The scope of this article is to present an overview the Density Functional based Tight Binding (DFTB) method and its applications. paper introduces basics DFTB standard formulation up second order. It also addresses methodological developments such as third order expansion, inclusion non-covalent interactions, schemes solve self-interaction error, implementation long-range short-range separation, treatment excited states via time-dependent scheme, in hybrid high-level/low level (DFT/DFTB or...

Abstract 2,4-Dihydroxybutyric acid (DHB) is a molecule with considerable potential as versatile chemical synthon. Notably, it may serve precursor for synthesis of the methionine analogue 2-hydroxy-4-(methylthio)butyrate, thus, targeting market in animal nutrition. However, no natural metabolic pathway exists biosynthesis DHB. Here we have therefore conceived three-step DHB starting from metabolite malate. The employs previously unreported malate kinase, semialdehyde dehydrogenase and...

We benchmark existing and improved self-consistent-charge density functional based tight-binding (SCC-DFTB) parameters for silver gold clusters as well bulk materials. In the former case, our benchmarks focus on both structural energetic properties of small-size AgN AuN (N from 2 to 13), medium-size with N = 20 55, finally larger nanoparticles 147, 309, 561. For materials, structural, energetics elastic are discussed. show that SCC-DFTB is quite satisfactory in reproducing essential...

Abstract Saccharides are ubiquitous biomolecules, but little is known about their interaction with, and assembly at, surfaces. By combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation self‐assembly of disaccharide sucrose on a Cu(100) surface subunit‐level imaging. employing multistage modeling approach in combination experimental data, can rationalize as well interactions between molecules, thereby yielding models observed...

State-of-the-art van der Waals (vdW) corrected density functional theory (DFT) is routinely used to overcome the failure of standard DFT in description molecule/surface long range interactions. However, systematic use dispersion forces model metallic surfaces could lead less accurate results than and effect these corrections on metal properties should be properly evaluated. In this framework, behavior two widely vdW methods (DFT-D2 vdW–DF/optB86b) has been evaluated six metals, i.e. Al, Cu,...

Atrazine, a pesticide belonging to the s-triazine family, is one of most employed pesticides. Due its negative impact on environment, it has been forbidden within European Union since 2004 but remains abundant in soils. For these reasons, behavior soils and water at atomic scale great interest. In this article, we have investigated, using DFT, adsorption atrazine onto two different clay surfaces: pyrophyllite an Mg-substituted named montmorillonite, with Ca2+ compensating cations surface....

Density-functional based tight-binding (DFTB) is an efficient quantum mechanical method that can describe a variety of systems, going from organic and inorganic compounds to metallic hybrid materials. The present topical review addresses the ability performance DFTB investigate energetic, structural, spectroscopic dynamical properties gold silver After brief overview theoretical basis DFTB, its parametrization transferability, we report past recent applications including small clusters,...

Bulk properties of hcp-Ti, relevant for the description dislocations, such as elastic constants, stacking faults and γ-surface, are computed using density functional theory (DFT) two central force embedded atom interaction models (Zope Mishin 2003 Phys. Rev. B 68 024102, Hammerschmidt et al 2005 71 205409). The results compared with previously published calculations, except pair potential which not appropriate metallic bond. comparison includes N-body (NB-CF) angular (NB-A) empirical...

Because of its importance in various aspects everyday life, silica is a material that has been the subject extensive research. Studies on amorphous phase have particularly benefited from contribution atomistic simulations to understand close relationships between structure and properties. In this context, main difficulty lies compromise had be made precision interactions need computed at an ab initio level important statistics required describe disorder. With advent machine learning...

The release of Ag+ ions into the environment through silica layers is a promising strategy for development anti-microbial surface coating devices. aim present study to provide some insight elementary mechanisms diffusion with objective proposing control strategies. Thanks interaction potentials based on neural networks, processes were studied via molecular dynamics simulations. Silver was found be anomalous and sub-diffusive, origin which could attributed deceleration temporal...

An extensive DFT search of (meta)stable structures the screw dislocation in hcp-Ti is presented. It reveals that stable core are never basal but always prismatic. This prismatic dissociates into two partial dislocations same or neighboring planes depending on initial position line, leading to either a symmetric an asymmetric core. alternative way defining region from electronic structure point view also proposed. evidences clearly character cores. We then introduce ansatz for straightforward...

Amine ligands are expected to drive the organization of metallic centers as well chemical reactivity silver clusters early growing during very first steps synthesis nanoparticles via an organometallic route. Density functional theory (DFT) computational studies have been performed characterize structure, atomic charge distribution, and planar two-dimensional (2D)/three-dimensional (3D) relative stability small-size (Agn, 2 ≤ n 7), with or without ethylamine (EA) ligand coordinated Ag...

Abstract Up to date, the influence of ambient air exposure on energetics and stability silver clusters has rarely been investigated compared in vacuum. Silver up 3000 atoms size, an amorphous carbon film, have exposed by atomic-resolution imaging aberration-corrected Scanning Transmission Electron Microscope. Ordered structures comprise more than half population, rest are amorphous. Here, we show that most common ordered isomer is icosahedron. These results contrast with published behaviour...

In the fight against antibiotic resistance, gold nanoparticles (AuNP) with antibiotics grafted on their surfaces have been found to be potent agents. Ampicillin-conjugated AuNPs thus reported overcome highly ampicillin-resistant bacteria. However, structure at atomic scale of these hybrid systems remains misunderstood. this paper, interface between an ampicillin molecule AMP and three flat facets Au(111), Au(110) Au(100) has investigated numerical simulations (dispersion-corrected DFT)....

Structural aspects of the Au147 cluster have been investigated through a density functional based tight binding global optimization involving parallel tempering molecular dynamics scheme with quenching followed by geometries relaxation at Density Functional Theory (DFT) level. The focus is put on competition between relaxed ordered regular and disordered (or amorphous) structures. present work shows that amorphous are relevant low energy candidates likely to contribute in finite temperature...

Silver nanoparticles (AgNPs) are widely used in the health-care sector and industrial applications because of their outstanding antibacterial activity. This bactericidal effect is mainly attributed to release Ag+ ions an aqueous medium, first step which dissolution AgNP via oxidation its surface by O2. With aim designing more durable less toxic devices, it desirable fine-tune rate into surrounding environment. can be achieved choosing adequate coating AgNPs, e.g., embedding a silica matrix....

We rationalize the experimentally observed variety of trehalose assemblies on Cu(100) by modeling based STM images and global optimization.

Scanning transmission electron microscopy experiments indicate that face-centered cubic (FCC) is the predominant ordered structure for Ag309 ± 7 nanoclusters, synthesized in vacuum. Historically, do not present a consensus on morphology at these sizes, whereas theoretical studies find icosahedral symmetry and decahedral shape nearby sizes. We employ density functional theory calculations to rationalize observations, considering both regular defective Ag nanoparticles (281–321 atoms). The...

Morphological competition between silver nanoparticles evolves under air exposure mainly due to temperature effects and interactions with surface contaminants.

Abstract The core structure of screw dislocations in -Ti was studied the cluster approach with ab initio DFT-GGA, and both quadrupole approaches a recently highly optimized EAM central force potential. With potential we have shown that finite-size effects, approach, are negligible down to size DFT calculations unambiguously preferential prismatic spreading for dislocation. Our results agreement previously published approximated using empirical or semi-empirical interaction models: only...

We investigate the dependence upon charge of heat capacities magic gold cluster Au20 obtained from density functional-based tight binding theory within parallel tempering molecular dynamics and multiple histogram method. The melting temperatures, determined capacity curves, are found to be 1102 K for neutral only 866 826 Au20+ Au20-. Both canonical microcanonical aspects transition discussed. A convex intruder, associated with a negative capacity, is evidenced in entropy case but absent...

Abstract Saccharides are ubiquitous biomolecules, but little is known about their interaction with, and assembly at, surfaces. By combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation self‐assembly of disaccharide sucrose on a Cu(100) surface subunit‐level imaging. employing multistage modeling approach in combination experimental data, can rationalize as well interactions between molecules, thereby yielding models observed...