Hybrid quantum mechanical/molecular mechanics calculations

Giese, T. J., and York, D. M. Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations. /. Chem. Phys., 127, doi 10.1063/l.2778428 [2007]. 

QM/MM Hybrid quantum-mechanical/molecular-mechanical calculations RPA Random phase approximation... 

A second approach is based on the methodology first explored in the seminal work by Warshel and Levitt as early as 1976 [21], and is the use of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations whereby a subsection of the system is treated by QM methods, the remainder (environment) is treated by standard molecular mechanics (MM) methods, and a coupling potential is used to connect the two regions [22], This methodology will then be exemplified with work developed in this group in recent years [23-26],... 

The second approach described here for inclusion of environment effects is the use of hybrid quantum mechanics/molecular mechanics methods (QM/MM). In a QM/MM calculation [21,22], the system is partitioned in two regions A QM region, typically consisting of a relatively small number of atoms relevant for the specific process being studied, and a MM region with all the remaining atoms. 

Despite the availability of fast computers and efficient codes for accurate quantum chemistry calculations, it is not likely in the near future that we will be able to study chemical reactions in proteins taking all the proteins atoms into quantum mechanical calculations. Hybrid methods in which different parts of large molecular systems are treated by different theoretical levels of methods are likely to play a key role in such studies for the coming decade or more. The ONIOM method we have developed is a versatile hybrid method that allows combining different quantum mechanical methods as well as molecular mechanics method in multiple layers, some features of... 

Molecular mechanics calculations have become a well established tool in the area of coordination chemistry, including the coordination chemistry of nickel375-379 where they are often applied for the analysis or the prediction of structures,380 the computation of isomer or conformer ratios and metal ion selectivities,381,382 and for simulating spectroscopic properties in combination with AOM calculations or by hybrid quantum mechanics/molecular mechanics (QMMM) methods.383,384 Details of the various approaches, e.g., the incorporation of d-electron stabilization energy... 

Abstract The applications of hybrid DFT/molecular mechanics (DFT/MM) methods to the study of reactions catalyzed by transition metal complexes are reviewed. Special attention is given to the processes that have been studied in more detail, such as olefin polymerization, rhodium hydrogenation of alkenes, osmium dihydroxylation of alkenes and hydroformylation by rhodium catalysts. DFT/MM methods are shown, by comparison with experiment and with full quantum mechanics calculations, to allow a reasonably accurate computational study of experimentally relevant problems which otherwise would be out of reach for theoretical chemistry. 

Duijnen, P.Th. van, Swart M. and Grozema F., QM/MM calculation of (hyper)polarizabilities with the DRFapproach., in Hybrid Quantum Mechanical and Molecular Mechanics Methods, J.Gao and M.A. Thompson, Editors. 1999, ACS Books Washington, DC. p. 220-232. 

Although few applications of these very recently implemented models have yet appeared, some calculations for free energies of transfer into aqueous solution are available.Polarization of the solute has been analyzed by reference to the molecular dipole moment,including comparison to a hybrid quantum mechanics/molecular mechanics approach,and the effect of aqueous solvation on conformational equilibria and simple nucleophilic reactions has been examined.] jo consideration of CDS solvation terms in conjunction with these models has appeared. 

Chaban GM, Gerber RB. Anharmonic vibrational spectroscopy of the glycine-water complex calculations for ab initio, empirical and hybrid quantum mechanics/molecular mechanics potentials. J Chem Phys 2001 115 1340-1348. 

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... 

To explain such facts, Linus Pauling proposed that the valence atomic orbitals in the molecule are different from those in the isolated atoms. Indeed, quantum-mechanical calculations show that if we mix specific combinations of orbitals mathematically, we obtain new atomic orbitals. The spatial orientations of these new orbitals lead to more stable bonds and are consistent with observed molecular shapes. The process of orbital mixing is called hybridization, and the new atomic orbitals are called hybrid orbitals. Two key points about the number and type of hybrid orbitals are that... 

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