Chemical reactions molecular dynamics

Supercritical water (SCW) presents a unique combination of aqueous and non-aqueous character, thus being able to replace an organic solvent in certain kinds of chemical synthesis. In order to allow for a better understanding of the particular properties of SCW and of its influence on the rate of chemical reactions, molecular dynamics computer simulations were used to determine the free energy of the SN2 substitution reaction of Cl- and CH3C1 in SCW as a function of the reaction coordinate [216]. The free energy surface of this reaction was compared with that for the gas-phase and ambient water (AW) [248], In the gas phase, an ion-dipole complex and a symmetric transition... 

Standard molecular mechanics (MM) force fields have been developed that provide a good description of protein structure and dynamics,21 but they cannot be used to model chemical reactions. Molecular dynamics simulations are very important in simulations of protein folding and unfolding,22 an area in which they complement experiments and aid in interpretation of experimental data.23 Molecular dynamics simulations are also important in drug design applications,24 and particularly in studies of protein conformational changes,25,26 simulations of the structure and function of ion channels and other membrane proteins,27-29 and in studies of biological macromolecular assemblies such as F-l-ATPase.30... 

M. Nagaoka, Y. Okuno, and T. Yamabe,/. Am. Chem. Soc., 113,769 (1991). The Chemical Reaction Molecular Dynamics Method and the Dynamic Transition State Proton Transfer Reaction in the Formamidine and Water Solvent System. 

I. Benjamin and K. R. Wilson, J. Chem. Phys., 90, 4176 (1989). Proposed Experimental Probes of Chemical Reaction Molecular Dynamics in Solution ICN Photodissodation. 

Nagaoka M, Okuno Y, Yamabe T (1991) The chemical reaction molecular dynamics method and the dynamic transition state proton transfer reaction in formamidine and water solvent system. J Am Chem Soc 113(3) 769-778... 

Nanoreactors also can be eqnipped with active sites such as transitional metal species. In this case, the restricted space in the NR can affect reaction rate and mechanism throngh additional interactions of the reactants and active sites and modihcation of the concentration of the reactant close to the active site [9]. In this context, immobilization of chiral active centers within porous materials has attracted much attention and there are numerous reports confirming the merit of nanospace confinement in the chemical reactions. Molecular dynamics simulations have been used to clarify the precise way in which enantioselectivities are enhanced [12],... 

Following the early studies on the pure interface, chemical and electrochemical processes at the interface between two immiscible liquids have been studied using the molecular dynamics method. The most important processes for electrochemical research involve charge transfer reactions. Molecular dynamics computer simulations have been used to study the rate and the mechanism of ion transfer across the water/1,2-dichloroethane interface and of ion transfer across a simple model of a liquid/liquid interface, where a direct comparison of the rate with the prediction of simple diffusion models has been made. ° ° Charge transfer of several types has also been studied, including the calculations of free energy curves for electron transfer reactions at a model liquid/liquid... 

Because of the fundamental importance of solvent-solute interactions in chemical reactions, the dynamics of solvation have been widely studied. However, most studies have focused on systems where charge redistribution within the solute is the dominant effect of changing the electronic stale.[I,2] Recently, Fourkas, Benigno and Berg studied the solvation dynamics of a nonpolar solute in a nonpolar solvent, where charge redistribution plays a minor role.[3,4] These studies showed two distinct dynamic components a subpicosecond, viscosity independent relaxation driven by phonon-like processes, and a slower, viscosity dependent structural relaxation. These results have been explained quantitatively by a theory of solvation based on mechanical relaxation of the solvent in response to changes in the molecular size of the solute on excitation.[6] Here, we present results on the solvation of a nonpolar solute, s-tetrazine, by a polar solvent, propylene carbonate over the temperature range 300-160 K. In this system, comparisons to several theoretical approaches to solvation are possible. 

M. W. Balk, C. L. Brooks III, and S. A. Adelman,/. Chem. Phys., 79, 804 (1983). Dynamics of Liquid State Chemical Reactions Photodissociation Dynamics and Geminate Recombination of Molecular Iodine in Liquid Solution. 

Optical metiiods, in both bulb and beam expermrents, have been employed to detemiine tlie relative populations of individual internal quantum states of products of chemical reactions. Most connnonly, such methods employ a transition to an excited electronic, rather than vibrational, level of tlie molecule. Molecular electronic transitions occur in the visible and ultraviolet, and detection of emission in these spectral regions can be accomplished much more sensitively than in the infrared, where vibrational transitions occur. In addition to their use in the study of collisional reaction dynamics, laser spectroscopic methods have been widely applied for the measurement of temperature and species concentrations in many different kinds of reaction media, including combustion media [31] and atmospheric chemistry [32]. 

The molecular beam and laser teclmiques described in this section, especially in combination with theoretical treatments using accurate PESs and a quantum mechanical description of the collisional event, have revealed considerable detail about the dynamics of chemical reactions. Several aspects of reactive scattering are currently drawing special attention. The measurement of vector correlations, for example as described in section B2.3.3.5. continue to be of particular interest, especially the interplay between the product angular distribution and rotational polarization. 

Herschbach D R 1987 Molecular dynamics of elementary chemical reactions Angew. Chem. 26 1221—43... 

The method of molecular dynamics (MD), described earlier in this book, is a powerful approach for simulating the dynamics and predicting the rates of chemical reactions. In the MD approach most commonly used, the potential of interaction is specified between atoms participating in the reaction, and the time evolution of their positions is obtained by solving Hamilton s equations for the classical motions of the nuclei. Because MD simulations of etching reactions must include a significant number of atoms from the substrate as well as the gaseous etchant species, the calculations become computationally intensive, and the time scale of the simulation is limited to the... 

Weakliem P C and Carter E A 1993 Surface chemical reactions studied via ab /n/f/o-derived molecular dynamics simulations fluorine etching of Si(IOO) J. Chem Phys. 98 737-45... 

Chemical reaction dynamics is an attempt to understand chemical reactions at tire level of individual quantum states. Much work has been done on isolated molecules in molecular beams, but it is unlikely tliat tliis infonnation can be used to understand condensed phase chemistry at tire same level [8]. In a batli, tire reacting solute s potential energy surface is altered by botli dynamic and static effects. The static effect is characterized by a potential of mean force. The dynamical effects are characterized by tire force-correlation fimction or tire frequency-dependent friction [8]. 

Before progressing, it is useful to review the dynamics of typical molecular systems. We consider three types scattering (chemical reaction), photodissociation, and bound-state photoabsorption (no reaction). 

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