scholarly journals Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding

2018 ◽  
Vol 9 (2) ◽  
pp. 399-405 ◽  
Author(s):  
Majid Mortazavi ◽  
Jan Gerit Brandenburg ◽  
Reinhard J. Maurer ◽  
Alexandre Tkatchenko
Keyword(s):  
Density Functional ◽  
Tight Binding ◽  
Molecular Crystals ◽  
Many Body ◽  
Structure And Stability ◽  
Inclusive Density

scholarly journals Structure and Stability of Molecular Crystals with Many Body Dispersion Inclusive Density Functional Tight Binding

2017 ◽  
Author(s):  
Majid Mortazavi ◽  
Jan Gerit Brandenburg ◽  
Reinhard J. Maurer ◽  
Alexandre Tkatchenko
Keyword(s):  
Structure Prediction ◽  
Density Functional ◽  
Materials Science ◽  
Tight Binding ◽  
Molecular Crystals ◽  
Dispersion Interactions ◽  
Many Body ◽  
Structure And Stability ◽  
Inclusive Density ◽  
Benchmark Database

<pre><p>Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semi-empirical electronic structure methods are computationally more efficient than their <i>ab initio </i>counterparts, allowing structure sampling with significant speed-ups. Here, we combine the Tkatchenko-Scheffler van-der-Waals method (TS) and the many body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) <i>via</i> a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speed-up of up to 3000 times compared to a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction. </p></pre>

scholarly journals Quantum mechanics of proteins in explicit water: The role of plasmon-like solute-solvent interactions

2019 ◽  
Vol 5 (12) ◽  
pp. eaax0024 ◽  
Author(s):  
Martin Stöhr ◽  
Alexandre Tkatchenko
Keyword(s):  
Density Functional ◽  
Van Der Waals ◽  
Tight Binding ◽  
Quantum Mechanical ◽  
Dispersion Interactions ◽  
Many Body ◽  
Biomolecular Systems ◽  
Range Interaction ◽  
Factors Affecting ◽  
Quantum Mechanical Approach

Quantum-mechanical van der Waals dispersion interactions play an essential role in intraprotein and protein-water interactions—the two main factors affecting the structure and dynamics of proteins in water. Typically, these interactions are only treated phenomenologically, via pairwise potential terms in classical force fields. Here, we use an explicit quantum-mechanical approach of density-functional tight-binding combined with the many-body dispersion formalism and demonstrate the relevance of many-body van der Waals forces both to protein energetics and to protein-water interactions. In contrast to commonly used pairwise approaches, many-body effects substantially decrease the relative stability of native states in the absence of water. Upon solvation, the protein-water dispersion interaction counteracts this effect and stabilizes native conformations and transition states. These observations arise from the highly delocalized and collective character of the interactions, suggesting a remarkable persistence of electron correlation through aqueous environments and providing the basis for long-range interaction mechanisms in biomolecular systems.

Simulation of the Diffusion Features of Point Defects in bcc Metals

2006 ◽  
Vol 249 ◽  
pp. 41-46
Author(s):  
Andrey S. Chirkov ◽  
Andrei V. Nazarov
Keyword(s):  
Point Defects ◽  
Density Functional ◽  
Tight Binding ◽  
Interatomic Potentials ◽  
Binding Theory ◽  
Many Body ◽  
Functional Theory ◽  
Bcc Metals ◽  
Diffusion Characteristics ◽  
The Density Functional Theory

This work is devoted to simulation of the diffusion features of point defects in bcc metals. The properties of point defects have been investigated with the usage of many-body interatomic potentials. This approach, based on the density-functional theory, permitted us to derive more adequate diffusion features of solids. This investigation is carried out within the framework of the Finnis-Sinclair formalism, developed for an assembly of N atoms and represents the secondmoment approximation of the tight-binding theory. We used a new model, based on the molecular static method for simulating the atomic structure near the defect and vacancy migration in pure metals. This approach gives the opportunity to simulate the formation and the migration volumes of the point defects, taking into consideration the influence of pressure on structure and consequently on energy. The diffusion characteristics of bcc α-Fe and anomalous β-Zr have been investigated.

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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