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.

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 Optical Properties and van der Waals-London Dispersion Interactions in Inorganic and Biomolecular Assemblies

2014 ◽  
Vol 1619 ◽  
Author(s):  
Daniel M. Dryden ◽  
Yingfang Ma ◽  
Jacob Schimelman ◽  
Diana Acosta ◽  
Lijia Liu ◽  
...  
Keyword(s):  
Optical Properties ◽  
Spectroscopic Ellipsometry ◽  
Density Functional ◽  
Type I Collagen ◽  
Strong Dependence ◽  
Van Der Waals ◽  
Fundamental Absorption Edge ◽  
Type I ◽  
Dispersion Interactions ◽  
London Dispersion

ABSTRACTThe optical properties and electronic structure of AlPO4, SiO2, Type I collagen, and DNA were examined to gain insight into the van der Waals-London dispersion behavior of these materials. Interband optical properties of AlPO4 and SiO2 were derived from vacuum ultraviolet spectroscopy and spectroscopic ellipsometry, and showed a strong dependence on the crystals’ constituent tetrahedral units, with strong implications for the role of phosphate groups in biological materials. The UV-Vis decadic molar absorption of four DNA oligonucleotides was measured, and showed a strong dependence on composition and stacking sequence. A film of Type I collagen was studied using spectroscopic ellipsometry, and showed a characteristic shoulder in the fundamental absorption edge at 6.05 eV. Ab initio calculations based on density functional theory corroborated the experimental results and provided further insights into the electronic structures, interband transitions and vdW-Ld interaction potentials for these materials.

scholarly journals Including dispersion in density functional theory for adsorption on flat oxide surfaces, in metal–organic frameworks and in acidic zeolites

2020 ◽  
Vol 22 (14) ◽  
pp. 7577-7585 ◽  
Author(s):  
Florian R. Rehak ◽  
GiovanniMaria Piccini ◽  
Maristella Alessio ◽  
Joachim Sauer
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Van Der Waals ◽  
Metal Organic Frameworks ◽  
Many Body ◽  
Functional Theory ◽  
Metal Organic ◽  
The Many ◽  
Acidic Zeolites ◽  
Better Than

Contrary to common believe, for eight adsorption cases, neither D3 or TS are an improvement compared to D2 nor van der Waals functionals or dDsC. Only the many body approaches are slightly better than D2(Ne) which uses Ne parameters for Mg2+ ions.

scholarly journals Including dispersion interactions in the ONETEP program for linear-scaling density functional theory calculations

2008 ◽  
Vol 465 (2103) ◽  
pp. 669-683 ◽  
Author(s):  
Quintin Hill ◽  
Chris-Kriton Skylaris
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Cost ◽  
Density Functional Theory Calculations ◽  
Binding Energies ◽  
Molecular Structures ◽  
Dispersion Interactions ◽  
Biomolecular Systems ◽  
Functional Theory ◽  
High Level

While density functional theory (DFT) allows accurate quantum mechanical simulations from first principles in molecules and solids, commonly used exchange-correlation density functionals provide a very incomplete description of dispersion interactions. One way to include such interactions is to augment the DFT energy expression by damped London energy expressions. Several variants of this have been developed for this task, which we discuss and compare in this paper. We have implemented these schemes in the ONETEP program, which is capable of DFT calculations with computational cost that increases linearly with the number of atoms. We have optimized all the parameters involved in our implementation of the dispersion correction, with the aim of simulating biomolecular systems. Our tests show that in cases where dispersion interactions are important this approach produces binding energies and molecular structures of a quality comparable with high-level wavefunction-based approaches.

scholarly journals Controlled On-Chip Single-Photon Transfer Using Photonic Crystal Coupled-Cavity Waveguides

2011 ◽  
Vol 2011 ◽  
pp. 1-13 ◽  
Author(s):  
Hubert Pascal Seigneur ◽  
Matthew Weed ◽  
Michael Niklaus Leuenberger ◽  
Winston Vaughan Schoenfeld
Keyword(s):  
High Efficiency ◽  
Nearest Neighbor ◽  
Single Photon ◽  
Tight Binding ◽  
Quantum Mechanical ◽  
Single Photons ◽  
Quantum Network ◽  
On Chip ◽  
Quantum Mechanical Approach ◽  
Coupled Cavity

To the end of realizing a quantum network on-chip, single photons must be guided consistently to their proper destination both on demand and without alteration to the information they carry. Coupled cavity waveguides are anticipated to play a significant role in this regard for two important reasons. First, these structures can easily be included within fully quantum-mechanical models using the phenomenological description of the tight-binding Hamiltonian, which is simply written down in the basis of creation and annihilation operators that move photons from one quasimode to another. This allows for a deeper understanding of the underlying physics and the identification and characterization of features that are truly critical to the behavior of the quantum network using only a few parameters. Second, their unique dispersive properties together with the careful engineering of the dynamic coupling between nearest neighbor cavities provide the necessary control for high-efficiency single-photon on-chip transfer. In this publication, we report transfer efficiencies in the upwards of 93% with respect to a fully quantum-mechanical approach and unprecedented 77% in terms of transferring the energy density contained in a classical quasibound mode from one cavity to another.

Sign in / Sign up

Export Citation Format

Share Document