QM/MM, hybrid

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-... 

Key words hydrosilylation, enantioselective catalysis, Car-Parrinello, ab initio molecular dynamics, combined QM/MM, hybrid methods... 

The Tripos [73] force field was used to perform the molecular mechanics calculations, augmented with parameters developed by Doman et al. [74] for the ferrocenyl ligand. In the QM/MM hybrid AIMD simulations, the electronic structure calculation was performed on a reduced system in which each of the substituents that have been removed from the QM part was replaced by a hydrogen atom, in order to saturate the valence of the QM boundary atoms. 

Meanwhile, cation - crown complexes were fully optimized by ab initio QM techniques in the gas phase, allowing to investigate the effect of electronic reorganization (mainly charge transfer + polarization effects) on the recognition properties/15,161 QM/MM hybrid methods which combine a QM representation of the ion coordination sphere with a MM representation of the more remote species, have been tested on 18C6/ cation complexes/17, 18] Typical applications of "computational approaches in supramolecular chemistry" up to 1994 can be found in ref. [191 There are also reviews on more specialized fields like calixarenes/20,21]... 

Further uses of pseudopotentials are numerous. The most obvious (and rather widely known ones) are to continue with the PP or MP Hamiltonians for a widely understood combination of the core and valence shells and to apply standard ab initio techniques to electrons in the valence subspace only. We do no elaborate further on this as the hybrid nature of the pseudopotential methods is rather obvious from the above and its more specific applications in a narrower QM/MM hybrid context will be described later. 

Since the suggestion of the sequential QM/MM hybrid method, Canuto, Coutinho and co-authors have applied this method with success in the study of several systems and properties shift of the electronic absorption spectrum of benzene [42], pyrimidine [51] and (3-carotene [47] in several solvents shift of the ortho-betaine in water [52] shift of the electronic absorption and emission spectrum of formaldehyde in water [53] and acetone in water [54] hydrogen interaction energy of pyridine [46] and guanine-cytosine in water [55] differential solvation of phenol and phenoxy radical in different solvents [56,57] hydrated electron [58] dipole polarizability of F in water [59] tautomeric equilibrium of 2-mercaptopyridine in water [60] NMR chemical shifts in liquid water [61] electron affinity and ionization potential of liquid water [62] and liquid ammonia [35] dipole polarizability of atomic liquids [63] etc. 

It is clear, at the moment, that the junction problem of QM/MM hybrid potentials is, as yet, unresolved. In all schemes the partitioning of a molecule should be done in a chemically sensible way — only single bonds should be broken and preferably those between non-polar atoms such as carbons. Additionally, if possible, the junction should be as far away as possible from the region of interest (e.g. where the reaction is occurring). And, above all, several partitionings should be tried so that the sensitivity of the results to the partitioning can be tested. 

QM/MM hybrid method with a QM core and MM environment SVD singular value decomposition... 

QM/MM hybrid quantum/classical (quantum mechanical/molecular mechanical)... 

Hybrid QM/MM Hybrid QM/MM is the combination of quantum mechanical (QM) and molecular mechanics (MM) methodologies in Monte Carlo and molecular dynamics calculations where the solute or chemically reacting part of the total system is treated quantum mechanically, whereas the rest of the system is treated in the MM approximation. 

MM is applicable to macromolecules such as enzymes, but cannot model the bond-breaking and bond-making that occurs within enzyme-substrate complexes at active sites. The solution is provided by a QM/MM hybrid approach, in which QM is used to model the active site and MM models are used for the rest of the enzyme structure. 

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

Excited-states simulations were mainly limited to small and medium-sized molecules before the 90s. However, many important photophysical processes, as for example, the photoisomerization of rhodopsin, take place in a biological environment, seldom not without the presence of an enzyme. To study photochemical processes in the large-size systems, alternative methods are required. One such method, the QM/MM method," was developed by Warshel and Levitt in 1976. This approach combines the accuracy of quantum chemical models with the speed of molecular mechanics. An alternative method to combine different quantum chemical approaches, the ONIOM method, was developed by Morokuma and co-workers." These methods were initially used in the context of ground-state reactions. Early applications of the QM/MM hybrid method to photochemical processes can be found as early as 1982," however, it was not until at the beginning of this century that the method started to be used extensively for photochemical and photophysical dynamics. To find representative investigations of that time consult the reference list." " ... 

QM-MM hybrid quantum mechanical-molecular mechanics method... 

QM calculations can be incorporated into mixed quantum-mechanical/molecular-mechanical (QM/MM) hybrid schemes, ih which only a relatively small part of the system (QM region) is treated within the electronic structure approach, while the remaining bulk of the system is described using molecular mechanics (MM). 

QM calculations can be incorporated into mixed quantum-mechanical/molecular-mechanical (QM/MM) hybrid... 

HCAII is one of the best-characterized enzymes and has therefore served as one of the first test cases to explore the capabilities of AIMD simulations for a first-principles modeling of enzymes. Several full-quantum and mixed QM/MM hybrid simulations have been performed for this system. In these studies the influence of the size of the quantum region and the representation of the electrostatic enviromnent of the protein have been tested. In addition, it was also possible to directly observe part of the enzymatic reaction cycle, namely the initial proton transfer steps from the zinc-boxmd water towards the proton acceptor group His64 located in the upper channel of the active site. In these proton transfer reactions a... 

In a QM calculation the wavefunction and, hence, the electron density of the system is determined. Thus, in a QM/MM hybrid potential calculation, in which there are electrostatic interactions between e QM and MM atoms, the electron density of the QM region will be influenced by the charges on the MM atoms. In contrast, in most MM force fields, the charges on the MM atoms are fixed parameters and so the MM charge distribution will not respond to changes in its environment. These MM polarization corrections can be significant in many systems and so some work has been done to try to include them. 

The dipole polarizability model can be readily adapted for use with QM/MM hybrid potentials. The major hurdle in doing so arises because the electric field at an MM atom will depend not only on the charge distribution of the MM atoms but also on that of the QM atoms as well. This means that both the induced dipoles on the MM atoms and the wavefunction of the atoms in the QM region must be determined self-consistently. In practice, this is achieved by an iterative procedure in which the MM dipoles and QM wavefunction are obtained at each cycle and the process repeated until convergence. 

Figure 3 The QM/MM hybrid potential approach applied to an enzymatic reaction. The atoms in red are QM while the rest of the atoms are MM light blue atoms are mobile while the purple ones are fixed and only feel the rest of the system through nonbonded interactions. The purple ring is the boundary region...

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