Reactive force-field quantum chemical methods

The process of adsorption and interaction of probe molecules such as ammonia, carbon monoxide as well as the whole spectrum of organic reactant molecules with zeolite catalysts has been the subject of numerous experimental and computational studies. These interaction processes are studied using several computational methods involving force fields (Monte Carlo, molecular dynamics emd energy minimization) or quantum chemical methods. Another paper [1] discusses the application of force field methods for studying several problems in zeolite chemistry. Theoretical quantum chemical studies on cluster models of zeolites help us to understand the electronic and catalytic properties of zeolite catalysts. Here we present a brief summary of the application of quantum chemical methods to understand the structure and reactivity of zeolites. 

Hybrid methods are characterized by a combination of quantum mechanical (QM) and molecular mechanical (MM) potentials. They treat the electronically important part of a large system by a quantum chemical method (e.g., ab initio, DFT, or semiempirical) and the remainder by a classical force field. They can provide an appropriate description for systems which are too large for a purely quantum chemical approach (even at the semiempirical level) and which contain regions that cannot be described classically (e.g., reactive centers with breaking and forming bonds, or chromophores where an electronic excitation takes place). 

The most basic approach to carry out MD simulations for larger systems is to use classical force fields. A variety of different force fields for molecular mechanics (MM) simulations has been developed,which are mainly intended to describe the non-reactive dynamics of large systems. In particular in the field of biochemistry force fields play an essential role to study the complex properties of large biomolecules. However, classical force fields require the specification of the connectivity of the atoms. Therefore, they are not able to describe chemical reactions, i.e., the making and breaking of bonds. To describe reactions, they can be combined with quantum mechanical (QM) methods in so-called QM/MM simulations. In recent years also reactive force fields , e.g. ReaxFF, have been introduced, which overcome this limitation. However, these reactive force fields are typically highly adapted to specific systems by analytic terms customized to describe e.g. certain bonding situations, and only a few applications have been reported so far. 

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. 

Computer experiments particularly use quantum chemical approaches that provide accurate result with intense computational cost. Classical or semiempirical methods on the other hand are able to simulate thousands or up to millions of atoms of a system with pairwise Lennard-Jones (LJ)-type potentials [104-107]. Thus, LJ-type potentials are very accurate for inert gas systems [108], whereas they are unable to describe reactions or they do so by predetermined reactive sites within the molecules of the reactive system [109]. van Duin and coworkers [109-115] developed bond-order-dependent reactive force field technique is called ReaxFF as a solution to the aforementioned problems. Therefore, ReaxFF force field is intended to simulate reactions. They are successfully implemented to study hydrocarbon combustion [112,115,116] that is based on C-H-0 combustion parameters, fuel cell [110,111], metal oxides [117-122], proteins [123,124], phosphates [125,126], and catalyst surface reactions and nanotubes [110-113] based on ReaxFF water parameters [127]. Bond order is the number of chemical bonds between a pair of atoms that depends only on the number and relative positions of other atoms that they interact with [127]. Parameterization of ReaxFFs is achieved using experimental and quantum mechanical data. Therefore, ReaxFF calculations are fairly accurate and robust. The total energy of the molecule is calculated as the combination of bonded and nonbonded interaction energies. 

Finally, it must be remembered that DFT and AIMD can be incorporated into the so-called mixed quantum mechanical/molec-ular mechanical (QM/MM) hybrid schemes [12, 13]. In such methods, only the immediate reactive region of the system under investigation is treated by the quantum mechanical approach -the effects of the surroundings are taken into account by means of a classical mechanical force field description. These DFT/MM calculations enable realistic description of atomic processes (e.g. chemical reactions) that occur in complex heterogeneous envir-... 

Traditional MD simulations can investigate the different residence times due to the hydrophobic property of the surface of the pores and then obtain different surface fluid transport coefficients and provide a reliable basis for the experimental design. Quantum chemical calculations can consider reactive molecules with different reaction mechanisms for the active surfice of pores the reactivity will also affect the transport fluid to some extent. MD simulation cannot reflect the chemical interaction between the particles and cannot simulate a chemical reaction, while quantum chemical calculations cannot be apphed to large systems. ReaxFF simulation method is a new simulation method rising in recent years it can simulate not only the transport process but also chemical reactions and can simulate transport and reaction in a large system at the same time, which can fill the gap between quantum chemistry and classical force field (empirical force field). It simulates the process with more reahstic method because we can not only obtain the transport properties of the fluid but also reflect a chemical reaction of fluid and the surface. 

The QM/MM PES is a preferred choice for large molecular systems such as a fully solvated protein because the method combines both the generality of quantum mechanical methods for treating chemical processes and the computational efSciency of a force field for large systems. This is important because the dynamic fluctuations of the enzyme and aqueous system have a major impact on the polarization of the species involved in the chemical reaction which, in turn, affects the chemical reactivity. 

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