Dynamic Simulation of the Migration of Oxygen Vacancy Defects in Rutile TiO2

2012 ◽  
Vol 1430 ◽  
Author(s):  
Jan M. Knaup ◽  
Michael Wehlau ◽  
Thomas Frauenheim
Keyword(s):  
Oxygen Vacancy ◽  
Dynamic Simulation ◽  
Electric Fields ◽  
Density Functional ◽  
Diffusion Processes ◽  
Tight Binding ◽  
Dynamic Simulations ◽  
Vacancy Defects ◽  
Barrier Heights ◽  
Large Dielectric Constant

ABSTRACTWe simulate the thermodynamics and kinetics of the drift/diffusion of oxygen vacancy defects in rutile TiO2, using the density-functional based tight-binding (DFTB) method. Both static and dynamic simulations have been performed. Results indicate that DFTB is well suited to examine the dynamic behavior of oxygen vacancies in TiO2. Detailed analysis shows, that strong model size dependence in relative diffusion barrier heights between different diffusion processes requires great care in defect diffusion simulations in TiO2. Thermodynamic results on the influence of an external electric field show that, due to the large dielectric constant, the coulomb driving force on oxygen vacancy diffusion is very small. Dynamic simulation of the influence of electric fields on the diffusion requires the use of advanced molecular dynamics acceleration schemes.

Oxygen vacancy defects in tantalum pentoxide: a density functional study

2003 ◽  
Vol 69 (2-4) ◽  
pp. 190-194 ◽  
Author(s):  
R. Ramprasad ◽  
Michael Sadd ◽  
Doug Roberts ◽  
Tom Remmel ◽  
Mark Raymond ◽  
...  
Keyword(s):  
Oxygen Vacancy ◽  
Density Functional ◽  
Tantalum Pentoxide ◽  
Functional Study ◽  
Density Functional Study ◽  
Vacancy Defects

scholarly journals Applying joint theoretical experimental research to aptamer modeling

2021 ◽  
pp. 105-106
Author(s):  
I.A. Shchugoreva ◽  
◽  
P.V. Artyushenko ◽  
F.N. Tomilin ◽  
D.I. Morozov ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemical ◽  
Density Functional ◽  
3D Structure ◽  
Tight Binding ◽  
Molecular Simulations ◽  
Molecular Structures ◽  
Dna Aptamer ◽  
Dynamic Simulations ◽  
Theoretical Methods

The aim of the research. In this work we studied the structure of LC-18 DNA aptamer, which exhibits specifi c binding to lung adenocarcinoma cells. Obtaining the 3D structure of the aptamer is necessary for understanding the mechanism of binding of the aptamer to the target. Th erefore, the aim of the research was modeling of the LC-18 aptamer spatial structure using combination of theoretical methods: DNA folding tools, quantum-chemical calculations and molecular dynamic simulations. Material and methods. Th e secondary structure of the LC-18 aptamer was predicted by using OligoAnalyzer and MFold online soft ware under the conditions typical small-angle X-ray scattering (SAXS) experiment. Th e molecular modeling of the aptamer was carried out using the Avogadro program. For prediction of the structure two computational methods were used: quantum-mechanical method with third-order density-functional tight-binding (DFTB3) and molecular dynamics (MD) with force fi elds. Results. In this paper it was shown that molecular simulations can predict structures from the SAXS experiments. OligoAnalyzer and MFold web servers have been used to generate a set of several likely models. However, more accurate calculations have showed that these models do not predict the relative importance of isomers. Meanwhile, application of quantum-chemical and molecular dynamics calculations have showed reliable molecular structures which have a small deviations from the experimental SAXS curves. Conclusion. Th is study demonstrates the approach for modeling 3D structures of DNA-aptamers in solution using both experimental and theoretical methods. It could be very helpful in designing more effi cient aptamers based on results obtained from molecular simulations.

scholarly journals Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules

2017 ◽  
Vol 38 (25) ◽  
pp. 2171-2185 ◽  
Author(s):  
Maja Gruden ◽  
Ljubica Andjeklović ◽  
Akkarapattiakal Kuriappan Jissy ◽  
Stepan Stepanović ◽  
Matija Zlatar ◽  
...  
Keyword(s):  
Density Functional ◽  
Organic Molecules ◽  
Tight Binding ◽  
Barrier Heights ◽  
Binding Models

Effect of Graphene/TiO2 (001) Interface on Threshold Voltage and Nonlinearity

NANO ◽  
2018 ◽  
Vol 13 (06) ◽  
pp. 1830004 ◽  
Author(s):  
Yuehua Dai ◽  
Shanshan Gong ◽  
Zhisheng Zhong ◽  
Fengyu Gao ◽  
Feifei Wang ◽  
...  
Keyword(s):  
Electric Field ◽  
Electric Fields ◽  
Threshold Voltage ◽  
Density Functional ◽  
Tight Binding ◽  
Resistive Transition ◽  
Design And Optimization ◽  
Interface Barrier ◽  
Iv Curves ◽  
Energy Package

In this work, the threshold voltage ([Formula: see text]) and nonlinearity (NL) of Graphene (Gra)/TiO2/Gra heterojunction were studied. First, the density functional tight binding (DFTB[Formula: see text]) and much more dynamics were used to investigate the IV curves and the resistive switching properties of TiO2 slab and Gra/TiO2/Gra heterojunction. The NL of Gra/TiO2/Gra heterojunction is stronger than that of the TiO2 slab. The [Formula: see text] of the resistive transition of the heterojunction is larger than that of the TiO2 slab. The tunneling probabilities and the Mulliken atomic population at the Gra/TiO2 interface under different electric fields were calculated by the Cambridge sequential total energy package (CASTEP). Results showed that both the parameters evidently increased under a certain numerical electric field. Finally, the movement of atom in the electric field and the change in the chemical bond were simulated by DFTB[Formula: see text] module. The effect of the Gra/TiO2 interface on [Formula: see text] and NL was further illustrated. Postponed [Formula: see text] and improved NL were found at the heterojunction relative to the TiO2 slab due to the presence of the interface barrier. This work provides guidance and reference for design and optimization of TiO2-based selectors.

Vapour Pressure Isotope Effect on Evaporation from Pure Organic Phases - a PIMD Approach

2020 ◽  
Author(s):  
Luis Vasquez ◽  
Agnieszka Dybala-Defratyka
Keyword(s):  
Path Integral ◽  
Vapour Pressure ◽  
Density Functional ◽  
Isotope Effects ◽  
Tight Binding ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Special Importance ◽  
Non Covalent Interactions ◽  
Covalent Interactions

<p></p><p>Very often in order to understand physical and chemical processes taking place among several phases fractionation of naturally abundant isotopes is monitored. Its measurement can be accompanied by theoretical determination to provide a more insightful interpretation of observed phenomena. Predictions are challenging due to the complexity of the effects involved in fractionation such as solvent effects and non-covalent interactions governing the behavior of the system which results in the necessity of using large models of those systems. This is sometimes a bottleneck and limits the theoretical description to only a few methods.<br> In this work vapour pressure isotope effects on evaporation from various organic solvents (ethanol, bromobenzene, dibromomethane, and trichloromethane) in the pure phase are estimated by combining force field or self-consistent charge density-functional tight-binding (SCC-DFTB) atomistic simulations with path integral principle. Furthermore, the recently developed Suzuki-Chin path integral is tested. In general, isotope effects are predicted qualitatively for most of the cases, however, the distinction between position-specific isotope effects observed for ethanol was only reproduced by SCC-DFTB, which indicates the importance of using non-harmonic bond approximations.<br> Energy decomposition analysis performed using the symmetry-adapted perturbation theory (SAPT) revealed sometimes quite substantial differences in interaction energy depending on whether the studied system was treated classically or quantum mechanically. Those observed differences might be the source of different magnitudes of isotope effects predicted using these two different levels of theory which is of special importance for the systems governed by non-covalent interactions.</p><br><p></p>

Quasi-Barrierless Submolecular Motion in Mechanically Interlocked Carbon Nanotubes

2020 ◽  
Author(s):  
Julia Villalva ◽  
Belén Nieto-Ortega ◽  
Manuel Melle-Franco ◽  
Emilio Pérez
Keyword(s):  
Density Functional ◽  
Close Contact ◽  
Tight Binding ◽  
Energetic Cost ◽  
Molecular Fragments ◽  
Activation Barriers ◽  
Flat Surfaces ◽  
Different Types ◽  
Atomically Flat ◽  
Derivatives Of

The motion of molecular fragments in close contact with atomically flat surfaces is still not fully understood. Does a more favourable interaction imply a larger barrier towards motion even if there are no obvious minima? Here, we use mechanically interlocked rotaxane-type derivatives of SWNTs (MINTs) featuring four different types of macrocycles with significantly different affinities for the SWNT thread as models to study this problem. Using molecular dynamics, we find that there is no direct correlation between the interaction energy of the macrocycle with the SWNT and its ability to move along or around it. Density functional tight-binding calculations reveal small (<2.5 Kcal·mol-1) activation barriers, the height of which correlates with the commensurability of the aromatic moieties in the macrocycle with the SWNT. Our results show that macrocycles in MINTs rotate and translate freely around and along SWNTs at room temperature, with an energetic cost lower than the rotation around the C−C bond in ethane.<br>

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