Molecular dynamics Car-Parinello

Mundy CJ, Colvin ME, Quong AA (2002) Irradiated guanine a Car-Parinello molecular dynamics study of dehydrogenation in the presence of an OH radical. J Phys Chem A 106 10063-10071 Murata-Kamiya N, Kamiya H, Muraoka M, Kaji H, Kasai H (1998) Comparison of oxidation products from DNA components byy-irradiation and Fenton-type reactions. J Radiat Res 38 121-131 Nabben FJ, van der Stroom HA, Loman H (1983) Inactivation of biologically active DNA by isopropanol and formate radicals. Int J Radiat Biol 43 495-504 Nakashima M, Hayon E (1979) Rates of reaction of inorganic phosphate radicals in solution. J Phys Chem 74 3290-3291... 

Keywords First-Principle Molecular Dynamics, Car-Parinello Molecular Dynamics, Density... 

Another method of controlling the temperature that can be used in CP MD is the stochastic thermostat of Andersen.27 In this approach the velocity of randomly selected nucleus is rescaled this corresponds in a way to the stochastic collisions with other particles in the system. Therefore, this approach is often called a stochastic collision method. The Andersen thermostat has recently been shown28 to perform very well in the Car-Parinello molecular dynamic simulations of bimolecular chemical reactions. 

In a very recent calculation by Markwick et al. targeted molecular dynamics methods were implemented in the framework of Car-Parinello molecular dynamics to study the nature of the double proton transfer [48]. They predict a concerted proton transfer reaction. In the very early stages of this reaction the system enters a vibrationally excited pretransitional state. Whereas in the global minima large amplitude fluctuations have been found in the pretransitional region, the frequency of these fluctuations is found to increase dramatically while the amplitude of the oscillation decreases when approaching the transition state. 

Ab initio MD simulations were not practical until the last decades of the 20th century due to their computational cost. In addition to rapid increase in computational power of modern computers, the factor of great importance for expansion of the ab initio molecular dynamics was a novel, practical scheme proposed by Car and Parinello.1 This methodology gave rise to a growing interest in ab initio MD and thus, quickly dominated the field. 

The main purpose of this chapter is to present the basics of ab initio molecular dynamics, focusing on the practical aspects of the simulations, and in particular, on modeling chemical reactions. Although CP-MD is a general molecular dynamics scheme which potentially can be applied in combination with any electronic structure method, the Car-Parinello MD is usually implemented within the framework of density functional theory with plane-waves as the basis set. Such an approach is conceptually quite distant from the commonly applied static approaches of quantum-chemistry with atom-centered basis sets. Therefore, a main... 

In this section we will briefly present the basic concepts of ab initio molecular dynamics within the Born-Oppenheimer and Car-Parinello approach. It is not our intention to cover the theoretical background of the Car-Parinello MD scheme in details. Instead we would like to concentrate on the practical aspects of the simulation and only briefly comment on the physical meaning of the basic parameters that must be specified in the input for a simulation. A more detailed discussion of the theoretical basis for the CP MD can be found in an excellent review article by Marx and Hutter.2... 

Figure 4-3. A comparison of the Car-Parinello and Bom-Oppenheimer molecular dynamics the potential energy (top) and temperature (kinetic energy, bottom) from the CP-MD and BO-MD simulations for ethylene, started from the same geometry and wave function. The results obtained form the simulations with the CPMD program13 (Troullier-Martins pseudopotentials,1415 time step of 4 a.u., fictitious mass 400 a.u., cut-off energy 70 Ry, unit cell 12 A x 12 A xl2 A)...

Car, R. and Parinello M., Unified approach for molecular dynamics and density-functional theory. Phys.Rev.Lett. (1985) 55 2471-2474. 

Some attempts to inclnde structural diffusion exist. The mechanism of proton transport in bulk water has been studied by various molecular modeling techniques like the Car-Parinello ab initio molecnlar dynamics simnlations (CPAIMD), mixed quan-tnm and classical mechanics technique (QM/MM), E " ... 

The first method is that of Car and Parinello, in which one performs molecular dynamics simulations for a large number (hundreds) of molecules, calculating the forces and energy from quantum mechanics for the whole assembly of molecules at each step. However, in order to be tractable, the calculations are carried out with DFT, but even then only for small molecules and requiring greater computational resources than are usually available. Also, the use of DFT restricts this method to systems in which electrostatic forces dominate ab initio methods could be used instead, but only at very large supercomputer centers. 

In the work by Shida et al. [45] a synchronous concerted double proton transfer is found to be the major mode of the reaction, which is confirmed in a recent molecular dynamics calculation by Wolf et al. [46]. In his molecular dynamics calculation the time evolution of the potential energy was additionally taken into account. The double proton transfer has also been investigated in a Car-Parinello ah initio molecular mechanics study by Miura et al. [41]. Quantum fluctuations are shown to cause significant deviations from the minimum energy path. While an asynchronous movement of the two protons close to the equilibrium structure was... 

The ah initio methods can be used in developing approximate classical expressions for the interactions present in these systems. The way in which this is done is the subject of this section. We note in passing that recent work on so-called ab initio molecular dynamics such as Car-Parinello MD [22-24] is blurring the distinction between purely ab initio methods and the classical simulation methods described below. In fact, the first ab initio M D simulation study of an ionic liquid was reported recently [21]. 

Hamiltonian models are classified according to then-level of approximation. The features of Schroedinger (S), Born-Oppenheimer (BO), and McMillan-Mayer (MM) level Hamiltonian models are exemplified in Table I by a solution of NaCl in H2O. The majority of investigations on electrolyte solutions are carried out at the MM level. BO-Level calculations are a precious tool for Monte Carlo and molecular dynamics simulations as well as for integral equation approaches. However, their importance is widely limited to stractural investigations. They, as well as the S-level models, have not yet obtained importance in electrochemical engineering. S-Level quantum-mechanical calculations mainly follow the Car-Parinello ab initio molecular dynamics method. 

The development of plane-wave pseudopotential methods for electronic structure calculations of solids (e.g., Payne et al. 1992) has also opened the door to real first-principles molecular dynamics simulations using the algorithm of Car and Parinello (1985). Here, we let the wavefimctions become part of the dynamics of the system. To do this, we introduce a fictitious kinetic energy associated with a dynamical motion of the wavefunction ... 

In this chapter we will review recent developments in modelling proton transport in different media. We will thereby narrow the topic to atomistic modelling of transport properties and processes only. The majority of studies in this area employ molecular dynamics (MD) to get insight into the mechanisms. For large systems classical force fields are used, small systems are often studied with ab-initio molecular dynamics, especially with Car-Parinello MD simulations. These methods are well known and documented, including their drawbacks, as e.g. finite-size effects in periodic simulations." Therefore, we will abandon explicit comments on the computational details, and refer the interested reader to the cited references or ordinary textbooks. 

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