A5026196545- Spectroscopy and Quantum Chemical Studies
- Advanced Chemical Physics Studies
- Photoreceptor and optogenetics research
- X-ray Diffraction in Crystallography
- Crystallization and Solubility Studies
- Molecular Junctions and Nanostructures
- Photochemistry and Electron Transfer Studies
- DNA and Nucleic Acid Chemistry
- Protein Structure and Dynamics
- Photosynthetic Processes and Mechanisms
- Neuroscience and Neuropharmacology Research
- Organic Electronics and Photovoltaics
- Crystallography and molecular interactions
- Light effects on plants
- Molecular spectroscopy and chirality
- Physics and Engineering Research Articles
- Mass Spectrometry Techniques and Applications
- Advanced biosensing and bioanalysis techniques
- Machine Learning in Materials Science
- Electron Spin Resonance Studies
- Boron and Carbon Nanomaterials Research
- Graphene research and applications
- Advanced Thermodynamics and Statistical Mechanics
- Advanced NMR Techniques and Applications
- Chemical Thermodynamics and Molecular Structure
Karlsruhe Institute of Technology
2016-2025
Institute of Nanotechnology
2025
Karlsruhe University of Education
2014-2024
The University of Sydney
2007-2022
Centenary Institute
2022
Constructor University
2009-2021
Cyprus University of Technology
2021
Heidelberg University
2002-2016
Memorial University of Newfoundland
2015
University of Wisconsin–Madison
2006-2014
We outline details about an extension of the tight-binding (TB) approach to improve total energies, forces, and transferability. The method is based on a second-order expansion Kohn-Sham energy in density-functional theory (DFT) with respect charge density fluctuations. zeroth order equivalent common standard non-self-consistent scheme, while at second transparent, parameter-free, readily calculable expression for generalized Hamiltonian matrix elements may be derived. These are modified by...
The self-consistent-charge density-functional tight-binding method (SCC-DFTB) is an approximate quantum chemical derived from density functional theory (DFT) based on a second-order expansion of the DFT total energy around reference density. In present study we combine earlier extensions and improve them consistently with, first, improved Coulomb interaction between atomic partial charges, second, complete third-order energy. These modifications lead us to next generation DFTB methodology...
We extend an approximate density functional theory (DFT) method for the description of long-range dispersive interactions which are normally neglected by construction, irrespective correlation function applied. An empirical formula, consisting R−6 term is introduced, appropriately damped short distances; corresponding C6 coefficient, calculated from experimental atomic polarizabilities, can be consistently added to total energy expression method. apply this DFT plus dispersion describe...
DFTB3 is a recent extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB) and derived from third order expansion density functional theory (DFT) total energy around given reference density. Being applied in combination with parametrization its predecessor (MIO), improves for hydrogen binding energies, proton affinities, transfer barriers. In present study, parameters especially designed are presented, performance evaluated small organic molecules focusing...
DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various approximating density functional theory (DFT), such as the based tight binding (DFTB) extended method, it enables simulations of large systems long timescales with reasonable accuracy while being considerably faster typical than respective ab initio methods. Based on DFTB framework, additionally offers...
A quantum mechanical/molecular mechanical (QM/MM) approach based on an approximate density functional theory, the so-called self-consistent charge tight binding (SCC-DFTB) method, has been implemented in CHARMM program and tested a number of systems biological interest. In gas phase, SCC-DFTB gives reliable energetics for models triosephosphate isomerase (TIM) catalyzed reactions. The rms errors compared to B3LYP/6-31+G(d,p) are about 2−4 kcal/mol; this is be contrasted with AM1, where...
The present status of development the density-functional-based tight-binding (DFTB) method is reviewed. As a two-centre approach to density-functional theory (DFT), it combines computational efficiency with reliability and transferability. Utilizing minimal-basis representation Kohn-Sham eigenstates superposition optimized neutral-atom potentials related charge densities for constructing effective many-atom potential, all integrals are calculated within DFT. Self-consistency included at...
The field of optogenetics uses channelrhodopsins (ChRs) for light-induced neuronal activation. However, optimized tools cellular inhibition at moderate light levels are lacking. We found that replacement E90 in the central gate ChR with positively charged residues produces chloride-conducting ChRs (ChloCs) only negligible cation conductance. Molecular dynamics modeling unveiled a high-affinity Cl(-)-binding site had been generated near gate. Stabilizing open state dramatically increased...
We report the parametrization of approximate density functional tight binding method, DFTB3, for sulfur and phosphorus. The is done in a framework consistent with our previous 3OB set established O, N, C, H, thus resulting parameters can be used to describe broad organic biologically relevant molecules. 3d orbitals are included parametrization, electronic chosen minimize errors atomization energies. tested using fairly diverse molecules biological relevance, focusing on geometries, reaction...
This paper reviews the basic principles of density-functional tight-binding (DFTB) method, which is based on theory as formulated by Hohenberg, Kohn and Sham (KS-DFT). DFTB consists a series models that are derived from Taylor expansion KS-DFT total energy. In lowest order (DFTB1), densities potentials written superpositions atomic potentials. The Kohn-Sham orbitals then expanded to set localized atom-centred functions, obtained for spherical symmetric spin-unpolarized neutral atoms...
The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method (Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density functional theory total energy expression, followed an approximation charge fluctuations monopoles and effective damped Coulomb interaction between atomic net charges. central assumptions behind this charge−charge are inverse relation size chemical hardness use fixed parameter independent state. While these approximations...
We present an extension to the recent 3OB parametrization of Density Functional Tight Binding Model DFTB31,2 for biological and organic systems. Parameters halogens F, Cl, Br, I have been developed use in covalently bound systems benchmarked on a test set 106 molecules (the 'OrgX' set), using bonding distances, angles, atomization energies, vibrational frequencies assess performance parameters. Additional testing has done with X40 40 supramolecular containing halogens,3 adding simple...
We introduce a database (HAB11) of electronic coupling matrix elements (H(ab)) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported this to assess performance three DFT methods decreasing computational cost, including constrained density...
In this paper we propose an extension of the self-consistent charge-density-functional tight-binding (SCC-DFTB) method [M. Elstner et al., Phys. Rev. B 58, 7260 (1998)], which allows calculation optical properties finite systems within time-dependent density-functional response theory (TD-DFRT). For a test set small organic molecules low-lying singlet excitation energies are computed in good agreement with first-principles and experimental results. The overall computational cost...
The atomic structures, electrical properties, and line energies for threading screw edge dislocations of wurtzite GaN are calculated within the local-density approximation. Both electrically inactive with a band gap free from deep levels. These results understood to arise relaxed core structures which similar ( $10\overline{1}0$) surfaces.
Properties of isolated intercalators (ethidium (E), daunomycin (D), ellipticine (EL), and 4,6'-diaminide-2-phenylindole (DAPI)) their stacking interactions with adenine···thymine (AT) guanine···cytosine (GC) nucleic acid base pairs were investigated by means a nonempirical correlated ab initio method. All exhibit large charge delocalization, none them (including the DAPI dication) exhibits site dominant charge. have polarizability are good electron acceptors, while donors. MP2/6-31G*(0.25)...
Motivated by the long-term goal of understanding vectorial biological processes such as proton transport (PT) in biomolecular ion pumps, a number developments were made to establish combined quantum mechanical/molecular mechanical (QM/MM) methods suitable for studying chemical reactions involving significant charge separation condensed phase. These summarized and discussed with representative problems. Specifically, free energy perturbation boundary potential treating long-range...
Abstract We compare the conformational distributions of Ace‐Ala‐Nme and Ace‐Gly‐Nme sampled in long simulations with several molecular mechanics (MM) force fields a fast combined quantum mechanics/molecular (QM/MM) field, which solute's intramolecular energy forces are calculated self‐consistent charge density functional tight binding method (SCCDFTB), solvent is represented by either one well‐known SPC TIP3P models. All MM give two main states for Ace‐Ala‐Nme, β α separated free barriers,...
Self-consistent charge density functional tight-binding (SCC-DFTB) is a semiempirical method based on theory and has in many cases been shown to provide relative energies geometries comparable accuracy full DFT or ab initio MP2 calculations using large basis sets. This article shows an implementation of the SCC-DFTB as part new QM/MM support AMBER 9 molecular dynamics program suite. Details examples applications are shown.
Starting from the eight B3LYP/6-31G* optimized N-acetyl-l-alanine N'-methylamide (AAMA) structures recently reported by Jalkanen and Suhai,1 we studied effect of hydration on AAMA geometries, relative energies, vibrational properties applying solvent continuum model, adding four explicit water molecules to each conformers, finally combining two approaches. For lowest energy AAMA+4H2O complexes, have calculated Hessians atomic polar tensors (APT), RHF/6-31G* axial (AAT), RHF/6-311+G**...
Rhodopsins can modulate the optical properties of their chromophores over a wide range wavelengths. The mechanism for this spectral tuning is based on response retinal chromophore to external stress and interaction with charged, polar, polarizable amino acids protein environment connected its large change in dipole moment upon excitation, electronic polarizability, structural flexibility. In work, we investigate accuracy computational approaches modeling changes absorption energies respect...