Hybrid QM/MM molecular dynamics

A. Magistrate, W. DeGrado, U. RothUsberger, and M. Klein (2003) Structural and Dynamical Characterization of Dizinc DPI, a Biomimetic Compound of Diiron Proteins via ab initio and Hybrid (QM/MM) Molecular Dynamics. J. Phys. Chem. B 107, p. 4182... 

In summary, ab initio and hybrid QM/MM molecular dynamics studies provide a valuable tool for the investigation of photoinduced CTI. Excited-state MD simulations of two small organic molecules, PSB5 and formaldimine, were carried out in order to assess the performance of different excited-state methods for the description of cis-trans isomerization reactions. In contrast to the majority of previous studies of the same model systems, our approach has the advantage to allow a completely unconstrained and unbiased relaxation of the excited molecule on its (3N-6)-dimensional PES. 

A more visual check of the process submitted to study is achieved by means of hybrid QM/MM Molecular Dynamics, which permits snapshots to be obtained which reproduce the geometry of the aminoacid surrounded by the solvent. In Figure 2.1.11 are shown four of these snapshots, corresponding to times of 200,270,405 and 440 femtoseconds after commencement of the process. 

Keywords Gas-liquid scattering Hybrid QM/MM molecular dynamics Interfacial chemistry Room temperature ionic liquids Squalane... 

R lak B, Yockel S, Kim D, Schatz GC (2008) Modeling reactive scattering of F(2P) at a liquid squalane interface a hybrid QM/MM molecular dynamics study. J Phys Chem A 113 7218-7226... 

Yockel S, Schatz GC (2010) Modeling 0(3P) and Ar scattering frrun the ionic liquid [emim] [N03] at 5 eV with hybrid QM/MM molecular dynamics. J Phys Orem B 114 14241-14248... 

Colombo MC et al (2008) Copper binding sites in the C-terminal domain of mouse prion protein a hybrid (QM/MM) molecular dynamics study. Proteins 70 1084-1098... 

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],... 

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. 

In this review we have seen examples representing three main types of biomolecules and biomodels proteins, nucleic acids, and lipids. Although it is not always classified as a biomolecule, water represents a fourth major type and it has been center stage in many of the examples we have treated. For each of these classes of biomolecules, DFT has played a major role in our work and in that of other workers. But this is not a one-man show we have also shown how DFT can be combined with molecular dynamics, either in the Bom-Oppenheimer-MD approach or in hybrid QM/MM methodologies. And we have shown examples that go beyond strictly Kohn-Sham DFT in the use of constraints that allow coimections with other theories and concepts, notably the Marcus theory of electron transfer. Finally, we have given a glimpse of some of the tools that can be used to analyze and interpret the DFT-based computations. 

The application of first-principles molecular dynamics to the study of organome-tallic systems or homogeneous catalytic processes in nmiaqueous solvents is certainly less extended than in water. Nevertheless, a survey of the literature shows that the number of AlMD-based studies in nonaqueous solvents is increasing. In many cases, due to the larger size of the complexes investigated and of the solvent molecules compared to in-water studies, the hybrid QM/MM approach is taken to simulate realistic model systems at a reduced computational cost. Simulations by means of first-principles molecular dynamics on ionic liquids [130] or frustrated Lewis pairs in organic solvents [131] are not covered here. 

To conclude this section we note that large molecular systems other than proteins have been the subject of hybrid QM/MM studies. Two such examples involve molecular dynamics simulations of surfaces using AMl/MM and PM3/MM potentials. In one the absorption of acetylene on a silicon surface was investigated [95] and in the other diamond surface reconstructions [96]. 

Pham VT et al (2010) The solvent shell structure of aqueous iodide X-ray absorption spectroscopy and classical, hybrid QM/MM and full quantum molecular dynamics simulations. Chem Phys 371 24—29... 

Hybrid QM/MM methods must be able to compute energy derivatives and forces to obtain geometry optimization and/or Molecular Dynamics simulations on the whole molecular system. Here again the recipes differ in the different formulations of hybrid QM/MM programs. 

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