Molecular dynamics chemical potential

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... 

Bash, P.A., Field, M.J.,Karplus, M. Free energy perturbation method for chemical reactions in the condensed phase A dynamical approach baaed on a combined quantum and molecular dynamics potential. J. Am. Chem. Soc. 109 (1987) 8092-8094. 

The thermodynamic properties that we have considered so far, such as the internal energy, the pressure and the heat capacity are collectively known as the mechanical properties and can be routinely obtained from a Monte Carlo or molecular dynamics simulation. Other thermodynamic properties are difficult to determine accurately without resorting to special techniques. These are the so-called entropic or thermal properties the free energy, the chemical potential and the entropy itself. The difference between the mechanical emd thermal properties is that the mechanical properties are related to the derivative of the partition function whereas the thermal properties are directly related to the partition function itself. To illustrate the difference between these two classes of properties, let us consider the internal energy, U, and the Fielmholtz free energy, A. These are related to the partition function by ... 

Just as one may wish to specify the temperature in a molecular dynamics simulation, so may be desired to maintain the system at a constant pressure. This enables the behavior of the system to be explored as a function of the pressure, enabling one to study phenomer such as the onset of pressure-induced phase transitions. Many experimental measuremen are made under conditions of constant temperature and pressure, and so simulations in tl isothermal-isobaric ensemble are most directly relevant to experimental data. Certai structural rearrangements may be achieved more easily in an isobaric simulation than i a simulation at constant volume. Constant pressure conditions may also be importai when the number of particles in the system changes (as in some of the test particle methoc for calculating free energies and chemical potentials see Section 8.9). 

Molecular dynamics studies can be done to examine how the path and orientation of approaching reactants lead to a chemical reaction. These studies require an accurate potential energy surface, which is most often an analytic... 

P. Zumbusch, W. Kulcke, G. Brunner. Use of alternating electric fields as antifouling strategy in ultrafiltration of biological suspensions. Introduction of a new experimental procedure for crossflow filtration. J Memb Sci 142-.15 (1998). R. L. Rowley, T. D. Shupe, M. W. Schuck. A direct method for determination of chemical potential with molecular dynamics simulations. 1. Pure components. Mol Phys 52 841, 1994. 

R. L. Rowley, M. Henrichsen. Calculation of chemical potential for structured molecules using osmotic molecular dynamics simulations. Fluid Phase Equil 137 15, 1997. 

Equilibrium Systems. Magda et al (12.) have carried out an equilibrium molecular dynamics (MD) simulation on a 6-12 Lennard-Jones fluid In a silt pore described by Equation 41 with 6 = 1 with fluid particle Interactions given by Equation 42. They used the Monte Carlo results of Snook and van Me gen to set the mean pore density so that the chemical potential was the same In all the simulations. The parameters and conditions set In this work were = 27T , = a, r = 3.5a, kT/e = 1.2, and... 

Molecular dynamics simulations of stretched gold nanowires The relative utility of different semiempirical potentials. Journal of Chemical Physics, 126, 144707-1-144707-6. 

All the macroscopic properties of polymers depend on a number of different factors prominent among them are the chemical structures as well as the arrangement of the macromolecules in a dense packing [1-6]. The relationships between the microscopic details and the macroscopic properties are the topics of interest here. In principle, computer simulation is a universal tool for deriving the macroscopic properties of materials from the microscopic input [7-14]. Starting from the chemical structure, quantum mechanical methods and spectroscopic information yield effective potentials that are used in Monte Carlo (MC) and molecular dynamics (MD) simulations in order to study the structure and dynamics of these materials on the relevant length scales and time scales, and to characterize the resulting thermal and mechanical proper-... 

Chelli R, Ciabatti S, Cardini G, Righini R, Procacci P (1999) Calculation of optical spectra in liquid methanol using molecular dynamics and the chemical potential equalization method. J Chem Phys... 

Fig. 3. Vibrational population distributions of N2 formed in associative desorption of N-atoms from ruthenium, (a) Predictions of a classical trajectory based theory adhering to the Born-Oppenheimer approximation, (b) Predictions of a molecular dynamics with electron friction theory taking into account interactions of the reacting molecule with the electron bath, (c) Born—Oppenheimer potential energy surface, (d) Experimentally-observed distribution. The qualitative failure of the electronically adiabatic approach provides some of the best available evidence that chemical reactions at metal surfaces are subject to strong electronically nonadiabatic influences. (See Refs. 44 and 45.)...

Quantum chemical methods are well established, accepted and of high potential for investigation of inorganic reaction mechanisms, especially if they can be applied as a fruitful interplay between theory and experiment. In the case of solvent exchange reactions their major deficiency is the limited possibility of including solvent effects. We demonstrated that with recent DFT-and ab initio methods, reaction mechanisms can be successfully explored. To obtain an idea about solvent effects, implicit solvent models can be used in the calculations, when their limitations are kept in mind. In future, more powerful computers will be available and will allow more sophisticated calculations to be performed. This will enable scientists to treat solvent molecules explicitly by ab initio molecular dynamics (e.g., Car-Parrinello simulations). The application of such methods will in turn complement the quantum chemical toolbox for the exploration of solvent and ligand exchange reactions. 

---