Car-Parrinello molecular dynamics study

O. Isayev et al., Are isolated nucleic acid bases really planar A Car-Parrinello molecular dynamics study. J. Phys. Chem. B 111, 3476-3480 (2007)... 

Y. Wu et al., On the Mechanisms of OH- Radical Induced DNA-Base Damage A Comparative Quantum Chemical and Car-Parrinello Molecular Dynamics Study. J. Phys. Chem. A 108, 2922-2929 (2004)... 

U. Rohrig, I. Prank, J. Hutter, A. Laio, J. VandeVondele, and U. Rothlisberger (2003) A QM/MM Car-Parrinello Molecular Dynamics Study of the Solvent Effects on the Ground State and on the Pirst Excited Singlet State of Acetone in Water. Chem. Phys. Chem. 4, p. 1177... 

Rohrig UF, Frank I, Hutter J, Laio A, VandeVondele J, Rothlisberger U (2003) QM/MM car-parrinello molecular dynamics study of the solvent effects on the ground stateand on the first excited singlet state of acetone in water. ChemPhysChem 4 1177-1182... 

Bhargava, B.L., and Balasubramanian, S., Intermolecular structure and dynamics in an ionic liquid A Car-Parrinello molecular dynamics simulation study of 1,3-dimethylimidazolium chloride, Chem. Phys. Lett., 417, 486-491, 2006. 

The mechanistic borderline between E2 and ElcB mechanisms has been studied under various conditions.1,2 The mechanism of the elimination reaction of 2-(2-fluoroethyl)-1-methylpyridinium has been explored explored by Car-Parrinello molecular dynamics in aqueous solution.3 The results indicated that the reaction mechanism effectively evolves through the potential energy region of the carbanion the carbon-fluoride bond breaks only after the carbon-hydrogen bond. 

Hybrid multiscale models enable us to focus on the relevant part of a system. For example, Leenders et al. studied the proton transfer process in the photoactive yellow protein (Figure 6.3) [9], They used Car-Parrinello molecular dynamics [10], a QM method for dynamics simulations, to describe the chromophore and its hydrogen-bonded network in the protein pocket (middle and right-hand circles). This was combined with a traditional MD force field of 28 600 atoms, simulating the entire protein in water (left-hand circle). 

DFT/MM calculations on ethylene polymerization by nickel diimine complexes have been applied within Car-Parrinello molecular dynamics simulations [40, 41]. A first set of calculations was used to refine the computed energy barrier for the termination step. The enthalpy barrier computed in the calculations described above was 18.6 kcal/mol, a value which decreased to 14.8 kcal/mol at 25 °C in the molecular dynamics calculation, in better agreement with experiment [40]. A second study analyzed the capture of the olefin by the catalyst [41], and found that this process, which has no en-thalpic barrier, has an entropic barrier. 

Both the experimental and theoretical studies indicate that the interactions between acetic acid and water molecules are more competitive in dilute aqueous solution. However to our knowledge, the specific interactions between acetic acid and water molecules are still not well understood, especially in such as the nature of hydrogen bonding, the bonds networking, the rule in architecture of larger hydration compounds, deprotonation of acetic acid in solution, stability of the hydrated proton, the local structure of its aqueous solution, and so on. In the present work, we have performed ab initio calculations on multi-hydrates (rich water hydration compounds) of acetic acid, and ab initio Car-Parrinello molecular dynamics (CPMD) [20] simulations on acetic acid monomer and water system (at dilute aqueous solution condition) to find something helpful for interpreting the nature of acetic acid aqueous solution. 

Boero et al. (1998) used Car-Parrinello molecular dynamics to study the polymerization of ethylene at titanium sites in MgCl2-supported Ziegler-Natta catalysts. Their objectives were to evaluate the reaction mechanism, in addition to determining the free energy profile of the polymerization process. Obviously, the characteristic time scale of this process is much greater than the picosecond time scale directly accessible by the simulation. Thus, it is not possible to observe the polymerization process via a straightforward Car-Parrinello simulation. 

Two important studies have predicted the melting point of sohd materials from first-principles calculations. Sugino and Car (1995) used Car-Parrinello molecular dynamics to estimate the melting point of silicon from first... 

We present a theoretical study of the oxidation reaction of NOj to NOj by dioxygen in the cages of sodalite. The combined Blue Moon Ensemble and Car Parrinello Molecular Dynamics approaches were used. 

We have studied the intracage oxidation NO2 + O2 —t NO3 in sodalite by means of the Blue Moon Ensemble and Car Parrinello Molecular Dynamics combined methods. The reaction was simulated by following the inverse reduction process. Such an approach has allowed an easier application of the BME sampling and could be of general interest. 

Section 2 provides a brief overview of the AIMD methodology mainly in the representation of Car-Parrinello molecular dynamics simulations. Bom-Oppenheimer molecular dynamics (BOMD) simulations (time-independent electronic structure) are introduced in a generalized formulation based on the work by Niklasson [7, 8]. This will be followed (Sect. 3) by some recent methodological advancements which allow for computationally more efficient simulations with better statistical sampling and which use more accurate electronic structure methods. After this, some examples from applied chemistry studied from AIMD will be given in Sect. 4. 

Recent advances in first-principles molecular dynamics (MD) calculations, which follow the Newtonian dynamics of classically treated nuclei, have made electronic-structure calculations applicable to the study of large systems where previously only classical simulations were possible. Examples of quantum-mechanical (QM) simulation methods are Born-Oppenheimer molecular dynamics (BOMD), Car-Parrinello molecular dynamics (CPMD), tight-binding molecular dynamics (TBMD), atom-centered density matrix propagation molecular dynamics (ADMPMD), and wavepacket ab idtb molecular dynamics (WPAIMD). 

Therefore, we decided to perform Car-Parrinello Molecular Dynamics (CPMD) on derivative IV and compared the quantum-chemistry results with the corresponding conventional molecular dynamics. Sampling of the puckering angle P during the study yielded the ID-free energy profiles reported in Fig. 7. The probability distribution is represented as a function of the coordinate P obtained from MD data, combining all values of 9m (see computational details). In these experiments, P and 0m are no... 

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