10.1002/jcc.540130110

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractThe semiempirical MO method SINDO1, originally suitable for first‐ and second‐row atoms, is extended to transition metals from scandium to zinc. The core Hamiltonian elements in a symmetrically orthogonalized atomic orbital (OAO) basis set are modified and the parameters are optimized to reproduce the experimental geometries, heats of formation, and ionization potentials. An application of the method to a selected number of molecules, as well as a comparison between calculated and experimental data is repor

ISSN:0192-8651    

DOI:10.1002/jcc.540130111

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY