摘要:

AbstractWe present investigations on the use of dielectric continuum models for the self‐consistent description of electrostatic solvent effects on the ground state of a molecule and on excitation energies. The electronic structure calculations have been carried out in the framework of the INDO and INDO/S‐CI method, respectively. We compare the performance of three implementations of the cavity model that all allow an arbitrary shape of the solute cavity. The procedures differ in the effort spent on the description of the charge density at the cavity surface. Two procedures in the vein of Miertus̆, Scrocco, and Tomasi (MST) rely upon point charges to model the reaction field and differ in the way the cavity surface is modeled. While one implementation divides the surface into flat triangular patches, the improved version uses curved triangles. Alternatively, we investigate a finite element method (FEM) for the calculation of the surface charge density. Applications to rod‐shaped organic molecules (including their charge transfer excitations) illustrate the superiority of the improved MST formalism over the primitive one, as it exhibits faster convergence of the results with increasing node density on the cavity surface. The FEM approach, which also employs curved surface patches, leads to a further improvement as it needs less computational effort, especially in the treatment of excited states. © 1993 John Wiley&So

ISSN:0192-8651    

DOI:10.1002/jcc.540140302

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractCombining the modified Urey–Bradley–Shimanouchi intramolecular potential energy function with an appropriate intermolecular energy function, normal coordinate calculations have been performed for both α and β anomers of glucose and for some deuterated analogs in the crystalline state. The overall agreement between the observed and calculated frequencies leads to an average error on the order of 3 and 5 cm−1for α and β glucose, respectively. In both cases, it is shown that the intermolecular potential energy terms are essential to reproduce perfectly the whole spectra, in particular for the hydroxyl stretching region, the anomeric and crystalline spectral regions, and the low‐frequency range. Moreover, the intermolecular interactions have a nonnegligible influence on the value of the intramolecular force constants. But, the potential energy distribution of vibrational modes are in accord with previous works performed for an isolated molecule. It is also important to point out that approximately the same set of force constants has been used for both molecules, differences existing only for the atoms involved in the anomeric configuration. Likewise, different charge distributions have been calculated and tested with different value of the dielectric constant. Charges determined by the AM1quantum mechanical procedure with a value of 3 for the dielectric constant have the merit to reproduce quite well the whole spectra and in particular the frequency range below 200 cm−1. © 1993 John W

ISSN:0192-8651    

DOI:10.1002/jcc.540140303

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractMolecular dynamics simulations of pure water employing two different empirical water models have been used to study the effects of different methods for truncation of long‐range interactions in molecular mechanics calculations. As has been observed previously in integral equation studies, “shifting” these interactions on an atom‐by‐atom basis was found to produce artificial structuring in the water and affect diffusion rates. In cases where some form of short‐range truncation must be used, the ST2 switching function applied on a group‐by‐group basis was found to be the most realistic procedure. If atom‐based shifting must be employed, a cutoff distance greater than or equal to 12.0 Å was found to be required to produce realistic results. © 1993 J

ISSN:0192-8651    

DOI:10.1002/jcc.540140304

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe nature of the tetrahedral H42+stationary point (minimum or triply degenerate saddle) depends remarkably upon the theoretical level employed. Harmonic vibrational analyses with, e.g., the 6‐31G** (and 6‐31 + +G**) and Dunning's [4s2p1d;2s1p] [D95(d,p)] basis sets using the standardpexponent suggest (erroneously) that theTdgeometry is a minimum at both the HF and MP2 levels. This is not the case at definitive higher levels. The C3H42+structure with an apical H is another example of the failure of the calculations with the 6‐31G**, 6‐311G**, and D95(d,p) basis sets. Even at MP2/6‐31G** and MP2/ cc‐pVDZ levels, theC3vstructure has no negative eigenvalues of the Hessian. Actually, this form is a second‐order saddle point as shown by the MP2/6‐31G** calculation with the optimized exponent. TheD4hmethane dication structure is also an example of the misleading performance of the 6‐31G** basis set. In all these cases, energy‐optimized hydrogenpexponents give the correct results, i.e., those found with more extended treatments. Optimized values of the hydrogen polarization function exponents eliminate these defects in 6‐31G** calculations. Species with higher coordinate hydrogens may also be calculated reliably by using more than one set ofpfunctions on hydrogen [e.g., the 6‐31G(d,2p) basis set]. Not all cases are critical. A survey of examples, also including some boron compounds, provides calibration. © 1

ISSN:0192-8651    

DOI:10.1002/jcc.540140305

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractIn a previous aqueous protein dynamics study, we compared the rms deviation relative to the crystal structure for distance‐dependent and constant dielectric models with and without a nonbonded cutoff. The structures obtained from a constant dielectric simulation with a cutoff were substantially different from the structures obtained from a distance‐dependent dielectric simulation, with and without cutoff, and a constant dielectric model without a cutoff. In fact, structures from the distance‐dependent dielectric simulations were insensitive to the nonbonded cutoff and in good agreement with the structures generated from the constant dielectric simulation without a cutoff. In addition, the solute‐solvent temperature differential and solvent evaporation artifacts, characteristic of the constant dielectric simulation with a cutoff, were not present for the distance‐dependent dielectric simulations. In this current work, we explore whether this dielectric‐dependent cutoff‐sensitive behavior for a constant dielectric model arises from the discontinuities in the forces at the nonbonded cutoff or from neglecting the structure‐stabilizing interactions beyond the nonbonded cutoff. We also examine the origin of the dielectric‐dependent artifacts, and its potential influence on the structural disparity. Several protocols for protein dynamics simulations are compared using both constant and distance‐dependent dielectric models, including implementation of a switching function and a nonbonded cutoff and two different temperature coupling algorithms. We show that the distance‐dependent dielectric model conserves energy in the SPASMS molecular mechanics and dynamics software for the time steps and nonbonded cutoffs commonly used in macromolecule simulations. Although the switching function simulation also conserved energy over a range of commonly used cutoffs, the constant dielectric model with a switching function yielded conformational results more similar to a constant dielectric simulation without a switching function than to a constant dielectric model without a nonbonded cutoff. Therefore, the conformational disparity between the dielectric models arises from neglecting important structure‐stabilizing interactions beyond the cutoff, rather than differences in energy conservation. © 1

ISSN:0192-8651    

DOI:10.1002/jcc.540140306

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractA fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long‐range nonbonded Coulomb and Lennard–Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1‐4 nonbonded interaction terms, coordinate restraints, and the SHAKE bond constraint algorithm. As far as we can determine, this is the first published description where a distributed‐memory MIMD parallel implementation of the SHAKE algorithm has been designed to treat not onlyhydrogen‐containing bondsbut alsoall heavy‐atom bonds, and where “shaken”crosslinksare supported as well. We discuss the subtasking and partitioning of an MD time‐step, load balancing the nonbonded evaluations, describe inalgorithmic detailhow parallelization of SHAKE was accomplished, and presentspeedup,efficiency, and benchmarking resultsachieved when this hypercube adaptation of the MD module AMBER was applied to several variant molecular systems. Results are presented for speedup and efficiency obtained on the nCUBE machine, using up to 128 processors, as well as benchmarks for performance comparisons with the CRAY YMP and FPS522 vector machines. © 1993 Jo

ISSN:0192-8651    

DOI:10.1002/jcc.540140307

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe stochastic search method coupled to MM3(92) has been used to locate as many conformers as possible for 6‐ to 11‐membered ring lactones,trans‐cycloalkenes, andcis‐cycloalkenes. A comparison was carried out between the conformers of lactones and cycloalkenes of the same ring size for each force field. These comparisons were carried out by means of (1)conformational distances, defined as the rms deviation between the dihedral angles of the conformers being compared, and (2),substitution, in which a lactone was transformed into an olefin and vice versa, trying to keep as much as possible the initial geometry, followed by reoptimization. It is found that cycloalkenes and lactones share many common characteristics. The thermodynamic information provided by MM3 was used to study the dependence of conformer population upon (1) temperature and (2) total number of conformers. © 1993 John Wiley&S

ISSN:0192-8651    

DOI:10.1002/jcc.540140308

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractWe report the development of a new approximate method of calculating molecular surface areas. Our technique is based upon the method of Sharake and Rupley but incorporates several major advances. First, we represent the state of surface points as bits in a bit string so we can utilize Boolean operations to simultaneously turn off multiple test points in one Boolean AND operation. Second, we use a series of Boolean mask look‐up tables to reduce the time complexity of the calculation of molecular surface area down to the same magnitude as doing a potential energy evaluation. When we use a 256 surface point sphere for all of the atoms in BPTI, a 454 nonhydrogen atom protein, and a 1.4‐Å solvent probe, we in general underestimate the total solvent‐accessible surface area (SASA) by approximately 1.25% with a correlation coefficient of 0.9990 over a wide range of conformations. The average CPU time required to calculate the SASA of a BPTI conformer is 0.58 s on an SGI 4D/220 workstation. We also describe a method by which we can calculate an approximate finite difference SASA gradient for BPTI in 0.79 of CPU time. © 1993 John Wiley&So

ISSN:0192-8651    

DOI:10.1002/jcc.540140309

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe electrostatic potential‐derived charges for the catecholamine neurotransmitter dopamine were calculated at the STO‐3G and 6‐31G* basis sets for six different molecular conformations. The degree of variance of the charges with changing conformations was examined. The 6‐31G* basis set produced charges that were more sensitive to changes in conformation than those derived from the STO‐3G electrostatic potentials. The implication of the charge variations in molecular mechanics calculations was also investigated. The molecular mechanics results in the gas phase exhibited a variance depending upon the charge set used. The force field calculations varied much less when aqueous solvation was included in the calculations through a continuum model. © 1993 John Wiley

ISSN:0192-8651    

DOI:10.1002/jcc.540140310

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractWe outline a procedure that resolves ambiguities in fitting nonlinear data by power series. As is well known, the coefficients in the regression equations depend upon the truncation of the power series. We outline the procedure in which the coefficients of the regression using a power expansion are independent of the degree of the polynomials used. This is achieved by considering mutual regression of descriptors and using residuals as novel variables. The derived regression equations show unusual numerical stability, i.e., the coefficients of the regression equations are constant and independent of the truncation of the power series. The process is illustrated in an example to show all details and facilitate duplicating the process for interested readers. The method described here complements recently outlined procedures for construction of orthogonal descriptors for use in multivariate regression analysis. © 1993 John Wiley&Sons, Inc

ISSN:0192-8651    

DOI:10.1002/jcc.540140311

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY