Self-consistent Charge Density-functional Tight-binding Method Research Articles

Structure and electrical properties of bilayer zigzag silicene nanoribbons depending on stone-wales and applied electric fields by SCC-DFTB method

The influence of geometry and electrical properties of Stone-Wales (SW) defects and an applied electric field on bilayer zigzag silicene nanoribbons (ZSiNRs) were investigated using the self-consistent charge density functional tight-binding (SCC-DFTB) method. The results show that concave deformation occurs at SW defects, leading to varying degrees of disruption in the original symmetrical structure. The overall stability of the marginal Stone-Wales (MSW) nanoribbons surpasses that of the central Stone-Wales (CSW) nanoribbons, SW-II type defects are prone to form in bilayer nanoribbons. The band gap of MSW defective nanoribbons expands significantly, realizing the transition from metallic to semi-metallic and semi-conductor properties. The electrons are transferred from the inner to the outer side of the nanoribbons, with a higher prevalence of defect nanoribbons compared to those that are perfect. The electric field intensity significantly alters the properties of both MSW-I and MSW-II defective nanoribbons.

Structure and electrical properties of double-walled silicon nanotubes depending on 585 defects and applied electric fields by SCC-DFTB method

The geometric structural and electronic properties of 585 defective double-walled silicon nanotubes (DWSiNTs) by using the self-consistent charge density functional tight-binding (SCC-DFTB) method. Furthermore, we investigated the impact of external electric field and intensity on the electronic properties. After the relaxation of perfect tubes, the structure of the tube changes significantly, and the winding direction of the tube wall changes. The buckling value of the tube wall is most closely related to the geometric shape and atomic arrangement order of tubes. The overall stability of zigzag tubes is higher than armchair tubes, and (6,6)@(10,10) stability is significantly affected by defects. The partially defected zigzag tubes change from direct band gap semiconductor properties to indirect band gap semi-metal properties. A transformation of the semiconductor-semimetal properties, direct-indirect band gap of DWSiNTs is realized. The charge transfer amplitude of the defect tubes is greater than the perfect tube. The applied electric field makes the stability of all tubes decrease linearly, and the stability of the defect tubes is higher than the perfect tube. Part of the electric field strength changes the defect tubes from semiconductor properties to semi-metal properties, and semi-metal properties to metal properties. These theoretical studies provide a reference for the preparation and future application of DWSiNTs.

Effects of Stone-Wales defects on structure and electrical properties of double-walled silicon nanotubes by SCC-DFTB method

In this work, the geometric structure, system stability, electrical properties and charge distribution of zigzag double-walled silicon nanotubes (DWSiNTs) (nin,0)@(nout,0) (nin = 5–7, nout = 8–13) perfect tubes and defective tubes with three types of Stone-Wales (SW) defects were studied using the self-consistent charge density functional tight-binding (SCC-DFTB) method. The change of the chirality index between the inner and outer walls was simulated. The results show that the symmetry of the structure disappears, and the warping of the tube wall changes from order to disorder after introducing SW defects. The warps of outer tube are obviously higher than that of inner tube. The perfect tubes with inner wall chirality index (6,0) are more stable than other tubes. SW defects of outer wall tubes have a higher effect on system stability than those of inner wall tubes. The difference of inner and outer wall chirality indices plays an obvious role in regulating the energy gap of the system, half of which are near-metal properties and the other half semiconductor properties, and the regulation range is 0.1075–0.8519 eV. All types of SW defects at all locations have a certain regulatory effect on the energy gap of DWSiNTs, and the effect of type III defect is the most obvious. The effect of atomic charge redistribution in the tube is related to the structure, and the charge transfer in a perfect tube is symmetrical. The number of electrons obtained at the defect is increased, and the electronegativity is stronger, due to the curvature of local atoms produced at the defect. This study provides a reference for the preparation and future application of DWSiNTs.

Early Events When Heating 1,1-Diamino-2,2-dinitroethylene: Self-Consistent Charge Density-Functional Tight-Binding Molecular Dynamics Simulations

A self-consistent charge density-functional tight-binding method combined with molecular dynamics (MD) simulations and static density functional theory (DFT) calculations is employed to reveal the initial steps responsible for the thermal decay of the low sensitive and high energetic material (EM) 1,1-diamino-2,2-dinitroethylene (FOX-7). Constant temperature heating and temperature-programmed heating are accounted in our MD simulations to resemble the practice. We find that the heating style has an impact on the initial decomposition mechanism of FOX-7. The N–O bond rupture to produce an O radical is observed for the first time in the temperature-programmed heating simulation from 300 to 3000 K, together with the C–NO2 bond cleavage. We also first capture the intra- and intermolecular hydrogen transferred structures in our constant temperature heating simulation at 3000 K, and in this case, the NO2 partition serves as another kind of primary step for thermally decaying FOX-7 too. Static DFT calculations s...

Improvement of the self-consistent-charge density-functional-tight-binding theory by a modified Mulliken charge

Although extensive efforts had been carried out to improve the accuracy of the self-consistent-charge density-functional-tight-binding (SCC-DFTB), the application of SCC-DFTB on biological systems (e.g., enzymes) is still limited. Our benchmark calculations show that the original SCC-DFTB/MM is not able to properly descript the human carboxylesterase 1 (CES1) catalyzed hydrolysis of d-threo-methylphenidate (dMD). In contrast to the ab initio QM/MM results, SCC-DFTB/MM underestimates the activation free energy barrier and renders the acylation process as a single-step reaction without a tetrahedral intermediate. It seems like that SCC-DFTB/MM misestimates the developing negative QM Mulliken charge of the substrate oxygen atom in the oxyanion hole. To improve the SCC-DFTB energy and the electrostatic interaction between QM (SCC-DFTB) and MM atoms, we adopt an optimization strategy for QM Mulliken charge, in which an empirical parameter is trained to fit the SCC-DFTB Mulliken charge to high-level DFT method along the reaction coordinate. Herein, the optimized Mulliken charge-based SCC-DFTB method is denoted as SCC-DFTBMR. Finally, benchmark and free energy calculations were performed to prove the applicability of SCC-DFTBMR to CES1-catalyzed reaction.

Effect of electronic excitation to intermolecular proton transfer in bulk nitromethane: Tuned parameter SCC-DFTB and first principles study

To understand the reaction mechanism involving hydrogen transfers through hydrogen-bond bridge, we carried out both Self-Consistent Charge Density Functional Tight-Binding (SCC-DFTB) calculations of bulk nitromethane and Density Functional Theory (DFT) calculations of singlet ground state/triplet excited state molecular nitromethane using B3LYP functional. Firstly, we tuned the repulsive parameters of the SCC-DFTB method for nitromethane with dataset calculated from DFT at B3LYP/6-311g level. The molecular dynamics simulations are carried out with tuned parameters to get the dynamical properties of the bulk nitromethane, and the static calculations are intended to give energy profile of the reaction process. These calculations indicate the excitation of nitromethane molecule making the proton transfer reactions possible, and lowering the reaction barrier.

Effect of defect and temperature on the mechanical and electronic properties of graphdiyne: A theoretical study

In the present work, the elastic properties (in-plane stiffness and Young's modulus) of graphdiyne, a two-dimensional lattice of sp–sp2-hybridized carbon atoms similar to graphene, are studied using a self-consistent charge density functional tight-binding (SCC-DFTB) method. The obtained results indicate that as the length of the graphdiyne increases in the x-direction, the in-plane stiffness and Young's modulus increase and finally approach constant values for longer lengths. Furthermore, based on the calculated density of states (DOS), we observed that graphdiyne is a semiconductor with a band gap energy of 0.43eV. A molecular dynamics simulation based on the SCC-DFTB method is also used to calculate the elastic properties of graphdiyne at five temperatures between 300 and 1500K. Our results indicate that the in-plane stiffness and Young's modulus of graphdiyne decrease as the temperature of the environment increases. Finally, we investigated the effect of different vacancies on the mechanical and electronic properties of graphdiyne. Our results reveal that increasing the number of removed carbon atoms leads to a decrease in the elastic parameters and band gap energy of graphdiyne.

SCC-DFTB calculation of the static first hyperpolarizability: From gas phase molecules to functionalized surfaces

The performance of the self-consistent charge density functional tight binding (SCC-DFTB) method for calculating the first hyperpolarizability of π-conjugated compounds has been assessed with respect to results obtained with high-level ab initio methods and density functional theory (DFT). The SCC-DFTB method performs similarly or better than DFT with the PBE XC functional. Thus, if for small π-conjugated linkers SCC-DFTB can reproduce trends, for longer chains the first hyperpolarizabilities are overestimated. In the case of push-pull thiophenes, the β values are strongly overestimated, as it is also the case with the B3LYP and PBE XC functionals. On the other hand, the SCC-DFTB method closely reproduces the evolution of β in p-disubstituted benzenes as a function of the donor and acceptor groups, as estimated at the MP2 level. The reliability of SCC-DFTB to determine the bond length alternation and the dihedral angles between the aromatic rings has also been tackled, demonstrating that both are underestimated. Overall, the SCC-DFTB calculations are of the same quality as those performed with the conventional PBE XC functional on which the method was parameterized but the SCC-DFTB calculations are computationally very little demanding, and it can therefore be adopted for very large systems for screening nonlinear optical materials as well as for assessing structure-property relationships. This is illustrated with an application on the first hyperpolarizability of an indolino-oxazolidine molecular switch grafted on a SiO2 surface. This has enabled to pinpoint (i) the effect of the surface on the donor/acceptor character of the linking substituent, (ii) the impact of molecular orientation, (iii) the role of a spacer between the π-conjugated switch and the surface, (iv) the global effect of the surface on the β contrast, and also (v) the fact that the molecular switches can maintain this contrast when adsorbed.

Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions

The self-consistent charge density functional tight binding (SCC-DFTB) method has been applied to hydroxide water clusters and a hydroxide ion in bulk water. To determine the impact of various implementations of SCC-DFTB on the energetics and dynamics of a hydroxide ion in gas phase and condensed phase, the DFTB2, DFTB2-γ(h), DFTB2-γ(h)+gaus, DFTB3-diag, DFTB3-diag+gaus, DFTB3-Full+gaus, and DFTB3-3OB implementations have been tested. Energetic stabilities for small hydroxide clusters, OH(-)(H2O)n, where n = 4-7, are inconsistent with the results calculated with the B3LYP and second order Møller-Plesset (MP2) levels of ab initio theory. The condensed phase simulations, OH(-)(H2O)127, using the DFTB2, DFTB2-γ(h), DFTB2-γ(h)+gaus, DFTB3-diag, DFTB3-diag+gaus, DFTB3-Full+gaus and DFTB3-3OB methods are compared to Car-Parrinello molecular dynamics (CPMD) simulations using the BLYP functional. The SCC-DFTB method including a modified O-H repulsive potential and the third order correction (DFTB3-diag/Full+gaus) is shown to poorly reproduce the CPMD computational results, while the DFTB2 and DFTB2-γ(h) method somewhat more closely describe the structural and dynamical nature of the hydroxide ion in condensed phase. The DFTB3-3OB outperforms the MIO parameter set but is no more accurate than DFTB2. It is also shown that the overcoordinated water molecules lead to an incorrect bulk water density and result in unphysical water void formation. The results presented in this paper point to serious drawbacks for various DFTB extensions and corrections for a hydroxide ion in aqueous environments.

Imogolite-like nanotubes: structure, stability, electronic and mechanical properties of the phosphorous and arsenic derivatives

Imogolite is a single-walled aluminosilicate nanotube (NT) found in nature that can be easily synthesized, as well as its analogue aluminogermanate NT. Based on geometrical assumptions and pKa values, species such as H3PO4, H3PO3, H3AsO3, H3AsO4 could also be candidates to form imogolite-like structures. In the present work, we provide insights about the stability, electronic, structural and mechanical properties of possible imogolite like NTs by means of self-consistent charge density-functional tight-binding method (SCC-DFTB). Similarly to aluminogermanate, where the tetrahedral silicate groups are replaced by germanate, in this work tetrahedral silicate groups are substituted by phosphate, phosphite, arsenate and arsenite units in the imogolite structure. Detailed analysis is focused on structural properties, strain energy, band gap and Mulliken charges distribution. The calculated strain energy curves for all studied zigzag imogolite-like NTs present well-defined minima, which change as a consequence of composition variation. Moreover, the strain energy curves of armchair imogolite-like NTs also present minima, although in all cases less stable than zigzags by at least 2.2 meV per atom. The insulating NT behaviour changes after internal modification from silicate to phosphate, phosphite, arsenate and arsenite, as well as the charge distribution inside and outside the nanotubes.

Structural Modification of TiO2 Surfaces in Bulk Water and Binding Motifs of a Functionalized C60 on TiO2 Anatase and Rutile Surfaces in Vacuo and in Water: Molecular Dynamics Studies

The nature of several TiO2 surfaces in liquid water, as well as the adsorption of a functionalized C60, L*C60 (where L is a carboxylic acid), on TiO2 anatase and rutile low index surfaces in vacuo and in liquid water have been studied at the self-consistent charge density functional tight-binding (SCC-DFTB) level of theory. It is shown that the SCC-DFTB method provides very good agreement with the high-level DFT data. The typical binding motif of L*C60@TiO2 is found to be the formation of a strong HC1C(O2H)O1–Ti5C/O1–Ti4C bond with a distance of 2.0–2.1 Å and a weaker HC1CO1O2–H···O2C/O2···H–O2C hydrogen bond. In some cases, a terminal OH of the linking group coordinates with a Ti–O–Ti bridging oxygen and loses the H to the surface. The adsorption energies in vacuum range between 21 and 82 kcal/mol depending on the surface. The density of states of these species reveals the presence of peaks below the surface conduction band upon ligand adsorption, which is due to the low-lying lowest unoccupied molecular orbitals (LUMOs) of the L*C60. Electron transfer from the surface to the ligand is thus possible via the initial UV photoexcitation of the surface followed by nonradiative relaxation of the excited electron to the LUMO of the ligand. This pattern was observed for all six surfaces considered in the present work. Solvation of C60@TiO2 in liquid water does not change the qualitative character of surface–ligand binding. In all cases, the ligand remains bound to the surface in the presence of water. The interaction of water molecules with the surface shows various patterns depending on the surface index. Anatase (101) and (100) surfaces favor nondissociative water adsorption, while anatase (001) and rutile (001), (110), and (101) surfaces show dissociative water adsorption which results in OH/OH2-terminated TiO2 surfaces. The latter finding is in agreement with several previous DFT studies reported by others.

Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment.

The solution conformations of biologically important mono- and di-α-d-arabinofuranosides were investigated using the dispersion-corrected self-consistent charge density functional tight binding (SCC-DFTB) and the AMBER/GLYCAM models. Simulations were performed using both long dynamics and umbrella sampling simulations. Angular distributions about the exocyclic C-C bonds and puckering distributions of the rings obtained from the SCC-DFTB model were quite different from those obtained with the AMBER/GLYCAM approach. The joint probability distribution of rotamer and ring puckering parameters reveals further discrepancies, while both methods predict weak correlation between exocyclic torsions and ring puckering. To assess the reliability of the simulations, ensemble-averaged vicinal proton-proton coupling constants ((3)JH,H) were calculated and compared directly to experimental NMR coupling constants. It is found that the (3)JH,H values obtained from the AMBER/GLYCAM simulations agree with experiment, while those obtained from the SCC-DFTB method, in most cases, differ from experimental (3)JH,H values. Potential energy surfaces (PES) along the exocyclic torsion obtained from ab initio and DFT calculations differ significantly from those obtained with the SCC-DFTB method. This study establishes that a high-quality all-atom force field would be more suitable than one of the superior semiempirical methods, SCC-DFTB, for investigation of rotamer populations and ring puckering in floppy ring systems such as furanosides.

Structural, Electronic, and Mechanical Properties of Single-Walled Chrysotile Nanotube Models

Structural, electronic, and mechanical properties of single-walled chrysotile nanotubes have been investigated using the self-consistent charge density-functional tight-binding method (SCC-DFTB). T...

Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water

The self-consistent charge density functional tight-binding (SCC-DFTB) method has been actively employed to study proton-transfer processes in biological systems. Recent studies in the literature employing SCC-DFTB reported that the method favors the Zundel form of the hydrated proton over the Eigen form, both in gas-phase water clusters and in bulk water, in disagreement with both higher-level calculations and experimental data. In this work, we explore the performance of SCC-DFTB for protonated gas-phase water clusters and bulk water (the latter both with and without an excess proton) with a modified O-H repulsive potential reported in our earlier work and with on-site third-order expansion of the DFT energy. Our results show that, with the proper set of published parameters, SCC-DFTB does correctly favor the Eigen form of the hydrated proton as compared to the Zundel form, both in gas-phase clusters and in the bulk; the amphiphilic character of the hydrated proton discussed in the literature has also been observed. The analyses do, however, bring forth remaining limitations in terms of the solvation structure around the hydrated proton as well as the structure of bulk water, which can guide future improvements of the method.

Effects of resonant scattering by probe contacts on nanoscale four-probe resistance measurements

The oscillation of the four-probe electric resistance of monatomic carbon chains as a function of electron energy was theoretically analysed on the basis of non-equilibrium Green's function formalism and the self-consistent charge density-functional tight-binding method. We constructed spectra from the spacing of the oscillation peaks in four-probe resistance spectra. The interference effect caused by multiple reflections and resonant scattering at the contacts were extracted separately from the peak spacing spectra. Analysis of the peak spacing spectra may provide a powerful tool to extract information about scattering processes in four-probe resistance measurements.

Structural, Electronic, and Mechanical Properties of Single-Walled Halloysite Nanotube Models

Halloysite is a clay mineral with stoichiometry Al2Si2O5(OH)4·nH2O that can grow into long tubules and is chemically similar to kaolinite. In this work we present a systematic study on the stability, electronic, and mechanical properties of zigzag and armchair single-walled halloysite nanotubes by means of the self-consistent charge density-functional tight-binding method (SCC-DFTB). The detailed analysis is focused on structural properties, strain energy, and band gap as a function of tube radii and Mulliken charge distribution. The strain energy of halloysite nanotubes does not have a monotonic character and the most stable structures should be observed in the region of radii above 24 Å, in agreement with experimental data. Analysis of the electronic density of states shows that all tubes are insulators. Our calculations predict that single-walled halloysite nanotubes have Young modulus in the same order of imogolite and inorganic nanotubes, but smaller than that of carbon nanotubes. Even though most of the properties are adequately described by simpler halloysite models, further studies on multiwalled and larger diameter tubes are in progress.

The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations

The self-consistent charge density functional tight binding (SCC-DFTB) method is a relatively new approximate electronic structure method that is increasingly used to study biologically relevant systems in aqueous environments. There have been several gas phase cluster calculations that indicate, in some instances, an ability to predict geometries, energies, and vibrational frequencies in reasonable agreement with high level ab initio calculations. However, to date, there has been little validation of the method for bulk water properties, and no validation for the properties of the hydrated excess proton in water. Presented here is a detailed SCC-DFTB analysis of the latter two systems. This work focuses on the ability of the original SCC-DFTB method, and a modified version that includes a hydrogen bonding damping function (HBD-SCC-DFTB), to describe the structural, energetic, and dynamical nature of these aqueous systems. The SCC-DFTB and HBD-SCC-DFTB results are compared to experimental data and Car-Parrinello molecular dynamics (CPMD) simulations using the HCTH/120 gradient-corrected exchange-correlation energy functional. All simulations for these systems contained 128 water molecules, plus one additional proton in the case of the excess proton system, and were carried out in a periodic simulation box with Ewald long-range electrostatics. The liquid water structure for the original SCC-DFTB is shown to poorly reproduce bulk water properties, while the HBD-SCC-DFTB somewhat more closely represents bulk water due to an improved ability to describe hydrogen bonding energies. Both SCC-DFTB methods are found to underestimate the water dimer interaction energy, resulting in a low heat of vaporization and a significantly elevated water oxygen diffusion coefficient as compared to experiment. The addition of an excess hydrated proton to the bulk water resulted in the Zundel cation (H(5)O(2)(+)) stabilized species being the stable form of the charge defect, which diffuses at a rate similar to the underlying water diffusion. These SCC-DFTB results differ significantly from other existing computational descriptions of the hydrated excess proton in water, as well as from the available experimental data.

Reformulating time-dependent density functional theory with non-orthogonal localized molecular orbitals

Time-dependent density functional theory (TDDFT) has broad application in the study of electronic response, excitation and transport. To extend such application to large and complex systems, we develop a reformulation of TDDFT equations in terms of non-orthogonal localized molecular orbitals (NOLMOs). NOLMO is the most localized representation of electronic degrees of freedom and has been used in ground state calculations. In atomic orbital (AO) representation, the sparsity of NOLMO is transferred to the coefficient matrix of molecular orbitals (MOs). Its novel use in TDDFT here leads to a very simple form of time propagation equations which can be solved with linear-scaling effort. We have tested the method for several long-chain saturated and conjugated molecular systems within the self-consistent charge density-functional tight-binding method (SCC-DFTB) and demonstrated its accuracy. This opens up pathways for TDDFT applications to large bio- and nano-systems.

Theoretical Study of Quantum Interference Effects on Nanoscale Four-probe Measurements

To analyze the interference effects on the oscillation of four-probe resistance of one-dimensional nanostructures in experiments, we performed numerical simulation of a nanoscale four-probe system consisting of monatomic carbon chains using self-consistent charge density-functional tight-binding method and nonequilibrium Green's function method. We constructed spectra of the peak spacing of calculated four-probe resistance spectra, and compared them with those expected from a simple model of interference due to multiple reflections between sample-probe contacts. From the peak spacing spectra, the interference effects caused by the multiple reflections and by resonant scattering at the sample-probe contacts are extracted separately. This result suggests that the peak spacing analysis is a potential tool to understand four-probe resistance measurements.

Theoretical study of four-probe resistance in nanoscale measurements: Monatomic carbon chains and (5,5)-carbon nanotubes

Simulations of four-probe resistance measurements of monatomic carbon chains and (5,5)-carbon nanotubes were carried out using the self-consistent charge density-functional tight-binding method and the Green's function method. The four-probe resistance spectra show oscillations depending on the probe geometries and become negative at specific electron energies. These features coincide qualitatively with those experimentally observed by Gao et al. [Phys. Rev. Lett. 95, 196802 (2005)]. It is shown that the resistance oscillations can be attributed to the interference of electron waves between the two voltage probes.