摘要:

AbstractSimulation data from an off‐lattice polymer model are compared with data from the Rouse model. The polymer model is built of sequentially connected rigid monomer units that represent the amide planes of a protein backbone. The time propagation of the dynamics of the polymer model is performed by a Monte Carlo method. The elementary Monte Carlo steps correspond to local confomational changes in a window of three consecutive monomer units. The time autocorrelation functions of end‐to‐end distances from segments within the linear chain molecule are considered in detail. Both models exhibit a stretched exponential decay pattern. A comparison of the data from the Rouse model and the computer simulation provide an estimate of the time unit of 15 ps for a full scan of the algorithm for local conformational changes along the chain. With a conservative estimate of the parameters governing the Rouse model this time unit is four orders of magnitude longer than the elementary time step of a conventional computer simulation of polymer dynamics based upon the classical equations of motion for all atoms. © 1992 by John Wiley&Son

ISSN:0192-8651    

DOI:10.1002/jcc.540130702

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractThe internal rotation in the HC(X)YCH2CH3(X,Y= O or S) series of molecules was studied by theab initioSCF‐MO method using 3‐21G and 3‐21G +d(ζ = 0.65S) basis sets. Energies and structures of several conformations of these molecules, determined by gradient geometry refinement, are reported and used to assess the effects of oxygen‐by‐sulphur substitution on molecular properties. The nature and relative importance of intramolecular interactions involving both the CH2CH3and the HC(X)Y(X,Y= O or S) fragments are also discussed. © 1992 by Joh

ISSN:0192-8651    

DOI:10.1002/jcc.540130703

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractA systematic derivation procedure that greatly facilitates the application of the Taylor method to the integration of kinetic models is developed. In addition, an algorithm that gives the integration step as a function of the required level of accuracy is proposed. Using the Taylor method, application of this algorithm is immediate and largely reduces the integration time. In addition, a new method of integration of kinetic models, whose most important feature is the self‐adaptability to the stiffness of the system along the integration process, is developed. This “stiffness‐adaptive” Taylor method (SAT method) makes use of several algorithms, combining them to meet the particular requirements of the integration of each species along the integration process. In comparison with the Runge–Kutta–Felhberg, Runge–Kutta–Calahan, Taylor, and Gear methods, the SAT method is the best to integrate non‐stiff and stiff kinetic systems, giving the best accuracy and the smallest computing time. © 1992 by Jo

ISSN:0192-8651    

DOI:10.1002/jcc.540130704

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractThe vibrational Stark effect of a series of small molecules has been calculated by means of the semiempirical AM1 method through addition of the electron–field interaction term in the one‐electron Hamiltonian. Optimized geometrical parameters along with harmonic frequencies and line intensities are determined for different strengths of the applied uniform electric field. The perturbed spectra are compared with theoretical studies carried out at theab initiolevel and with experimental results. The vibrational Stark effect of the retinal molecule is also computed, showing that this kind of study is feasible in systems of biochemical interest. © 1992 by John Wiley&Sons,

ISSN:0192-8651    

DOI:10.1002/jcc.540130705

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractA semi‐empirical NDDO method, generalized from a similar scheme at the CNDO/2 level developed previously, is presented to treat very large molecules. The extended molecular system is divided into a relatively small subsystem where substantial chemical changes take place and an environment remaining more‐or‐less unperturbed during the process. Expanding the wave function on an atomic hybrid basis an SCF procedure is performed for the subsystem in the field of the iteratively determined electronic distribution of the environment. A computer program has been written for the IBM RISC System/6000 530 computer and several test calculations were done for a variety of large classical molecules, like substituted aliphatic hydrocarbons, water oligomers, and a heptapeptide. Protonation energies, proton transfer potential curves, rotational barriers, atomic net charges, and HOMO and LUMO energies, as computed by the exact version of the NDDO method, are fairly well reproduced by our approximation if the subsystem is appropriately defined. © 1992 by John Wiley&Son

ISSN:0192-8651    

DOI:10.1002/jcc.540130706

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractA bond and group equivalent scheme that allows the calculation of heats of formation for carboxylic acids and esters fromab initio6‐31G* energies has been developed. For a group of 16 compounds, the rms error for the calculated heats of formation was 0.64 kcal/mol. Heats of formation have been predicted for an additional seven compounds for which the experimental values are either unknown or suspect. © 1992 by John Wiley&Sons, I

ISSN:0192-8651    

DOI:10.1002/jcc.540130707

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractThe molecular electrostatic potential (MEP) distribution of anisole, chlorobenzene, and fluorobenzene obtained from STO‐3G, 3‐21G, and 6‐31G* basis setab initioand MNDO and AM1 semiempirical wave functions is investigated to explain the differences among the MEP features obtained for polychlorodibenzo‐p‐dioxins. The main topological features as well as the absoltue and relative minima location obtained fromab initiocalculations are independent from the choice of the basis set. MNDO calculations are in good agreement with theab initioones in the case of anisole and fluorobenzene, while they incorrectly describe the MEP of chlorobenzene. The AM1 fails to localize the absolute minimum of fluorobenzene and does not find the minimum above the chlorobenzene chlorine atom. The poor agreement of both semiempirical methods withab initiofor any kind of chlorinated compounds is confirmed by results obtained for chloreothylene and chloroethane. We hypothesize that the main problem concerning these methods is that they freeze a too large amount of electrons in the atomic core of elements belonging to the second row, which makes for a wrong description of the core–valence electron interactions. Results obtained by modifying the AM1 parameters related to these interactions confirm our hypothesis. © 1992 by John Wil

ISSN:0192-8651    

DOI:10.1002/jcc.540130708

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractIn this article we present an extension of our modified MM2(80) force field MM2MOD in which a potential function for hydrogen bonding in alcohols and ethers is included. The results of applying MM2(85), MM2(87), and MM2MOD on ethylene glycol, 2‐methoxyethanol and 1,3‐propanediol are reported and compared with available experimental data andab initioresults. It is concluded that hydrogen bonding plays an important role in determining the molecular conformations of these systems. © 1992 by John Wiley&Sons,

ISSN:0192-8651    

DOI:10.1002/jcc.540130709

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractApplication of MNDO, AM1, PM3, MNDO/H, and MNDO/M methods to a set of compounds with intramolecular hydrogen bonds suggested that none of these methods accurately modeled the characteristics of the hydrogen bonds. Since the MNDO/H and MNDO/M methods work well for intermolecular hydrogen bonds, we followed their example and modified MNDO for intramolecular hydrogen bonds by altering the empirical core–core repulsion energy function for all pairs of atoms involved in intramolecular O‐HO bonds. The resulting modified method models the behavior of these bonds quite well, especially as regards their geometry and the barrier to proton transfer. © 1992 by John Wiley&Son

ISSN:0192-8651    

DOI:10.1002/jcc.540130710

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractThe electronic structure of cobalt silicide clusters Co7Si7and Si7Co7was studied in comparison to that of Co19and Si17clusters under the scope of the MINDO/SR method. Clusters Co7Si7and Si7Co7represent the environment of a cobalt atom and that of a silicon atom in the cobalt monosilicide bulk, respectively. It is found that the CoSi bond is essentiallyspin character with an indirect participation (by electrostatic interaction) of the cobaltdorbitals. Our calculations show a charge transfer from silicon to thedorbitals of cobalt viasp–spinteraction with an internalsp–dhybridization. The theoretical density of states for cobalt silicide clusters are reported and compared with experimental results of surface spectroscopies. © 1992 by John Wiley&Son

ISSN:0192-8651    

DOI:10.1002/jcc.540130711

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY