Theoretical tools, molecular modeling

One of the most powerful theoretical tools for modeling carbohydrate solution systems on a microscopic scale and evaluating the degree of flexibility of these molecules is the molecular dynamics technique (MD) which has become popular over the last two decades. The first reported works of MD carbohydrate simulation appeared in 1986 and since then an in-... 

Simulation methods have been proved to be useful in the study of many different molecular systems, in particular in the case of flexible polymers chains [ 14]. According to the variety of structures and the theoretical difficulties inherent to branched structures, simulation work is a very powerful tool in the study of this type of polymer, and can be applied to the general problems outHned above. Sometimes, this utility is manifested even for behaviors which can be explained with simple theoretical treatments in the case of linear chains. Thus, the description of the theta state of a star chain cannot be performed through the use of the simple Gaussian model. The adequate simulation model and method depend strongly on the particular problem investigated. Some cases require a realistic representation of the atoms in the molecular models [10]. Other cases, however, only require simplified coarse-grained models, where some real mon-... 

Chemists seeking to use computational chemistry to support experimental efforts now have three generd theoretical tools available to them force field or molecular mechanics models, ab initio molecular orbital (MO) models and semiempirical MO models (1). Each of these tools have strengths and weaknesses which must be evaluated to determine which is most appropriate for a given applications. 

The distinction between the various dissociation schemes (with the exception of multiphoton dissociation) is rather artificial from the formal point of view. Common to direct dissociation, predissociation, and unimolecular decay is the possibility of state-specificity, i.e., the dependence of the dissociation on the quantum state of the parent molecule (Manz and Parmenter 1989). The absorption of a single photon uniquely defines the energy in the dissociative state. As we will demonstrate in subsequent chapters, one can treat all three classes of fragmentation with the same basic theoretical tools. However, the underlying molecular dynamics is quite different demanding different interpretation models. 

The advent of high-speed computers, availability of sophisticated algorithms, and state-of-the-art computer graphics have made plausible the use of computationally intensive methods such as quantum mechanics, molecular mechanics, and molecular dynamics simulations to determine those physical and structural properties most commonly involved in molecular processes. The power of molecular modeling rests solidly on a variety of well-established scientific disciplines including computer science, theoretical chemistry, biochemistry, and biophysics. Molecular modeling has become an indispensable complementary tool for most experimental scientific research. 

Molecular modeling includes a collection of computer-based tools of varying theoretical soundness, which make it possible to explain, and eventually predict, the properties of molecular systems on the basis of their composition, geometry, and electronic structure. The need for such modeling arises while studying and/or developing various chemical products and/or processes. The raison d etre of molecular modeling is provided by chemical thermodynamics and chemical kinetics, the basic facts of which are assumed to be known to the reader.1... 

Ab initio calculations of electronic wave functions are well established as useful and powerful theoretical tools to investigate physical and chemical processes at the molecular level. Many computational packages are available to perform such calculations, and a variety of mathematical methods exist to approximate the solutions of the electronic hamiltonian. Each method is based (or should be) on a well defined physical model, specified by a certain partition of the electronic hamiltonian, in such a way as to include a subset of all the interactions present in the exact one. It is expected that this subset contains the most important effects to describe consistently the situation of interest. The identification of which physical interactions to include is a major step in developing and applying quantum chemical theory to the study of real problems. 

Agatonovich-Kustrin S, Beresford R, Yusof APM (2001) ANN modeling of the penetration across a polydimethylsiloxane membrane from theoretically derived molecular descriptors. J Pharm Biomed Anal 25 227-237 Baroni M, Costantino G, Cruciani G et aL (1993) Generating optimal linear PLS estimations (GOLPE) An advanced chemometric tool for handling 3D-QS AR problems. Quant Struct-Act Relat 12 9-20... 

The unique features of our system enable us to use three different theoretical tools — a molecular dynamics simulation, models which focus on the repulsion between atoms and a statistical approach, based on an information theory analysis. What enables us to use a thermodynamic-like language under the seemingly extreme nonequilibrium conditions are the high density, very high energy density and the hard sphere character of the atom-atom collisions, that contribute to an unusually rapid thermalization. These conditions lead to short-range repulsive interactions and therefore enable us to use the kinematic point of view in a useful way. 

Molecular dynamics (MD) simulations, the most suitable theoretical tool for the investigation of internal motions, can be used to explore both equilibrium properties and time-dependent phenomena. Based on both experimental and theoretical observations two models for the internal motion of proteins have been suggested. Within the framework of the first model internal motions arise from harmonic or quasi-harmonic vibrations that occur in a single multidimensional well on the potential energy surface [4,5,6,7]. The second model assumes that motions are a superposition of oscillations within a well and... 

For example, MD simulations are practically the only theoretical tool to give information about various molecular processes behind intermolecular NMR relaxation. MD can also be used to separate the different intramolecular relaxation mechanisms from each other- typically a challenging problem to the experimentalists. In addition, it can be used to evaluate motional models, assumed to be valid in interpretation of NMR results. The topics covered in this chapter will demonstrate how MD simulations can be used as an ideal partner to the NMR relaxation experiment - at the same time as the experimental results can be used to refine the used theoretical models to describe liquids and solutions. It is clear that the both parts, theoreticians and experimentalists, will find a close collaboration beneficial. 

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