Hybrid quantum mechanical/force field

J. Wang, R. J. Boyd, and A. Laaksonen, J. Cbem. Pbys., 104, 7261. A Hybrid Quantum Mechanical Force Field Molecular Dynamics Simulation of Liquid Methanol Vibrational Frequency Shifts as a Probe of the Quantum Mechanical/Molecular Mechanical Coupling. 

J. Wang, R.J. Boyd, and A. Laaksonen, A hybrid quantum mechanical force field molecular dynamics simulation of liquid methanol Vibrational fiie-quency shifts as a probe of the quantum mechanical molecular mechanical coupling, J. Chem. Phys., 104(1996), 7261-7269. 

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... 

Direct dynamics calculations of the type just described, with all degrees of freedom included, are very expensive if the local quadratic approximations to the potential energy surface are obtained from an ab initio computation. In applications we have used a hybrid parameterized quantum-mechanical/force-field method, designed to simulate the CASSCF potential for ground and covalent excited states. A force field is used to describe the inert molecular a-framework, and a parameterized Heisenberg Hamiltonian is used to represent the CASSCF active orbitals in a valence bond space. Applications include azulene and benzene excited state decay dynamics. 

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-... 

In an attempt to aid interpretation of the IR spectrum of MbCO we decided to model the full protein by use of a hybrid quantum mechanics/molecular mechanics approach (QM/MM), to evaluate changes in the CO stretching frequency for different protein conformations. The QM/MM method used [44] combines a first-principles description of the active center with a force-field treatment (using the CHARMM force field) of the rest of the protein. The QM-MM boundary is modeled by use of link atoms (four in the heme vinyl and propionate substituents and one on the His64 residue). Our QM region will include the CO ligand, the porphyrin, and the axial imidazole (Fig. 3.13). The vinyl and propionate porphyrin substituents were not included, because we had previously found they did not affect the properties of the Fe-ligand bonds (Section 3.3.1). It was, on the other hand, crucial to include the imidazole of the proximal His (directly bonded to the... 

The inter/intramolecular potentials that have been described may be viewed as classical in nature. An alternative is a hybrid quantum-mechanical/classical approach, in which the solute molecule is treated quantum-mechanically, but interactions involving the solvent are handled classically. Such methods are often labeled QM/MM, the MM reflecting the fact that classical force fields are utilized in molecular mechanics. An effective Hamiltonian Hefl is written for the entire solute/solvent system ... 

The study of the enantioselective hydrosilylation reaction was performed with a series of combined quantum mechanics/molecular mechanics (QM/MM) calculations [26, 30] within the computational scheme of ab initio (AIMD) (Car-Parrinello) [62] molecular dynamics. The AIMD approach has been described in a number of excellent reviews [63-66], AIMD as well as hybrid QM/MM-AIMD calculations [26, 47] were performed with the ab initio molecular dynamics program CPMD [67] based on a pseudopotential framework, a plane wave basis set, and periodic boundary conditions. We have recently developed an interface to the CPMD package in which the coupling with a molecular mechanics force field has been implemented [26, 68],... 

Where quantum chemical methods have been used to study problems in medicinal chemistry and drug design, it has usually been combined with a continuum approximation [90,107-112], rather than explicit simulation, for the solvent effect. As noted, molecular simulations with an explicit solvent are traditionally performed using classical force fields. The reason for this is obvious quantum mechanical calculations are too time consuming. The coupling of QM with continuum approximations has therefore become convenient. However, the so-called hybrid quantum mechanical and... 

Relative pK calculations are also useful to predict the acidity of electronically excited species, taking the ground-state value as reference. Gao et al. [59] used the TCI cycle to predict the pK of the first singlet excited state of phenol (PhOH ). The calculations were performed using a hybrid quantum mechanical and molecular mechanical method (QM/MM) where the solute is treated quantum mechanically while the solvent molecules are represented by an MM force field. They obtained a ApK (PhOH PhOH ) of —8.6 + 0.1 pK units, implying a pK value of 1.4 for PhOH. ... 

The late Pierre Claverie was one of the most influential French researchers in the field of intermolecular interactions. His work dedicated to the foundation of molecular force fields and their links with quantum chemistry was truly visionary. Since about 1970, Claverie has pointed out the importance of taking polarization effects into account in molecular mechanics, and he proposed the concept of self-encased different levels of computations regarding solvent effects, thereby showing the road to the present development of hybrid quantum mechanics/molecular mechanics (QMVMM) methods. 

Cisneros, G. A., Tholander, S. N., Parisel, 0., Darden, T. A., Hiking, D., Perera, L., and Piquemal, J.-P, [2008], Simple formulas for improved point-charge electrostatics in classical force fields and hybrid quantum mechanical/molecular mechanical embedding, Int. J. Quantum Chem. 108, pp. 1905-1912, doi 10,1002/qua.21675. 

Many chemical and biological processes call for a quantum treatment, due to a chemical reaction, electronic excitation or necessity of a more accurate description. Hybrid quantum mechanics/molecular mechanics (QM/MM) approach, pioneered by Warshel and coworkers [50], provides means to represent a part of the system with a rigorous ab initio method while modeling the rest of the S5 em with a classical force field. The QM/MM Hamiltonian of the combined system can be represented as ... 

M. A. Thompson, /. Phys. Chem., 99, 4794 (1995). Hybrid Quantum Mechanical-Molecular Mechanical Force Field Development for Large Flexible Molecules A Molecular Dynamics Study of 18-Crown-6. 

Hybrid simulation techniques [5, 28, 31, 53, 80,103] proved as another family of approaches with important significance in chemical sciences. Since quantum mechanical (QM) based computation techniques [21, 34, 86] are prohibitively expensive when applied to large systems and simplified molecular mechanical (MM, also referred to as force fields) potential models [24,45,49,72] are in many cases not sufficiently accurate to investigate a chemical process, the advantages of both techniques are combined into a single computational framework. These hybrid quantum mechanical/molecular mechanical (QM/MM) approaches partition the system into a high- and a low-level zone. While the chemical most relevant region of the system is treated accurately via a suitable QM technique, efficient MM potentials... 

Piquemal JP et al (2008) Simple formulas for improved point-charge electrostatics in classical force fields and hybrid quantum mechanical/molecular mechanical embedding. Int J Quantum Chem 108 1905-1912... 

The fundamental idea behind the use of hybrid potentials is that a system is partitioned into several regions which are then modeled with different levels of approximation. The atoms from the residues or molecules that are participating in the reaction process, or atoms that are rich in electrons, such as metals, are treated quantum mechanically. The rest of the system is described by standard molecular mechanics force fields. Finally a boundary region is defined to account for the finite size of the system. 

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