Density-functional Tight-binding Method Research Articles

Reduction pathway of glutaredoxin 1 investigated with QM/MM molecular dynamics using a neural network correction.

Glutaredoxins are small enzymes that catalyze the oxidation and reduction of protein disulfide bonds by the thiol-disulfide exchange mechanism. They have either one or two cysteines in their active site, resulting in different catalytic reaction cycles that have been investigated in many experimental studies. However, the exact mechanisms are not yet fully known, and to our knowledge, no theoretical studies have been performed to elucidate the underlying mechanism. In this study, we investigated a proposed mechanism for the reduction of the disulfide bond in the protein HMA4n by a mutated monothiol Homo sapiens glutaredoxin and the co-substrate glutathione. The catalytic cycle involves three successive thiol-disulfide exchanges that occur between the molecules. To estimate the regioselectivity of the different attacks, classical molecular dynamics simulations were performed and the trajectories analyzed regarding the sulfur-sulfur distances and the attack angles between the sulfurs. The free energy profile of each reaction was obtained with hybrid quantum mechanical/molecular mechanical metadynamics simulations. Since this required extensive phase space sampling, the semi-empirical density functional tight-binding method was used to describe the reactive cysteines. For an accurate description, we used specific reaction parameters fitted to B3LYP energies of the thiol-disulfide exchange and a machine learned energy correction that was trained on coupled-cluster single double perturbative triple [CCSD(T)] energies of thiol-disulfide exchanges. Our calculations show the same regiospecificity as observed in the experiment, and the obtained barrier heights are about 12 and 20 kcal/mol for the different reaction steps, which confirms the proposed pathway.

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.

Efficient simulation of resonance Raman spectra with tight-binding approximations to density functional theory.

Resonance Raman spectroscopy has long been established as one of the most sensitive techniques for detection, structure characterization, and probing the excited-state dynamics of biochemical systems. However, the analysis of resonance Raman spectra is much facilitated when measurements are accompanied by Density Functional Theory (DFT) calculations that are expensive for large biomolecules. In this work, resonance Raman spectra are therefore computed with the Density Functional Tight-Binding (DFTB) method in the time-dependent excited-state gradient approximation. To test the accuracy of the tight-binding approximations, this method is first applied to typical resonance Raman benchmark molecules, such as β-carotene, and compared to results obtained with pure and range-separated exchange-correlation functionals. We then demonstrate the efficiency of the approach by considering a computationally challenging heme variation. Overall, we find that the vibrational frequencies and excited-state properties (energies and gradients) that are needed to simulate the spectra are reasonably accurate and suitable for interpretation of experiments. We can therefore recommend DFTB as a fast computational method to interpret resonance Raman spectra.

Hybrid Carbon Nanotubes-Graphene Nanostructures: Modeling, Formation, Characterization.

A technology for the formation and bonding with a substrate of hybrid carbon nanostructures from single-walled carbon nanotubes (SWCNT) and reduced graphene oxide (rGO) by laser radiation is proposed. Molecular dynamics modeling by the real-time time-dependent density functional tight-binding (TD-DFTB) method made it possible to reveal the mechanism of field emission centers formation in carbon nanostructures layers. Laser radiation stimulates the formation of graphene-nanotube covalent contacts and also induces a dipole moment of hybrid nanostructures, which ensures their orientation along the force lines of the radiation field. The main mechanical and emission characteristics of the formed hybrid nanostructures were determined. By Raman spectroscopy, the effect of laser radiation energy on the defectiveness of all types of layers formed from nanostructures was determined. Laser exposure increased the hardness of all samples more than twice. Maximum hardness was obtained for hybrid nanostructure with a buffer layer (bl) of rGO and the main layer of SWCNT—rGO(bl)-SWCNT and was 54.4 GPa. In addition, the adhesion of rGO to the substrate and electron transport between the substrate and rGO(bl)-SWCNT increased. The rGO(bl)-SWCNT cathode with an area of ~1 mm2 showed a field emission current density of 562 mA/cm2 and stability for 9 h at a current of 1 mA. The developed technology for the formation of hybrid nanostructures can be used both to create high-performance and stable field emission cathodes and in other applications where nanomaterials coating with good adhesion, strength, and electrical conductivity is required.

(Invited) Simulating Dynamic Excitons Via Quantum Molecular Dynamics: A Case Study in Lead Halide Perovskites

The ultrafast electronic and structural dynamics invoked by photoexcitation, i.e., “dynamic exciton” phenomena, not only are important in the context of practical applications such as solar cells, but also raise many questions from the viewpoint of fundamental science. Experimental measurement, computational simulations, and theoretical interpretation will be the three pillars for deciphering the dynamic exciton phenomena.From the viewpoint of computational simulations, molecular dynamics (MD) techniques combined with quantum chemical calculations, i.e., quantum molecular dynamics (QMD), has been the popular tool to simulate the dynamic exciton phenomena. The quantum chemical calculations, which are typically conducted on the basis of the density-functional theory (DFT), require the large computational resources and time. These have been the limiting factors for the accessible spatial and time scales by the QMD simulations.To extend the coverage of simulations to more complex, large-scale systems, we have developed efficient excited-state QMD methods that can include nonadiabatic effects. Our method combines the density-functional tight binding (DFTB) method, which is an approximate DFT, and the surface hopping method, which is a theoretical framework to incorporate the nonadiabatic effects into the QMD simulations. The method was further improved to be suitable for condensed-phase simulations explicitly including the environment, i.e., solvent, by using a “divide-and-conquer” style quantum chemical calculation technique. These theoretical framework enables us to simulate the coupled electronic–structural dynamics in excited states of systems consisting of 102–103 atoms[1,2,3].In addition, using the developed method, we conducted the real-time simulations of the ultrafast processes invoked by photoexcitation of lead iodide perovskites, which are known as the key materials for perovskite solar cells. The dissociation of the exciton into the positive and negative charge carriers was observed. Moreover, the hot carrier cooling, where the charge carriers dissipate excess energy via the electron–phonon coupling and relax to the band edges, was also tracked. Finally, the direct evidence of the polaron formation, where the structural deformation is induced by the presence of charge carriers, was observed. These results highlight the importance of the coupling between electronic and structural degrees of freedom.In the talk, recent improvements in the methodology and future perspectives will also be presented[5].

The effect of molecular decoration on formation of curved and twisted graphene

The formation of curved and twisted ThMoB4-type sheet graphene (TSG) surface via adsorption of the ethylene carbonate(EC) solvent molecule has been theoretically investigated. The calculation has been performed by one of the extended self-consistent-charge density-functional tight-binding methods named as GFN1-xTB. During the calculation, six different possibilities of decorations for EC molecule have been tried. These decorations are considered thermodynamically stable for TSG surface. We obtained the optimized lattice parameters, surface areas and adsorption energies (Ead) for six surface decorations. We reveal that the value of Ead is the main reason for the difference in the formation of the surface. The zigzag configuration of the graphene results in the positive and large Ead value of +4.4 eV leading to the curved surface which is bending toward the adsorbed molecule. In the case of adsorption of EC which is decorated at the armchair site, the surface is perfectly twisted due to the Ead value of -2.45 eV. Furthermore, the change in UV–vis/IR spectrum concerning the formation of the structure has been analyzed. Our results claim that this type of graphene structure can be a candidate for the application of chemical or biological sensing.

Effect of Functionalization with Potassium Atoms on the Electronic Properties of a 3D Glass-like Nanomaterial Reinforced with Carbon Nanotubes: In Silico Study

In this paper, using the self-consistent charge density-functional tight-binding (SCC DFTB) method, we perform an in silico study of the effect of functionalization by potassium atoms on the electronic properties of a new configuration of the glass-like carbon (GLC) reinforced with (4,4) and (6,5) single-walled carbon nanotubes (SWCNTs). The method of classical molecular dynamics was used to obtain energetically stable GLC configurations with different mass fractions of potassium. It is found that with an increase in the mass fraction of SWCNTs, the elasticity of GLC increases. It is shown that when the GLC structure reinforced with SWCNTs is filled with potassium, the number of available electronic states at the Fermi level increases compared to GLC without nanotubes, which significantly improves the emission and electrophysical characteristics of the carbon nanomaterial. For most structures, at a potassium/carbon mass ratio of 1:100 (0.01), an increase in the Fermi energy is observed, and, hence, a decrease in the work function. The maximum decrease in the work function by ~0.3 eV was achieved at a mass ratio of potassium/carbon of 1:4.5 (0.23) for GLC reinforced with (6,5) SWCNTs. It is revealed that, at a mass ratio of potassium/carbon of 1:28.5 (0.035), the quantum capacitance of GLC reinforced with (4,4) and (6,5) SWCNTs increases by ~9.4% (1752.63 F/g) and 24.1% (2092.04 F/g), respectively, as compared to GLC without nanotubes (1587.93 F/g). Based on the results obtained, the prospects for the application of the proposed GLC configuration in emission electronics devices are predicted.

Effects of chiral index, vacancy defects and external electric field on the structures and electronic properties of DWSiNTs by SCC-DFTB calculations

As a new candidate material, silicon nanotubes (SiNTs) have been widely studied. However, various types of structural defects and external electric field are usually inescapability introduced in the experimental process of SiNTs synthesis. Structures, stability and electronic properties of the materials especially for double-walled silicon nanotubes (DWSiNTs) require to be considered. In this work, effects of vacancy defects and external electric field on properties of the geometrically structural optimization and electronic properties of DWSiNTs zigzag (3,0)@(7,0) and armchair (3,3)@(7,7) are studied via the self-consistent charge density functional tight binding (SCC-DFTB) method. The results of us show that the regular arrangement of the atoms, quantum molecular descriptors, distribution of charge, the degree of warping, stability, energy gap and Fermi energy levels intensely hinge on the chirality index of the tube and impacts of vacancy defects and electric field. Especially, the appearance of monovacancy and the change of vacancy density have the most significant effect on the band gap. For the pristine tubes, the charges transfer from the inside to the outside along the radial direction of the tube exhibiting an axisymmetric distribution. With the introduction of defects, the range of the charge transfer is broadened dramatically. The direction of charge transfer in the applied electric field is always opposite to the field direction. Our work may provide a new route to tune the electronic properties of DWSiNTs and opens a wider field of its application in nano-electronic devices.

Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions.

We present a fast, accurate, and robust approach for determination of free energy profiles and kinetic isotope effects for RNA 2'-O-transphosphorylation reactions with inclusion of nuclear quantum effects. We apply a deep potential range correction (DPRc) for combined quantum mechanical/molecular mechanical (QM/MM) simulations of reactions in the condensed phase. The method uses the second-order density-functional tight-binding method (DFTB2) as a fast, approximate base QM model. The DPRc model modifies the DFTB2 QM interactions and applies short-range corrections to the QM/MM interactions to reproduce ab initio DFT (PBE0/6-31G*) QM/MM energies and forces. The DPRc thus enables both QM and QM/MM interactions to be tuned to high accuracy, and the QM/MM corrections are designed to smoothly vanish at a specified cutoff boundary (6 Å in the present work). The computational speed-up afforded by the QM/MM+DPRc model enables free energy profiles to be calculated that include rigorous long-range QM/MM interactions under periodic boundary conditions and nuclear quantum effects through a path integral approach using a new interface between the AMBER and i-PI software. The approach is demonstrated through the calculation of free energy profiles of a native RNA cleavage model reaction and reactions involving thio-substitutions, which are important experimental probes of the mechanism. The DFTB2+DPRc QM/MM free energy surfaces agree very closely with the PBE0/6-31G* QM/MM results, and it is vastly superior to the DFTB2 QM/MM surfaces with and without weighted thermodynamic perturbation corrections. 18O and 34S primary kinetic isotope effects are compared, and the influence of nuclear quantum effects on the free energy profiles is examined.

Designing 1D correlated-electron states by non-Euclidean topography of 2D monolayers

Two-dimensional (2D) bilayers, twisted to particular angles to display electronic flat bands, are being extensively explored for physics of strongly correlated 2D systems. However, the similar rich physics of one-dimensional (1D) strongly correlated systems remains elusive as it is largely inaccessible by twists. Here, a distinctive way to create 1D flat bands is proposed, by either stamping or growing a 2D monolayer on a non-Euclidean topography-patterned surface. Using boron nitride (hBN) as an example, our analysis employing elastic plate theory, density-functional and coarse-grained tight-binding method reveals that hBN’s bi-periodic sinusoidal deformation creates pseudo- electric and magnetic fields with unexpected spatial dependence. A combination of these fields leads to anisotropic confinement and 1D flat bands. Moreover, changing the periodic undulations can tune the bandwidth, to drive the system to different strongly correlated regimes such as density waves, Luttinger liquid, and Mott insulator. The 1D nature of these states differs from those obtained in twisted materials and can be exploited to study the exciting physics of 1D quantum systems.

Comprehensive Study of the Chemistry behind the Stability of Carboxylic SWCNT Dispersions in the Development of a Transparent Electrode.

Single-walled carbon nanotubes (SWCNTs) are well-known for their excellent electrical conductivity. One promising application for SWCNT-based thin films is as transparent electrodes for uncooled mid-IR detectors (MIR). In this paper, a combination of computational and experimental studies were performed to understand the chemistry behind the stability of carboxylic SWCNTs (SWCNTs-COOH) dispersions in different solvents. A computational study based on the density functional tight-binding (DFTB) method was applied to understand the interactions of COOH-functionalized carbon nanotubes with selected solvents. Attention was focused on understanding how the protonation of COOH groups influences the binding energies between SWCNTs and different solvents. Thin film electrodes were prepared by alternately depositing PEI and SWCNT-COOH on soda lime glass substrates. To prepare a stable SWCNT dispersion, different solvents were tested, such as deionized (DI) water, ethanol and acetone. The SWCNT-COOH dispersion stability was tested in different solvents. Samples were prepared to study the relationship between the number of depositions, transparency in the MIR range (2.5–5 µm) and conductivity, looking for the optimal thickness that would satisfy the application. The MIR transparency of the electrode was reduced by 20% for the thickest SWCNT layers, whereas sheet resistance values were reduced to 150–200 kΩ/sq.

A General Use QSAR-ARX Model to Predict the Corrosion Inhibition Efficiency of Drugs in Terms of Quantum Mechanical Descriptors and Experimental Comparison for Lidocaine.

A study of 250 commercial drugs to act as corrosion inhibitors on steel has been developed by applying the quantitative structure-activity relationship (QSAR) paradigm. Hard-soft acid-base (HSAB) descriptors were used to establish a mathematical model to predict the corrosion inhibition efficiency (IE%) of several commercial drugs on steel surfaces. These descriptors were calculated through third-order density-functional tight binding (DFTB) methods. The mathematical modeling was carried out through autoregressive with exogenous inputs (ARX) framework and tested by fivefold cross-validation. Another set of drugs was used as an external validation, obtaining SD, RMSE, and MSE, obtaining 6.76%, 3.89%, 7.03%, and 49.47%, respectively. With a predicted value of IE% = 87.51%, lidocaine was selected to perform a final comparison with experimental results. By the first time, this drug obtained a maximum IE%, determined experimentally by electrochemical impedance spectroscopy measurements at 100 ppm concentration, of about 92.5%, which stands within limits of 1 SD from the predicted ARX model value. From the qualitative perspective, several potential trends have emerged from the estimated values. Among them, macrolides, alkaloids from Rauwolfia species, cephalosporin, and rifamycin antibiotics are expected to exhibit high IE% on steel surfaces. Additionally, IE% increases as the energy of HOMO decreases. The highest efficiency is obtained in case of the molecules with the highest ω and ΔN values. The most efficient drugs are found with pKa ranging from 1.70 to 9.46. The drugs recurrently exhibit aromatic rings, carbonyl, and hydroxyl groups with the highest IE% values.

Combining classical molecular docking with self-consistent charge density-functional tight-binding computations for the efficient and quality prediction of ligand binding structure

To improve the successful prediction rate of the existing molecular docking methods, a new docking approach is proposed that consists of three steps: generating an ensemble of docked poses with a conventional docking method, performing clustering analysis of the ensemble to select the representative poses, and optimizing the representative structures with a low-cost quantum mechanics method. Three quantum mechanics methods, self-consistent charge density-functional tight-binding, ONIOM(DFT:PM6), and ONIOM(SCC-DFTB:PM6), are tested on 18 ligand-receptor bio-complexes. The rate of successful binding pose predictions by the proposed self-consistent charge density-functional tight-binding docking method is the highest, at 67%. The self-consistent charge density-functional tight-binding docking method should be useful for the structure-based drug design.

Pareto Optimization of Oligomer Polarizability and Dipole Moment Using a Genetic Algorithm.

High-performance electronic components are highly sought after in order to produce increasingly smaller and cheaper electronic devices. Drawing inspiration from inorganic dielectric materials, in which both polarizability and polarization contribute, organic materials can also maximize both. For a large set of small molecules drawn from PubChem, a Pareto-like front appears between the polarizability and dipole moment, indicating the presence of an apparent trade-off between these two properties. We tested this balance in π-conjugated materials by searching for novel conjugated hexamers with simultaneously large polarizabilities and dipole moments with potential use for dielectric materials. Using a genetic algorithm (GA) screening technique in conjunction with an approximate density functional tight-binding method for property calculations, we were able to efficiently search chemical space for optimal hexamers. Given the scope of chemical space, using the GA technique saves considerable time and resources by speeding up molecular searches compared to a systematic search. We also explored the underlying structure-function relationships, including sequence and monomer properties, that characterize large polarizability and dipole moment regimes.

Electronic properties and behavior of carbon network based on graphene and single-walled carbon nanotubes in strong electrical fields: quantum molecular dynamics study

Using the self-consistent-charge density-functional tight-binding method (SCC-DFTB) and extended lagrangian DFTB-based molecular dynamics, we performed in silico studies of the behavior of graphene–nanotube hybrid structures that are part of a branched 3D carbon network in strong electrical fields. It has been established that strong fields with strength ranging from 5 to 10 V nm−1 cause oscillating deformations of the atomic framework with a frequency in the range from 1.22 to 1.38 THz. It has been revealed that the oscillation frequency is determined primarily by the topology of the atomic framework of graphene–nanotube hybrid, while the electric field strength has an effect within 1%–2%. A further increase in electric field strength reduces the oscillation frequency to 0.7 THz, which accompanies the partial destruction of the atomic framework. The critical value of the electric field strength when the graphene is detached from the nanotube is ∼20 V nm−1.

3 + 2] Cycloadditions and Retrocycloadditions of Niobium Imido Complexes: An Experimental and Computational Mechanistic Study.

We demonstrate reactivity between a β-diketiminate-supported niobium(III) imido complex and alkyl azides to form niobatetrazene complexes (BDI)Nb(NtBu)(RNNNNR) (BDI = N,N-bis(2,6-diisopropylphenyl)-3,5-dimethyl-β-diketiminate; R = cyclohexyl (1), benzyl (2)). Intriguingly, niobatetrazene complexes 1 and 2 can be interconverted via addition of an appropriate alkyl azide, likely through a series of concerted [3 + 2] cycloaddition and retrocycloaddition reactions in which π-loaded bis(imido) intermediates are formed. The bis(imido) intermediates were trapped upon addition of alkyl isocyanides to yield five-coordinate bis(imido) complexes (BDI)Nb(NtBu)(NCy)(CNR) (R = tert-butyl (4a), cyclohexyl (4b)). Two computational methods─density functional theory and density functional tight binding (DFTB)─were employed to calculate the lowest energy pathway across the potential energy surface for this multistep transformation. Reaction path calculations for individual cycloaddition or retrocycloaddition processes along the multistep reaction pathway showed that these transformations occur via a concerted, yet highly asynchronous mechanism, in which the two bond-breaking or -making events do not occur simultaneously. The use of the DFTB method in this work highlights its advantages and utility for studying transition metal systems.

Role of the Backbone when Optimizing Functional Groups─A Theoretical Study Based on an Improved Inverse-Design Approach.

We present an improved inverse-design approach for automatically identifying molecular (or other) systems with optimal values for prechosen properties. The new approach uses SMILES (simplified molecular input line entry system) to describe molecular structures efficiently, a genetic algorithm to optimize the molecules automatically, and the DFTB+ (self-consistent charge density functional tight-binding) method to calculate electronic properties. Thereby, almost every class of materials─even macromolecules or monomers─can be studied easily. Without crossover operators but with only mutation operators, the genetic algorithm is more adaptive to SMILES while keeping its efficiency. DFTB+ is more accurate than the DFTB method used in our previous inverse-design approach for the study of excited states and charge transfer processes. The improved approach is applied to optimize benzene, pyridine, pyridazine, pyrimidine, and pyrazine derivatives for seven electronic properties, which all are highly relevant and important for the performance of molecules in solar cells. We found that for some electronic properties, the precise composition and structure of the backbone have remarkable impacts on the value of the electronic properties and/or on the set of functional groups that leads to the best performance. On the contrary, for other properties, these effects are less pronounced. The reasonable optimal functional groups and/or substitution patterns are reported.

DNA-Mimicking Metal-Organic Frameworks with Accessible Adenine Faces for Complementary Base Pairing.

Biologically derived metal–organic frameworks (Bio-MOFs) are significant, as they can be used in cutting-edge biomedical applications such as targeted gene delivery. Herein, adenine (Ade) and unnatural amino acids coordinate with Zn2+ to produce biocompatible frameworks, KBM-1 and KBM-2, with extremely defined porous channels. They feature an accessible Watson–Crick Ade face that is available for further hydrogen bonding and can load single-stranded DNA (ssDNA) with 13 and 41% efficiency for KBM-1 and KBM-2, respectively. Treatment of these frameworks with thymine (Thy), as a competitive guest for base pairing with the Ade open sites, led to more than 50% reduction of ssDNA loading. Moreover, KBM-2 loaded Thy-rich ssDNA more efficiently than Thy-free ssDNA. These findings support the role of the Thy-Ade base pairing in promoting ssDNA loading. Furthermore, theoretical calculations using the self-consistent charge density functional tight-binding (SCC-DFTB) method verified the role of hydrogen bonding and van der Waals type interactions in this host–guest interface. KBM-1 and KBM-2 can protect ssDNA from enzymatic degradation and release it at acidic pH. Most importantly, these biocompatible frameworks can efficiently deliver genetic cargo with retained activity to the cell nucleus. We envisage that this class of Bio-MOFs can find immediate applicability as biomimics for sensing, stabilizing, and delivering genetic materials.

Annihilation dynamics of a dislocation pair in graphene: Density-functional tight-binding molecular dynamics simulations and first principles study

The time evolution of a dislocation pair in graphene is investigated by performing subnanosecond-scale molecular dynamics simulations based on the density-functional tight-binding method. The simulations show the self-healing behavior of the graphene lattice, resulting in complete annihilation of dislocations, that is, the formation of the pristine graphene structure. To understand the mechanism of the structural developments, first principles calculations are performed for the principal dislocation structures observed in the density-functional tight-binding/molecular dynamics simulations. We reveal the characteristic bonding states in the area around the dislocation structures by bond analyses based on the Wiberg bond index and crystal orbital Hamilton population approaches. The unusual local bonding states mainly originate from geometrical features of the out-of-plane deformation of the dislocation structures. The annihilation processes of dislocations in graphene are discussed in relation to the local bonding states of the dislocation structures.

Benchmarks of the density functional tight-binding method for redox, protonation and electronic properties of quinones.

Organic materials with controllable molecular design and sustainable resources are promising electrode materials. Crystalline quinones have been investigated in a variety of rechargeable battery chemistries due to their ubiquitous nature, voltage tunability and environmental friendliness. In acidic electrolytes, quinone crystals can undergo proton-coupled electron transfer (PCET), resulting in charge storage. However, the detailed mechanism of this phenomenon remains elusive. To model PCET in crystalline quinones, force field-based methods are not viable due to variable redox states of the quinone molecules during battery operation and computationally efficient quantum mechanical methods are strongly desired. The semi-empirical density functional tight-binding (DFTB) method has been widely used to study inorganic crystalline systems and biological systems but has not been comprehensively benchmarked for studying charge transport in quinones. In this work, we benchmark the third order variant of DFTB (DFTB3) for the reduction potential of quinones in aqueous solution, energetics of proton transfer between quinones and between quinones and water, and structural and electronic properties of crystalline quinones. Our results reveal the deficiencies of the DFTB3 method in describing the proton affinity of quinones and the structural and electronic properties of crystalline quinones, and highlight the need for further development of the DFTB method for describing charge transport in crystalline quinones.