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MD Trajectories (md + trajectory)

Distribution by Scientific Domains

Chemistry	100%

Selected Abstracts

Temperature effects on the UV,Vis electronic spectrum of trans-stilbene

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2001
S. P. Kwasniewski
Abstract The ultraviolet (UV),Visible absorption spectrum of trans-stilbene (tS) is computed at different temperatures by coupling molecular dynamics (MD) simulations with the classical MM3 force field to ZINDO/S-CIS calculations of vertical excitation energies and transition dipole moments. The selection of a large number of structures along the MD trajectories enables a consistent treatment of temperature effects in the vacuum, whereas the ZINDO/S-CIS calculations permit a reliable treatment of electron correlation and relaxation, taking account of multistate interactions in the final state. Thermal motions are found to alter very differently the width and shape of bands. Structural alterations such as the stretching and the torsion of the vinyl single and double bonds very strongly influence the appearance of the first valence state, pertaining to the highest occupied and lowest unoccupied molecular orbital (HOMO,LUMO) transition. At temperatures less than 400 K, these are found to yield a merely Gaussian and very pronounced thermal broadening of the related band (A), up to nearly 30 nm, together with a minor blue shift of its maximum ,max. In contrast, a red shift by several nanometers occurs due to thermal motions for the remaining three valence bands. As can be expected, the broadening intensifies at higher temperatures, and for the A-band, becomes markedly asymmetric when T exceeds 400 K. The combination of MD(MM3) and ZINDO/S-CIS computations enables also consistent calculations of hot bands, which are forbidden by symmetry at 0 K. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source]

Study on the inhibitory mechanism and binding mode of the hydroxycoumarin compound NSC158393 to HIV-1 integrase by molecular modeling

BIOPOLYMERS, Issue 9 2009
Ming Liu
Abstract Human immunodeficiency virus type 1 integrase (IN) is an essential enzyme in the life cycle of this virus and also an important target for the study of anti-HIV drugs. In this work, the binding modes of the wild type IN core domain and the two mutants, that is, W132G and C130S, with the 4-hydroxycoumarin compound NSC158393 were evaluated by using the "relaxed complex" molecular docking approach combined with molecular dynamics (MD) simulations. Based on the monomer MD simulations, both of the two substitutions affect not only the stability of the 128,136 peptides, but also the flexibility of the functional 140s loop. In principle, NSC158393 binds the 128,136 peptides of IN; however, the specific binding modes for the three systems are various. According to the binding mode of NSC158393 with WT, NSC158393 can effectively interfere with the stability of the IN dimer by causing a steric hindrance around the monomer interface. Additionally, through the comparative analysis of the MD trajectories of the wild type IN and the IN-NSC158393 complex, we found that NSC15893 may also exert its inhibitory function by diminishing the mobility of the function loop of IN. Three key binding residues, that is, W131, K136, and G134, were discovered by energy decomposition calculated with the Molecular Mechanics Generalized Born Surface Area method. Characterized by the largest binding affinity, W131 is likely to be indispensable for the ligand binding. All the above results are consistent with experiment data, providing us some helpful information for understanding the mechanism of the coumarin-based inhibitors. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 700,709, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source]

Computer Simulation of Long Side-Chain Substituted Poly(phenylene vinylene) Polymers

CHEMPHYSCHEM, Issue 3 2004
Hsiao-Ching Yang
Abstract A molecular dynamics (MD) simulation was employed to investigate structure features and segment orientation of four poly(phenylene vinylene) (PPV) derivatives with long, flexible side chains at room temperature. In the simulations, the main chains of the polymers were found to be semirigid and exhibit a tendency to coil into ellipsoidal helices or form zigzag conformations of limited regularity. The simulations show that continuous quasi-coplanar segments along the backbone are in a range of ,2,4 repeat units. The ordered orientation and coupling distance of interchain aromatic rings can be correlated with optical properties of materials. A simplified quantum-mechanical method was developed to investigate optical properties based on MD trajectories. The method was tested to simulate the absorption spectra of four PPV derivatives. The absorption maxima of the calculated spectra are in reasonable agreement with experimental data. This work implies that long-range electron transfer along the backbones of these polymers may not occur, but may be mediated by interchain interactions. [source]

Computational Study of the Lipase-Mediated Desymmetrisation of 2-Substituted-Propane-1,3-Diamines

CHEMBIOCHEM, Issue 18 2009
Eduardo García-Urdiales Dr.
Abstract The enantioselectivity displayed by the lipase from Pseudomonas cepacia towards a wide range of prochiral 2-substituted-propane-1,3-diamines was studied by means of molecular dynamics simulations (MDS). In all cases the enzyme allows the recovery of the corresponding amino carbamates of R configuration. However, the enantioselectivity is only synthetically useful if no ortho substituent is present and the aromatic ring is directly bonded to the 2-carbon of the 1,3-diamine core. Analysis of the MDS trajectories revealed that the homologation of 2-aryl substituents by means of a methylene group lowers enantioselectivity by alleviating the conformational tension of the slow-reacting orientations due to unfavourable intramolecular contacts between the ortho carbons of the aryl group and the nucleophilic nitrogen, as well as between the chiral carbon and the oxyanion. Additionally, the relative solvent accessible surfaces of the atoms of the aryl ring nicely correlate with the effect of the location of the substituent on enantioselectivity. [source]