Force field, quantum theory

Quantum dynamics effects for hydride transfer in enzyme catalysis have been analyzed by Alhambra et. al., 2000. This process is simulated using canonically variational transition-states for overbarrier dynamics and optimized multidimensional paths for tunneling. A system is divided into a primary zone (substrate-enzyme-coenzyme), which is embedded in a secondary zone (substrate-enzyme-coenzyme-solvent). The potential energy surface of the first zone is treated by quantum mechanical electronic structure methods, and protein, coenzyme, and solvent atoms by molecular mechanical force fields. The theory allows the calculation of Schaad-Swain exponents for primary (aprim) and secondary (asec) KIE... 

Giese, T. J., Chen, H., Dissanayake, T, Giamba u, G. M., Heldenbrand, H., Huang, M., Kuechler, E. R., Lee, T.-S., Panteva, M. T, Radak, B. K., and York, D. M. [2013]. A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields, /. Chem. Theory Comput. 9,1417-1427. 

AMI AMBER A Program for Simulation of Biological and Organic Molecules CHARMM The Energy Function and Its Parameterization Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Divide and Conquer for Semiempirical MO Methods Electrostatic Catalysis Force Fields A General Discussion Force Fields CFF GROMOS Force Field Hybrid Methods Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Methods Mixed Quantum-Classical Methods MNDO MNDO/d Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Parameterization of Semiempirical MO Methods PM3 Protein Force Fields Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mecha-nics/Molecular Mechanics (QM/MM) SINDOI Parameterization and Application. 

Before 1980, force field and semiempircal methods (such as CNDO, MNDO, AMI, etc.) [1] were used exclusively to study sulfur-containing compounds due to the lack of computer resources and due to inefficient quantum-chemical programs. Unfortunately, these computational methods are rather hmit-ed in their reliability. The majority of the theoretical studies under this review utilized ab initio MO methods [2]. Not only ab initio MO theory is more reliable, but also it has the desirable feature of not relying on experimental parameters. As a consequence, ab initio MO methods are apphcable to any systems of interest, particularly for novel species and transition states. 

Computational chemists in the pharmaceutical industry also expanded from their academic upbringing by acquiring an interest in force field methods, QSAR, and statistics. Computational chemists with responsibility to work on pharmaceuticals came to appreciate the fact that it was too limiting to confine one s work to just one approach to a problem. To solve research problems in industry, one had to use the best available technique, and this did not mean going to a larger basis set or a higher level of quantum mechanical theory. It meant using molecular mechanics or QSAR or whatever. 

Keywords Polarizable force field, Molecular orbital and valence bond theory, Nuclear quantum... 

Quantum mechanics is essential for studying enzymatic processes [1-3]. Depending on the specific problem of interest, there are different requirements on the level of theory used and the scale of treatment involved. This ranges from the simplest cluster representation of the active site, modeled by the most accurate quantum chemical methods, to a hybrid description of the biomacromolecular catalyst by quantum mechanics and molecular mechanics (QM/MM) [1], to the full treatment of the entire enzyme-solvent system by a fully quantum-mechanical force field [4-8], In addition, the time-evolution of the macromolecular system can be modeled purely by classical mechanics in molecular dynamicssimulations, whereas the explicit incorporation... 

Equation (4-5) can be directly utilized in statistical mechanical Monte Carlo and molecular dynamics simulations by choosing an appropriate QM model, balancing computational efficiency and accuracy, and MM force fields for biomacromolecules and the solvent water. Our group has extensively explored various QM/MM methods using different quantum models, ranging from semiempirical methods to ab initio molecular orbital and valence bond theories to density functional theory, applied to a wide range of applications in chemistry and biology. Some of these studies have been discussed before and they are not emphasized in this article. We focus on developments that have not been often discussed. 

One tool for working toward this objective is molecular mechanics. In this approach, the bonds in a molecule are treated as classical objects, with continuous interaction potentials (sometimes called force fields) that can be developed empirically or calculated by quantum theory. This is a powerful method that allows the application of predictive theory to much larger systems if sufficiently accurate and robust force fields can be developed. Predicting the structures of proteins and polymers is an important objective, but at present this often requires prohibitively large calculations. Molecular mechanics with classical interaction potentials has been the principal tool in the development of molecular models of polymer dynamics. The ability to model isolated polymer molecules (in dilute solution) is well developed, but fundamental molecular mechanics models of dense systems of entangled polymers remains an important goal. 

Molecular mechanics force fields rest on four fundamental principles. The first principle is derived from the Bom-Oppenheimer approximation. Electrons have much lower mass than nuclei and move at much greater velocity. The velocity is sufficiently different that the nuclei can be considered stationary on a relative scale. In effect, the electronic and nuclear motions are uncoupled, and they can be treated separately. Unlike quantum mechanics, which is involved in determining the probability of electron distribution, molecular mechanics focuses instead on the location of the nuclei. Based on both theory and experiment, a set of equations are used to account for the electronic-nuclear attraction, nuclear-nuclear repulsion, and covalent bonding. Electrons are not directly taken into account, but they are considered indirectly or implicitly through the use of potential energy equations. This approach creates a mathematical model of molecular structures which is intuitively clear and readily available for fast computations. The set of equations and constants is defined as the force... 

In this section, we give a brief overview of theoretical methods used to perform tribological simulations. We restrict the discussion to methods that are based on an atomic-level description of the system. We begin by discussing generic models, such as the Prandtl-Tomlinson model. Below we explore the use of force fields in MD simulations. Then we discuss the use of quantum chemical methods in tribological simulations. Finally, we briefly discuss multiscale methods that incorporate multiple levels of theory into a single calculation. 

Figure 5. Normal modes for vibration of tetrahedral [Cr04] (chromate). There are four distinct vibrational frequencies, including one doubly-degenerate vibration (E symmetry) and two triply-degenerate vibrations (F2 symmetry), for a total of nine vibrational modes. Arrows show the characteristic motions of each atom during vibration, and the length of each arrow is proportional to the magnitude of atomic motion. Only F2 modes involve motion of the central chromium atom, and as a result their vibrational frequencies are affected by Cr-isotope substitution. The normal modes shown here were calculated with an ab initio quantum mechanical model, using hybrid Hartree-Fock/Density Functional Theory (B3LYP) and the 6-31G(d) basis set—other ab initio and empirical force-field models give very similar results.

Hypercube, Inc. at http //www.hyper.com offers molecular modeling packages under the HyperChem name. HyperChem s newest version, Hyper-Chem Release 7.5, is a full 32-bit application, developed for the Windows 95, 98, NT, ME, 2000, and XP operating systems. Density Functional Theory (DFT) has been added as a basic computational engine to complement Molecular Mechanics, Semiempirical Quantum Mechanics and ab initio Quantum Mechanics. The DFT engine includes four combination or hybrid functions, such as the popular B3-LYP or Becke-97 methods. The Bio+ force field in HyperChem represents a version of the Chemistry at HARvard using Molecular Mechanics (CHARMM) force field. Release 7.5 of HyperChem updates... 

The term computational chemistry can refer in its broadest sense to a wide range of methods that have been developed to give insight into the fundamental behavior of chemical species. Such methods include, but are not necessarily limited to, those related to quantum mechanics (1), molecular mechanics (or force-field calculations) (2), perturbation theory (3), graph theory (4), or statistical thermodynamics (5). For the purposes of this chapter, comments will be restricted to force-field and quantum-based calculations, since these are the techniques that have been used in work on lignin. Furthermore, these methods have been reviewed in a very readable book by Clark (6). 

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