Computer Simulation of Molecular Structures

Many problems in force field investigations arise from the calculation of Coulomb interactions with fixed charges, thereby neglecting possible mutual polarization. With that obvious drawback in mind, Ulrich Sternberg developed the COSMOS (Computer Simulation of Molecular Structures) force field [30], which extends a classical molecular mechanics force field by serai-empirical charge calculation based on bond polarization theory [31, 32]. This approach has the advantage that the atomic charges depend on the three-dimensional structure of the molecule. Parts of the functional form of COSMOS were taken from the PIMM force field of Lindner et al., which combines self-consistent field theory for r-orbitals ( nr-SCF) with molecular mechanics [33, 34]. 

The linkage of microscopic and macroscopic properties is not without challenges, both theoretical and experimental. Statistical mechanics and thermodynamics provide the connection between molecular properties and the behavior of macroscopic matter. Coupled with statistical mechanics, computer simulation of the structure, properties, and dynamics of mesoscale models is now feasible and can handle the increase in length and time scales. 

None of the methods currently used to study molecular dynamics can span the whole time range of motions of interest, from picoseconds to seconds and minutes. However, the structural resolution of a method is of equal importance. A method has to not only provide information about the existence of motions with definite velocities but also to identify what structural element is moving and what is the mechanism of motion. Computer simulation of molecular dynamics has proved to be a very important tool for the development of theories concerning times and mechanisms of motions in proteins. In this approach, the initial coordinates and forces on each atom are input into the calculations, and classical equations of motions are solved by numerical means. The lengthy duration of the calculation procedure, even with powerful modem computers, does not permit the time interval investigated to be extended beyond hundreds of picoseconds. In addition, there are strong... 

In some cases, one is interested in the structures of complex fluids only at the continuum level, and the detailed molecular structure is not important. For example, long polymer molecules, especially block copolymers, can form phases whose microstructure has length scales ranging from nanometers almost up to microns. Computer simulations of such structures at the level of atoms is not feasible. However, composition field equations can be written that account for the dynamics of some slow variable such as 0 (x), the concentration of one species in a binary polymer blend, or of one block of a diblock copolymer. If an expression for the free energy / of the mixture exists, then a Ginzburg-Landau type of equation can sometimes be written for the time evolution of the variable 0 with or without flow. An example of such an equation is (Ohta et al. 1990 Tanaka 1994 Kodama and Doi 1996)... 

Computer simulation of molecular dynamics is concerned with solving numerically the simultaneous equations of motion for a few hundred atoms or molecules that interact via specified potentials. One thus obtains the coordinates and velocities of the ensemble as a function of time that describe the structure and correlations of the sample. If a model of the induced polarizabilities is adopted, the spectral lineshapes can be obtained, often with certain quantum corrections [425,426]. One primary concern is, of course, to account as accurately as possible for the pairwise interactions so that by carefully comparing the calculated with the measured band shapes, new information concerning the effects of irreducible contributions of inter-molecular potential and cluster polarizabilities can be identified eventually. Pioneering work has pointed out significant effects of irreducible long-range forces of the Axilrod-Teller triple-dipole type [10]. Very recently, on the basis of combined computer simulation and experimental CILS studies, claims have been made that irreducible three-body contributions are observable, for example, in dense krypton [221]. 

Estimated rate constants for the various electron-transfer steps, together with approximate reduction potentials, are displayed in Figure 6.39. For each step, the forward rate is orders of magnitude faster than the reverse reaction. The rapid rates suggest that attempts to obtain x-ray structures of intermediates (especially the early ones ) will not be successful. However, molecular dynamics methods are being explored in computer simulations of the structures of various intermediates. Within a few years we may begin to understand why the initial steps are so fast. 

Two sets of methods for computer simulations of molecular fluids have been developed Monte Carlo (MC) and Molecular Dynamics (MD). In both cases the simulations are performed on a relatively small number of particles (atoms, ions, and/or molecules) of the order of 100simulation supercell. The interparticle interactions are represented by pair potentials, and it is generally assumed that the total potential energy of the system can be described as a sum of these pair interactions. Very large numbers of particle configurations are generated on a computer in both methods, and, with the help of statistical mechanics, many useful thermodynamic and structural properties of the fluid (pressure, temperature, internal energy, heat capacity, radial distribution functions, etc.) can then be directly calculated from this microscopic information about instantaneous atomic positions and velocities. 

We carry out computer simulations in the hope of understanding bulk, macroscopic properties in temis of the microscopic details of molecular structure and interactions. This serves as a complement to conventional experiments, enabling us to leam something new something that cannot be found out in other ways. 

Material properties can be further classified into fundamental properties and derived properties. Fundamental properties are a direct consequence of the molecular structure, such as van der Waals volume, cohesive energy, and heat capacity. Derived properties are not readily identified with a certain aspect of molecular structure. Glass transition temperature, density, solubility, and bulk modulus would be considered derived properties. The way in which fundamental properties are obtained from a simulation is often readily apparent. The way in which derived properties are computed is often an empirically determined combination of fundamental properties. Such empirical methods can give more erratic results, reliable for one class of compounds but not for another. 

Computer simulations of electron transfer proteins often entail a variety of calculation techniques electronic structure calculations, molecular mechanics, and electrostatic calculations. In this section, general considerations for calculations of metalloproteins are outlined in subsequent sections, details for studying specific redox properties are given. Quantum chemistry electronic structure calculations of the redox site are important in the calculation of the energetics of the redox site and in obtaining parameters and are discussed in Sections III.A and III.B. Both molecular mechanics and electrostatic calculations of the protein are important in understanding the outer shell energetics and are discussed in Section III.C, with a focus on molecular mechanics. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

Contemporary s Tithetic chemists know detailed information about molecular structures and use sophisticated computer programs to simulate a s Tithesis before trying it in the laboratory. Nevertheless, designing a chemical synthesis requires creativity and a thorough understanding of molecular structure and reactivity. No matter how complex, every chemical synthesis is built on the principles and concepts of general chemistry. One such principle is that quantitative relationships connect the amounts of materials consumed and the amounts of products formed in a chemical reaction. We can use these relationships to calculate the amounts of materials needed to make a desired amount of product and to analyze the efficiency of a chemical synthesis. The quantitative description of chemical reactions is the focus of Chapter 4. 

Molecular dynamics and Monte Carlo simulations have been extensively applied to molten salts since 1968 to study structure, thermodynamic properties, and dynamic properties from a microscopic viewpoint. Several review papers have been published on computer simulation of molten salts. " Since the Monte Carlo method cannot yield dynamic properties, MD methods have been used to calculate dynamic properties. 

Garofalini, S.H. (1990) Molecular dynamics computer simulations of silica surface structure and adsorption of water molecules, J. Non-Cryst. Solids, 120, 1. 

Molecular spectra can be analyzed for spectrometric or for spectroscopic purposes. The term spectrometric usually refers to compound identification (linking a signal to a known structure) and to the determination of its concentration. The term spectroscopic stands for interpretation of the spectrum in terms of structure (chemical, electronic, nuclear, etc.). In this chapter we will look as some theoretical and practical aspects of a key spectrometric application of bioEPR, namely, the determination of the concentration of paramagnets, also known as spin counting. Subsequently, we consider the generation of anisotropic powder EPR patterns in the computer simulation of spectra, a basic technique that underlies both spectrometric and spectroscopic applications of bioEPR. 

Sometimes the theoretical or computational approach to description of molecular structure, properties, and reactivity cannot be based on deterministic equations that can be solved by analytical or computational methods. The properties of a molecule or assembly of molecules may be known or describable only in a statistical sense. Molecules and assemblies of molecules exist in distributions of configuration, composition, momentum, and energy. Sometimes, this statistical character is best captured and studied by computer experiments molecular dynamics, Brownian dynamics, Stokesian dynamics, and Monte Carlo methods. Interaction potentials based on quantum mechanics, classical particle mechanics, continuum mechanics, or empiricism are specified and the evolution of the system is then followed in time by simulation of motions resulting from these direct... 

The molecular models can be used in computational simulations of functional mechanisms to generate and/or probe specific mechanistic hypotheses for structural changes involved in the various states of the receptors, both wild-type and mutant constructs. The structural context makes these hypotheses testable in collaborative experiments designed to probe specific predictions and refine functional insights (for comprehensive review, see ref. [5]). 

Beyond the clusters, to microscopically model a reaction in solution, we need to include a very big number of solvent molecules in the system to represent the bulk. The problem stems from the fact that it is computationally impossible, with our current capabilities, to locate the transition state structure of the reaction on the complete quantum mechanical potential energy hypersurface, if all the degrees of freedom are explicitly included. Moreover, the effect of thermal statistical averaging should be incorporated. Then, classical mechanical computer simulation techniques (Monte Carlo or Molecular Dynamics) appear to be the most suitable procedures to attack the above problems. In short, and applied to the computer simulation of chemical reactions in solution, the Monte Carlo [18-21] technique is a numerical method in the frame of the classical Statistical Mechanics, which allows to generate a set of system configurations... 

The main goal of the molecular dynamics computer simulation of ionic solvation and adsorption on a metal surface has been to test the above model and to provide more quantitative information about the different factors that influence the structure of hydrated ions at the interface. Unfortunately, most of the experimental information about these issues has been obtained from indirect measurements such as capacity and current-potential plots, although in recent years in situ experimental techniques have begun to provide an accurate test of the above model. For a recent review of experimental techniques and the theory of ionic adsorption at the water/metal interface, see the excellent paper by Philpott. ... 

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