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Density functional tight binding approach utilized to study X-ray-induced transitions in solid materials.

ABSTRACT: Intense X-ray pulses from free-electron lasers can trigger ultrafast electronic, structural and magnetic transitions in solid materials, within a material volume which can be precisely shaped through adjustment of X-ray beam parameters. This opens unique prospects for material processing with X rays. However, any fundamental and applicational studies are in need of computational tools, able to predict material response to X-ray radiation. Here we present a dedicated computational approach developed to study X-ray induced transitions in a broad range of solid materials, including those of high chemical complexity. The latter becomes possible due to the implementation of the versatile density functional tight binding code DFTB+ to follow band structure evolution in irradiated materials. The outstanding performance of the implementation is demonstrated with a comparative study of XUV induced graphitization in diamond.

SUBMITTER: Lipp V

PROVIDER: S-EPMC8799736 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Density-functional tight-binding for phosphine-stabilized nanoscale gold clusters.

Project description:We report a parameterization of the second-order density-functional tight-binding (DFTB2) method for the quantum chemical simulation of phosphine-ligated nanoscale gold clusters, metalloids, and gold surfaces. Our parameterization extends the previously released DFTB2 "auorg" parameter set by connecting it to the electronic parameter of phosphorus in the "mio" parameter set. Although this connection could technically simply be accomplished by creating only the required additional Au-P repulsive potential, we found that the Au 6p and P 3d virtual atomic orbital energy levels exert a strong influence on the overall performance of the combined parameter set. Our optimized parameters are validated against density functional theory (DFT) geometries, ligand binding and cluster isomerization energies, ligand dissociation potential energy curves, and molecular orbital energies for relevant phosphine-ligated Au n clusters (n = 2-70), as well as selected experimental X-ray structures from the Cambridge Structural Database. In addition, we validate DFTB simulated far-IR spectra for several phosphine- and thiolate-ligated gold clusters against experimental and DFT spectra. The transferability of the parameter set is evaluated using DFT and DFTB potential energy surfaces resulting from the chemisorption of a PH3 molecule on the gold (111) surface. To demonstrate the potential of the DFTB method for quantum chemical simulations of metalloid gold clusters that are challenging for traditional DFT calculations, we report the predicted molecular geometry, electronic structure, ligand binding energy, and IR spectrum of Au108S24(PPh3)16.

| S-EPMC8163209 | biostudies-literature

Assessment of the Density Functional Tight Binding Method for Protic Ionic Liquids.

Project description:Density functional tight binding (DFTB), which is ?100-1000 times faster than full density functional theory (DFT), has been used to simulate the structure and properties of protic ionic liquid (IL) ions, clusters of ions and the bulk liquid. Proton affinities for a wide range of IL cations and anions determined using DFTB generally reproduce G3B3 values to within 5-10 kcal/mol. The structures and thermodynamic stabilities of n-alkyl ammonium nitrate clusters (up to 450 quantum chemical atoms) predicted with DFTB are in excellent agreement with those determined using DFT. The IL bulk structure simulated using DFTB with periodic boundary conditions is in excellent agreement with published neutron diffraction data.

| S-EPMC4196743 | biostudies-literature

Database of Wannier tight-binding Hamiltonians using high-throughput density functional theory.

Project description:Wannier tight-binding Hamiltonians (WTBH) provide a computationally efficient way to predict electronic properties of materials. In this work, we develop a computational workflow for high-throughput Wannierization of density functional theory (DFT) based electronic band structure calculations. We apply this workflow to 1771 materials (1406 3D and 365 2D), and we create a database with the resulting WTBHs. We evaluate the accuracy of the WTBHs by comparing the Wannier band structures to directly calculated spin-orbit coupling DFT band structures. Our testing includes k-points outside the grid used in the Wannierization, providing an out-of-sample test of accuracy. We illustrate the use of WTBHs with a few example applications. We also develop a web-app that can be used to predict electronic properties on-the-fly using WTBH from our database. The tools to generate the Hamiltonian and the database of the WTB parameters are made publicly available through the websites https://github.com/usnistgov/jarvis and https://jarvis.nist.gov/jarviswtb .

| S-EPMC8044170 | biostudies-literature

DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB).

Project description:The self-consistent-charge density-functional tight-binding method (SCC-DFTB) is an approximate quantum chemical method derived from density functional theory (DFT) based on a second-order expansion of the DFT total energy around a reference density. In the present study we combine earlier extensions and improve them consistently with, first, an improved Coulomb interaction between atomic partial charges, and second, the complete third-order expansion of the DFT total energy. These modifications lead us to the next generation of the DFTB methodology called DFTB3, which substantially improves the description of charged systems containing elements C, H, N, O, and P, especially regarding hydrogen binding energies and proton affinities. As a result, DFTB3 is particularly applicable to biomolecular systems. Remaining challenges and possible solutions are also briefly discussed.

| S-EPMC3509502 | biostudies-literature

Density Functional Tight Binding Theory Approach for the CO<sub>2</sub> Reduction Reaction Paths on Anatase TiO<sub>2</sub> Surfaces.

Project description:Herein, we have investigated the CO2 reduction paths on the (101) anatase TiO2 surface using an approach based on the density functional tight binding (DFTB) theory. We analyzed the reaction paths for the conversion of carbon dioxide to methane by performing a large number of calculations with intermediates placed in various orientations and locations at the surface. Our results show that the least stable intermediate is CO2H and therefore a key bottleneck is the reduction of CO2 to formic acid. Hydrogen adsorption is also weak and would also be a limiting factor, unless very high pressures of hydrogen are used. The results from our DFTB approach are in good agreement with the hybrid functional based density functional theory calculations presented in the literature.

| S-EPMC7557987 | biostudies-literature

Tight-binding approach to penta-graphene.

Project description:We introduce an effective tight-binding model to discuss penta-graphene and present an analytical solution. This model only involves the ?-orbitals of the sp(2)-hybridized carbon atoms and reproduces the two highest valence bands. By introducing energy-dependent hopping elements, originating from the elimination of the sp(3)-hybridized carbon atoms, also the two lowest conduction bands can be well approximated - but only after the inclusion of a Hubbard onsite interaction as well as of assisted hopping terms. The eigenfunctions can be approximated analytically for the effective model without energy-dependent hopping elements and the optical absorption is discussed. We find large isotropic absorption ranging from 7.5% up to 24% for transitions at the ?-point.

| S-EPMC4778137 | biostudies-literature

Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

Project description:Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies. The encouraging results for the diverse sets of reactions studied here suggest that DFTB models, especially the most recent third-order version (DFTB3/3OB augmented with dispersion correction), in most cases provide satisfactory description of organic chemical reactions with accuracy almost comparable to popular DFT methods with large basis sets, although larger errors are also seen for certain cases. Therefore, DFTB models can be effective for mechanistic analysis (e.g., transition state search) of large (bio)molecules, especially when coupled with single point energy calculations at higher levels of theory. © 2017 Wiley Periodicals, Inc.

| S-EPMC5554453 | biostudies-literature

Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method.

Project description:An important element determining the time requirements of Born-Oppenheimer molecular dynamics (BOMD) is the convergence rate of the self-consistent solution of Roothaan equations (SCF). We show here that improved convergence and dynamics stability can be achieved by use of a Lagrangian formalism of BOMD with dissipation (DXL-BOMD). In the DXL-BOMD algorithm, an auxiliary electronic variable (e.g., the electron density or Fock matrix) is propagated and a dissipative force is added in the propagation to maintain the stability of the dynamics. Implementation of the approach in the self-consistent charge density functional tight-binding method makes possible simulations that are several hundred picoseconds in lengths, in contrast to earlier DFT-based BOMD calculations, which have been limited to tens of picoseconds or less. The increase in the simulation time results in a more meaningful evaluation of the DXL-BOMD method. A comparison is made of the number of iterations (and time) required for convergence of the SCF with DXL-BOMD and a standard method (starting with a zero charge guess for all atoms at each step), which gives accurate propagation with reasonable SCF convergence criteria. From tests using NVE simulations of C(2)F(4) and 20 neutral amino acid molecules in the gas phase, it is found that DXL-BOMD can improve SCF convergence by up to a factor of two over the standard method. Corresponding results are obtained in simulations of 32 water molecules in a periodic box. Linear response theory is used to analyze the relationship between the energy drift and the correlation of geometry propagation errors.

| S-EPMC3160450 | biostudies-other

Efficient Computation of Structural and Electronic Properties of Halide Perovskites Using Density Functional Tight Binding: GFN1-xTB Method.

Project description:In recent years, metal halide perovskites (MHPs) for optoelectronic applications have attracted the attention of the scientific community due to their outstanding performance. The fundamental understanding of their physicochemical properties is essential for improving their efficiency and stability. Atomistic and molecular simulations have played an essential role in the description of the optoelectronic properties and dynamical behavior of MHPs, respectively. However, the complex interplay of the dynamical and optoelectronic properties in MHPs requires the simultaneous modeling of electrons and ions in relatively large systems, which entails a high computational cost, sometimes not affordable by the standard quantum mechanics methods, such as density functional theory (DFT). Here, we explore the suitability of the recently developed density functional tight binding method, GFN1-xTB, for simulating MHPs with the aim of exploring an efficient alternative to DFT. The performance of GFN1-xTB for computing structural, vibrational, and optoelectronic properties of several MHPs is benchmarked against experiments and DFT calculations. In general, this method produces accurate predictions for many of the properties of the studied MHPs, which are comparable to DFT and experiments. We also identify further challenges in the computation of specific geometries and chemical compositions. Nevertheless, we believe that the tunability of GFN1-xTB offers opportunities to resolve these issues and we propose specific strategies for the further refinement of the parameters, which will turn this method into a powerful computational tool for the study of MHPs and beyond.

| S-EPMC8479810 | biostudies-literature

Comprehensive Assessment of GFN Tight-Binding and Composite Density Functional Theory Methods for Calculating Gas-Phase Infrared Spectra.

Project description:Vibrational spectroscopy is a valuable and widely used analytical tool for the characterization of chemical substances. We investigate the performance of semiempirical quantum mechanical GFN tight-binding and force-field methods for the calculation of gas-phase infrared spectra in comparison to experiment and low-cost (B3LYP-3c) density functional theory. A data set of 7247 experimental references was used to evaluate method performance based on automatic spectra comparison. Various quantitative spectral similarity measures were employed for the comparison between theory and experiment and for determining empirical scaling factors. It is shown that the scaling of atomic masses provides an accurate yet simple alternative to standard global frequency scaling in density functional theory (DFT) and semiempirical calculations. Furthermore, the method performance for 58 exemplary transition metal complexes was investigated. The efficient DFT composite method B3LYP-3c, that was introduced in the course of this work, was found to be excellently suited for general IR spectra calculations. The GFN1- and GFN2-xTB tight-binding methods clearly outperformed the PMx competitors. Conformational changes were investigated for a subset of the data and are found to have a mediocre strong influence on the simulated spectra suggesting that the corresponding elaborate sampling steps may be neglected in automated compound identification workflows.

| S-EPMC8378236 | biostudies-literature

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