Applications of Ab Initio Molecular Dynamics

1 Exploring Structurally Complex Materials Liquids and Amorphous Phases 

07 times larger than the crystal density and an amorphous density equal to the crystal density. 

Once the structures of liquid and amorphous InP have been generated using MD simulations, various properties of these materials can be explored. To give just one example, the structure of disordered materials is often characterized using the radial distribution function  

p(r) is the average density of atoms found in a thin shell at a radius r from an arbitrary atom in the material, and p is the average density of the entire material. For very small values of r, g(r) — 0, since atoms cannot overlap one another. For large values of r, on the other hand, g(r) — 1, because atoms that are separated from one another by large distances in a disordered material are not influenced by one another. The distribution functions calculated by Lewis et al. for liquid and amorphous InP are shown in Fig. 9.4. As might be expected, the amorphous material has considerably more structure than the liquid. One important feature in the amorphous material is the peak in the P-P distribution near r 2.2 A. This peak shows the existence of P-P bonds in the amorphous material, a kind of bond that does not exist in the crystalline solid. 

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Applications of Ab-Initio Molecular Dynamics Simulations in Chemistry and Polymer Science... 

This review serves as an overview of modem aspects concerning methodology as well as applications of ab initio molecular dynamics simulations. 

The Kohn-Sham theory made a dramatic impact in the field of ab initio molecular dynamics. In the 1985, Car and Parrinello38 introduced a new formalism to study dynamics of molecular systems in which the total energy functional defined as in the Kohn-Sham formalism proved to be instrumental for practical applications. In the Car-Parrinello method (CP), the equations of motion are based on a Lagrangian (Lcp) which includes fictitious degrees of freedom associated with the electronic state. It is defined as ... 

In the present chapter, we will focus on the simulation of the dynamics of photoexcited nucleobases, in particular on the investigation of radiationless decay dynamics and the determination of associated characteristic time constants. We use a nonadiabatic extension of ab initio molecular dynamics (AIMD) [15, 18, 21, 22] which is formulated entirely within the framework of density functional theory. This approach couples the restricted open-shell Kohn-Sham (ROKS) [26-28] first singlet excited state, Su to the Kohn-Sham ground state, S0, by means of the surface hopping method [15, 18, 94-97], The current implementation employs a plane-wave basis set in combination with periodic boundary conditions and is therefore ideally suited to condensed phase applications. Hence, in addition to gas phase reference simulations, we will also present nonadiabatic AIMD (na-AIMD) simulations of nucleobases and base pairs in aqueous solution. 

Serianni AS, Chipman DM (1987) Furanose ring conformation The application of ab-initio molecular orbital calculations to the structure and dynamics of erythrofuranose and threofuranose rings. J Am Chem Soc 109 5297 - 5303... 

We have seen that many-body-based methods provide an ab-initio way to treat the Coulomb correlation in an N electron system without the expensive cost of QMC calculations. However, they are computationally more demanding than routine LDA-KS calculations and, hence, the feasibility of their application to complex systems is unclear, especially in the context of ab-initio molecular dynamics calculations, where many total-energy evaluations are required. As described in Sect. 5.3, the main problem when constructing approximations to E c [n] is related to its inherent non-analytical character which is due to the specific way in which the KS mapping between the real and the fictitious systems is done. However, this is not the only possible realisation of DFT and recently, new DFT methods have been proposed [112,113]. In these generalised Kohn-Sham schemes (GKS) the actual electron system is mapped onto a fictitious one in which particles move in an effective non-local potential. As a result of this, it is possible to describe structmal properties at the same (or better) level than LDA/GGA but improving on its description of quasiparticle properties. 

Blochl, P. E., Margl, P, Schwarz, K., 1996, Ab Initio Molecular Dynamics With the Projector Augmented Wave Method in Chemical Applications of Density Functional Theory, Laird, B. B., Ross, R. B., Ziegler, T. (eds.), American Chemical Society, Washington DC. 

The coupled DFT/MM formalism can be regarded as an intermediate approximation between ab initio molecular dynamics, and classical molecular mechanics. Being so, the range of its applicability extends to problems not treatable by molecular mechanics, chemical reactions for instance. The possibility of restricting quantum-mehcanical treatment to well-localized regions also makes it computationally advantageous over supermolecule ab initio simulations. It is important to note that this formalism does not differ whether applied to study biochemical reactions or to study reactions taking place in an other microscopic environment. This makes it possible to test any implementation on problems for which there... 

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. 

In this chapter, a short introduction to DFT and to its implementation in the so-called ab initio molecular dynamics (AIMD) method will be given first. Then, focusing mainly on our own work, applications of DFT to such fields as the definition of structure-activity relationships (SAR) of bioactive compounds, the interpretation of the mechanism of enzyme-catalyzed reactions, and the study of the physicochemical properties of transition metal complexes will be reviewed. Where possible, a case study will be examined, and other applications will be described in less detail. 

A proposal for the comprehensive study of chemical processes in a variety of important condensed-phase systems using modern theoretical methodology has been presented. The primary goals of the research are to provide microscopic information on the mechanisms and structural and dynamical properties of the chemical systems proposed for investigation, to test the applicability of modern ab initio molecular dynamics (MD) by comparison with experiment, and to develop and apply novel ab initio MD techniques in simulating complex chemical systems. The proposed research will contribute to the forefront of modern theoretical chemistry and address a number of important technological issues. The PI has carefully attempted to demonstrate his knowledge, ability, and resources to carry out the proposed research projects. 

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