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Molecular Mechanics Calculations (molecular + mechanic_calculation)
Selected AbstractsStudies of Adjacent Re-Entry Folds of Chains of Syndiotactic l,2-Poly(1,3-butadiene) by Molecular Mechanics CalculationsMACROMOLECULAR THEORY AND SIMULATIONS, Issue 2 2007Roberto Napolitano Abstract The mode of packing and the adjacent re-entry folds of chains of syndiotactic 1,2-poly(1,3-butadiene) have been studied by molecular mechanics calculations with the use of various sets of potential functions. The results of the packing analysis indicate that the crystal grows preferentially along the [100] and [110] directions. Models of fold have been built up on an infinite ab surface completely covered by adjacent re-entry folds in the (100) and (110) planes. The results of energy minimizations show that several almost isoenergetic folds, constituted by four monomeric units, can be realized in the (100) planes, while the fold in the (110) planes has higher energy. The calculated value of the work of fold is in satisfactory agreement with that derived by crystallization kinetics reported in literature. [source] Synthesis of new enantiomerically pure macrocycles containing phenanthroline subunitsCHIRALITY, Issue 6 2006Federica Colombo Abstract New enantiomerically pure macrocycles have been prepared by combining 1,10-phenanthroline 2,9-dicarboxylic acid and two ,-amino-acids linked through spacers. Different diamine linkers have been employed in order to modify the dimensions and the properties of the macrocycles whose structures have been studied by 1H and 13C NMR spectroscopy. The ability of the (L)-valine containing macrocycles to bind metal ions and phenolic molecules has been investigated by 1H NMR experiments and Molecular Mechanics calculations. Chirality, 2006. © 2006 Wiley-Liss, Inc. [source] Molecular mechanics calculations on carbonyl compounds.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2001Abstract Open-chain aliphatic ketones were studied with the molecular mechanics (MM4) force field. A total of seven compounds were examined. Structures were well fit, including moments of inertia. Rotational barriers, vibrational spectra, and dipole moments were also well fit. The overall root mean square errors for MM3 and MM4 were 0.27 and 0.18%, respectively, for the six moments of inertia (known experimentally for two compounds) and 31 and 20 cm,1, respectively, for the vibrational frequencies (over 99 weighted modes). © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1426,1450, 2001 [source] From quantum chemistry and the classical theory of polar liquids to continuum approximations in molecular mechanics calculations,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Sergio A. Hassan Abstract Biological macromolecules and other polymers belong to the class of mesoscopic systems, with characteristic length scale of the order of a nanometer. Although microscopic models would be the preferred choice in theoretical calculations, their use in computer simulations becomes prohibitive for large systems or long simulation times. On the other hand, the use of purely macroscopic models in the mesoscopic domain may introduce artifacts, with effects that are difficult to assess and that may compromise the reliability of the calculations. Here is proposed an approach with the aim of minimizing the empirical nature of continuum approximations of solvent effects within the scope of molecular mechanics (MM) approximations in mesoscopic systems. Using quantum chemical methods, the potential generated by the molecular electron density is first decomposed in a multicenter-multipole expansion around predetermined centers. The monopole and dipole terms of the expansion at each site create electric fields that polarize the surrounding aqueous medium whose dielectric properties can be described by the classical theory of polar liquids. Debye's theory allows a derivation of the dielectric profiles created around isolated point charges and dipoles that can incorporate Onsager reaction field corrections. A superposition of screened Coulomb potentials obtained from this theory makes possible a simple derivation of a formal expression for the total electrostatic energy and the polar component of the solvation energy of the system. A discussion is presented on the physical meaning of the model parameters, their transferability, and their convergence to calculable quantities in the limit of simple systems. The performance of this continuum approximation in computer calculations of amino acids in the context of an atomistic force field is discussed. Applications of a continuum model based on screened Coulomb potentials in multinanosecond simulations of peptides and proteins are briefly reviewed. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2002Pengyu Ren Abstract A protocol is described for the treatment of molecular polarization in force field calculations. The resulting model is consistent in that both inter- and intramolecular polarization are handled within a single scheme. An analytical formula for removing intramolecular polarization from a set of atomic multipoles for an arbitrary static structure or conformation is given. With the help of the intramolecular polarization, these permanent atomic multipoles can then be applied in modeling alternative conformations of a molecule. Equipped with this simple technique, one can derive transferable electrostatic parameters for peptides and proteins using flexible model compounds such as dipeptides. The proposed procedure is tested for its ability to describe the electrostatic potential around various configurations of the N -methylacetamide dimer. The effect of different intramolecular polarization schemes on the accuracy of a force field model of the electrostatic potential of alanine dipeptide is investigated. A group-based scheme for including direct intramolecular polarization is shown to be most successful in accounting for the conformational dependence of electrostatic potentials. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1497,1506, 2002 [source] Synthesis, stereochemistry and adsorption studies of new spiranes and polyspiranes containing 1,2-dithiolane unitsJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 3 2007Radu A. Gropeanu The synthesis and stereochemistry of a series of new cyclic disulfides containing (poly)spirane 1,2-dithiolane units are reported. Also included is a study of the self-assembled monolayers (SAMs) of these compounds on a gold surface. The characteristics of the resultant SAMs were determined by IR spectroscopy using molecular mechanics calculations. [source] Synthesis, conformation and biological activity of linear and cyclic Thr6 -bradykinin analogues containing N -benzylglycine in place of phenylalanine,JOURNAL OF PEPTIDE SCIENCE, Issue 12 2001L. Biondi Abstract Three linear Thr6 -bradykinin analogues in which either one or both the two phenylalanine residues in the peptide sequence have been substituted by N -benzylglycine (BzlGly) and their head-to-tail cyclic analogues were synthesized and tested on an isolated rat duodenum preparation. The linear (BzlGly5,Thr6 -BK, BzlGly8,Thr6 -BK and BzlGly5,8,Thr6 -BK) and the cyclic (cyclo BzlGly5,Thr6 -BK, cyclo BzlGly8,Thr6 -BK and cyclo BzlGly5,8,Thr6 -BK) peptoid-like analogues were characterized by amino acid analysis, optical rotation, analytical HPLC and MALDI-TOF mass spectroscopy. The conformational features of both the linear and cyclic derivatives were investigated by FT-IR and CD measurements. Preliminary molecular mechanics calculations were also performed on some synthetic peptides. Pharmacological screening using the relaxation of the isolated rat duodenum preparation showed that incorporation of N -benzylglycine at positions 5 and/or 8 in the linear Thr6 -BK causes a substantial decrease in potency. Comparable incorporation in cyclo Thr6 -BK, at position 8, or 5 and 8, resulted in nearly inactive analogues. However, cyclo BzlGly5,Thr6 -BK showed a potency which is of the same order of magnitude as for cyclo -BK and cyclo Thr6 -BK. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd. [source] New mathematic model for predicting chiral separation using molecular docking: Mechanism of chiral recognition of triadimenol analoguesJOURNAL OF SEPARATION SCIENCE, JSS, Issue 14 2009Guoqing Zhang Abstract The purpose of this paper was to study the enantioseparation mechanism of triadimenol compounds by carboxymethylated (CM)-,-CD mediated CE. All the enantiomers were separated under the same experimental conditions to study the chiral recognition mechanism using a 30 mM sodium dihydrogen phosphate buffer at pH 2.2 adjusted by phosphoric acid. The inclusion courses between CM-,-CD and enantiomers were investigated by the means of molecular docking technique. It was found that there were at least three points (one hydrophobic bond and two hydrogen bonds) involved in the interaction of each enantiomer with the chiral selectors. A new mathematic model has been built up based on the results of molecular mechanics calculations, which could analyze the relationship between the resolution of enantioseparation and the interaction energy in the docking area. Comparing the results of the separation by CE, the established mathematic model demonstrated good capability to predict chiral separation of triadimenol enantiomers using CM-,-CD mediated CE. [source] Studies of Adjacent Re-Entry Folds of Chains of Syndiotactic l,2-Poly(1,3-butadiene) by Molecular Mechanics CalculationsMACROMOLECULAR THEORY AND SIMULATIONS, Issue 2 2007Roberto Napolitano Abstract The mode of packing and the adjacent re-entry folds of chains of syndiotactic 1,2-poly(1,3-butadiene) have been studied by molecular mechanics calculations with the use of various sets of potential functions. The results of the packing analysis indicate that the crystal grows preferentially along the [100] and [110] directions. Models of fold have been built up on an infinite ab surface completely covered by adjacent re-entry folds in the (100) and (110) planes. The results of energy minimizations show that several almost isoenergetic folds, constituted by four monomeric units, can be realized in the (100) planes, while the fold in the (110) planes has higher energy. The calculated value of the work of fold is in satisfactory agreement with that derived by crystallization kinetics reported in literature. [source] On the Crystal Structure of Isotactic cis -1,4-Poly(1,3-pentadiene)MACROMOLECULAR THEORY AND SIMULATIONS, Issue 8 2006Roberto Napolitano Abstract Summary: A comparison between the crystal structure of isotactic cis -1,4-poly(1,3-pentadiene) previously predicted by molecular mechanics calculations and that successively determined by other authors by experimental data is reported. The agreement between the two structures is very good as far as the space group, the unit cell parameters and the conformation of the polymer chain are concerned. The mode of packing of the chains proposed in the experimental crystal structure is very similar to that found as relative minimum in the previous energy calculations. The coexistence, in different amounts, of these two modes of packing is suggested by the analysis of the simulated X-ray spectra and by the results of new energy calculations. A mode of packing of chains of isotactic cis -1,4-poly(1,3-pentadiene). [source] The use of MPA amide for the assignment of absolute configuration of a sterically hindered cyclic secondary amine by ,mix and shake' NMR methodMAGNETIC RESONANCE IN CHEMISTRY, Issue 1 2008Jinhai Gao Abstract We present here a new method using methoxyphenylacetic acid (MPA) as the chiral derivatizing agent (CDA) for the assignment of absolute configuration of cyclic secondary amines. The MPA amides were prepared using the purification-free ,mix and shake' method. A detailed conformational analysis for the two diastereomeric amides was conducted by 2D NMR experiments and molecular mechanics calculations. We have established that, in the most stable conformation of each syn rotamer of MPA amides, the H-, in the MPA moiety is oriented toward the bulky substituent group at the asymmetric carbon in the chiral amine, presumably to avoid steric and/or electrostatic interactions. The observed NMR data were correlated with the conformational model to allow unambiguous assignment of absolute configuration of secondary amines. The results demonstrate that the MPA can be used as a useful CDA in the case of sterically crowded cyclic secondary amines from which the MTPA amides are usually difficult to make. Copyright © 2008 John Wiley & Sons, Ltd. [source] 1H and 13C NMR spectral data for a tricyclic derivative of a Diels,Alder adductMAGNETIC RESONANCE IN CHEMISTRY, Issue 1 2006Susimaire Pedersoli Abstract A complete NMR analysis with full assignment for 1H and 13C NMR spectral data for 5-(acetyloxy)-3-hydroxy-9,10-dimethoxy-6-oxo-11-oxatricyclo[6.2.1.02,7]undec-2-yl acetate (8) is described. This compound was prepared by rapid hydrogenation of the unstable Diels,Alder adduct obtained from the reaction between 3,4-dimethoxyfuran (4) and 2,5-diacetoxy-1,4-benzoquinone (5). Full homonuclear hydrogen coupling constants measurements and molecular mechanics calculations were performed for the determination of the relative stereochemistry. Copyright © 2005 John Wiley & Sons, Ltd. [source] Identification of possible kinetically significant anion-binding sites in human serum transferrin using molecular modeling strategiesBIOPOLYMERS, Issue 2 2004Elizabeth Ambrose Amin Abstract Certain anions have been shown experimentally to influence the rate of iron release from human serum transferrin (HST), implying the existence of one or more allosteric kinetically significant anion- binding (KISAB) sites on or near the surface of the protein. A rank-ordered selection of potential HST KISAB sites has been obtained using a novel three-stage molecular modeling strategy. The crystal structure of HST (1A8E.pdb) was first subjected to a heuristic analysis, in which positively charged and hydrogen-bonding residues on or near the surface of the protein were identified. In this stage, a preliminary electrostatic potential map was also calculated, yielding six preliminary sites. Next, energy-grid calculations were conducted in order to identify anion,protein interaction energy minima, which resulted in the inclusion of three additional sites. Finally, three anions already shown experimentally to demonstrate varied effects on HST iron-release kinetics were placed at each potential site; molecular dynamics and molecular mechanics calculations were performed in order to elucidate the hydrogen-bonding environment around each anion of the protein as well as to calculate anion,protein-binding energies. © 2003 Wiley Periodicals, Inc. Biopolymers 73: 205,215, 2004 [source] Metal Binding Properties of Fluorescent Analogues of Trichogin GA,IV: A Conformational Study by Time-Resolved Spectroscopy and Molecular Mechanics InvestigationsCHEMBIOCHEM, Issue 1 2009Mariano Venanzi Prof. Abstract The metal ion binding properties of two fluorescent analogues of trichogin GA,IV, which is a natural undecapeptide showing significant antimicrobial activity, were studied by circular dichroism, time-resolved optical spectroscopy, and molecular mechanics calculations. Binding of CaII and GdIII to the peptides investigated was shown to promote a structural transition from highly helical conformations to folded structures characterized by formation of a loop that embedded the metal ion. Time-resolved spectroscopy revealed that peptide dynamics is also remarkably affected by ion binding: peptide-backbone motions slowed down to the microsecond time scale. Finally, molecular mechanics calculations emphasized the role of the central Gly5-Gly6 motif, which allowed for the twisting of the peptide segment that gave rise to the formation of the binding cavity. [source] Aromatic,Carbohydrate Interactions: An NMR and Computational Study of Model SystemsCHEMISTRY - A EUROPEAN JOURNAL, Issue 25 2008Sophie Vandenbussche Ir. Abstract The interactions of simple carbohydrates with aromatic moieties have been investigated experimentally by NMR spectroscopy. The analysis of the changes in the chemical shifts of the sugar proton signals induced upon addition of aromatic entities has been interpreted in terms of interaction geometries. Phenol and aromatic amino acids (phenylalanine, tyrosine, tryptophan) have been used. The observed sugar,aromatic interactions depend on the chemical nature of the sugar, and thus on the stereochemistries of the different carbon atoms, and also on the solvent. A preliminary study of the solvation state of a model monosaccharide (methyl ,-galactopyranoside) in aqueous solution, both alone and in the presence of benzene and phenol, has also been carried out by monitoring of intermolecular homonuclear solvent,sugar and aromatic,sugar NOEs. These experimental results have been compared with those obtained by density functional theory methods and molecular mechanics calculations. [source] Enthalpy change on mixing a couple of S - and R -enantiomers of some chiral compounds at 298.15 KCHIRALITY, Issue 8 2006Takayoshi Kimura Abstract Enthalpy change on the mixing of R - and S -enantiomers of chiral liquid compounds such as dimethyl malate (1), methyl 3-hydroxylbutanoate (2), 2-butanol (3), ethyl 4-chloro-3-hydroxylbutanoate (4), 1,3,3-trimethylbicycle-[2.2.1]heptan-2-one (5), 3,7-dimethyl-6-octenal (6), and 8-bromo-2,6-dimethyl-2-octene (7) is measured over the entire range of mole fractions at 298.15 K, albeit very small values. The mixing of chiral liquids of R - 1 + S - 1, R - 2 + S - 2, R - 3 + S - 3, R - 6 + S - 6, and R - 7 + S - 7 produces enthalpic destabilization over the entire range of mole fractions, while that of R - 4 + S - 4 and R - 5 + S - 5 shows enthalpic stabilization over entire compositions. Enthalpy change on mixing at an equimolar concentration and the intermolecular interaction obtained by the molecular mechanics calculations show a linear correlation, except for a few compounds measured. Chirality, 2006. © 2006 Wiley-Liss, Inc. [source] | ||||||||||