摘要:

AbstractThe conformational features of a large number of hydroperoxidesROOH and peroxidesROOR′, whereRandR′ are alkyl groups of different and increasing size and phenyl rings, includingorthosubstituted derivatives, were obtained from molecular mechanics calculations by employing a standard package. For the molecules of small molecular size, comparison was carried out with the results ofab initiocalculations. Heats of formation were also obtained from molecular mechanics for hydroperoxides and peroxides: The values are, in general, overestimated. For the molecules containing the CF3group, the calculated values are subject to large errors and heats of formation were obtained fromab initiototal energies in the “atom equivalents” scheme. To estimate the homolytic dissociation energies of the different bonds in the peroxide molecules, heats of formation ofR·, ·OR, and ·OORradicals were employed and several of them had to be calculated. Different approaches were employed—molecular mechanics calculations,ab initioenergies within the atom equivalent and isodesmic reaction schemes, and Benson's group additivity rule; values consistent within the different calculation methods were chosen for estimating dissociation energies. The bond dissociation energies indicate different trends in these molecules as a function of the nature of theRandR′ groups and the possible electronic effects operating in these molecules are discussed. © 1993 John

ISSN:0192-8651    

DOI:10.1002/jcc.540140402

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractSemiempirical (AM1) molecular orbital theory has been used to investigate the oxidation of alcohols at the active site of liver alcohol dehydrogenase (LADH). The model active site consists of a zinc dication coordinated to two methyl‐mercaptans (Cys‐46, Cys‐176), an imidazole (His‐67), and a water. An imidazole (His‐51) hydrogen bonded to a hydroxy‐acetate (Ser‐48) forms the remote base. AM1 calculations that address the two distinct steps in the catalytic mechanism of ethanol oxidation by LADH are reported. These two steps are: (1) the deprotonation of ethanol by imidazole (His‐51) via hydrogen‐bonded hydroxy‐acetate (Ser‐48), creating a proton relay system; and (2) the rate‐limiting hydride transfer step from ethanol C1 to nicotinamide adenine dinucleotide (NAD+), leading to product formation. Detailed calculations have been used to resolve the unsolved problems of mechanisms that have been suggested on the basis of kinetic data and crystal structures of several LADH complexes. We investigated two possible mechanisms for the deprotonation of ethanol, by zinc‐bound OH−and by direct deprotonation of zinc‐bound ethanol by imidazole via hydroxyacetate (Ser‐48). Our calculations show that there is no need for LADH to activate a water molecule at the active site as in many other zinc enzymes. This result agrees with experimental evidence. Our calculations also indicate that substrates are bound in an inner‐sphere‐pentacoordinated complex to the active site zincion. In this case, spectroscopic investigations agree with our results but crystallographic data do not. The highest activation energy is found for the hydride transfer, in agreement with the experiment. Finally, we proposed an alternative mechanism for the mode of action of LADH based upon our r

ISSN:0192-8651    

DOI:10.1002/jcc.540140403

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractA systematic SCF study has been undertaken to compare the conventionala posterioriBoys–Bernardi BSSE correction scheme with our recent CHA/F method in which BSSE is excluded ina priorimanner. Potential curves have been obtained for nine simple hydrogen‐bonded systems by using nine different basis sets for each. It is concluded that the difference between thea posterioriBB and thea prioriCHA schemes diminishes much faster when the basis set improves than BSSE disappears from the uncorrected SCF results. This fact gives an additional confidence in the CHA results, permitting one to draw the explicit conclusion that, at the SCF level of theory, thea prioriCHA/F scheme can be considered the ultimate solution of the BSSE problem for weakly bonded systems. © 1993 John Wiley&Sons,

ISSN:0192-8651    

DOI:10.1002/jcc.540140404

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractA procedure to represent atomic electron charge densities [L. Fernandez Pacios,J. Phys. Chem.,95, 10653 (1991);J. Phys. Chem.,96, 7294 (1992)] is here generalized to obtain simple analytical functions for potential energy contributions. Based upon suitable functions to describe atomic electron densities in a physically meaningful form, the procedure is developed to define density‐dependent analytical expressions for the electrostatic (classical) and exchange (quantum) potentials by means of proper approximate functionals. Calculations of correlation energies by using various density‐functional approaches are also performed. The whole scheme is used to represent Hartree–Fock limit atomic wave functions by Clementi–Roetti. This way, a set of analytically simple, nonbasis set‐dependent functions are defined with the aim to be further implemented in energy decomposition schemes for molecular interactions studies using atomic instead of electronic building blocks. © 1993 John Wiley

ISSN:0192-8651    

DOI:10.1002/jcc.540140405

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractA procedure is reported for the prediction of dense crystal structures of C‐, H‐, N‐, O‐, and F‐containing organic compounds in the primitive triclinic, monoclinic, and orthorhombic space groups with Z ≤ 4. The crystal environments of molecules in 242 crystal structures have been analyzed to determine the common coordination sphere pattens. This led to the development of the MOLPAK (MOLecular PAcKing) program, which uses a rigid‐body molecular structure probe to build packing arrangements (possible crystal structures) in the various space groups. A MOLPAK search, which involves the investigation of all unique orientations of a central molecule and the construction of the appropriate coordination patterns about the central molecule, provides a 3‐D map of minimum unit cell volume as a function of the orientation of the central molecule. MOLPAK uses a repulsion‐only potential and a preset threshold to place molecules in contact with each other. The 5–10 smallest volume packing arrangements from a search are subjected to a lattice energy minimization refinement with the WMIN program to yield possible crystal structures. The results are described from the analyses of several known compounds starting with the crystal molecular structures as the MOLPAK search probes in the P1, P21, P21/c, and P212121space groups. In addition, several examples are given in which the search probes were created by AM1 geometry optimization of preliminary molecular models. More extensive data are given in supplementary tables. © 1993

ISSN:0192-8651    

DOI:10.1002/jcc.540140406

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractConformational analysis of bradykinin (BK), a nonapeptide of the sequence RPPGFSPFR, was accomplished using annealed molecular dynamics (AMD) at 1000 K in BIOGRAF 2.2. One hundred anneal cycles produced 100 conformations over approximately 2000 ps. These conformations were compared to structures derived by nuclear magnetic resonance (NMR) methods for similar shape and energy. Energy minimization of relevant conformations using both BIOGRAF 2.2 and AMBER 3.0a revealed that the AMD‐determined conformations are in the same energy range as the NMR‐determined structures. Also, the shape of the relevant conformations appeared similar, suggesting that AMD is a good tool for the conformational analysis of small peptide ligands. © 1993 John Wiley&Sons,

ISSN:0192-8651    

DOI:10.1002/jcc.540140407

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractParallelization of the SCF method for closed‐shell molecules on the highly parallel transputer‐based system PARAM is described. The parallelization has been implemented on three different hardware and software environments: (1) a network of bare 64 transputers; (2) configuration 1 plus a back‐end file system (BFS); and (3) configuration 2 with one INTEL i860 processor. The evaluation of electron repulsion integrals (ERIs) and setting up of the Fock matrix is carried out in parallel on 64 nodes using minimal communication strategies. A good load balance is achieved for ERI evaluation with the help of bounds, local symmetry features, and the shell concept, as well as a data randomization technique, resulting into almost linear speedup (for ERI evaluation). In configurations 2 and 3, BFS is used for parallel storage and retrieval of ERIs. Further, in 3 matrix operations are implemented as remote procedure calls on the i860 processor. Routine techniques of level shifting and extrapolation are used for accelerating SCF convergence. The resulting package, INDMOL, has been tested for some randomly selected molecules having up to 255 contractions. Using configuration 3, a factor of 2 to 5 in computation time is obtained over 1, for the systems for which the ERIs cannot be stored in the distributed core memory. In summary, a heterogeneous system, as in configuration 3, can indeed be optimally exploited for programming peculiar diverse requirements of the SCF procedure. © 1993 John Wiley&Son

ISSN:0192-8651    

DOI:10.1002/jcc.540140408

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractWe present an improvement to Johnson, Gill, and Pople's results for reducing the cost of using the McMurchie–DavidsonRNLMrecurrence relation for one‐center integrals. Recursive replacement of singly referenced and single‐term auxiliary integrals results in floating point operation (FLOP) savings of up to 11% and explicit auxiliary integral calculation reductions of up to 76% with respect to the full list and up to 46% with respect to FLOP‐reduced lists with no replacement. The programs are written in the string‐manipulation language Convert; one of the programs automatically generates a FORTRAN subroutine given an integral list. © 1993 John Wiley

ISSN:0192-8651    

DOI:10.1002/jcc.540140409

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractMolecular mechanics is a fast developing discipline with new methods and potential fields appearing every year. A versatile molecular mechanics program supports many methods and potential fields that make it unavoidably large. There are problems writing and maintaining large programs with traditional methods because of data and other dependencies. Modular programming provides a solution. A program is developed as a collection of highly independent modules containing only related data structures and procedures. These entities are isolated in the module and access to them is provided through a well‐defined and controlled interface. The high degree of independence circumscribes programming errors. Most of all, it reduces the cost of revising the program as only a small part of the program needs to be read and understood for each revision. We implemented a molecular mechanics program,yammp, using the modular programming method. © 1993 John Wiley&Sons, I

ISSN:0192-8651    

DOI:10.1002/jcc.540140410

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractOne of the features of the polypeptide backbone is that it represents a flexible chain that contains almost rigid CONH peptide bonds. One may try to substitute one or more such bonds by another relatively rigid unit to maintain the overall conformational properties of the backbone and at the same time modify some other properties of the molecule (“pseudopeptide”), such as the ability to form hydrogen bonds. By a detailed conformational analysis, it is shown that the carboncarbon double bond is quite isosteric with the peptide bond and for this reason suitable for such a substitution. This is accomplished by applying molecular mechanics in calculation of the ϕ, ψ maps for pseudopeptide analogs of theN‐acetyl‐Ala‐NHMe molecule. © 1993 John

ISSN:0192-8651    

DOI:10.1002/jcc.540140411

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY