Study of reduction processes over cerium oxide surfaces with atomic hydrogen using ultra accelerated quantum chemical molecular dynamics

Ceria plays an important role in catalysis, due to its ability to store and release oxygen depending on the condition present in the catalyst environment. To analyze the role of ceria in catalytic reactions, it is necessary to know the details of the interaction of ceria surface with environmentally sensitive molecules. This study was conducted using ultra accelerated quantum chemical molecular dynamics. Its purpose was to investigate the reduction process of the (1 1 1) and (1 1 0) surfaces of ceria with atomic hydrogen as well as water desorption mechanisms from the surfaces. This simulation demonstrated that when a high-energy colliding hydrogen atoms are adsorbed on the ceria, it pulls up an O atom from the ceria surfaces and results in the formation of a H₂O molecule. This is the first dynamics simulation related to such reduction processes based on quantum chemistry.     

Chemical reaction dynamics of PeCB and TCDD decomposition: A tight‐binding quantum chemical molecular dynamics study with first‐principles parameterization

The decomposition reaction dynamics of 2,3,4,4′,5‐penta‐chlorinated biphenyl (2,3,4,4′,5‐PeCB), 3,3′,4,4′,5‐penta‐chlorinated biphenyl (3,3′,4,4′,5‐PeCB), and 2,3,7,8‐tetra‐chlorinated dibenzo‐p‐dioxin (2,3,7,8‐TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first‐principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first‐principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4′,5‐PeCB, 3,3′,4,4′,5‐PeCB, and 2,3,7,8‐TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Superionic Conduction in Co‐Vacant P2‐NaxCoO2 Created by Hydrogen Reductive Elimination

The layered P2‐Na_xMO₂ (M: transition metal) system has been widely recognized as electronic or mixed conductor. Here, we demonstrate that Co vacancies in P2‐Na_xCoO₂ created by hydrogen reductive elimination lead to an ionic conductivity of 0.045 S cm^?1 at 25 °C. Using in situ synchrotron X‐ray powder diffraction and Raman spectroscopy, the composition of the superionic conduction phase is evaluated to be Na_0.61(H₃O)_0.18Co_0.93O₂. Electromotive force measurements as well as molecular dynamics simulations indicate that the ion conducting species is proton rather than hydroxide ion. The fact that the Co‐stoichiometric compound Na_x(H₃O)_yCoO₂ does not exhibit any significant ionic conductivity proves that Co vacancies are essential for the occurrence of superionic conductivity.     

Investigation of the dissociative adsorption for cyclopropane on the copper surface by density functional theory and quantum chemical molecular dynamics method

The dissociative adsorption of cyclopropane on the copper surface was studied using quantum chemical molecular dynamics method with “Colors-Excite” code and density functional theory by Amsterdam Density Functional program (ADF2000). The excited state of cyclopropane was used as adsorbate to simulate the dissociated adsorption under an irradiation energy of ca. 10 eV. One of the C-C bonds in cyclopropane was broken and the two new bonds between cyclopropane and copper surface were formed. The electrons transferred from the copper atoms to cyclopropane with a value of about 0.2e. The shorter distances between the carbons and surface copper atoms showed the existence of strong interaction. Consistently, the results indicated metallacyclopentane was the most possible intermediate species in dissociative adsorption by ADF2000 and “Colors-Excite” method.     

Communication: The reason why +c ZnO surface is less stable than -c ZnO surface: first-principles calculation

It has been experimentally shown that an O(-c)-polar ZnO surface is more stable than a Zn(+c)-polar surface in H(2) ambient. We applied first-principles calculations to investigating the polarity dependence on the stability at the electronic level. The calculations revealed that the -c surface terminated with H atom was stable maintaining a wurtzite structure, whereas the +c surface was unstable due to the change of coordination numbers of Zn at the topmost surface from four (wurtzite) to six (rock salt). This causes the generation of O(2) molecules, resulting in instability at the +c surface.     

Tribochemical reaction dynamics of phosphoric ester lubricant additive by using a hybrid tight-binding quantum chemical molecular dynamics method

To study the atomistic behavior of the phosphoric ester molecule on the nascent Fe surface under boundary lubrication conditions, we adopted a hybrid tight-binding quantum chemical molecular dynamics method. First, we investigated chemical interactions between phosphoric ester and the nascent Fe surface. Phosphoric ester was shown to interact with the nascent Fe surface, forming both covalent and ionic bonds. Formation and dissociation dynamics of covalent bonds during tribochemical reaction was clearly observed during the simulation. The effect of friction condition on the tribochemical reaction dynamics was then studied, and it was indicated that friction would influence the formation and the dissociation of covalent bonds. By using a hybrid tight-binding quantum chemical molecular dynamics method, we obtained insights on initial tribochemical reaction processes for the formation of tribofilm from the phosphoric ester molecule on the nascent Fe surface.     

Enhanced gas-sensing behaviour of Ru-doped SnO2 surface: A periodic density functional approach

A theoretical study on Ru-doped rutile SnO₂(1 1 0) surface has been carried out by means of periodic density functional theory (DFT) at generalized gradient approximation (GGA-RPBE) level with a periodic supercell approach. Electronic structure analysis was performed based on the band structure and partial density of states. The results provide evidence that the electronic structures of SnO₂(1 1 0) surface are modified by the surface Ru dopant, in which Ru 4d orbital are located at the edge of the band gap region. It is demonstrated that molecular oxygen adsorption characteristics on stoichiometric SnO₂(1 1 0) surface are changed from endothermic to exothermic due to the existence of surface Ru dopant. The dissociative adsorption of molecular oxygen on the Ru_5c/SnO₂(1 1 0) surface is exothermic, which indicates that Ru could act as an active site to increase the oxygen atom species on SnO₂(1 1 0) surface. Our present study reveals that the Ru dopant on surface is playing both electronic and chemical role in promoting the SnO₂ gas-sensing property.     

Influence of nanometer scale film structure of ZDDP tribofilm on Its mechanical properties: A computational chemistry study

We investigated the influence of a nanometer scale film structure of a tribofilm generated from zinc dialkyldithiophosphate (ZDDP) anti-wear additive on its mechanical properties using a combined molecular dynamics (MD) and finite element (FE) method. The frictional behavior of an interface between a native iron oxide layer on steel surface and zinc metaphosphate - regarded as a model material of ZDDP tribofilm - was firstly studied using the MD method. The results showed that the iron atoms in the oxide layer diffused into the phosphate layer during the friction process. The zinc atoms in the phosphate layer also diffused into the oxide layer. Significant interdiffusion of iron and zinc atoms was observed with increasing simulation time. Thus, metallic phosphate with a gradient composition of iron and zinc atoms was formed on the phosphate/oxide interface. We then constructed an axisymmetric nanoindentation simulation model from the MD-derived structures at a certain simulation time and carried out a FE calculation. As a result, we found that the rubbed ZDDP tribofilm, including the phosphate with the gradient composition of metallic atoms, showed larger contact stiffness and hardness. The combined MD/FE simulation indicates that the tribofilm becomes stiffer and harder due to the interdiffusion of iron and zinc atoms on the tribofilm/oxide interface. We have found that the gradient composition formation in ZDDP tribofilm during friction process influences on its mechanical properties.     

A graph theoretical approach to the effect of mutation on the flexibility of the DNA binding domain of p53 protein

Tumor suppressor protein p53 becomes inactive due to mutation on its DNA binding core domain leading to misbehavior of this protein and preventing its interaction with DNA. In the present study, changes of the protein conformation by five hot spot mutations of T-p53C were assessed preventing the mutants wild-type (WT) behavior. While studies of this nature were undertaken both experimentally and theoretically, the focus is fundamentally on the effects of the mutation on the dynamics of the protein. Hence, the basic concept underlying this study is the change in flexibility or rigidity of the protein. It was found that stable variant T-p53C (PDB-ID: 1uol) that is structurally and functionally very close to wild-type p53 is the most rigid structure and each single carcinogenic mutation on it makes the structure more flexible. We hypothesize that these changes of the molecule’s flexibility disrupt the network of hydrogen bonds associated with the interaction of WT not only at interaction but in the internal structures of the mutants as well, which prevents them from interacting in the WT fashion loosing the anti-cancer properties of WT.