Molecular dynamics simulations quantum mechanics

In molecular dynamics simulations, quantum mechanics is used to calculate the energy of the quantum system but the motion of the whole system is treated classically. Taking account of the quantum character of the motion does not invalidate eqn (16.1), but it gives rise to nuclear quantum mechanical (NQM) effects which change AG and the transmission coefficient k. Zero point energy effects contribute to AG while dynamical effects such as tunnelling and transitions to excited vibrational states contribute to k. Various approaches have been proposed to evaluate these contributions. 

Mata et al have determined the dynamic polarizability and Cauchy moments of liquid water by using a sequential molecular dynamics(MD)/ quantum mechanical (QM) approach. The MD simulations are based on a polarizable model of liquid water while the QM calculations on the TDDFT and EOM-CCSD methods. For the water molecule alone, the SOS/TDDFT method using the BHandHLYP functional closely reproduces the experimental value of a(ffl), provided a vibrational correction is assumed. Then, when considering one water molecule embedded in 100 water molecules represented by point charges, a(co) decreases by about 4%. This decrease is slightly reduced when the QM part contains 2 water molecules but no further effects are observed when enlarging the QM part to 3 or 4 water molecules. These molecular properties have then been employed to simulate the real and imaginary parts of the dielectric constant of liquid water. 

Progress in the theoretical description of reaction rates in solution of course correlates strongly with that in other theoretical disciplines, in particular those which have profited most from the enonnous advances in computing power such as quantum chemistry and equilibrium as well as non-equilibrium statistical mechanics of liquid solutions where Monte Carlo and molecular dynamics simulations in many cases have taken on the traditional role of experunents, as they allow the detailed investigation of the influence of intra- and intemiolecular potential parameters on the microscopic dynamics not accessible to measurements in the laboratory. No attempt, however, will be made here to address these areas in more than a cursory way, and the interested reader is referred to the corresponding chapters of the encyclopedia. 

Field, M.J., Bash, P.A., Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem. 11 (1990) 700-733. 

The principal idea behind the CSP approach is to use input from Classical Molecular Dynamics simulations, carried out for the process of interest as a first preliminary step, in order to simplify a quantum mechanical calculation, implemented in a subsequent, second step. This takes advantage of the fact that classical dynamics offers a reasonable description of many properties of molecular systems, in particular of average quantities. More specifically, the method uses classical MD simulations in order to determine effective... 

Field M J, P A Bash and M Karplus 1990. A Combined Quantum Mechanical and Molecular Mechanical Potential for Molecular Dynamics Simulations. Journal of Computational Chemistry 11 700-733. 

Combined Quantum and Molecular Mechanical Simulations. A recentiy developed technique is one wherein a molecular dynamics simulation includes the treatment of some part of the system with a quantum mechanical technique. This approach, QM/MM, is similar to the coupled quantum and molecular mechanical methods introduced by Warshel and Karplus (45) and at the heart of the MMI, MMP2, and MM3 programs by AUinger (60). These latter programs use quantum mechanical methods to treat the TT-systems of the stmctures in question separately from the sigma framework. 

Armrmanto, R., Schwenk, C.F. and Rode, B.M. (2003) Structure and Dynamics of Hydrated Ag (I) Ab Initio Quantum Mechanical-Molecular Mechanical Molecular Dynamics Simulation. The Journal of Physical Chemistry A, 107, 3132-3138. 

Equation (4-5) can be directly utilized in statistical mechanical Monte Carlo and molecular dynamics simulations by choosing an appropriate QM model, balancing computational efficiency and accuracy, and MM force fields for biomacromolecules and the solvent water. Our group has extensively explored various QM/MM methods using different quantum models, ranging from semiempirical methods to ab initio molecular orbital and valence bond theories to density functional theory, applied to a wide range of applications in chemistry and biology. Some of these studies have been discussed before and they are not emphasized in this article. We focus on developments that have not been often discussed. 

Lu ZY, Zhang YK (2008) Interfacing ab initio quantum mechanical method with classical Drude os-illator polarizable model for molecular dynamics simulation of chemical reactions. J Chem Theory Comput 4(8) 1237-1248... 

Wang S, Hu P, Zhang Y (2007) Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis the case of histone lysine methyltransferase set7/9. J Phys Chem B ASAP... 

The computational details for both the quantum mechanical and FEP studies using molecular dynamics simulations are described elsewhere.9 In brief, the gas-phase free energies (AGgas) were calculated using energies... 

Molecular dynamics simulations, with quantum-mechanically derived energy and forces, can provide valuable insights into the dynamics and structure of systems in which electronic excitations or bond breaking processes are important. In these cases, conventional techniques with classical analytical potentials, are not appropriate. Since the quantum mechanical calculation has to be performed many times, one at each time step, the choice of a computationally fast method is crucial. Moreover, the method should be able to simulate electronic excitations and breaking or forming of bonds, in order to provide a proper treatment of those properties for which classical potentials fail. 

In some situations we have performed finite temperature molecular dynamics simulations [50, 51] using the aforementioned model systems. On a simplistic level, molecular dynamics can be viewed as the simulation of the finite temperature motion of a system at the atomic level. This contrasts with the conventional static quantum mechanical simulations which map out the potential energy surface at the zero temperature limit. Although static calculations are extremely important in quantifying the potential energy surface of a reaction, its application can be tedious. We have used ah initio molecular dynamics simulations at elevated temperatures (between 300 K and 800 K) to more efficiently explore the potential energy surface. 

---