Molecular dynamics with quantum

It seems that surface hopping (also called Molecular Dynamics with Quantum Transitions, MDQT) is a rather heavy tool to simulate proton dynamics. A recent and promising development is path integral centroid dynamics [123] that provides approximate dynamics of the centroid of the wavefunctions. Several improvements and applications have been published [123, 124, 125, 126, 127, 128). 

Hammes-Schiffer, S., Tully, J.C. Proton transfer in solution Molecular dynamics with quantum transitions. J. Chem. Phys. 101 (1994) 4657 667. 

Table II Comparison of the ratio k/k E °f quantum rate k over k, which is the TST result corrected for zero-point energy in the reactant well. Also shown are the Landail-Zener and centroid calculations67 and the molecular dynamics with quantum transition result.68...

Since the dielectric continuum representation of the solvent has significant limitations, the molecular dynamics simulation of PCET with explicit solvent molecules is also an important direction. One approach is to utilize a multistate VB model with explicit solvent interactions [34-36] and to incorporate transitions among the adiabatic mixed electronic/proton vibrational states with the Molecular Dynamics with Quantum Transitions (MDQT) surface hopping method [39, 40]. The MDQT method has already been applied to a one-dimensional model PCET system [39]. The advantage of this approach for PCET reactions is that it is valid in the adiabatic and non-adiatic limits as well as in the intermediate regime. Furthermore, this approach is applicable to PCET in proteins as well as in solution. 

Hwang et al.131 were the first to calculate the contribution of tunneling and other nuclear quantum effects to enzyme catalysis. Since then, and in particular in the past few years, there has been a significant increase in simulations of QM-nuclear effects in enzyme reactions. The approaches used range from the quantized classical path (QCP) (e.g., Refs. 4,57,136), the centroid path integral approach,137,138 and vibrational TS theory,139 to the molecular dynamics with quantum transition (MDQT) surface hopping method.140 Most studies did not yet examine the reference water reaction, and thus could only evaluate the QM contribution to the enzyme rate constant, rather than the corresponding catalytic effect. However, studies that explored the actual catalytic contributions (e.g., Refs. 4,57,136) concluded that the QM contributions are similar for the reaction in the enzyme and in solution, and thus, do not contribute to catalysis. 

S. Y. Kim and S. Hammes-Schiffer (2003) Molecular dynamics with quantum transitions for proton transfer Quantum treatment of hydrogen and donorac-ceptor motions. J. Chem. Phys. 119, pp. 4389-4398... 

MDQT Molecular dynamics with quantum transition MM Molecular mechanics... 

The free-energy profile is calculated by the FEP/US method (see section 16.3.3.3). However, at each step of the molecular dynamics simulation, the vibrational energy and the wave function of the transferred proton are determined from a three-dimensional Schrodinger equation and are included in the FEP/US procedure. In addition, dynamical effects due to transitions among proton vibrational states are calculated with a molecular dynamics with quantum transition (MDQT) procedure in which the proton wave function evolution is determined by a time-dependent Schrodinger equation. This procedure is combined with a reactive flux approach to calculate the transmission... 

Molecular dynamics with quantum mechanical methods is reviewed in... 

Solution - Molecular-Dynamics with Quantum Transitions. 

To the disappointment of Lilly s guest relations department, Lilly s Cray-2 was later replaced with a Cray J90, a mundane-looking machine. But the J90 was more economical, especially because it was leased. The supercomputers were almost always busy with molecular dynamics and quantum mechanical calculations [100]. Of the personnel at the company, the computational chemists were the main beneficiaries of supercomputing. 

The research of Paul Brumer and his colleagues addresses several fundamental problems in theoretical chemical physics. These include studies of the control of molecular dynamics with lasers.98 In particular, the group has demonstrated that quantum interference effects can be used to control the motion of molecules, opening up a vast new area of research. For example, one can alter the rate and yield of production of desirable molecules in chemical reactions, alter the direction of motion of electrons in semiconductors, and change the refractive indices of materials etc. by creating and manipulating quantum interferences. In essence, this approach, called coherent control, provides a method for manipulating chemistry at its most fundamental level.99... 

The approach has been tested by controlling nuclear wavepacket motion in a two-dimensional model system [23], The relative simplicity of the system makes it possible to compare the semiclassical results with exact quantum ones. Numerical applications to the control of HCN-CNH isomerization [24] demonstrates that the new semiclassical formulation of optimal control theory provides an effective and powerful tool for controlling molecular dynamics with many degrees of freedom. 

Unfortunately, quantitatively reliable quantum chemical calculations of nucleation rates for atmospherically relevant systems would require the application of both high-level electronic structure methods and complicated anharmonic thermochemical analysis to large cluster structures. Such computations are therefore computationally too expensive for currently available computer systems, and will likely remain so for the foreseeable future. Instead, a synthesis of different approaches will probably be necessary. In the future, successful nucleation studies are likely to contain combinations of the best features of both classical (Monte Carlo and molecular dynamics) and quantum chemical methods, with the ultimate objective being a chemically accurate, complete configurational sampling. 

Conformational study of glycal-type neuraminidase inhibitors has been undertaken by lorga and co-workers using a combined approach of conformational analysis, molecular dynamics and quantum chemistry. /hh couplings have been calculated for the resulting conformations by the use of several already published empirical equations and compared with the experimental ones. Several examples of nucleosides and carbohydrates whose structures were obtained with the help of Vrh couplings are given in Table 2. 

C. S. Carmer, B. Weiner, and M. Frenklach, J. Chem. Phys., 99, 1356 (1993). Molecular Dynamics with Combined Quantum and Empirical Potentials C2H2 Adsorption on Si(lOO). 

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