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Classical Molecular Dynamics (classical + molecular_dynamics)

Distribution by Scientific Domains

Chemistry	85%

Terms modified by Classical Molecular Dynamics

classical molecular dynamics simulation

Selected Abstracts

Spectroscopic Properties in the Liquid Phase: Combining High-Level Ab Initio Calculations and Classical Molecular Dynamics

CHEMPHYSCHEM, Issue 1 2006
Michele Pavone Dr.
Abstract We present an integrated computational tool, rooted in density functional theory, the polarizable continuum model, and classical molecular dynamics employing spherical boundary conditions, to study the spectroscopic observables of molecules in solution. As a test case, a modified OPLS-AA force field has been developed and used to compute the UV and NMR spectra of acetone in aqueous solution. The results show that provided the classical force fields are carefully reparameterized and validated, the proposed approach is robust and effective, and can also be used by nonspecialists to provide a general and powerful complement to experimental techniques. [source]

Electron transport enhanced molecular dynamics for metals and semi-metals,

INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 8-9 2010
Reese E. Jones
Abstract In this work we extend classical molecular dynamics by coupling it with an electron transport model known as the two temperature model. This energy balance between free electrons and phonons was first proposed in 1956 by Kaganov et al. but has recently been utilized as a framework for coupling molecular dynamics to a continuum description of electron transport. Using finite element domain decomposition techniques from our previous work as a basis, we develop a coupling scheme that preserves energy and has local control of temperature and energy flux via a Gaussian isokinetic thermostat. Unlike the previous work on this subject, we employ an efficient, implicit time integrator for the fast electron transport which enables larger stable time steps than the explicit schemes commonly used. A number of example simulations are given that validate the method, including Joule heating of a copper nanowire and laser excitation of a suspended carbon nanotube with its ends embedded in a conducting substrate. Published in 2010 by John Wiley & Sons, Ltd. [source]

Temperature dependence of structure and dynamics of the hydrated Ca2+ ion according to ab initio quantum mechanical charge field and classical molecular dynamics

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2010
Len Herald V. Lim
Abstract Simulations using ab initio quantum mechanical charge field molecular dynamics (QMCF MD) and classical molecular dynamics using two-body and three-body potentials were performed to investigate the hydration of the Ca2+ ion at different temperatures. Results from the simulations demonstrate significant effects of temperature on solution dynamics and the corresponding composition and structure of hydrated Ca2+. Substantial increase in ligand exchange events was observed in going from 273.15 K to 368.15 K, resulting in a redistribution of coordination numbers to lower values. The effect of temperature is also visible in a red-shift of the ion-oxygen stretching frequencies, reflecting weakened ligand binding. Even the moderate increase from ambient to body temperature leads to significant changes in the properties of Ca2+ in aqueous environment. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source]

Bifunctional Catalysis by Natural Cinchona Alkaloids: A Mechanism Explained

CHEMISTRY - A EUROPEAN JOURNAL, Issue 32 2009
Clotilde
Abstract The use of bifunctional chiral catalysts, which are able to simultaneously bind and activate two reacting partners, currently represents an efficient and reliable strategy for the stereoselective preparation of valuable chiral compounds. Cinchona alkaloids such as quinine and quinidine, simple organic molecules generously provided by Nature, were the first compounds to be proposed to operate through a cooperative catalysis. To date, a full mechanistic characterization of the dual catalysis mode of cinchona alkaloids has proven a challenging objective, due to the transient, non-covalent nature of the involved catalyst,substrate interactions. Here, we propose a mechanistic rationale on how natural cinchona alkaloids act as efficient bifunctional catalysts by using a broad range of computational methods, including classical molecular dynamics, a mixed quantum mechanical/molecular mechanics (QM/MM) approach, and correlated ab-initio calculations. We also unravel the origin of enantio- and diastereoselectivity, which is due to a specific network of hydrogen bonds that stabilize the transition state of the rate-determining step. The results are validated by experimental evidence. [source]

Computational Study of the Phosphoryl Transfer Catalyzed by a Cyclin-Dependent Kinase

CHEMISTRY - A EUROPEAN JOURNAL, Issue 30 2007
Marco De, Vivo Dr.
Abstract A cyclin-dependent kinase, Cdk2, catalyzes the transfer of the ,-phosphate from ATP to a threonine or serine residue of its polypeptide substrates. Here, we investigate aspects of the reaction mechanism of Cdk2 by gas-phase density functional calculations, classical molecular dynamics, and Car,Parrinello QM/MM simulations. We focus on the role of the conserved Asp127 and on the nature of the phosphoryl transfer reaction mechanism catalyzed by Cdk2. Our findings suggest that Asp127 is active in its deprotonated form by assisting the formation of the near-attack orientation of the substrate serine or threonine. Therefore, the residue does not act as a general base during the catalysis. The mechanism for the phosphoryl transfer is a single SN2-like concerted step, which shows a phosphorane-like transition state geometry. Although the resulting reaction mechanism is in agreement with a previous density functional study of the same catalytic reaction mechanism (Cavalli et,al., Chem. Comm.2003, 1308,1309), the reaction barrier is considerably lower when QM/MM calculations are performed, as in this study (,42,kcal,mol,1 QM vs. ,24,kcal,mol,1 QM/MM); this indicates that important roles for the catalysis are played by the protein environment and solvent waters. Because of the high amino acid sequence conservation among the whole family of cyclin-dependent kinases (CDKs), these results could be general for the CDK family. [source]