Critical assessment of machine-learned repulsive potentials for the density functional based tight-binding method: A case study for pure silicon.

We investigate the feasibility of improving the semi-empirical density functional based tight-binding method through a general and transferable many-body repulsive potential for pure silicon using a common machine-learning framework. Atomic environments using atom centered symmetry functions fed into flexible neural-networks allow us to overcome the limited pair potentials used until now with the ability to train simultaneously on a large variety of systems. We achieve an improvement on bulk systems with good performance on energetic, vibrational, and structural properties. Contrarily, there are difficulties for clusters due to surface effects. To deepen the discussion, we also put these results into perspective with two fully machine-learned numerical potentials for silicon from the literature. This allows us to identify both the transferability of such approaches together with the impact of narrowing the role of machine-learning models to reproduce only a part of the total energy.

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations.

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 methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green's functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.

The role of tryptophans in the UV-B absorption of a UVR8 photoreceptor--a computational study.

Arabidopsis thaliana UV RESISTANCE LOCUS8 (UVR8) has been identified as a photoreceptor for ultraviolet-B (UV-B). Tryptophan (Trp) residues have been shown to play a critical role in the response to UV-B irradiation in UVR8. In this work, we explore the spectroscopic behaviors of Trps in different protein environments of the UVR8 structure using the time-dependent density functional tight-binding (TD-DFTB) scheme. We show that W233 exhibits the longest absorption wavelength, highlighting its potential as a terminal Trp chromophore in the UV-B harvesting antenna. Our electronic and optical property analyses using various amino acid models support the important roles of W285 and W233 in sensing UV-B light at longer absorption wavelengths (∼290 nm). We also provide evidence for the specific function of W94 in absorption at the longest wavelengths (305.8 nm in cluster II and 304.5 nm in cluster III). To these findings, we also add information about the influence of the arginine and aspartic acid residues surrounding the Trp pyramid on the particular absorption bands (280-300 nm) that are characteristic of the UV-B photoreceptor.

Accurate hydrogen bond energies within the density functional tight binding method.

The density-functional-based tight-binding (DFTB) approach has been recently extended by incorporating one-center exchange-like terms in the expansion of the multicenter integrals. This goes beyond the Mulliken approximation and leads to a scheme which treats in a self-consistent way the fluctuations of the whole dual density matrix and not only its diagonal elements (Mulliken charges). To date, only the performance of this new formalism to reproduce excited-state properties has been assessed (Domínguez et al. J. Chem. Theory Comput., 2013, 9, 4901-4914). Here we study the effect of our corrections on the computation of hydrogen bond energies for water clusters and water-containing systems. The limitations of traditional DFTB to reproduce hydrogen bonds has been acknowledged often. We compare our results for a set of 22 small water clusters and water-containing systems as well as for five water hexadecamers to those obtained with the DFTB3 method. Additionally, we combine our extension with a third-order energy expansion in the charge fluctuations. Our results show that the new formalisms significantly improve upon original DFTB.

Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method.

Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.

Optimal surface functionalization of silicon quantum dots.

Surface functionalization is a critical step for Si nanocrystals being used as biological probes and sensors. Using density-functional tight-binding calculations, we systematically investigate the optical properties of silicon quantum dots (SiQDs) with various termination groups, including H, CH(3), NH(2), SH, and OH. Our calculations reveal that capping SiQDs with alkyl group (-Si-C-) induces minimal changes in the optical spectra, while covering the surface with NH(2), SH, and OH results in evident changes compared to hydrogenated SiQDs. The structural deformations and electronic property changes due to surface passivation were shown to be responsible for the above-described features. Interestingly, we find that the optical properties of SiQDs can be controlled by varying the S coverage on the surface. This tuning effect may have important implications in device fabrications.

Geometric and excited-state properties of 1,4-bis(benzothiazolylvinyl)benzene interacting with 2,2',2' '-(1,3,5-phenylene)tris[1-phenyl-1H-benzimidazole] studied by a density-functional tight-binding method.

The energetics and luminescent property of a guest molecule, 1,4-bis(benzothiazolylvinyl)benzene (BT), interacting with a host molecule, 2,2',2' '-(1,3,5-phenylene)tris[1-phenyl-1H-benzimidazole] (TPBI), in organic light-emitting diodes are studied by performing excited-state calculations using a time-dependent density-functional tight-binding method complemented with dispersion energy. It is found that the overlap between the TPBI emission and the BT absorption spectra shows an efficient energy transfer from the host molecule to the guest molecule when they are excited. The planar BT molecule becomes distorted when it is mixed with TPBI, resulting in a blue luminescence around 475 nm. The separation of the TPBI + BT mixture on a graphite surface is found to be energetically favorable, consistent with experimental observation.

Stacking dependence of carrier transport properties in multilayered black phosphorous.

We present the effect of different stacking orders on carrier transport properties of multi-layer black phosphorous. We consider three different stacking orders AAA, ABA and ACA, with increasing number of layers (from 2 to 6 layers). We employ a hierarchical approach in density functional theory (DFT), with structural simulations performed with generalized gradient approximation (GGA) and the bandstructure, carrier effective masses and optical properties evaluated with the meta-generalized gradient approximation (MGGA). The carrier transmission in the various black phosphorous sheets was carried out with the non-equilibrium green's function (NEGF) approach. The results show that ACA stacking has the highest electron and hole transmission probabilities. The results show tunability for a wide range of band-gaps, carrier effective masses and transmission with a great promise for lattice engineering (stacking order and layers) in black phosphorous.

Extensions of the Time-Dependent Density Functional Based Tight-Binding Approach.

The time-dependent density functional based tight-binding (TD-DFTB) approach is generalized to account for fractional occupations. In addition, an on-site correction leads to marked qualitative and quantitative improvements over the original method. Especially, the known failure of TD-DFTB for the description of σ → π* and n → π* excitations is overcome. Benchmark calculations on a large set of organic molecules also indicate a better description of triplet states. The accuracy of the revised TD-DFTB method is found to be similar to first principles TD-DFT calculations at a highly reduced computational cost. As a side issue, we also discuss the generalization of the TD-DFTB method to spin-polarized systems. In contrast to an earlier study, we obtain a formalism that is fully consistent with the use of local exchange-correlation functionals in the ground state DFTB method.

Electron Transport Suppression from Tip-π State Interaction on Si(100)-2 × 1 Surfaces.

We investigate the electron transport between a scanning tunneling microscope tip and Si(100)-2 × 1 surfaces with four distinct configurations by performing calculations using density functional theory and the nonequilibrium Green's function method. Interestingly, we find that the conducting mechanism is altered when the tip-surface distance varies from large to small. At a distance larger than the critical value of 4.06 Å, the conductance is increased with a reduction in distance owing to the π state arising from the silicon dimers immediately under the tip; this in turn plays a key role in facilitating a large transmission probability. In contrast, when the tip is closer to the substrate, the conductance is substantially decreased because the π state is suppressed by the interaction with the tip, and its contribution in the tunneling channels is considerably reduced.

Resonant electron heating and molecular phonon cooling in single C60 junctions.

We study heating and heat dissipation of a single C(60) molecule in the junction of a scanning tunneling microscope by measuring the electron current required to thermally decompose the fullerene cage. The power for decomposition varies with electron energy and reflects the molecular resonance structure. When the scanning tunneling microscope tip contacts the fullerene the molecule can sustain much larger currents. Transport simulations explain these effects by molecular heating due to resonant electron-phonon coupling and molecular cooling by vibrational decay into the tip upon contact formation.

Analytical excited state forces for the time-dependent density-functional tight-binding method.

An analytical formulation for the geometrical derivatives of excitation energies within the time-dependent density-functional tight-binding (TD-DFTB) method is presented. The derivation is based on the auxiliary functional approach proposed in [Furche and Ahlrichs, J Chem Phys 2002, 117, 7433]. To validate the quality of the potential energy surfaces provided by the method, adiabatic excitation energies, excited state geometries, and harmonic vibrational frequencies were calculated for a test set of molecules in excited states of different symmetry and multiplicity. According to the results, the TD-DFTB scheme surpasses the performance of configuration interaction singles and the random phase approximation but has a lower quality than ab initio time-dependent density-functional theory. As a consequence of the special form of the approximations made in TD-DFTB, the scaling exponent of the method can be reduced to three, similar to the ground state. The low scaling prefactor and the satisfactory accuracy of the method makes TD-DFTB especially suitable for molecular dynamics simulations of dozens of atoms as well as for the computation of luminescence spectra of systems containing hundreds of atoms.

Theoretical Studies on Optical and Electronic Properties of Propionic-Acid-Terminated Silicon Quantum Dots.

The origin and stability of photoluminescence (PL) are critical issues for silicon nanoparticles to be used as biological probes. Optical and electronic properties of propionic-acid (PA) -terminated silicon quantum dots (SiQDs) were studied using the density-functional tight-binding method. We find that the adsorbed PA molecules slightly affect the structure of silicon core. The PA adsorption does not change the optical properties of SiQDs, while it substantially decreases the ionization potentials in the excited state and results in some new active orbitals with adjacent energies around the Fermi energy level. Accordingly, the modified surface of SiQDs can serve as a reaction substrate to oxygen and solvent molecules, which is responsible for the increase in both PL stability and water solubility.

New type of charged defect in amorphous chalcogenides.

We report on density-functional-based tight-binding simulations of a series of amorphous arsenic sulfide models. In addition to the charged coordination defects previously proposed to exist in chalcogenide glasses, a novel defect pair, [As(4)](-)-[S(3)](+), consisting of a fourfold coordinated arsenic site in a seesaw configuration and a threefold coordinated sulfur site in a near-planar trigonal configuration, was found in several models. The valence-alternation pairs [S(3)](+)-S-1 are converted into [As(4)](-)-[S(3)](+) pairs under HOMO-to-LUMO electronic excitation. This structural transformation is accompanied by a decrease in the size of the HOMO-LUMO band gap, which suggests that such transformations could contribute to photodarkening in these materials.

A global investigation of excited state surfaces within time-dependent density-functional response theory.

This work investigates the capability of time-dependent density functional response theory to describe excited state potential energy surfaces of conjugated organic molecules. Applications to linear polyenes, aromatic systems, and the protonated Schiff base of retinal demonstrate the scope of currently used exchange-correlation functionals as local, adiabatic approximations to time-dependent Kohn-Sham theory. The results are compared to experimental and ab initio data of various kinds to attain a critical analysis of common problems concerning charge transfer and long range (nondynamic) correlation effects. This analysis goes beyond a local investigation of electronic properties and incorporates a global view of the excited state potential energy surfaces.