Nickel molecular dynamics simulations

The rest of this paper will be organized as follows In the next section we describe a set of interatomic potentials which we have developed to model iron-nickel alloys and report the calculational techniques of molecular dynamics simulations which we... 

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. 

However, details of this process including the mode of urea binding, the protonation state of individual surround protein residues, and the exact identity of the nucleophile are still under debate. Cyanate also was proposed as a possible intermediate in the urease mechanism (33). Recent quantum chemical calculations and molecular dynamics simulations indicated that hydrolytic and ehmination mechanisms might indeed compete, and that both are viable reaction channels for urease (34—37). Finally, an important issue is Why does urease require nickel as the metal of choice, whereas most other metallohydrolases use zinc While it was speculated that, inter alia, the relatively rigid and stable coordination environment around the Ni(II) ions as opposed to the higher kinetic lability and lower thermodynamic stability of Zn(II) complexes might play a role (31), this fundamental question has not yet been answered. 

The results presented in Fig. 4 show the evolution of the number of adsorbed benzene in the different system as a function of the simulation time. The ReaxFF force field allows the creation and breaking of covalent bonds between the different atoms of the system during the molecular dynamics simulation. In fliis work, we considered that a benzene molecule was adsorbed, if it formed at least one bond with the Ni (100), Ni (111), or Raney-Nickel surface, respectively. In the first 5 ps, the benzene adsorption is comparable for all three systems evaluated, i.e. both clean Ni surfaces and Raney Ni model. After the first 5 ps, about 6-7 % of benzene molecules have been adsorbed. In the very beginning of the simulation time, the adsorption process is even faster on Ni (100) and Ni (111) surface (blue and green line in Fig. 4) compared to the catalyst (purple line). After the first few ps, the adsorption on Ni (100) surface (blue line in Fig. 4) remains rather constant and does not increase much. After 25 ps, only about 12 % of benzene have been adsorbed. In contrast to this finding, the benzene adsorption on the Ni (111) surface and the Raney Ni model system (green and purple line in Fig. 4) increases more... 

Gunes, B., 8c Erkoc, S. (2000). Melting and fragmentation of nickel nanparticles Molecular-dynamics simulations. International Journal of Modern Physics, 11,1567. 

Immobilization of Fl-ATPase asPsy subcomplex on solid surface by polyhistidine interaction with Ni-NTA (Noji et al. 1997) (Reprinted from Materials Science and Engineering A, 423, Yang ZY and Zhao YP, QM/MM and classical molecular dynamics simulation of His-tagged peptide immobilization on nickel surface, 84-91, Copyright (2006), with permission from Elsevier)... 

M. Odelius, C. Ribbing, and J. Kowalewski, Spin dynamics under the Hamiltonian varying with time in discete steps Molecular dynamics-based simulation of electron and nuclear spin relaxation in aqueous nickel(II)., J. Chem. Phys., 104(1996), 3181-3188. 

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