摘要:

AbstractAn expanded form of the Wiener number is suggested for characterization of molecular graphs and structure‐property correlations. The simple, computer‐oriented method for counting of the novel index is briefly discus

ISSN:0192-8651    

DOI:10.1002/jcc.540110802

出版商:John Wiley&Sons, Inc.    

年代:1990

数据来源: WILEY

摘要:

AbstractA new strategy to evaluate accurate electrostatic charges from semiempirical wave functions is reported. The rigorous quantum mechanical molecular electrostatic potentials computed from both MNDO and AM1 wave functions are fitted to the point‐charge molecular electrostatic potential to obtain the electrostatic charges. The reliability of this strategy is tested by comparing the semiempirical electrostatic charges for 21 molecules with the semiempirical Mulliken charges and with the ab initio STO‐3G and 6‐31G* electrostatic charges. The ability of the dipoles derived from the semiempirical electrostatic and Mulliken charges as well as from the SCF charge distributions to reproduce the ab initio 6‐31G* electrostatic dipoles and the gas phase experimental values is determined. The statistical analysis clearly point out the goodness of the semiempirical electrostatic charges, specially when the MNDO method is used. The excellent relationships found between the MNDO and 6‐31G* electrostatic charges permit to define a scaling factor which allows to accurately reproduce the 6‐31G* electrostatic charge distribution as well as the experimental dipoles from the semiempirical electrosta

ISSN:0192-8651    

DOI:10.1002/jcc.540110803

出版商:John Wiley&Sons, Inc.    

年代:1990

数据来源: WILEY

摘要:

AbstractThe geometry, electronic structure, and photoelectron spectra of Sb2and Sb4have been investigated employing the LCGTO‐MP‐LSD method. For both molecules the geometrical and spectroscopic constants computed using the VWN potential are in very good agreement with the available experimental data. The HeI photoelectron spectra were computed with different potentials (Xα, GL, HL, BH, and VWN). The calculated spectra are in excellent agreement with the experimental ones and the use of the VWN potential gives the most accurate results. The reliable results for molecules complement those for the Sb atom and show that the proposed LSD Model Potential is able to give an accurate description of the structural and spectroscopic properties of the title molec

ISSN:0192-8651    

DOI:10.1002/jcc.540110804

出版商:John Wiley&Sons, Inc.    

年代:1990

数据来源: WILEY

摘要:

AbstractThe effect of the addition of diffuse functions ofsptype on the first row atoms (and/or ofdtype on phosphorus) to a MINI‐1 minimal basis set is evaluated by comparing the SCF description of the interaction energy and its decomposition, counterpoise (CP) corrected and uncorrected for basis set superposition errors (BSSEs), with that produced by extended basis sets (6‐31G** and 3‐21G+) as well as by basis sets (6‐31G** + VPSand (2d)S), previously successfully tested, designed to minimize the BSSE. The systems considered are a few anions (F−, HCOO−, H2PO−4) H‐bonded to water; the basis set performance on a different geometry (bifurcated instead of linear) of the phosphate‐water adduct was also considered. An additional comparison with the interaction energy in a neutral dimer, (HF)2, was carried out. The addition of diffuse functions to the MINI‐1 basis set, instead of resorting to extended basis sets, seems to be a sensible choice for anions. The equilibrium distance is shifted towards the reference basis set value at the CP corrected level as well as at the uncorrected one. The spread of the energy due to the basis set is hardly distinguishable when the CP corrected values are plotted. The description of the interaction energy in dimers involving phosphorus is improved usingdtyp

ISSN:0192-8651    

DOI:10.1002/jcc.540110805

出版商:John Wiley&Sons, Inc.    

年代:1990

数据来源: WILEY

摘要:

AbstractThe organization of the highly vectorizable molecular dynamics simulation program ARGOS is described. The specific choice of the data structure and the separation of the calculation of interactions involving solutes and solvent molecules allows a considerable improvement in computation speed. Illustrative results are given for the NEC SX‐2/400 supercomputer. For the simulation of a large biological molecule in water a speedup factor of 5 is obtained as a result of vectorization of the code to 87%. The parts of the code used in a simulation of pure water could be vectorized to 98%, leading to an overall speedup factor due to vectorization of 13. The simulation of pure water runs over 300 times faster on the SX‐2/400 than on the VAX 8

ISSN:0192-8651    

DOI:10.1002/jcc.540110806

出版商:John Wiley&Sons, Inc.    

年代:1990

数据来源: WILEY

摘要:

AbstractMolecular mechanics provides an excellent means of generating reasonable chemical structures in a short amount of time. Using a classical representation, a molecule can be partitioned into a collection ofn‐fold atomic interactions, each with an associated force constant. In order for a calculation to proceed, all of the required force constants must be known. This article presents a method of rapidly determining the values for missing parameters using appropriately scaled quantum chemical technique

ISSN:0192-8651    

DOI:10.1002/jcc.540110807

出版商:John Wiley&Sons, Inc.    

年代:1990

数据来源: WILEY

摘要:

AbstractIntermolecular potential functions have been developed for use in computer simulations of alkyl ethers. The simple OPLS model was adopted and parameterized to yield good descriptions of bimolecular and ion‐molecule complexes as well as to reproduce experimental thermodynamic properties of liquid ethers. The principal testing featured Monte Carlo statistical mechanics simulations for liquid dimethyl ether (DME), ethyl methyl ether (EME), diethyl ether (DEE), and tetrahydrofuran (THF). Average errors of 1–3% are obtained for the computed densities and heats of vaporization including results for THF at pressures up to 5000 atm. The torsional motion about the central CO bonds in EME and DEE was included in the simulations using rotational potential functions fit to results of molecular mechanics (MM2) calculations. The liquid‐state environment is found to have negligible effect on the conformational equ

ISSN:0192-8651    

DOI:10.1002/jcc.540110808

出版商:John Wiley&Sons, Inc.    

年代:1990

数据来源: WILEY

摘要:

AbstractA quadrature‐point‐driven implementation of the standard Rys polynomial method for computing two‐electron repulsion integrals of gaussian basis functions has been found to be both concise and openended with respect to the angular momentum of the gaussian functions (i.e.,s,p,d,f,g,…). These are important features in certain applications, such as molecular properties and property gr

ISSN:0192-8651    

DOI:10.1002/jcc.540110809

出版商:John Wiley&Sons, Inc.    

年代:1990

数据来源: WILEY

摘要:

AbstractAtom‐centered partial charges which exactly reproduce the lowest several multipoles of a molecule's charge distribution can be obtained in a straightforward and convenient manner from the output of existing electronic structure calculations. The multipole constraint method is demonstrated by a computation of partial charges for the twenty common amino acids. The electron density employed here, derived from a semiempirical MNDO calculation, incorporates Slater‐type orbitals which imbue it with the exponential fall‐off vital to electronic tunneling calculations. In addition, a procedure based on these charges is described which divides the original electron density into two components, a large component with a simple electrostatic potential, and a much smaller residual whose several lowest multipoles v

ISSN:0192-8651    

DOI:10.1002/jcc.540110810

出版商:John Wiley&Sons, Inc.    

年代:1990

数据来源: WILEY

摘要:

AbstractFree energy perturbation calculations were performed to determine the free energy of binding associated with the presence of perhaps an unusual hydroxyl group in the transition state analog of nebularine, an inhibitor of the enzyme adenosine deaminase. The presence of a single hydroxyl group in this inhibitor has been found to contribute −9.8 kcal/mol to the free energy of binding, with a 108‐fold increase in the binding affinity by the enzyme. In this work, we calculate the difference in solvation free energy for the 1,6‐dihydropurine complex versus that of the 6‐hydroxyl‐1,6‐dihydropurine complex to determine if this marked increase in binding affinity is attributed to an unusually hydrophobic hydroxyl group. The calculated ΔGassociated for the solvation free energy is −11.8 kcal/mol. This large change in the solvation free energy suggests that this hydroxyl is instead unusually hydrophilic and that the difference in free energy of interaction for the two inhibitors to the enzyme must be at least ca. 20 kcal/mol. Although the crystal structure for adenosine deaminase is currently not known, we attempt to mimic the nature of the active site by constructing models which simulate the enzyme‐inhibitor complex. We present a first attempt at determining the change in free energy of binding for a system in which structural data for the enzyme is incomplete. To do this, we construct what we believe is a minimal model of the binding between adenosine deaminase and an inhibitor. The active site is simulated as a single charged carboxyl group which can form a hydrogen bond with the hydroxyl group of the analog. Two different carboxyl anion models are used. In the first model, the association is modeled between an acetic acid anion and the modified inhibitor. The second model consists of a hydrophobic amino acid pocket with an interior Glu residue in the active site. From these models we calculate the change in free energy of association and the overall change in free energy of binding. We calculate the free energies of interaction both in the absence and presence of water. We conclude from this that the presence of a single suitably placed‐CO−2group probably cannot explain the binding effect of the‐OH group and that additional interactions will be found in the adenosine

ISSN:0192-8651    

DOI:10.1002/jcc.540110811

出版商:John Wiley&Sons, Inc.    

年代:1990

数据来源: WILEY