Self-consistent Charge Density Research Articles

Self-consistent charge and dipole density functional tight binding method and application to carbon-based systems

The density functional tight binding (DFTB) method is a fast, semi-empirical, total energy electronic structure method based upon and parameterized to density functional theory (DFT). The standard self-consistent charge (SCC) DFTB approximates the charge fluctuations in a system using a multipole expansion truncated to the monopole term. For systems with asymmetric charge distributions, such as might be induced by an applied external field, higher terms in the multipole expansion are likely to be important. We have extended the formalism to include dipoles (SCCD), have implemented the method computationally, and test it by calculating the response of various carbon nanotubes and fullerenes to an applied electric field. A comparison of polarizabilities with experimental data or more sophisticated DFT calculations indicates a substantial improvement over standard SCC-DFTB. We also discuss the issues surrounding parameterization of the new SCCD-DFTB scheme.

Electronic properties of graphene with single vacancy and Stone-Wales defects

The first principles calculations have been performed based on self-consistent charge density functional tight-binding in order to examine the electronic properties of graphene with single vacancy (SV) and Stone-Wales (SW) defects. We have optimized structures of pristine graphene and graphene with SV and SW defects. The bond lengths, current-voltage curve and transmission probability have been calculated. We found that the bond length for relaxed graphene is 1.43Å while for graphene with SV and SW defects the bond lengths are 1.41Å and 1.33Å, respectively. For the SV defect, the arrangement of atoms with three nearest neighbors indicates sp2 bonding. While for SW defect, the arrangement of atoms suggests nearly sp bonding. From the current-voltage curve for graphene with defects we have determined that the behavior of the I–V curves is nonlinear. It is also found that the SV and SW defects cause to decrease the current compared to the pristine graphene case. Furthermore, the single vacancy defect reduces the current more than the Stone-Wales defect. Moreover, we observed that by increasing the voltage from zero to 1V new peaks near Fermi level in the transmission probability curves have been created.

Assessment of semi-empirical molecular orbital calculations for describing magnetic interactions

We report a thorough comparison between the spin-unrestricted semi-empirical molecular orbital (SE-UMO) and density functional theory (UDFT) calculations for a variety of π-conjugated diradical molecules which exhibit through-bond magnetic exchange interactions. The spin-unrestricted neglect of diatomic differential overlap (NDDO)-based methods (UPM6 and UrPM6) and self-consistent charge density functional tight-biding (UDFTB) are examined. The UCAM-B3LYP method is used as a representative of UDFT. We have found that NDDO-based and UDFTB methods give different performances with respect to the results of UCAM-B3LYP. The degree of diradical character in the target systems decreases in the order of UPM6>UrPM6≈UCAM-B3LYP>UDFTB. The conventional UPM6 and UDFTB calculations tend to overestimate and underestimate the diradical character, respectively, whereas UrPM6 is able to provide much the same results as UCAM-B3LYP. This is convincing evidence that UrPM6 will be useful for in silico screening of materials science at much lower computational cost.

Self-consistent mapping: Effect of local environment on formation of magnetic moment in α−FeSi2

The Hohenberg-Kohn theorem establishes a basis for mapping the exact energy functional to a model one provided that their charge densities coincide. We suggest to use a mapping in a similar spirit, but here the parameters of the formulated multiorbital model should minimize the difference between the self-consistent charge and spin densities. The analysis of the model allows for detailed understanding of the role played by different parameters of the model in the physics of interest. After finding the areas of interest in the phase diagram of the model, we return to the ab initio calculations and check if the effects discovered are confirmed or not. Because of the last controlling step, we call this approach hybrid self-consistent mapping approach (HSCMA). As an example of the approach we present a study of the effect of silicon atoms substitution by the iron atoms and vice versa on the magnetic properties in the iron silicide $\ensuremath{\alpha}\ensuremath{-}{\mathrm{FeSi}}_{2}$. We find that while the stoichiometric $\ensuremath{\alpha}\ensuremath{-}{\mathrm{FeSi}}_{2}$ is nonmagnetic, the substitutions generate different magnetic structures depending on the type of local environment of the substitutional Fe atoms. Besides, contrary to the commonly accepted statement that the destruction of the magnetic moment is controlled only by the number of Fe-Si nearest neighbors, we find that actually it is controlled by the Fe-Fe next-nearest-neighbor hopping parameter. This finding led us to the counterintuitive conclusion: an increase of Si concentration in ${\mathrm{Fe}}_{1\ensuremath{-}x}{\text{Si}}_{2+x}$ ordered alloys may lead to ferromagnetism. The calculation within GGA-to-DFT confirms this conclusion.

Adsorption on a nanoporous organic polymer for clean energy applications: A multiscale modeling study using density functional tight binding approach

Adsorption of carbon dioxide, methane and hydrogen on the novel ferrocenyl-nanoporous organic polymer was studied from an approximate density-functional method. Geometric, energetic and electronic parameters are obtained using the self-consistent charge density functional tight binding (SCC-DFTB) spin polarized approach and prove a mechanism of adsorption governed by physisorption processes. In order to gain a deeper understanding of the effect of temperature on the adsorption-desorption process, an SCC-DFTB/MD simulation is implemented which enabled a satisfactory agreement with the experimental results reported in the literature.

On-the-Fly QM/MM Docking with Attracting Cavities.

We developed a hybrid quantum mechanical/molecular mechanical (QM/MM) on-the-fly docking algorithm to address the challenges of treating polarization and selected metal interactions in docking. The algorithm is based on our classical docking algorithm Attracting Cavities and relies on the semiempirical self-consistent charge density functional tight-binding (SCC-DFTB) method and the CHARMM force field. We benchmarked the performance of this approach on three very diverse data sets: (1) the Astex Diverse set of 85 common noncovalent drug/target complexes formed both by hydrophobic and electrostatic interactions; (2) a zinc metalloprotein data set of 281 complexes, where polarization is strong and ligand/protein interactions are dominated by electrostatic interactions; and (3) a heme protein data set of 72 complexes, where ligand/protein interactions are dominated by covalent ligand/iron binding. Redocking performance of the on-the-fly QM/MM docking algorithm was compared to the performance of classical Attracting Cavities, AutoDock, AutoDock Vina, and GOLD. The results demonstrate that the QM/MM code preserves the high accuracy of most classical scores on the Astex Diverse set, while it yields significant improvements on both sets of metalloproteins at moderate computational cost.

Atomistic Insights into Chemical Interface Damping of Surface Plasmon Excitations in Silver Nanoclusters

A detailed description of the mechanism underlying chemical interface damping (CID) in silver nanoclusters is presented. The effect of adsorbates on the surface plasmon excitation in silver nanoclusters is explored by means of a method based on time-dependent self-consistent charge density functional tight binding (TD-SCC-DFTB). By using this tool, we have calculated the homogeneous line width of the surface plasmon resonance (SPR) band for both naked and capped silver nanoclusters. A new picture explaining the decreased lifetime of the surface plasmon excitations is provided, in which coupling between particles states via adsorbate states enhances the natural dephasing mechanism of the surface plasmon excitation. To the best of our knowledge, this is the first report that addresses this topic from a fully atomistic time-dependent approach considering nanosized particles.

Stepwise Simulation of 3,5-Dihydro-5-methylidene-4H-imidazol-4-one (MIO) Biogenesis in Histidine Ammonia-lyase.

A 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) electrophilic moiety is post-translationally and autocatalytically generated in homotetrameric histidine ammonia-lyase (HAL) and other enzymes containing the tripeptide Ala-Ser-Gly in a suitably positioned loop. The backbone cyclization step is identical to that taking place during fluorophore formation in green fluorescent protein from the tripeptide Ser-Tyr-Gly, but dehydration, rather than dehydrogenation by molecular oxygen, is the reaction that gives rise to the mature MIO ring system. To gain additional insight into this unique process and shed light on some still unresolved issues, we have made use of extensive molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations implementing the self-consistent charge density functional tight-binding method on a fully solvated tetramer of Pseudomonas putida HAL. Our results strongly support the idea that mechanical compression of the reacting loop by neighboring protein residues in the precursor state is absolutely required to prevent formation of inhibitory main-chain hydrogen bonds and to enforce proper alignment of donor and acceptor orbitals for bond creation. The consideration of the protein environment in our computations shows that water molecules, which have been mostly neglected in previous theoretical work, play a highly relevant role in the reaction mechanism and, more importantly, that backbone cyclization resulting from the nucleophilic attack of the Gly amide lone pair on the π* orbital of the Ala carbonyl precedes side-chain dehydration of the central serine.

Fragmentation network of doubly charged methionine: Interpretation using graph theory.

The fragmentation of doubly charged gas-phase methionine (HO2CCH(NH2)CH2CH2SCH3) is systematically studied using the self-consistent charge density functional tight-binding molecular dynamics (MD) simulation method. We applied graph theory to analyze the large number of the calculated MD trajectories, which appears to be a highly effective and convenient means of extracting versatile information from the large data. The present theoretical results strongly concur with the earlier studied experimental ones. Essentially, the dication dissociates into acidic group CO2H and basic group C4NSH10. The former may carry a single or no charge and stays intact in most cases, whereas the latter may hold either a single or a double charge and tends to dissociate into smaller fragments. The decay of the basic group is observed to follow the Arrhenius law. The dissociation pathways to CO2H and C4NSH10 and subsequent fragmentations are also supported by ab initio calculations.

Optimizing the Photovoltaic Properties of CdTe Quantum Dot–Porphyrin Nanocomposites: A Theoretical Study

By using the self-consistent charge density functional tight binding method, we explore the photovoltaic properties of CdTe quantum dot (CdTeQD)–porphyrin nanocomposites. It is well-known that for dye-sensitized solar cell (DSSCs) applications, the composite system should have a type-II band alignment that hinders the recombination of charge carriers, thereby improving the photovoltaic performance. The emphasis of our tight-binding calculations is to find the suitable CdTeQD–porphyrin nanocomposites that can offer better performance for solar energy conversion. By analyzing the electronic energy levels of the composite systems we have shown that the axially coordinated Zn-tetraphenylporphyrin (ZnTPP) functionalized CdTe quantum dot (ZnTPP–CdTeQD) nanocomposites are really promising materials for application in DSSCs, as they produce type-II band alignment for all the composites irrespective of the size of CdTeQDs. The time-dependent density functional theory (TDDFT) calculations demonstrate that the size ...

A network approach to unravel correlated ion pair dynamics in protic ionic liquids. The case of triethylammonium nitrate

The intermolecular interactions in the title compound are investigated using self-consistent charge density functional based tight binding molecular dynamics. Emphasis is put on the analysis of correlated motions of ion pairs using ideas of network theory. At equilibrium such correlations are not very pronounced on average. However, there exist sizable local correlations for cases where two cations share the same anion via two NHO-hydrogen bonds. The effect of an external perturbation, which artificially introduces a sudden local heating of an NH-bond, is investigated using nonequilibrium molecular dynamics. Here, it is found that the average NH bond vibrational relaxation time is about 5.3ps. This energy redistribution is rather nonspecific with respect to the ion pairs and does not lead to long-range correlations spreading from the initially excited ion pair.

Band gap engineering in silicene: A theoretical study of density functional tight-binding theory

In this work, we performed first principles calculations based on self-consistent charge density functional tight-binding to investigate different mechanisms of band gap tuning of silicene. We optimized structures of silicene sheet, functionalized silicene with H, CH3 and F groups and nanoribbons with the edge of zigzag and armchair. Then we calculated electronic properties of silicene, functionalized silicene under uniaxial elastic strain, silicene nanoribbons and silicene under external electrical fields. It is found that the bond length and buckling value for relaxed silicene is agreeable with experimental and other theoretical values. Our results show that the band gap opens by functionalization of silicene. Also, we found that the direct band gap at K point for silicene changed to the direct band gap at the gamma point. Also, the functionalized silicene band gap decrease with increasing of the strain. For all sizes of the zigzag silicene nanoribbons, the band gap is near zero, while an oscillating decay occurs for the band gap of the armchair nanoribbons with increasing the nanoribbons width. At finally, it can be seen that the external electric field can open the band gap of silicene. We found that by increasing the electric field magnitude the band gap increases.

Nonadiabatic Molecular Dynamics for Thousand Atom Systems: A Tight-Binding Approach toward PYXAID.

Excited state dynamics at the nanoscale requires treatment of systems involving hundreds and thousands of atoms. In the majority of cases, depending on the process under investigation, the electronic structure component of the calculation constitutes the computation bottleneck. We developed an efficient approach for simulating nonadiabatic molecular dynamics (NA-MD) of large systems in the framework of the self-consistent charge density functional tight binding (SCC-DFTB) method. SCC-DFTB is combined with the fewest switches surface hopping (FSSH) and decoherence induced surface hopping (DISH) techniques for NA-MD. The approach is implemented within the Python extension for the ab initio dynamics (PYXAID) simulation package, which is an open source NA-MD program designed to handle nanoscale materials. The accuracy of the developed approach is tested with ab initio DFT and experimental data, by considering intraband electron and hole relaxation, and nonradiative electron-hole recombination in a CdSe quantum dot and the (10,5) semiconducting carbon nanotube. The technique is capable of treating accurately and efficiently excitation dynamics in large, realistic nanoscale materials, employing modest computational resources.

ES2MS: An interface package for passing self-consistent charge density and potential from Electronic Structure codes To Multiple Scattering codes

We present an interface package, called ES2MS, for passing self-consistent charge density and potential from Electronic Structure (ES) codes To Multiple Scattering (MS) codes. MS theory is based on the partitioning of the space by atomic-size scattering sites, so that the code provides the charge densities and potentials for each scattering site. For pseudo potential codes, the interface solves Poisson equation to construct the all-electron potential on the radial mesh which is used to solve the transition operators (T-matrix) and Green’s functions in MS codes. We show the algorithm of the interface and the example for X-ray absorption spectra of graphene. Program summaryProgram title: ES2MS-1.0Catalogue identifier: AFAB_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFAB_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 3351816No. of bytes in distributed program, including test data, etc.: 82576761Distribution format: tar.gzProgramming language: Fortran 90, FORTRAN 77.Computer: Any.Operating system: Linux, Mac OSX, Windows.RAM: Several hundred Mega BytesClassification: 7.2.Nature of problem: Reconstruction of full-potential for Multiple Scattering codes from external charge densities, data transformation between cartesian supercell mesh onto radial meshes of real space cluster.Solution method: The pseudo-potential and the all-electron charge density from a Projector-Augmented-Wave electronic structure method (here: VASP) are read. Inside the augmentation spheres, the charge density is interpolated onto the radial mesh of the Multiple Scattering code. The all-electron full-potential is obtained by solving the Poisson equation with proper boundary conditions on the surface of the spheres as given by the pseudopotential. Outside the spheres, the charge density and potential are interpolated from the cartesian mesh onto the radial mesh. By rotating and shifting the coordinates of the cluster used in the Multiple Scattering code, the code finds the corresponding point in the unit cell of the Electronic Structure code.Additional comments: !!!!! The distribution file for this program is over 82 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!!Running time: A few tens of seconds

Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations.

This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment.

Dynamics of the Formation of the Nitrogen-Vacancy Center in Diamond

AbstractWe present results of simulations of the energetics and dynamics involved in the realization of the NV (nitrogen-vacancy) center in diamond. We use the self-consistent charge-density functional tight-binding approximation and show that when the nitrogen resides on a single substitutional site, it fails to attract a vacancy, hence no NV center can be formed. However, if it occupies a split interstitial site and two vacancies reside on the second or third neighbor sites, an NV center will form following annealing at temperatures as low as 300°C and 650°C, respectively. These results provide guidelines to experimentalists on how to increase the efficiency of NV formation in diamond.

X-ray absorption spectra of graphene and graphene oxide by full-potential multiple scattering calculations with self-consistent charge density

The x-ray absorption near-edge structure of graphene, graphene oxide, and diamond is studied by the recently developed real-space full potential multiple scattering (FPMS) theory with space-filling cells. It is shown how accurate potentials for FPMS can be generated from self-consistent charge densities obtained with other schemes, especially the projector augmented wave method. Compared to standard multiple scattering calculations in the muffin-tin approximation, FPMS gives much better agreement with experiment. The effects of various structural modifications on the graphene spectra are well reproduced. (1) Stacking of graphene layers increases the peak intensity in the higher energy region. (2) The spectrum of the C atom located at the edge of a graphene sheet shows a prominent pre-edge structure. (3) Adsorption of oxygen gives rise to the so-called interlayer-state peak. Moreover, O K-edge spectra of graphene oxide are calculated for three types of bonding, C-OH, C-O-C, and C-O, and the proportions of these bondings at 800 degrees C are deduced by fitting them to the experimental spectrum.

Electronic and electrical properties of silicon nanowire-single wall carbon nanotube junction as a nanoelectronic switch

In this work, we performed first principles calculations based on self-consistent charge density functional tight-binding to investigate how the overlapping length of two inter-shell structure effect on the electronic and electrical properties of silicon nanowire-single wall carbon nanotube junction. By computing of density of state, current–voltage curve, conductance and transmission probability, it is found that the binding energy, charge transferring between two structures and conductance changes with the overlapping length. Our results show that charge transferring between the two structures is not affected by overlapping length. Also, we found that the current increases by increasing the overlapping length. At finally, the conductance increase from the zero to the high amount of overlapping length as an off and on states of a nanometer switch.

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization.

Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.

SCC-DFTB parameters for simulating hybrid gold-thiolates compounds.

We present a parametrization of a self-consistent charge density functional-based tight-binding scheme (SCC-DFTB) to describe gold-organic hybrid systems by adding new Au-X (X = Au, H, C, S, N, O) parameters to a previous set designed for organic molecules. With the aim of describing gold-thiolates systems within the DFTB framework, the resulting parameters are successively compared with density functional theory (DFT) data for the description of Au bulk, Aun gold clusters (n = 2, 4, 8, 20), and Aun SCH3 (n = 3 and 25) molecular-sized models. The geometrical, energetic, and electronic parameters obtained at the SCC-DFTB level for the small Au3 SCH3 gold-thiolate compound compare very well with DFT results, and prove that the different binding situations of the sulfur atom on gold are correctly described with the current parameters. For a larger gold-thiolate model, Au25 SCH3 , the electronic density of states and the potential energy surfaces resulting from the chemisorption of the molecule on the gold aggregate obtained with the new SCC-DFTB parameters are also in good agreement with DFT results.