Theory and Modelling for the Nanoscale: The $$spds$$ * Tight Binding Approach

2012 ◽  
pp. 19-39 ◽  
Author(s):  
R Benchamekh ◽  
M Nestoklon ◽  
J.-M Jancu ◽  
P Voisin
Keyword(s):  
Tight Binding

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>

Communication: Photoinduced Carbon Dioxide Binding with Surface-Functionalized Silicon Quantum Dots

2018 ◽  
Author(s):  
Oscar A. Douglas-Gallardo ◽  
Cristián Gabriel Sánchez ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Quantum Dots ◽  
Atmospheric Carbon Dioxide ◽  
Density Functional ◽  
Tight Binding ◽  
Carbon Dioxide Concentration ◽  
Research Area ◽  
Silicon Quantum Dots ◽  
Dependent Model ◽  
Photoinduced Charge

<div> <div> <div> <p>Nowadays, the search of efficient methods able to reduce the high atmospheric carbon dioxide concentration has turned into a very dynamic research area. Several environmental problems have been closely associated with the high atmospheric level of this greenhouse gas. Here, a novel system based on the use of surface-functionalized silicon quantum dots (sf -SiQDs) is theoretically proposed as a versatile device to bind carbon dioxide. Within this approach, carbon dioxide trapping is modulated by a photoinduced charge redistribution between the capping molecule and the silicon quantum dots (SiQDs). Chemical and electronic properties of the proposed SiQDs have been studied with Density Functional Theory (DFT) and Density Functional Tight-Binding (DFTB) approach along with a Time-Dependent model based on the DFTB (TD-DFTB) framework. To the best of our knowledge, this is the first report that proposes and explores the potential application of a versatile and friendly device based on the use of sf -SiQDs for photochemically activated carbon dioxide fixation. </p> </div> </div> </div>

Trace-map invariant and zero-energy states of the tight-binding Rudin-Shapiro model

1992 ◽  
Vol 46 (6) ◽  
pp. 3296-3304 ◽  
Author(s):  
Mihnea Dulea ◽  
Magnus Johansson ◽  
Rolf Riklund
Keyword(s):  
Tight Binding ◽  
Zero Energy ◽  
Trace Map ◽  
Energy States

scholarly journals Cobalt-based magnetic Weyl semimetals with high-thermodynamic stabilities

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Wei Luo ◽  
Yuma Nakamura ◽  
Jinseon Park ◽  
Mina Yoon
Keyword(s):  
Tight Binding ◽  
Three Dimensional ◽  
Interlayer Coupling ◽  
First Principles Calculation ◽  
Optimization Approach ◽  
Binding Model ◽  
Nodal Lines ◽  
Weyl Semimetal ◽  
Topological Quantum ◽  
First Time

AbstractRecent experiments identified Co3Sn2S2 as the first magnetic Weyl semimetal (MWSM). Using first-principles calculation with a global optimization approach, we explore the structural stabilities and topological electronic properties of cobalt (Co)-based shandite and alloys, Co3MM’X2 (M/M’ = Ge, Sn, Pb, X = S, Se, Te), and identify stable structures with different Weyl phases. Using a tight-binding model, for the first time, we reveal that the physical origin of the nodal lines of a Co-based shandite structure is the interlayer coupling between Co atoms in different Kagome layers, while the number of Weyl points and their types are mainly governed by the interaction between Co and the metal atoms, Sn, Ge, and Pb. The Co3SnPbS2 alloy exhibits two distinguished topological phases, depending on the relative positions of the Sn and Pb atoms: a three-dimensional quantum anomalous Hall metal, and a MWSM phase with anomalous Hall conductivity (~1290 Ω−1 cm−1) that is larger than that of Co2Sn2S2. Our work reveals the physical mechanism of the origination of Weyl fermions in Co-based shandite structures and proposes topological quantum states with high thermal stability.

scholarly journals Herb-target virtual screening and network pharmacology for prediction of molecular mechanism of Danggui Beimu Kushen Wan for prostate cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hong Li ◽  
Andrew Hung ◽  
Angela Wei Hong Yang
Keyword(s):  
Prostate Cancer ◽  
Binding Affinity ◽  
Molecular Mechanisms ◽  
Biological Activities ◽  
Tight Binding ◽  
Experimental Studies ◽  
Network Pharmacology ◽  
High Morbidity ◽  
High Binding ◽  
High Binding Affinity

AbstractProstate cancer (PCa) is a cancer that occurs in the prostate with high morbidity and mortality. Danggui Beimu Kushen Wan (DBKW) is a classic formula for patients with difficult urination including PCa. This study aimed to investigate the molecular mechanisms of DBKW for PCa. We obtained DBKW compounds from our previous reviews. We identified potential targets for PCa from literature search, currently approved drugs and Open Targets database and filtered them by protein–protein interaction network analysis. We selected 26 targets to predict three cancer-related pathways. A total of 621 compounds were screened via molecular docking using PyRx and AutoDock Vina against 21 targets for PCa, producing 13041 docking results. The binding patterns and positions showed that a relatively small number of tight-binding compounds from DBKW were predicted to interact strongly and selectively with three targets. The top five high-binding-affinity compounds were selected to generate a network, indicating that compounds from all three herbs had high binding affinity against the 21 targets and may have potential biological activities with the targets. DBKW contains multi-targeting agents that could act on more than one pathway of PCa simultaneously. Further studies could focus on validating the computational results via experimental studies.

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