Dihedral Distortions Research Articles

Simulation of Titanium Metal/Titanium Dioxide Etching with Chlorine and Hydrogen Chloride Gases Using the ReaxFF Reactive Force Field

In this study, a new ReaxFF reactive force field has been developed to describe reactions in Ti/O/Cl/H materials. This force field was applied to etching simulations for titanium metal and titanium dioxide with chlorine and hydrogen chloride gases. The ReaxFF force field parameters are fitted against a quantum mechanical (QM) training set containing structures and energies related to bond dissociations, angle and dihedral distortions, and reactions between titanium and chlorine gases as well as heats of formation of TiClx crystals. These newly developed Ti-Cl force field parameters were combined with a recently developed Ti-O-H force field. ReaxFF accurately reproduces the QM training set for structures and energetics of small clusters and TiClx crystals. In the etching simulations, titanium and titanium dioxide slab models with chlorine and hydrogen chloride gases were used in molecular dynamics simulations. The etching ratio between HCl and Cl2 are compared to experimental results, and satisfactory results are obtained, indicating that this ReaxFF extension provides a useful tool for studying the atomistic-scale details of the etching process.

Development of a ReaxFF Reactive Force Field for Titanium Dioxide/Water Systems

A new ReaxFF reactive force field has been developed to describe reactions in the Ti-O-H system. The ReaxFF force field parameters have been fitted to a quantum mechanical (QM) training set containing structures and energies related to bond dissociation energies, angle and dihedral distortions, and reactions between water and titanium dioxide, as well as experimental crystal structures, heats of formation, and bulk modulus data. Model configurations for the training set were based on DFT calculations on molecular clusters and periodic systems (both bulk crystals and surfaces). ReaxFF reproduces accurately the QM training set for structures and energetics of small clusters. ReaxFF also describes the relative energetics for rutile, brookite, and anatase. The results of ReaxFF match reasonably well with those of QM for water binding energies, surface energies, and H2O dissociation energy barriers. To validate this ReaxFF description, we have compared its performance against DFT/MD simulations for 1 and 3 monolayers of water interacting with a rutile (110) surface. We found agreement within a 10% error between the DFT/MD and ReaxFF water dissociation levels for both coverages.

Development and Application of a ReaxFF Reactive Force Field for Oxidative Dehydrogenation on Vanadium Oxide Catalysts

We have developed a new ReaxFF reactive force field to describe accurately reactions of hydrocarbons with vanadium oxide catalysts. The ReaxFF force field parameters have been fit to a large quantum mechanics (QM) training set containing over 700 structures and energetics related to bond dissociations, angle and dihedral distortions, and reactions between hydrocarbons and vanadium oxide clusters. In addition, the training set contains charge distributions for small vanadium oxide clusters and the stabilities of condensed-phase systems. We find that ReaxFF reproduces accurately the QM training set for structures and energetics of small clusters. Most important is that ReaxFF describes accurately the energetics for various oxidation states of the condensed phases, including V2O5, VO2, and V2O3 in addition to metallic V (V0). To demonstrate the capability of the ReaxFF force field for describing catalytic processes involving vanadium oxides, we performed molecular dynamics (MD) simulation for reactions of a gas of methanol exposed to the (001) surface of V2O5. We find that formaldehyde is the major product, in agreement with experiment. These studies find that water desorption from surface VIII sites is facilitated by interlayer bonding.

Theoretical calculations of hypersurfaces of the 13C chemical shift anisotropy in the C [dbnd]O⋯H [sbnd]N hydrogen bond and the benefit for the ab initio structure determination

We investigated the influence of structural changes on the anisotropic part of the carbonyl 13C chemical shift tensor in a model complex containing hydrogen bonded cyanuric acid and pyrrole. The model was chosen for its chemical resemblance to cyameluric acid. In the solid state this compound comprises three different hydrogen bonds which are well distinguishable based on the anisotropy parameters δ aniso and η of the carbonyl 13C atoms. The variation of six relevant structural variables in the model system produced hypersurfaces for the isotropic shift, δ aniso and η. Our goal was to investigate whether such surfaces can be used for the ab initio structure determination of hydrogen bonds. With a medium size basis set it could be shown that although the absolute values differ DFT describes the relative change in δ aniso and η close to the quality of MP2 calculations. Due to the high dimensionality of the hypersurface we had to reduce the number of variables in our study. We systematically created subsurfaces each described by three of the six variables and investigated their isolated influence on the NMR observables. We identified the most important structure parameters and on this base built a minimal model. For a fixed NO distance the hydrogen bond arrangement was altered by two angular variations and one dihedral distortion. In this model evidence was found that the η surfaces for different NO distances exhibit a uniform shape and can be transformed into one another by a simple shift and multiplication by a mean factor. Furthermore, the experimental parameters δ aniso and η of cyameluric acid were taken as a base for the extraction of structures from the hypersurfaces. δ aniso and η unequivocally selected ensembles of similar structure and the COHN arrangement in two of the three cyameluric hydrogen bonds could be predicted with good quality from the theoretical model. Our results show that it is possible to predict the distance and at least qualitatively the orientation in a hydrogen bond environment from an analysis of the anisotropic part of the 13C chemical shift tensor.

Free Energy and Structural Pathways of Base Flipping in a DNA GCGC Containing Sequence

Structural distortions of DNA are essential for its biological function due to the genetic information of DNA not being physically accessible in the duplex state. Base flipping is one of the simplest structural distortions of DNA and may represent an initial event in strand separation required to access the genetic code. Flipping is also utilized by DNA-modifying and repair enzymes to access specific bases. It is typically thought that base flipping (or base-pair opening) occurs via the major groove whereas minor groove flipping is only possible when mediated by DNA-binding proteins. Here, umbrella sampling with a novel center-of-mass pseudodihedral reaction coordinate was used to calculate the individual potentials of mean force (PMF) for flipping of the Watson–Crick (WC) paired C and G bases in the CCATGC G CTGAC DNA dodecamer. The novel reaction coordinate allowed explicit investigation of the complete flipping process via both the minor and major groove pathways. The minor and major groove barriers to flipping are similar for C base flipping while the major groove barrier is slightly lower for G base flipping. Minor groove flipping requires distortion of the WC partner while the flipping base pulls away from its partner during major groove flipping. The flipped states are represented by relatively flat free energy surfaces, with a small, local minimum observed for the flipped G base. Conserved patterns of phosphodiester backbone dihedral distortions during flipping indicate their essential role in the flipping process. During flipping, the target base tracks along the respective grooves, leading to hydrogen-bonding interactions with neighboring base-pairs. Such hydrogen-bonding interactions with the neighboring sequence suggest a novel mechanism of sequence dependence in DNA dynamics.

Electronic Structure of Platinum in Silicon

The negatively charged state of substitutional platinum in silicon is observable by electron paramagnetic resonance (EPR). The g-tensor of the EPR spectrum (labelled Si-Pt[I]) reveals orthorhombic-I symmetry of the centre. The principal g-values, which are g[110] = 1.3867, g[11̄0] = 1.4266 and g[001] = 2.0789, respectively, deviate significantly from the pure spin value g = 2.0023, indicating substantial contributions from orbital momentum. The g-tensor data were analysed on a model of one electron, with spin S = 1/2, in an orbital triplet state, L = 1. Spin-orbit coupling and crystal field interactions of cubic, tetragonal or orthorhombic symmetry were included in the model. The theoretical analysis can account in a satisfactory manner for the experimentally observed values. The electronic structure of Pt- is concluded to be the 5d96s6p configuration. This is consistent with predominant bonding of platinum with two silicon neighbours and dihedral distortion. The results are incompatible with alternative models, such as the vacancy model or a 5d-version of the Ludwig-Woodbury model. The orbital g-factor is reduced by about 30% by covalency.

Crystal field theory and EPR parameters in D2 d and C2 v distorted tetrahedral copper(II) complexes

Calculations of the orbital energy vs tetrahedral ( D 2 d and C 2 v ) distortion parameters are reported for copper complexes on the assumption of constant metal-ligand distance. The possible ground states of the complexes are considered and the respective spin Hamiltonian parameters vs distortion parameters dependences are calculated. Comparison with experiment led to good agreement: the relation between the orbital splittings and dihedral distortion angle is found to be linear for symmetry C 2 v in a wide range of distortion of the regular tetrahedron, and distortion of the D 2 d crystal field has a compensatory effect lowering the hfs splitting from 4 p-orbital admixture into the ground-state wavefunction.