Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics
نویسندگان
چکیده
sorption results9 revealed that the iron surface was mostly covered by promoter oxides of AI, Ca, and K. Postreaction XPS results also revealed a C( Is) XPS peak of weak to moderate intensity centered at 284.1-283.7 eV. This binding energy approaches those (ca. 283.5 eV) reported for iron cat bide^.^^*'^ More convincing evidence for carbide formation was obtained from TPHT results collected after reaction studies like those displayed in Figure 1 in which methane was the only product. After reaction at temperatures below 340 OC, only small amounts of reactive carbon could be distinguished with maximum methane desorption rates near 300 OC. However, for higher reaction temperatures, large amounts of methane were produced with a maximum rate just above 400 OC. Since XPS results revealed only small amounts of carbonaceous residue on top of the catalyst surface, this reactive carbon must be associated with carbiding of the catalyst. Consequently, it appears that the active carbon incorporation catalyst is carbided iron. This conclusion is well supported by bulk carbon to iron stoichiometries of 0.1-0.25 estimated from the TPHT peak areas which were adequate to represent 40-60'36 conversion to bulk carbides such as Fe,C or FeSC2. Moreover, preliminary results from studies using bona fide iron carbides have shown similar catalytic b e h a ~ i o r . ~
منابع مشابه
Introducing critical residues in the human prion protein and its Asp 178 Asn mutant by molecular dynamics simulation
The molecular dynamics (MD) simulation method is used to assess structural details for humanprion protein (hereafter PrPN) and its Asp178 Asn mutant (hereafter PrPm) which causes fatalfamilial insomnia disease. The results reveal that the flexibility and instability increase in PrPmcould be related to specific amino acids exposed to the solvent. Solvation free energy of PrPm is 20kjmot1nni2 mor...
متن کاملDynamics of Macro–Nano Mechanical Systems; Fixed Interfacial Multiscale Method
The continuum based approaches don’t provide the correct physics in atomic scales. On the other hand, the molecular based approaches are limited by the length and simulated process time. As an attractive alternative, this paper proposes the Fixed Interfacial Multiscale Method (FIMM) for computationally and mathematically efficient modeling of solid structures. The approach is applicable to mult...
متن کاملA comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations
We study how the results of molecular dynamics (MD) simulations are affected by various choices during the setup, e.g., the starting velocities, the solvation, the location of protons, the conformation of His, Asn, and Gln residues, the protonation and titration of His residues, and the treatment of alternative conformations. We estimate the binding affinity of ligands to four proteins calculat...
متن کاملMolecular Docking Based on Virtual Screening, Molecular Dynamics and Atoms in Molecules Studies to Identify the Potential Human Epidermal Receptor 2 Intracellular Domain Inhibitors
Human epidermal growth factor receptor 2 (HER2) is a member of the epidermal growth factor receptor family having tyrosine kinase activity. Overexpression of HER2 usually causes malignant transformation of cells and is responsible for the breast cancer. In this work, the virtual screening, molecular docking, quantum mechanics and molecular dynamics methods were employed to study protein–ligand ...
متن کاملSolvation Force in Hard Ellipsoid Molecular Liquids with Rod-Sphere and Rod- Surface Interactions
In previous work, one of us calculated the Solvation force of hard ellipsoid fluid with hard Gaussian overlap potential using hard needle wall interaction and non-linear equation proposed by Grimson- Rickyazen. In present work, using density functional theory and extended restricted orientation model, the solvation force of hard ellipsoid fluid in presence of more realistic rod- sphere and rod-...
متن کاملApplication of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems.
The difference-based adaptive solvation quantum mechanics/molecular mechanics (adQM/MM) method (J. Chem. Theory Comput.2009, 5, 2212) as implemented in the Amber software was applied to the study of several chemical processes in solution. The adQM/MM method is based on an efficient selection scheme that enables quantum-mechanical treatment of the active region of a molecular system in solution ...
متن کامل