Computational studies chemical dynamics simulations

P. A. J Hilbers and K. Esselink, Parallel computing and molecular dynamics simulations , Computer Simulations in Chemical Physics, Proc. of the NATO advanced study institute on new perspectives in computer simulations in chemical physics, 473-95, 1993. 

Figure 4.49 reprinted with permission from Pranata J and W L Jorgensen. Computational Studies on FK506 Conformational Search and Molecular Dynamics Simulations in Water. The Journal of the American Chemical Society 113 9483-9493. 1991 American Chemical Society. 

Interestingly, in the experiments devoted solely to computational chemistry, molecular dynamics calculations had the highest representation (96-98). The method was used in simulations of simple liquids, (96), in simulations of chemical reactions (97), and in studies of molecular clusters (98). One experiment was devoted to the use of Monte Carlo methods to distinguish between first and second-order kinetic rate laws (99). One experiment used DFT theory to study two isomerization reactions (100). 

What is next Several examples were given of modem experimental electrochemical techniques used to characterize electrode-electrolyte interactions. However, we did not mention theoretical methods used for the same purpose. Computer simulations of the dynamic processes occurring in the double layer are found abundantly in the literature of electrochemistry. Examples of topics explored in this area are investigation of lateral adsorbate-adsorbate interactions by the formulation of lattice-gas models and their solution by analytical and numerical techniques (Monte Carlo simulations) [Fig. 6.107(a)] determination of potential-energy curves for metal-ion and lateral-lateral interaction by quantum-chemical studies [Fig. 6.107(b)] and calculation of the electrostatic field and potential drop across an electric double layer by molecular dynamic simulations [Fig. 6.107(c)]. 

The main advantage of the MFA is that it permits one to dramatically reduce the computational requisites associated with the study of solvent effects. This allows one to focus attention on the solute description, and it consequently becomes possible to use calculation levels similar to those usually employed in the study of systems and processes in the gas phase. Furthermore, in the case of ASEP/MD this high level description of the solute is combined with a detailed description of the solvent structure obtained from molecular dynamics simulations. Thanks to these features ASEP/MD [8] enables the study of systems and processes where it is necessary to have simultaneously a good description of the electron correlation of the solute and the explicit consideration of specific solute-solvent interactions, such as for VIS-UV spectra [9] or chemical reactivity [10]. 

Quantum chemical methods are valuable tools for studying atmospheric nucle-ation phenomena. Molecular geometries and binding energies computed using electronic structure methods can be used to determine potential parameters for classical molecular dynamic simulations, which in turn provide information on the dynamics and qualitative energetics of nucleation processes. Quantum chemistry calculations can also be used to obtain accurate and reliable information on the fundamental chemical and physical properties of molecular systems relevant to nucleation. Successful atmospheric applications include investigations on the hydration of sulfuric acid and the role of ammonia, sulfur trioxide and/or ions... 

Unsteady-state or dynamic simulation accounts for process transients, from an initial state to a final state. Dynamic models for complex chemical processes typically consist of large systems of ordinary differential equations and algebraic equations. Therefore, dynamic process simulation is computationally intensive. Dynamic simulators typically contain three units (i) thermodynamic and physical properties packages, (ii) unit operation models, (hi) numerical solvers. Dynamic simulation is used for batch process design and development, control strategy development, control system check-out, the optimization of plant operations, process reliability/availability/safety studies, process improvement, process start-up and shutdown. There are countless dynamic process simulators available on the market. One of them has the commercial name Hysis [2.3]. 

NMR spectroscopy is a very useful tool for determining the local chemical surroundings of various atoms. Komin et al studied theoretically this for the adenine molecule of Fig. 20 both in vacuum and in an aqueous solution using different computational approaches. In all cases, density-functional calculations were used for the adenine molecule, but as basis functions they used either a set of localized functions (marked loc in Table 45) or plane waves (marked pw). Furthermore, in order to include the effects of the solvent they used either the polarizable continuum approach (marked PCM) or an explicit QM/MM model with a force field for the solvent and a molecular-dynamics approach for optimizing the structure (marked MD). In that case, the chemical shifts were calculated as averages over 40 snapshots from the molecular-dynamics simulations. Finally, in one case, an extra external potential from the solvent acting on the solute was included, too, marked by the asterisk in the table. 

So far, our discussion has focussed on stationary quantum chemical methods, which yield results for fixed atomic nuclei, i.e. for frozen molecular structures like minimum structures on the Born-Oppenheimer potential energy surface. Processes in supramolecular assemblies usually feature prominent dynamical effects, which can only be captured through explicit molecular dynamics or Monte Carlo simulations [95-98]. Molecular dynamics simulations proved to be a useful tool for studying the detailed microscopic dynamic behavior of many-particle systems as present in physics, chemistry and biology. The aim of molecular dynamics is to study a system by recreating it on the computer as close to nature as possible, i.e. by simulating the dynamics of a system in all microscopic detail over a physical length of time relevant to properties of interest. 

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