Search results for "computational"
showing 10 items of 5884 documents
Metallacrown Complexes Reaching the Nanosize Regime
2018
Abstract The chapter discusses the merit of metallacrown complexes to achieve multifunctional and multidimensional molecular materials. It introduces basic design strategies for discrete metallacrown complexes and discusses the predictability of molecular properties. Thereafter, it reviews two of the most outstanding molecular properties of metallacrown complexes, namely, the magnetic and luminescence characteristics. Most interestingly, for metallacrown complexes, such properties could be combined in one single molecule, giving rise to stable “multifunctional” molecular materials. Moreover, MCs are suitable building blocks to construct multidimensional coordination polymers. The chapter pr…
Structure-based statistical analysis of transmembrane helices
2012
Recent advances in determination of the high-resolution structure of membrane proteins now enable analysis of the main features of amino acids in transmembrane (TM) segments in comparison with amino acids in water-soluble helices. In this work, we conducted a large-scale analysis of the prevalent locations of amino acids by using a data set of 170 structures of integral membrane proteins obtained from the MPtopo database and 930 structures of water-soluble helical proteins obtained from the protein data bank. Large hydrophobic amino acids (Leu, Val, Ile, and Phe) plus Gly were clearly prevalent in TM helices whereas polar amino acids (Glu, Lys, Asp, Arg, and Gln) were less frequent in this …
A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase.
2007
Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Diketo acids such as L-731,988 and S-1360 are potent and selective inhibitors of HIV-1 IN. In this study, we used molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy between HIV-1 IN and L-731,988 and 10 of its derivatives and analogues. This hybrid methodology has the advantage that it includes quantum effects such as ligand polarisation upon binding, which can be very important when highly polarisable groups are embedded in anisotropic environments, as for example in metal-c…
Conformational studies of the Emp-AKH peptide using Molecular and Langevin Dynamics methods
1998
The secondary structure of the member of the AKH/RPCH family has been studied by Molecular Dynamics and Langevin Dynamics methods. Molecular dynamics simulation were performed in vacuum, model aqueous solution and simulated membrane. Langevin dynamics simulation was performed using the friction factor γ equal to 2 ps-1. Molecular dynamics as well as Langevin Dynamics simulation were conducted at 300 K. All minimum energy conformers have similar backbone structure characterised by the turn consisted out of 3 amino acids, Thr, Pro and Asn7. Structures obtained from Molecular Dynamics simulation are characterised by the lack of hydrogen bonds whereas the structure obtained form Langevin Dynami…
Spectrophotometric determinations of binding constants between cyclodextrins and aromatic nitrogen substrates at various pH values
2001
The inclusion capacity of native β-cyclodextrin (1) and mono-(6-amino-6-deoxy)-β-cyclodextrin (2) versus aromatic compounds having a nitro or an amino group or both has been investigated at three different pH values. Molecular interactions in inclusion complexes have also been investigated by means of molecular mechanics (MM2/QD) models. Electrostatic and van der Waals interactions and the formation of a hydrogen bond between the donor amino group and the oxygen atom of the secondary hydroxyl group seem to be the more important contributions in determining complex stability. The inclusion capacity of two different cyclodextrins versus aromatic compounds has been investigated at three differ…
Estimation of pKa shifts in weak polyacids using a simple molecular model: effects of strong polybases, hydrogen bonding and divalent counterion bind…
2004
Abstract The pKa values of ionizable groups in macromolecules can be significantly different than those of the isolated groups in solution. We have estimated theoretically the changes in the dissociation constant of a weak acid (a) in the vicinity of another ionizable group (b) on the basis of the theoretical approach by Hill (J. Am. Chem. Soc. 78 (1956) 3330) for matching pairs of interacting sites on two large molecules. Three cases are considered for group b: the strong base, the same weak acid as group a with hydrogen bonding between them, and the same weak acid as group a with divalent counterion binding. The pKa shifts are evaluated in each case as a function of the interaction energy…
Quantitative characterization of the global electrophilicity pattern of some reagents involved in 1,3-dipolar cycloaddition reactions
2003
Abstract The global electrophilicity power, ω, of a series of dipoles and dipolarophiles commonly used in 1,3-dipolar cycloadditions may be conveniently classified within a unique relative scale. The effects of chemical substitution on the electrophilicity of molecules have been evaluated using a representative set of electron-withdrawing and electron-releasing groups for a series of dipoles including nitrone, nitrile oxide and azide derivatives. The absolute scale of electrophilicity is used to rationalize the chemical reactivity of these species as compared to the static reactivity pattern of the reagents involved in the Diels–Alder reactions.
The Mössbauer effect and collective motions in glass-forming liquids and polymeric networks
1994
Glass-forming liquids, synthetic polymers and biopolymers share essential properties. Dynamic processes in these complex systems are characterized by cooperative motions with wide distributions of time scales, which manifest themselves in broad quasielastic lines in the Mossbauer spectrum. In this article, the application of the Mossbauer effect to the study of structural dynamics in complex systems is discussed.
Reactivity of the carbon-carbon double bond towards nucleophilic additions. A dft analysis
2004
Abstract The global and local electrophilicity indexes have been used to characterize the reactivity pattern of the CC double bond towards nucleophilic addition reactions. A wide family of molecules including ketones, esters, anhydrides, nitriles and nitrocompounds containing appropriate substitution on the CC double bond have been classified within an unique scale of reactivity. The predictive capability of the theoretical model is tested against a series of benzylidenemalononitriles and substituted α-nitrostilbenes.
Spectrophotometric study on the thermodynamics of binding of α- and β-cyclodextrin towards some p-nitrobenzene derivativesElectronic supplementary in…
2003
Binding properties of native α- and β-cyclodextrin towards some nitrobenzene derivatives have been studied by means of UV-vis spectrophotometry. The former host is able to form complexes having 1 : 1 and 1 : 2 stoichiometric ratios with these guests, while only 1 : 1 complexes are detected with the latter host. A careful analysis of the thermodynamic parameters for complexation equilibria, under the perspective of the enthalpy–entropy compensation effect, reveals that binding abilities of the two different hosts are subject to different features.