Density-functional Tight-binding Simulations Research Articles

A density functional tight-binding based strategy for modeling ion bombardment and its application to Ar bombardment of silicon nitride

In many modern applications, it is important to understand mechanisms of non-equilibrium chemistry and physics that are driven by low energy ion bombardment of solid surfaces. However, the study of these processes has been challenging as it demands a relatively unique balance between chemical fidelity and computational cost. To this end, we have proposed and constructed a new, high-throughput simulation pipeline based on density functional tight binding simulations. Additionally, we have extended the parameter set pbc-0-3 with the addition of Ar, thereby enabling the simulation of Ar bombardment. This pipeline was then applied to study the structural and compositional evolution of silicon nitride (SiN) under Ar bombardment. We identified a possible rate limiting step of bombardment-driven sputtering of SiN and suggested underlying mechanisms of Si and N removal. Damage from the bombardment, including generation of surface defects and Ar implantation, are further discussed. These findings and the newly developed simulation framework will serve as a useful foundation for further research in processes driven by ion bombardment.

Investigating the effect of electrostatic field on electronic structures of C58N2 molecules from SCC-DFTB simulations

Self-consistent charge density functional tight-binding simulations are performed to investigate the effect of externally electrostatic field on nitrogen-doped fullerene C58N2 molecules. Based on the obtained geometric structures of twenty-three C58N2 configurations, electric field is applied to six selected configurations. We analyze the effects of the direction and strength of the electric field on the HOMO and LUMO energy levels, chemical potential, energy gap, dipole moment, Mulliken populations on atoms, and the variations of molecular orbitals at HOMO and LUMO energy levels of these configurations. The calculation results show that the electric field can change them. The effects of the electric field on the Mulliken charge distribution on the atoms in each configuration present complex patterns, and changing electric field’s direction and strength significantly affect the molecular orbitals. Here, variation of electric field direction can change the phase of molecular orbitals of the configuration having relatively high energy, and the change in the strength of the electric field has a more pronounced effect on the electron distribution at the LUMO levels.

Photoresponse of Solution-Synthesized Graphene Nanoribbon Heterojunctions on Diamond Indicating Phototunable Photodiode Polarity

Graphene nanoribbon heterostructures and heterojunctions have attracted interest as next-generation molecular diodes with atomic precision. Their mass production via solution methods and prototypical device integration remains to be explored. Here, the bottom-up solution synthesis and characterization of liquid-phase-processable graphene nanoribbon heterostructures (GNRHs) are demonstrated. Joint photoresponsivity measurements and simulations provide evidence of the structurally defined heterostructure motif acting as a type-I heterojunction. Real-time, time-dependent density functional tight-binding simulations further reveal that the photocurrent polarity can be tuned at different excitation wavelengths. Our results introduce liquid-phase-processable, self-assembled heterojunctions for the development of nanoscale diode circuitry and adaptive hardware.

GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems.

Metadynamics calculations of large chemical systems with ab initio methods are computationally prohibitive due to the extensive sampling required to simulate the large degrees of freedom in these systems. To address this computational bottleneck, we utilized a GPU-enhanced density functional tight binding (DFTB) approach on a massively parallelized cloud computing platform to efficiently calculate the thermodynamics and metadynamics of biochemical systems. To first validate our approach, we calculated the free-energy surfaces of alanine dipeptide and showed that our GPU-enhanced DFTB calculations qualitatively agree with computationally-intensive hybrid DFT benchmarks, whereas classical force fields give significant errors. Most importantly, we show that our GPU-accelerated DFTB calculations are significantly faster than previous approaches by up to two orders of magnitude. To further extend our GPU-enhanced DFTB approach, we also carried out a 10 ns metadynamics simulation of remdesivir, which is prohibitively out of reach for routine DFT-based metadynamics calculations. We find that the free-energy surfaces of remdesivir obtained from DFTB and classical force fields differ significantly, where the latter overestimates the internal energy contribution of high free-energy states. Taken together, our benchmark tests, analyses, and extensions to large biochemical systems highlight the use of GPU-enhanced DFTB simulations for efficiently predicting the free-energy surfaces/thermodynamics of large biochemical systems.

Polarization Controlled Assembly of Ultrathin Thiorphan Nanostructures on ZnO Surface Facets

Despite the importance of thiorphan as a small molecule with vital biological roles, its interactions with zinc oxide (ZnO) nanomaterials that are prospective in drug delivery and theranostic applications have not yet been sufficiently explored. Here the impact of surface polarity of different ZnO facets on thiorphan adsorption is studied both experimentally by atomic force microscopy (AFM) and angle resolved X-ray photoelectron spectroscopy (XPS) and theoretically by force field molecular dynamics (FFMD) and density functional tight binding simulations (DFTB). Polar ZnO surfaces cause the formation of thiorphan nanodots, where the size of the nanodots depends on the direction of dipoles: small (4 nm) nanodots are formed on Zn-face ZnO, while large (25 nm) nanodots are formed on O-face ZnO. Nonpolar ZnO surfaces cause self-assembly into layered nanoislands with characteristic 4 nm layer thickness, which subsequently merge into rigid nanolayers. The self-assembly is shown to be controlled solely by the effect of surface dipole electric field orientation and magnitude, whereas effects of surface chemistry or solution are negligible. The results thus also show a way for controlling the assembly of thiorphan and other molecular nanomaterials for diverse applications.

DFTB investigations of structures and electron states for a decahedron Ti7 cluster on graphene on electrical level

We performed self-consistent charge density functional tight binding simulations to investigate the interactions between a decahedron Ti 7 cluster and graphene. Different adsorption behaviors of the cluster on perfect and defective graphene are characterized by adsorption energy, chemical potential, HOMO-LUMO energy gap, charge density differences, Mulliken populations on atoms, and molecular orbitals on HOMO and LUMO energy levels. Simulation results show that relatively contacting orientations of the cluster and graphene as well as adsorption positions greatly affect adsorption's packing configurations. The defective graphene improves high possibility for strongly binding the metal cluster. Apparent charge transfer occurs from the cluster to graphene for the adsorption on defective graphene. The molecular orbitals on the HOMO and LUMO energy levels present differences for different adsorption configurations. • A decahedron Ti 7 cluster and graphene • Different adsorption behaviors of the cluster on perfect and defective graphene • Adsorption energy, chemical potential, HOMO-LUMO energy gap • Charge density differences, Mulliken populations on atoms, and molecular orbitals on HOMO and LUMO energy levels

Performance and interaction mechanism of a new highly efficient benzimidazole-based epoxy resin for corrosion inhibition of carbon steel in HCl: A study based on experimental and first-principles DFTB simulations

Thanks to their excellent properties, epoxy resins are the first choice for many engineering applications. In this regard, herein, a new epoxy resin, namely 1-(oxiran-2-ylmethyl-1H-benzo[d]imidazole (BIZ epoxy), was synthesized and characterized by nuclear magnetic resonance (1H, 13C NMR) and Fourier transform infrared-attenuated total reflection (FTIR-ATR)) techniques. The corrosion inhibition properties of prepared epoxy resin for carbon steel (CS) in 1.0 mol/L HCl were evaluated using electrochemical and scanning electron microscope (SEM) techniques. Furthermore, reactivity and interaction mechanisms between epoxy resin molecule and the iron surface were investigated using quantum chemical parameters (QCPs) and Density-Functional Tight-Binding (DFTB). Electrochemical studies by potentiodynamic polarization curves (PPC) and electrochemical impedance spectroscopy (EIS) showed that the BIZ epoxy acted as a barrier against the acid corrosion of CS with an inhibition efficiency of 93 % at 1 mmol/L. The adsorption of BIZ epoxy followed the Langmuir adsorption isotherm and was found to be a physicochemical process. The SEM analysis showed a significant difference in surface morphology of CS after inhibition due to the formation of a protective barrier. DFTB simulation of BIZ epoxy – Fe(110) surface revealed the formation of a chemical bond and several long-range van der Waals interactions. The projected density of states (PDOS) of isolated and adsorbed systems confirmed the physicochemical nature of interactions between inhibitor molecule and Fe(110) surface.

Investigating the effect of electric field on the adsorption of C60 onto graphene from density functional tight-binding simulations

Self-consistent charge density functional tight-binding simulations are performed to investigate the adjustments of adsorption behaviors of C60 onto perfect or defective graphene owing to the applied electrical field. For the C60 adsorbed on the perfect graphene, the effect of the applied electrical field on the physical adsorption is visually displayed from the Mulliken charges on the atoms of the C60-graphene nanohybrid systems. When the C60 is adsorbed on the graphene with one vacancy, the differential charge density and optimized geometry as well as the adsorption energy are used to identify chemical, physical, or no adsorption. The applied electric field can adjust adsorption behaviors for some configurations accompanying with the atom arrangements in the graphene.

Strong Structural and Electronic Binding of Bovine Serum Albumin to ZnO via Specific Amino Acid Residues and Zinc Atoms.

ZnO biointerfaces with serum albumin have attracted noticeable attention due to the increasing interest in developing ZnO-based materials for biomedical applications. ZnO surface morphology and chemistry are expected to play a critical role on the structural, optical, and electronic properties of albumin-ZnO complexes. Yet there are still large gaps in the understanding of these biological interfaces. Herein we comprehensively elucidate the interactions at such interfaces by using atomic force microscopy and nanoshaving experiments to determine roughness, thickness, and adhesion properties of BSA layers adsorbed on the most typical polar and non-polar ZnO single-crystal facets. These experiments are corroborated by force field (FF) and density-functional tight-binding (DFTB) calculations on ZnO-BSA interfaces. We show that BSA adsorbs on all the studied ZnO surfaces while interactions of BSA with ZnO are found to be considerably affected by the atomic surface structure of ZnO. BSA layers on the surface have the highest roughness and thickness, hinting at a specific upright BSA arrangement. BSA layers on surface have the strongest binding, which is well correlated with DFTB simulations showing atomic rearrangement and bonding between specific amino acids (AAs) and ZnO. Besides the structural properties, the ZnO interaction with these AAs also controls the charge transfer and HOMO-LUMO energy positions in the BSA-ZnO complexes. This ZnO facet-specific protein binding and related structural and electronic effects can be useful for improving the design and functionality of ZnO-based materials and devices.

Davis Computational Spectroscopy Workflow-From Structure to Spectra.

We describe an automated workflow that connects a series of atomic simulation tools to investigate the relationship between atomic structure, lattice dynamics, materials properties, and inelastic neutron scattering (INS) spectra. Starting from the atomic simulation environment (ASE) as an interface, we demonstrate the use of a selection of calculators, including density functional theory (DFT) and density functional tight binding (DFTB), to optimize the structures and calculate interatomic force constants. We present the use of our workflow to compute the phonon frequencies and eigenvectors, which are required to accurately simulate the INS spectra in crystalline solids like diamond and graphite as well as molecular solids like rubrene. We have also implemented a machine-learning force field based on Chebyshev polynomials called the Chebyshev interaction model for efficient simulation (ChIMES) to improve the accuracy of the DFTB simulations. We then explore the transferability of our DFTB/ChIMES models by comparing simulations derived from different training sets. We show that DFTB/ChIMES demonstrates ∼100× reduction in computational expense while retaining most of the accuracy of DFT as well as yielding high accuracy for different materials outside of our training sets. The DFTB/ChIMES method within the workflow expands the possibilities to use simulations to accurately predict materials properties of increasingly complex structures that would be unfeasible with ab initio methods.

Density Functional Tight-Binding Simulations Reveal the Presence of Surface Defects on the Quartz (101)–Water Interface

Density Functional Tight-Binding Simulations Reveal the Presence of Surface Defects on the Quartz (101)–Water Interface

Thickness-Dependence of Surface Reconstruction on the (001) Surface of Ultrathin Silicon Nanosheets by Density Functional Tight Binding Simulations

The influences of the thickness of ultrathin Si nanosheets on the (001) surface morphologies and charge distribution were identified by using density functional tight binding (DFTB) simulations. The differences in structure and electronic properties were elucidated on the basis of bond lengths, bond angle distribution, and arrangement patterns in (001) surface atoms of Si nanosheets with their thickness decreasing from 1.5 nm to 0.4 nm. The surface atoms in some nanosheets present perfect zig-zag patterns in their dimers. The amounts of the trimers are far less than those of the dimers in the surface. The formation of the dimers lowers the surface energy of the nanosheets. Analysis of Mülliken gross populations indicates that there is the charge transfer from the inner part of the nanosheet to the surface. The moving distance and direction of the surface atoms can affect the charge distribution.

Protein Molecular Dynamics Simulations with Approximate QM: What Can We Learn?

Classical force fields are essential for computer simulations of proteins and are typically parameterized to reproduce secondary and tertiary structure of isolated proteins. However, while protein-protein interactions are ubiquitous in nature, they are not considered in parameterization efforts and are far less understood than isolated proteins. A better characterization of intermolecular interactions is widely recognized as a key to revolutionizing drug and therapeutic developments with high-throughput computational screening. Urgently needed is a critical assessment of the performance of modern protein force fields against first-principles electronic structure methods and experiments. In a daring step toward this goal, we here describe a comparison of peptide folding dynamics as predicted by a molecular mechanics force field on the one hand and by an approximate electronic structure quantum mechanical (QM) method based on density-functional tight-binding (DFTB) on the other. We further compare the dynamics from straightforward DFTB simulations with a near-linear scaling version of DFTB for massively parallel computation based on the fragment molecular orbital (FMO-DFTB) method. We illustrate differences between the phenomenology of the folding dynamics from these three methods for a small model peptide, as well as charge polarization and dynamic fluctuations, point out possible correlations and implications for force field developers, and discuss the lessons learned that might become applicable to future predictive high-throughput computer screening for personalized neoantigen cancer therapy.

Influence of temperature on the displacement threshold energy in graphene

The atomic structure of nanomaterials is often studied using transmission electron microscopy. In addition to image formation, the energetic electrons impinging on the sample may also cause damage. In a good conductor such as graphene, the damage is limited to the knock-on process caused by elastic electron-nucleus scattering. This process is determined by the kinetic energy an atom needs to be sputtered, i.e. its displacement threshold energy Ed. This is typically assumed to have a fixed value for all electron impacts on equivalent atoms within a crystal. Here we show using density functional tight-binding simulations that the displacement threshold energy is affected by thermal perturbations of atoms from their equilibrium positions. This effect can be accounted for in the estimation of the displacement cross section by replacing the constant threshold energy value with a distribution. Our refined model better describes previous precision measurements of graphene knock-on damage, and should be considered also for other low-dimensional materials.

Hydrogen bonding in the protic ionic liquid triethylammonium nitrate explored by density functional tight binding simulations.

The applicability of the density functional based tight binding (DFTB) method to the description of hydrogen bond dynamics and infrared (IR) spectroscopy is addressed for the exemplary protic ionic liquid triethylammonium nitrate. Potential energy curves for proton transfer in gas and liquid phases are shown to be comparable to the high level coupled cluster theory in the thermally accessible range of bond lengths. Geometric correlations in the hydrogen bond dynamics are analyzed for a cluster of six ion pairs. Comparing DFTB and DFT data lends further support for the reliability of the DFTB method. Therefore, DFTB bulk simulations are performed to quantify the extent of geometric correlations in terms of Pauling's bond order model. Further, IR absorption spectra are obtained using DFTB and analyzed putting emphasis on the signatures of hydrogen bonding in the NH-stretching and far IR hydrogen bond range.

Effect of edge passivation on the mechanical properties of phosphorene nanoribbons

Using density functional tight binding simulations, we studied the edge structures, edge elastic properties, deformation and failure behavior of phosphorene nanoribbons (PNRs) with edges passivated by hydrogen atoms. Two primary types of edge, that is, arm-chair (AC) and zig-zag (ZZ), were examined. It was found that edge relaxation primarily occurred within three atomic rows near the passivated edges, in the form of alteration in bond length and angle. The edge passivation was able to lessen the edge relaxation and reduce the edge stresses and elastic moduli. For AC PNRs under tension, three deformation stages were identified: linear elastic, bond rotation and bond stretching. At ε≈ 0.5, intra-row bonds fracture in a double-row-wise manner in the interior of the sample, leading to fragmentation of AC PNRs. For ZZ PNRs under tension, inter-row bonds are stretched directly. At ε≈ 0.18, a fraction of the inter-row bonds break randomly, leading to the failure of ZZ PNRs. Interestingly, the edge passivation increases both the failure strain (Δε/ε≈ 80%) and strength (Δσ/σ≈ 26%) of ZZ PNRs significantly, but the failure strain (Δε/ε≈ 2%) and strength (Δσ/σ≈ 5%) of AC PNRs only slightly.

The structure and elastic properties of phosphorene edges

We investigated the edge atomic structures and elastic properties of defect-free phosphorene nanoribbons (PNRs). Density functional tight binding simulations were used to optimize two main edge configurations: armchair (AC) and zigzag (ZZ). It was found that the energy relaxation of PNRs leads to the noticeable changes in edge atomic configurations. The effective width of the edge region, which includes all the atoms involved in the edge relaxation, was found to contain approximately three atomic rows near the edge for both AC and ZZ PNRs. We further extracted the edge stress and modulus for the ZZ and AC edges. Both the AC and ZZ edge stresses of PNRs are positive, indicating tensile stress at the edges. In addition, both the AC and ZZ edge moduli are positive. However, the edge elastic modulus and edge stress of ZZ PNRs are about three times larger than those of AC PNRs. Furthermore, we showed that the tensile edge stresses along ZZ and AC edges are able to cause distortion in freestanding phosphorene nanoribbons. Our results highlight the importance of accounting for edge stresses in the design and fabrication of PNRs.

Adsorption of a Hydrogen Atom on a Graphene Flake Examined with Quantum Trajectory/Electronic Structure Dynamics

Adsorption of atomic hydrogen colliding with C37H15, a planar “flake” of graphene, is examined using a hybrid quantum trajectory/electronic structure (QTES) dynamics for the values of the collision energies below 2.0 eV. The entire system of 53 atoms is represented by a quantum trajectory ensemble. The quantum correction on dynamics is included for the adsorbing hydrogen. The electronic structure is computed on-the-fly using the density functional tight binding (DFTB) method. The highest probability of adsorption is obtained for the kinetic energy of incident hydrogen in the range from 0.1 to 0.9 eV. Adsorption mechanism involves transfer of the collision energy to the graphene flake and projection of the carbon atom of the forming CH bond, accompanying sp3 hybridization of orbitals. The QTES–DFTB simulations with and without the quantum correction show that localization of the proton wave function and details of the mixed quantum/classical description of light and heavy nuclei greatly influence the adsor...

A Delocalized Proton-Binding Site within a Membrane Protein

The role of protein-bound water molecules in protein function and catalysis is an emerging topic. Here, we studied the solvation of an excess proton by protein-bound water molecules and the contribution of the surrounding amino acid residues at the proton release site of the membrane protein bacteriorhodopsin. It hosts an excess proton within a protein-bound water cluster, which is hydrogen bonded to several surrounding amino acids. Indicative of delocalization is a broad continuum absorbance experimentally observed by time-resolved Fourier transform infrared spectroscopy. In combination with site-directed mutagenesis, the involvement of several amino acids (especially Glu-194 and Glu-204) in the delocalization was elaborated. Details regarding the contributions of the glutamates and water molecules to the delocalization mode in biomolecular simulations are controversial. We carried out quantum mechanics/molecular mechanics (QM/MM) self-consistent charge density functional tight-binding simulations for all amino acids that have been experimentally shown to be involved in solvation of the excess proton, and systematically investigated the influence of the quantum box size. We compared calculated theoretical infrared spectra with experimental ones as a measure for the correct description of excess proton delocalization. A continuum absorbance can only be observed for small quantum boxes containing few amino acids and/or water molecules. Larger quantum boxes, including all experimentally shown involved amino acids, resulted in narrow absorbance bands, indicating protonation of a single binding site in contradiction to experimental results. We conclude that small quantum boxes seem to reproduce representative extreme cases of proton delocalization modes: proton delocalization only on water molecules or only between Glu-194 and Glu-204. Extending the experimental spectral region to lower wave numbers, a water-delocalized proton reproduces the observed continuum absorbance better than a glutamate-shared delocalized proton. However, a full agreement between QM simulations and experimental results on the delocalized excess proton will require a larger quantum box as well as more sophisticated QM/MM methods.

Relative Stability of Graphene Nanoflakes Under Environmentally Relevant Conditions

The stability of finite-sized graphene nanostructures under different conditions is contingent on the stability of the highly reactive undercoordinated atoms around the circumference. Chemical passivation is a convenient way of stabilizing the edges and corners, provided the conditions support adsorption. In this paper we examine the stabilities of hydrogen, oxygen, hydroxyl, and water functionalization of the edges of graphene nanoflakes using a combination of ab initio thermodynamics and self-consistent charge density functional tight-binding simulations. We find that the adsorption of hydrogen and oxygen on graphene nanoflakes is selective and sensitive to the edge and corner structure and the local environment. Under hydrogen-rich conditions (or in vacuo), we find that armchair edges are preferred, whereas under oxygen-rich conditions the stability of the zigzag edge is enhanced. In addition to this, we find that the types of corners play an important role, and the presence of acute 60° corners is thermodynamically preferred, particularly under humid conditions. In each case, the adsorption efficiency is related to the temperature and the pressure, which may be used to stabilize one type of structure or another.