Car-Parrinello molecular dynamics simulations

Thar J, Reckien W, Kirchner B (2007) Car-Parrinello Molecular Dynamics Simulations and Biological Systems. 268 133-171... 

Laio, A. VandeVondele, J. Rothlisberger, U., A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations, J. Chem. Phys. 2002,116, 6941-6947... 

In this section we focused our attention to a rationalization of the factors determining the stereoselectivity through ab initio mixed quantum/classical (QM/MM) Car-Parrinello molecular dynamic simulations. We have used the same basic computational approach used in Section 3 to explore the potential energy surface of the reaction. Since the catalyst system, 1, is relatively large, we have used the combined QM/MM model system B as shown in Figure 3 and described in subsections 2.1 and 3.1. 

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. 

Figure 6.3 Three snapshots of MD and Car—Parrinello molecular dynamics simulations of the photoactive yellow protein, showing the entire protein (left), the pocket containing the chromophore (middle), and the chromophore itself (right). Thanks to Dr. Elske Leenders and Dr. Evert Jan Meijer for the simulation snapshots.

Carloni, P. and Rothlisberger, U. (2001) Simulations of enzymatic systems perspectives from Car-Parrinello molecular dynamics simulations. Theor. Comp. Chem., 9, 215. 

The energy surface for the E2/S 2 reaction between ethyl fluoride and fluoride ion was calculated using the hills method within a Car-Parrinello molecular dynamics simulation.113 The S 2 reaction was found to occur faster than the E2 reaction. The results demonstrated that this theoretical method can determine the potential energy surfaces where competing concerted reactions occur via different transition states. 

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. 

Tamura R, Takahashi H, Fujimoto D, Ushio T (2007) Mechanism and Scope of Preferential Enrichment, a Symmetry-Breaking Enantiomeric Resolution Phenomenon. 269 53-82 Thar J, Reckien W, Kirchner B (2007) Car-Parrinello Molecular Dynamics Simulations and Biological Systems. 268 133-171... 

SIMULATIONS OF ENZYMATIC SYSTEMS PERSPECTIVES FROM CAR-PARRINELLO MOLECULAR DYNAMICS SIMULATIONS... 

I. Bako, J. Butter, and G. PaUnkas (2002) Car-Parrinello molecular dynamics simulation of the hydrated calcium ion. J. Chem. Phys. 117, p. 9838... 

P. Carloni and U. Rothlisberger (2001) Simulations of Enzymatic Systems Perspectives from Car-Parrinello Molecular Dynamics Simulations. In Theoretical Biochemistry - Processes and Properties of Biological Systems, ed. L. Eriksson Elsevier Science, pp. 215-251... 

K. Spiegel, U. Rothlisberger, and P. Carloni (2004) Cisplatin Binding to DNA Oligomers from Hybrid Car-Parrinello Molecular Dynamics Simulations. J. Phys. Chem. B 108, p. 2699... 

Fig. 12.4. Left The dipole moment in Debye plotted against the time step. Right Distribution of dipole moments (left-hand-side region smaller dipole moments right-hand-side region larger dipole moments). Both data sets were calculated from a Car-Parrinello molecular dynamics simulation of an isolated tetralactam macrocycle [227].

Perspectives from Car-Parrinello Molecular Dynamics Simulations. In Theoretical Biochemistry - Processes and Properties of Biological Systems-, L. 

Keywords Ab initio molecular dynamics simulations Always stable predictor-corrector algorithm Associated liquids Basis set Bom-Oppenheimer molecular dynamics simulations Car-Parrinello molecular dynamics simulations Catalysis Collective variable Discrete variable representation Dispersion Effective core potential Enhanced sampling Fictitious mass First-principles molecular dynamics simulations Free energy surface Hartree-Fock exchange Ionic liquids Linear scaling Metadynamics Nudged elastic band Numerically tabulated atom-centered orbitals Plane waves Pseudopotential Rare event Relativistic electronic structure Retention potential Self consistent field SHAKE algorithm ... 

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. 

The basic idea of Car-Parrinello molecular dynamics simulations can be expressed by A two-component quantum-classical problem is mapped onto a two-component purely classical problem with employing the constraints that quantum mechanics has to be fulfilled at all times [3]. 

DFT and Car-Parrinello molecular dynamics simulations have been used to study aggregation effects in model aldols, using the lithium enolates of acetaldehyde and acetone, with formaldehyde and acetone as electrophiles. The core of the aggregates is Li 0 ... 

Alkane functionalization is a highly desirable chemical transformation. The Shilov system [112], based on Pp and complexes, constimtes an early proposal for hydrocarbon oxidation in aqueous solution (Fig. 7). The rate-limiting step of the catalytic cycle, namely, C-H bond activation, was investigated by Vidossich et al. by means of Car-Parrinello molecular dynamics simulations in explicit water [113]. The authors considered the PtCl2(H20)(CH4) species, in both cis and trans configurations, solvated with 32 water molecules in a cubic box of 10 A edge treated under periodic boundary conditions. 

Carre, A., Horbach, J., Ispas, S., and Kob, W. (2008) New fitting scheme to obtain effective potential from Car-Parrinello molecular-dynamics simulations application to sihca, Eur. Lett., 82,17001. 

Early Car-Parrinello molecular dynamics simulations of small silicon clusters Si (n< 10) have been carried out to obtain zero temperature structures and structural properties at finite temperature [118]. 

Bako, L, Hutter, J., Palink s, G. (2006). Car-Parrinello molecular dynamics simulation of liquid formic acid. Journal of Physical Chemistry A, 110,2188. 

Dal Peraro, M., Ruggerone, P, Raugei, S., Gervasio, F. L., Carloni, P. (2007). Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Current Opinion in Structural Biology, 17,149. 

The above values are obtained using non-relativistic values calculated at the CCSD level of theory combined with relativistic corrections derived from the Dirac-Hartree-Fock method, plus dynamic and solvent effects estimated from cluster calculations involving water molecules that have been generated from Car-Parrinello molecular dynamics simulations. 

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