Tight-binding Density Functional Theory Research Articles

Dirac cones in bipartite square-octagon lattice: A theoretical approach.

Dirac cones are difficult to achieve in a square lattice with full symmetry. Here, we have theoretically investigated a bipartite tetragonal lattice composed of tetragons and octagons using both Tight-Binding (TB) model and density functional theory (DFT) calculations. The TB model predicts that the system exhibits nodal line semi-metallic properties when the on-site energies of all atoms are identical. When the on-site energies differ, the formation of an elliptical Dirac cone is predicted. Its physical properties (anisotropy, tilting, merging, and emerging) can be regulated by the hopping energies. An exact analytical formula is derived to determine the position of the Dirac point by the TB parameters, and a criterion for the existence of Dirac cones is obtained. The "divide-and-coupling" method is applied to understand the origin of the Dirac cone, which involves dividing the bands into several groups and examining the couplings among inter-groups and intra-groups. Various practical systems computed by DFT methods, e.g., t-BN, t-Si, 4,12,2-graphyne, and t-SiC, are also examined, and they all possess nodal lines or Dirac cones as predicted by the TB model. The results provide theoretical foundation for designing novel Dirac materials with tetragonal symmetry.

Shadow Molecular Dynamics and Atomic Cluster Expansions for Flexible Charge Models.

A shadow molecular dynamics scheme for flexible charge models is presented where the shadow Born-Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, is modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born-Oppenheimer molecular dynamics (BOMD) [Eur. Phys. J. B 2021, 94, 164]. XL-BOMD provides stable dynamics while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO2) and a molecular system of liquid water. The combined ACE+XL-QEq molecular dynamics simulations are stable over a wide range of temperatures both for the oxide and for the molecular systems and provide a precise sampling of the Born-Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO2, predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.

Adaptive Peptide Molecule as the Promising Highly-Efficient Gas-Sensor Material: In Silico Study.

Gas sensors are currently employed in various applications in fields such as medicine, ecology, and food processing, and serve as monitoring tools for the protection of human health, safety, and quality of life. Herein, we discuss a promising direction in the research and development of gas sensors based on peptides-biomolecules with high selectivity and sensitivity to various gases. Thanks to the technique developed in this work, which uses a framework based on the density-functional tight-binding theory (DFTB), the most probable adsorption centers were identified and used to describe the interaction of some analyte molecules with peptides. The DFTB method revealed that the physical adsorption of acetone, ammonium, benzene, ethanol, hexane, methanol, toluene, and trinitrotoluene had a binding energy in the range from -0.28 eV to -1.46 eV. It was found that peptides may adapt to the approaching analyte by changing their volume up to a maximum value of approx. 13%, in order to confine electron clouds around the adsorbed molecule. Based on the results obtained, the prospects for using the proposed peptide configurations in gas sensor devices are good.

Environmental and Nuclear Quantum Effects on Double Proton Transfer in the Guanine-Cytosine Base Pair.

In the present letter, we investigate the double proton transfer (DPT) tautomerization process in guanine-cytosine (GC) DNA base pairs. In particular, we study the influence of the biological environment on the mechanism, the kinetics and thermodynamics of such DPT. To this end, we present a molecular dynamics (MD) study in the tight-binding density functional theory framework, and compare the reactivity of the isolated GC dimer with that of the same dimer embedded in a small DNA structure. The impact of nuclear quantum effects (NQEs) is also evaluated using Path Integral based MD. Results show that in the isolated dimer, the DPT occurs via a concerted mechanism, while in the model biological environment, it turns into a stepwise process going through an intermediate structure. One of the water molecules in the vicinity of the proton transfer sites plays an important role as it changes H-bond pattern during the DPT reaction. The inclusion of NQEs has the effect of speeding up the tautomeric-to-canonical reaction, reflecting the destabilization of both the tautomeric and intermediate forms.

Machine Learning Frontier Orbital Energies of Nanodiamonds.

Nanodiamonds have a wide range of applications including catalysis, sensing, tribology, and biomedicine. To leverage nanodiamond design via machine learning, we introduce the new data set ND5k, consisting of 5089 diamondoid and nanodiamond structures and their frontier orbital energies. ND5k structures are optimized via tight-binding density functional theory (DFTB) and their frontier orbital energies are computed using density functional theory (DFT) with the PBE0 hybrid functional. From this data set we derive a qualitative design suggestion for nanodiamonds in photocatalysis. We also compare recent machine learning models for predicting frontier orbital energies for similar structures as they have been trained on (interpolation on ND5k), and we test their abilities to extrapolate predictions to larger structures. For both the interpolation and extrapolation task, we find the best performance using the equivariant message passing neural network PaiNN. The second best results are achieved with a message passing neural network using a tailored set of atomic descriptors proposed here.

Investigation of electronic and thermal properties of CoCrFe and CoCrFeNi high entropy alloys via extended tight-binding DFT computational method

In this study, CoCrFe and CoCrFeNi transition high entropy alloys (HEAs) are modelled by extended tight-binding density functional theory (DFT) method. Also, the geometric optimizations, band structures, density of states (DOS), thermodynamic properties and phonon dispersion curves of alloys are investigated to give a detailed information. The results show that the covalent d–d bonding between Fe-Cr is occurred because of strong metallic Cr–Fe interactions. The entropy (S) value increases gradually with the addition of Ni element to the CoCrFe alloy. The heat capacity (Cv) increases due to the harmonic effect of the phonons in the range of 0-400 K and then, close to the classic limit at high temperatures with 0.82 J/mol.K and 0.94 J/mol.K for the CoCrFe and the CoCrFeNi. The alloy systems exhibit metallic properties because the DOS of the metals have a nonzero value at the Fermi energy level. Also, the addition of element Ni to the CoCrFe alloy system causes a decrease in phonon frequencies.

Thermal stability and decomposition mechanisms of hexatetracarbon: Tight-binding molecular dynamics and density functional theory study

In this work, we carry out molecular dynamics and ab initio modeling to determine the thermal decomposition channels and thermal stability of the recently proposed 2D carbon allotrope, hexatetracarbon (HTC). To take into account the role of edges in the initialization of decay, we considered finite size cluster models of HTC passivated by hydrogen. Four models were selected for the study: [Formula: see text], [Formula: see text] [Formula: see text] and [Formula: see text]. Molecular dynamics and hyperdynamics was carried out using the NTBM non-orthogonal tight-binding model. For ab initio calculations, we used the electron density functional theory with the B3LYP three-parameter hybrid functional and the 6-311G[Formula: see text] electronic basis set. Prismane [Formula: see text] demonstrated the highest stability due to the high energy barrier of 1.5 eV preserving its decomposition. Larger clusters possessed lower barriers in the 0.65–0.9 eV range. We concluded that the HTC edges are unstable at room temperatures. However, the destruction of some interlayer bonds can result in strain relaxation and increase of stability. We believe that HTC could exist at room temperatures in the form of nanosized quantum dots that appeared from bilayer graphene under high pressure.

Mechanical properties and deformation-driven band gap tuning on [N]-Carbophenes

A new class of two-dimensional carbon-based materials, N-carbophenes, is studied using tight binding density functional theory. The present study addresses the influence of strain on band gap opening for N-Carbophenes where 3 ≤ N ≤ 9. We found that both uniaxial and biaxial strains can lead to significant changes in the electronic structure of N-carbophenes. One unexpected effect was the existence of a maximum value for the band gaps for strains in the range 13%≤ɛ≤15% and that increasing ɛ above that range can cause a reduction in the band gap. The origin of the band gap openings is due to the stretching of C–C bonds in the N-carbophene 4-member rings.

Graph-based quantum response theory and shadow Born-Oppenheimer molecular dynamics.

Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations [A. M. N. Niklasson et al., J. Chem. Phys. 144, 234101 (2016)] is adapted to the most recent shadow potential formulations of extended Lagrangian Born-Oppenheimer molecular dynamics, including fractional molecular-orbital occupation numbers [A. M. N. Niklasson, J. Chem. Phys. 152, 104103 (2020) and A. M. N. Niklasson, Eur. Phys. J. B 94, 164 (2021)], which enables stable simulations of sensitive complex chemical systems with unsteady charge solutions. The proposed formulation includes a preconditioned Krylov subspace approximation for the integration of the extended electronic degrees of freedom, which requires quantum response calculations for electronic states with fractional occupation numbers. For the response calculations, we introduce a graph-based canonical quantum perturbation theory that can be performed with the same natural parallelism and linear scaling complexity as the graph-based electronic structure calculations for the unperturbed ground state. The proposed techniques are particularly well-suited for semi-empirical electronic structure theory, and the methods are demonstrated using self-consistent charge density-functional tight-binding theory both for the acceleration of self-consistent field calculations and for quantum-mechanical molecular dynamics simulations. Graph-based techniques combined with the semi-empirical theory enable stable simulations of large, complex chemical systems, including tens-of-thousands of atoms.

Evaluation of tight-binding DFT performance for the description of organic photochromes properties.

Photochromic molecules are widely studied and developed for their many potential applications. To optimize the required properties through theoretical models, a considerable chemical space is to be explored, and their environment in devices is to be accounted for.. To this end, cheap and reliable computational methods can be powerful tools to steer synthetic developments. As ab initio methods remain costly for extensive studies (in terms of the size of the system and/or number of molecules), semiempirical methods such as density functional tight-binding (TB) could offer a good compromise between accuracy computational cost. However, these approaches necessitate benchmarking on the families of compounds of interest. Thus, the aim of the present study is to evaluate the accuracy of several key features calculated with TB methods (DFTB2, DFTB3, GFN2-xTB, and LC-DFTB2) for three sets of photochromic organic molecules: azobenzene (AZO), norbornadiene/quadricyclane (NBD/QC), and dithienylethene (DTE) derivatives. The features considered here are the optimized geometries, the difference in energy between the two isomers (ΔE), and of the energies of the first relevant excited states. All the TB results are compared to those obtained with DFT methods and state-of-the-art electronic structure calculation methods: DLPNO-CCSD(T) for ground states and DLPNO-STEOM-CCSD for excited states. Our results show that, overall, DFTB3 is the TB method leading to the best results for the geometries and the ΔE values and can be used alone for these purposes for NBD/QC and DTE derivatives. Single point calculations at the r2SCAN-3c level using TB geometries allow circumventing the deficiencies of the TB methods in the AZO series. For electronic transition calculations, the range separated LC-DFTB2 method is the most accurate TB method tested for AZO and NBD/QC derivatives, in close agreement with the reference.

Photoemission Study of One-Dimensional Electronic States of (6,5), (6,6), and (7,4) Single-Walled Carbon Nanotubes

We have investigated the one-dimensional electronic states of single-walled carbon nanotubes (SWCNTs) with diameters ranging from 0.8–1.4 nm by optical absorption, photoemission, and inverse photoemission measurements. In the photoemission spectra of (6,5) SWCNTs and (6,6)- and (7,4)-enriched SWCNTs, spike structures caused by Van Hove singularities (VHSs) are clearly observed. The observed VHS positions are compared with the positions calculated using the tight-binding model and density functional theory. A large curvature affects the electronic states of metallic SWCNTs with small diameters.

A comprehensive study of the velocity, momentum and position matrix elements for Bloch states: Application to a local orbital basis

We present a comprehensive study of the velocity operator, \hat{\boldsymbol{v}}=\frac{i}{\hbar} [\hat{H},\hat{\boldsymbol{r}}]\,𝐯̂=iℏ[Ĥ,𝐫̂], when used in crystalline solids calculations. The velocity operator is key to the evaluation of a number of physical properties and its computation, both from a practical and fundamental perspective, has been a long-standing debate for decades. Our work summarizes the different approaches found in the literature, but never connected before in a comprehensive manner. In particular we show how one can compute the velocity matrix elements following two different routes. One where the commutator is explicitly used and another one where the commutator is avoided by relying on the Berry connection. We work out an expression in the latter scheme to compute velocity matrix elements, generalizing previous results. In addition, we show how this procedure avoids ambiguous mathematical steps and how to properly deal with the two popular gauge choices that coexist in the literature. As an illustration of all this, we present several examples using tight-binding models and local density functional theory calculations, in particular using Gaussian-type localized orbitals as basis sets. We show how the the velocity operator cannot be approximated, in general, by the k-gradient of the Bloch Hamiltonian matrix when a non-orthonormal basis set is used. Finally, we also compare with its real-space evaluation through the identification with the canonical momentum operator when possible. This comparison offers us, in addition, a glimpse of the importance of non-local corrections, which may invalidate the naive momentum-velocity correspondence.

Investigation of plasmon relaxation mechanisms using nonadiabatic molecular dynamics.

Hot carriers generated from the decay of plasmon excitation can be harvested to drive a wide range of physical or chemical processes. However, their generation efficiency is limited by the concomitant phonon-induced relaxation processes by which the energy in excited carriers is transformed into heat. However, simulations of dynamics of nanoscale clusters are challenging due to the computational complexity involved. Here, we adopt our newly developed Trajectory Surface Hopping (TSH) nonadiabatic molecular dynamics algorithm to simulate plasmon relaxation in Au20 clusters, taking the atomistic details into account. The electronic properties are treated within the Linear Response Time-Dependent Tight-binding Density Functional Theory (LR-TDDFTB) framework. The relaxation of plasmon due to coupling to phonon modes in Au20 beyond the Born-Oppenheimer approximation is described by the TSH algorithm. The numerically efficient LR-TDDFTB method allows us to address a dense manifold of excited states to ensure the inclusion of plasmon excitation. Starting from the photoexcited plasmon states in Au20 cluster, we find that the time constant for relaxation from plasmon excited states to the lowest excited states is about 2.7ps, mainly resulting from a stepwise decay process caused by low-frequency phonons of the Au20 cluster. Furthermore, our simulations show that the lifetime of the phonon-induced plasmon dephasing process is ∼10.4fs and that such a swift process can be attributed to the strong nonadiabatic effect in small clusters. Our simulations demonstrate a detailed description of the dynamic processes in nanoclusters, including plasmon excitation, hot carrier generation from plasmon excitation dephasing, and the subsequent phonon-induced relaxation process.

Theoretically probing the relationship between barrier length and resistance in Al/AlO[formula omitted]/Al tunnel junctions

Al/AlOx/Al tunnel junctions, also known as Josephson Junctions, are key components of many established and emerging electronic devices. They are an essential component of superconducting qubits. A major drawback is a lack of understanding of how the amorphous AlOx barrier influences the electron transport properties. In this work we combined Tight Binding Density Functional Theory (DFTB) with Non Equilibrium Greens Function (NEGF) to study computationally several Al/AlOx/Al with different barrier lengths. The simulations reveal a weak exponential relationship between barrier length and resistance of the device. However, considerable variability is found between junctions of similar barrier length. The calculations provide evidence of an “effective” barrier length significantly smaller than the actual (physical) barrier length. The resistance and effective barrier is found to be sensitively influenced by the local atomic structure of the amorphous barrier, which explains the junction to junction variability.

Nonadiabatic molecular dynamics simulations based on time-dependent density functional tight-binding method.

Nonadiabatic excited state molecular dynamics underpin many photophysical and photochemical phenomena, such as exciton dynamics, and charge separation and transport. In this work, we present an efficient nonadiabatic molecular dynamics (NAMD) simulation method based on time-dependent density functional tight-binding (TDDFTB) theory. Specifically, the adiabatic electronic structure, an essential NAMD input, is described at the TDDFTB level. The nonadiabatic effects originating from the coupled motions of electrons and nuclei are treated by the trajectory surface hopping algorithm. To improve the computational efficiency, nonadiabatic couplings between excited states within the TDDFTB method are derived and implemented using an analytical approach. Furthermore, the time-dependent nonadiabatic coupling scalars are calculated based on the overlap between molecular orbitals rather than the Slater determinants to speed up the simulations. In addition, the electronic decoherence scheme and a state reassigned unavoided crossings algorithm, which has been implemented in the NEXMD software, are used to improve the accuracy of the simulated dynamics and handle trivial unavoided crossings. Finally, the photoinduced nonadiabatic dynamics of a benzene molecule are simulated to demonstrate our implementation. The results for excited state NAMD simulations of benzene molecule based on TDDFTB method compare well to those obtained with numerically expensive time-dependent density functional theory. The proposed methodology provides an attractive theoretical simulation tool for predicting the photophysical and photochemical properties of complex materials.

A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides.

Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers (Phys. Chem. Chem. Phys.2020, 22, 7169−719232073075 and J. Chem. Theory. Comput.2019, 15, 2847–286230943025) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.

Atomistic Modeling of the Electrical Conductivity of Single‐Walled Carbon Nanotube Junctions

Carbon nanotubes (CNTs) have many interesting properties that make them a focus of research in a wide range of technological applications. In CNT films, the bottleneck in charge transport is typically attributed to higher resistance at CNT junctions, leading to electrical transport characteristics that are quite different from individual CNTs. Previous simulations confirm this; however, a systematic study of transport across junctions is still lacking in the literature. Herein, density functional tight binding (DFTB) theory combined with the nonequilibrium Green's functions (NEGF) method is used to systematically calculate current across a range of CNT junctions. A random sampling approach is used to sample an extensive library of junction structures. The results demonstrate that the conductivity of CNT contacts depends on the overlap area between nanotubes and exponentially on the distances between the carbon atoms of the interacting CNTs. Two models based solely on the atomic positions of carbon atoms within the nanotubes are developed and evaluated: a simple equation using only the smallest C–C separation and a more sophisticated model using the positions of all C atoms. These junction current models can be used to predict transport in larger‐scale simulations where the CNT fabric structure is known.

Quantum Perturbation Theory Using Tensor Cores and a Deep Neural Network.

Time-independent quantum response calculations are performed using Tensor cores. This is achieved by mapping density matrix perturbation theory onto the computational structure of a deep neural network. The main computational cost of each deep layer is dominated by tensor contractions, i.e., dense matrix-matrix multiplications, in mixed-precision arithmetics, which achieves close to peak performance. Quantum response calculations are demonstrated and analyzed using self-consistent charge density-functional tight-binding theory as well as coupled-perturbed Hartree-Fock theory. For linear response calculations, a novel parameter-free convergence criterion is presented that is well-suited for numerically noisy low-precision floating point operations and we demonstrate a peak performance of almost 200 Tflops using the Tensor cores of two Nvidia A100 GPUs.

Modification of benzoindenothiophene-based organic dye with fused thiophenes for efficient dye-sensitized solar cells

Recently low-energy-gap benzoindenothiophene (BIT)-based organic dyes have been experimentally sensitized to dye-sensitized solar cells (DSSCs) with impressive 10.9% power conversion efficiency. This paper presents a computational study of the modification of BIT-based dyes with fused thiophene moieties to build novel low band gap sensitizers. Density functional theory (DFT), tight-binding DFT, and time dependent DFT (TDDFT) approaches are used to demonstrate the electronic and optical properties of the BIT dyes and dye/(TiO2)46 complexes. Our calculations show that the structural modification by using fused thiophenes can effectively lower the band gap of the BIT dyes by 0.07–0.12 eV and affect the optical properties of BIT dyes. Enlarging the thiophene unit in BIT with thienothiophene and dithienothiophene improves the oscillator strength by 14%–25%, while the lowest-energy absorption peak basically remains at 559 nm. The incorporation of cyclopentadithiophene unit leads to a significant 47 nm red-shift of absorption peak and a 25% enhanced oscillator strength, compared to the original BIT dye. Those fused thiophenes modified BIT dyes also demonstrate ideal molecular orbital distribution patterns and ultra-fast injection time at the dye/(TiO2)46 interface. Our calculations provide useful guidance for the molecular design of novel naphthalene-based dyes for DSSC optimizations.

Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition

Cysteine proteases are an important target for the development of inhibitors that could be used as drugs to regulate the activity of these kinds of enzymes involved in many diseases, including COVID-19. For this reason, it is important to have methodological tools that allow a detailed study of their activity and inhibition, combining computational efficiency and accuracy. We here explore the performance of different quantum mechanics/molecular mechanics methods to explore the inhibition reaction mechanism of the SARS-CoV-2 3CL protease with a hydroxymethyl ketone derivative. We selected two density functional theory (DFT) functionals (B3LYP and M06-2X), two semiempirical Hamiltonians (AM1d and PM6), and two tight-binding DFT methods (DFTB3 and GFN2-xTB) to explore the free energy landscape associated with this reaction. We show that it is possible to obtain an accurate description combining molecular dynamics simulations performed using tight-binding DFT methods and single-point energy corrections at a higher QM description. The use of a computational strategy that provides reliable results at a reasonable computational cost could assist the in silico screening of possible candidates during the design of new drugs directed against cysteine proteases.