Search results for "DENSITY FUNCTIONAL THEORY"

Combined spectroscopic and theoretical analysis of the binding of a water-soluble perylene diimide to DNA/RNA polynucleotides and G-quadruplexes.

2021

We present here a combined spectroscopic and theoretical analysis of the binding of N,N’-bis(2-(1-piperazino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide dichloride (PZPERY) to different biosubstrates. Absorbance titrations and circular dichroism experiments, melting studies and isothermal calorimetry (ITC) titrations reveal a picture where the binding to natural double-stranded DNA is very different from that to double and triple-stranded RNAs (poly(A)∙poly(U) and poly(U)∙poly(A)⁎poly(U)). As confirmed also by the structural and energetic details clarified by density functional theory (DFT) calculations, intercalation occurs for DNA, with a process driven by the combination of aggr…

New Austalides from the Sponge-Associated Fungus Aspergillus sp.

2011

Chromatographic separation of a crude extract obtained from the fungus Aspergillus sp., isolated from the Mediterranean sponge Tethya aurantium, yielded five new meroterpenoid metabolites, austalides M–Q (1–5), together with nine known compounds (6–13). The structures of the new compounds were unambiguously elucidated on the basis of extensive 1D and 2D NMR methods and by mass spectral analysis. Furthermore, the absolute configurations of 1 and 4 were determined by time-dependent density functional theory electronic circular dichroism (TDDFT ECD) calculations, allowing the assignment of the absolute configuration of analogous compounds 2, 3, and 5. The calculations revealed that the conform…

Duality theory for multi-marginal optimal transport with repulsive costs in metric spaces

2018

In this paper we extend the duality theory of the multi-marginal optimal transport problem for cost functions depending on a decreasing function of the distance (not necessarily bounded). This class of cost functions appears in the context of SCE Density Functional Theory introduced in "Strong-interaction limit of density-functional theory" by M. Seidl.

Disorder and interactions in systems out of equilibrium : the exact independent-particle picture from density functional theory

2017

Density functional theory (DFT) exploits an independent-particle-system construction to replicate the densities and current of an interacting system. This construction is used here to access the exact effective potential and bias of non-equilibrium systems with disorder and interactions. Our results show that interactions smoothen the effective disorder landscape, but do not necessarily increase the current, due to the competition of disorder screening and effective bias. This puts forward DFT as a diagnostic tool to understand disorder screening in a wide class of interacting disordered systems.

Toward an Understanding of Molecular Mechanism of Domino Cycloadditions. Density Functional Theory Study of the Reaction between Hexafluorobut-2-yne …

1998

Modeling ?-lactam interactions in aqueous solution through combined quantum mechanics-molecular mechanics methods

1999

Adiabatic versus non-adiabatic electron transfer at 2D electrode materials

2021

2D electrode materials are often deployed on conductive supports for electrochemistry and there is a great need to understand fundamental electrochemical processes in this electrode configuration. Here, an integrated experimental-theoretical approach is used to resolve the key electronic interactions in outer-sphere electron transfer (OS-ET), a cornerstone elementary electrochemical reaction, at graphene as-grown on a copper electrode. Using scanning electrochemical cell microscopy, and co-located structural microscopy, the classical hexaamineruthenium (III/II) couple shows the ET kinetics trend: monolayer > bilayer > multilayer graphene. This trend is rationalized quantitatively through th…

Density-functional tight-binding for beginners

2009

This article is a pedagogical introduction to density-functional tight-binding (DFTB) method. We derive it from the density-functional theory, give the details behind the tight-binding formalism, and give practical recipes for parametrization: how to calculate pseudo-atomic orbitals and matrix elements, and especially how to systematically fit the short-range repulsions. Our scope is neither to provide a historical review nor to make performance comparisons, but to give beginner's guide for this approximate, but in many ways invaluable, electronic structure simulation method--now freely available as an open-source software package, hotbit.

Quantum Monte Carlo study of high pressure solid molecular hydrogen

2013

We use the diffusion quantum Monte Carlo (DMC) method to calculate the ground state phase diagram of solid molecular hydrogen and examine the stability of the most important insulating phases relative to metallic crystalline molecular hydrogen. We develop a new method to account for finite-size errors by combining the use of twist-averaged boundary conditions with corrections obtained using the Kwee-Zhang-Krakauer (KZK) functional in density functional theory. To study band-gap closure and find the metallization pressure, we perform accurate quasi-particle many-body calculations using the $GW$ method. In the static approximation, our DMC simulations indicate a transition from the insulating…

Ab initio modelling of UN grain boundary interfaces

2012

The uranium mononitride (UN) is a material considered as a promising candidate for Generation-IV nuclear reactor fuels. Unfortunately, oxygen in air affects UN fuel performance and stability. Therefore, it is necessary to understand the mechanism of oxygen adsorption and further UN oxidation in the bulk and at surface. Recently, we performed a detailed study on oxygen interaction with UN surface using density functional theory (DFT) calculations. We were able to identify an atomistic mechanism of UN surface oxidation consisting of several important steps, starting with the oxygen molecule dissociation and finishing with oxygen atom incorporation into vacancies on the surface. However, in re…