Self-consistent Tight-binding Method Research Articles

BODIPY-DERIVATIVES AS PHOTOSENSITIZERS IN PHOTODYNAMIC THERAPY: THE RELATIONSHIP BETWEEN ELECTRONIC PROPERTIES AND LIGHT ABSORPTION EFFICIENCY

In this study, the structural and electronic properties of BODIPY and its twelve derivates, including meso-amino, meso-alkoxy, meso-phenyl, meso-alkyl and other compounds, were investigated using an accurate and broadly parametrized self-consistent tight-binding quantum chemical method named GFN2-xTB. The influence of the substituent groups on the geometrical parameters, the HOMOLUMO gap, and electronic properties of BODIPYs was analyzed. The obtained results have shown that the presence of substituents at the R2 position did not significantly change the structural parameters of BODIPY. The electron-acceptor or electron-donor substituents in the meso-position have different effects on the electronic parameters of the molecules. A correlation between the global electrophilicity index and the HOMO-LUMO gap was found. Among the studied systems, the BODIPY-derivative with a -NO2 group at the meso-position was evaluated as the most promising candidate for photosensitizers in PDT.

Effects of chiral indices on the atomic arrangements and electronic properties of Si double-walled nanotubes (6,min)@(9,mout) (min = 0 to 6, mout = 0 to 9) by SCC-DFTB calculations

The geometric structural optimization and electronic properties of double-walled silicon nanotubes (DWSiNTs) (6, min)@(9, mout) (min= 0 to 6, mout= 0 to 9) are studied in terms of the self-consistent charge density functional tight binding (SCC-DFTB) method. In particular, a cross-section configuration transformation of the DWSiNTs affected by the different inner and outer wall chiral indices is explored. It seems that six different shapes including circular-like, ellipse-like, trilateral-like, quadrilateral-like, pentagon-like, and hexagon-like shapes appear. The interactions between the atoms in the inner and outer walls possess most of the atoms in sp3 hybridization, followed in sp2 hybridization, with very few in high-order hypervalent states. The chiral indices of the inner and outer walls as well as the cross-section configuration of the tube have obvious effects on the stability of the DWSiNTs. The DWSiNTs (6,5)@(9,7), (6,6)@(9,8), and (6,6)@(9,9) show metal characteristic: others exhibit semiconductor properties with a narrow band gap. Furthermore, the possibility of tuning the band structure by changing the chiral indices is demonstrated to help for the performance needs of different devices, inducing a metal-semiconductor transition and direct-indirect band gap transition. These theoretical studies provide references for the preparation, and future application, of DWSiNTs.

Energy stability and electronic properties of carbon nanotorus at a localized breaking of interatomic bonds: computer modeling

This paper is devoted to the study of the dynamic processes that occur in the carbon nanotorus during localized breaking of interatomic bonds, and to the analysis of the influence of these processes on the electronic properties of carbon nanotorus. The object of research is a carbon nanotorus with chirality indices (13, 0) with a diameter of 20 nm and a thickness of 1 nm obtained as a result of defect-free folding of a zigzag carbon nanotube of appropriate geometric dimensions into a ring. The behavior of the nanotorus is modeled by the molecular dynamics method using a modified Brenner potential to describe the interaction between atoms. It is shown that over time, the nanotorus straightens into a nanotube, while maintaining energy stability. It is found that the process of nanotorus straightening is accompanied by the appearance of deformation wave-like bends propagating at a speed of 200 m/s along the atomic network of the structure. These bends lead to deformation of the nanotorus and numerous local breaks in the bonds between atoms. However, broken bonds are restored within a few femtoseconds before the structure relaxes in energy, therefore, in general, the atomic framework of the nanotorus remains defect-free after rectification. The results of calculating the distribution of the density of electronic states (DOS) of a nanotorus by the self-consistent charge density functional tight-binding (SCC-DFTB) quantum method showed that at the moment of localized breaking of interatomic bonds around the circumference of the tubular framework, the nanotorus loses its semiconductor properties, becoming a gapless conductor. The discovered physical phenomenon explains the process of nanotorus formation during synthesis accompanied by multiple ruptures of the nanotori and reverse closure of the nanotubes into the nanotori.

Reduced graphene oxide/NH2-MIL-125(Ti) composite: Selective CO2 photoreduction to methanol under visible light and computational insights into charge separation

Abstract The development of visible-light active photocatalysts is highly desirable for CO2 reduction to hydrocarbons and alcohols using sunlight. Here, we report the metal-organic frameworks (MOF) of amino-benzene dicarboxylate with titanium oxocluster center (NH2-MIL-125(Ti)) and modified with reduced graphene oxide (RGO), RGO-NH2-MIL-125(Ti), ideal for the visible-light-driven photocatalytic reduction of CO2 to hydrocarbons and methanol. The catalyst provides high quantum efficiency and selectivity for methanol. The cluster model and self-consistent charge density functional tight binding methods were used to investigate the photogenerated charge separation for NH2-MIL-125(Ti). The quantum modelling suggests that holes were accumulated in the central ring Ti8O8(OH)4, where strongly adsorbed electron donor, triethanolamine, undergoes photooxidation while electrons were located in the organic ligand of MOF including the NH2 group. The binding affinity of NH2 reaction sites to CO2 possibly work to improve the photocatalytic reduction of CO2 to methanol. The RGO also play an important role for charge separation and better photocatalytic reduction with RGO-NH2-MIL-125(Ti).

Adsorption of NO2, HCN, HCHO and CO on pristine and amine functionalized boron nitride nanotubes by self-consistent charge density functional tight-binding method

The adsorptions of toxic gases including NO2, HCN, HCHO and CO molecules on the pristine and amine functionalized (5,0) single-wall boron nitride nanotubes (BNNTs) are investigated based on self-consistent charge density functional tight-binding (SCC-DFTB) method. The calculated results indicate that the pristine (5,0) BNNT exhibits weak adsorption for the gas molecules. Based on the calculated adsorption energy, interaction distances and charge transfer, amine functionalization at a boron atom of the pristine (5,0) BNNT enhances the sensitivity of the pristine (5,0) BNNT toward the gas molecules. The electronic densities of state results reveal that new local states in the vicinity of Fermi level for adsorption between amine functionalized BNNT and the gas molecules significantly appear. This confirms the improved sensitivity of the pristine (5,0) BNNT functionalized with amine for adsorption of the toxic gases. This study is expected to provide a useful guidance on gas sensing application of pristine and amine functionalized BNNTs for detection of the toxic gases at room temperature.

Theoretical investigation of electronic bandgaps of semiconducting single-walled carbon nanotubes using semi-empirical self-consistent tight binding and ab-inito density functional methods

We perform a comprehensive theoretical study of electronic band gaps of semiconducting single-walled carbon nanotubes (SWNTs) with different sets of chiral indices using semi-empirical tight binding and density functional (DFT) based ab-initio methods. In particular, self-consistent extended Huckel (EH-SCF) and self-consistent Slater Koster (SK-SCF) tight binding models are used as semi-empirical methods, whereas the DFT based LDA-1/2 and Tran-Blaha (TB09) meta-GGA schemes are used as ab-initio methods. The calculations are performed for 1) (n, m) chiral SWNTs for which experimental optical gaps have been reported 2) (9, 0), (12, 0) and (15, 0) ‘metallic’ zigzag SWNTs for which small bad gaps have been reported 3) Pairs of SWNTs having same diameters but different chiral angles 4) (n, 0) zigzag SWNTs with From the comparison of bands gaps of tubes with same diameter, the electronic band gaps are found to vary with chiral angles with opposing trend as compared to that reported for experimental optical band gaps. This result may be expected to have important implications for self-energy corrections and/or exciton binding energies and their dependence on chiral angles. The hopping parameter obtained from fitting EH-SCF and SK-SCF bandgap data, is found to be in good agreement with that obtained from fitting experimental data. In general, the band gap values of SWNTs computed using semi-empirical EH-SCF and SK-SCF methods are quite close (within ∼ 5%) to those computed using DFT-based LDA-1/2 and TB09 meta-GGA methods. The results suggest that self-consistent semi-empirical methods can be expected to provide similar accuracy in results as that expected from more computationally challenging ab-intio DFT based LDA-1/2 and TB09 meta-GGA methods.

TETT-functionalized TiO2 nanoparticles for DOX loading: a quantum mechanical study at the atomic scale.

In this work, we present a quantum mechanical investigation, based on the self-consistent charge density functional tight-binding (SCC-DFTB) method, of the functionalization with silane-type ligands (TETT) of a spherical TiO2 nanoparticle of realistic size (2.2 nm containing 700 atoms) to create an efficient nanosystem for simultaneous photodynamic therapy and drug transport. We determine the mechanism of the TETT ligand anchoring and its stability under thermal treatment, through molecular dynamics simulations at 300 K. Then, we build a medium and a full coverage model (22 and 40 TETTs, respectively) and analyze the interaction among TETT ligands and between the ligands and the surface. Finally, on the fully covered nanoparticle, we succeed in localizing two minimum energy structures for an attached doxorubicin anticancer molecule (DOX) and provide the atomistic details for both the covalent and the non-covalent (electrostatic) types of interaction. A future development of this work will be the investigation of the loading capacity of this drug delivery system and of the pH effect of the surrounding aqueous environment.

SCC-DFTB-PIMD Method To Evaluate a Multidimensional Quantum Free-Energy Surface for a Proton-Transfer Reaction.

The self-consistent charge density functional tight binding method was combined with the path-integral molecular dynamics method for the first time to evaluate the two-dimensional free-energy surface including nuclear quantum effects of a proton-transfer reaction in a 2,4-dichlorophenol-trimethylamine complex. A statistically converged two-dimensional quantum free-energy surface was evaluated by the multidimensional blue moon ensemble method. The accuracy was guaranteed by optimizing the repulsive potential between the sp3-hybridized nitrogen and hydrogen atoms in a SCC-DFTB3 parameter set for the system to reproduce high-level quantum chemical calculations. The present study illustrates the usefulness of this new approach to investigate nuclear quantum effects in various realistic proton-transfer reactions.

Distinctive optoelectronic properties of nanostructured MoS2 bilayers

We theoretically investigate the electronic and optical properties of nanostructured ${\mathrm{MoS}}_{2}$ bilayers, consisting of vertically stacked monolayer (ML) of pristine ${\mathrm{MoS}}_{2}$ and ML of periodic triangular nanoplatelets or holes. Our calculations reveal that the interplay between edge atoms in periodic nanostructures, size of nanostructures, and distances between them, control the appearance and size of the band gaps, and optical response, including the number and intensity of peaks; the nanostructured bilayers with periodic nanoplatelets in particular exhibit rich optical properties. Specifically, we find the electronic states, originating from the atoms of the ML with either periodic nanoplatelets or holes, get embedded between electronic states of pristine ${\mathrm{MoS}}_{2}$ ML, but now with red- and blueshifted valence and conduction bands, respectively. For a ML with periodic nanoplatelets, electronic states originate primarily from $p$ orbitals of S atoms, and for a ML with periodic holes, they originate from $d$ orbitals of Mo atoms. The electronic structure is accessed through the self-consistent tight-binding (SCTB) method, which is the extension of our tested parametrized TB model that includes nonorthogonal ${sp}^{3}{d}^{5}$ orbitals and spin-orbit coupling. We systematically examine the parameters in our SCTB to avoid possible distortion of electronic states, ensuring high quality of our predictions.

Effect of side gates doping on graphene self-switching nano-diode rectification

Based on the self-consistent charge density functional tight-binding method, the electrical properties and rectification behavior of graphene self-switching nanodiodes with B and N atoms doped side gates are investigated. The doping changes the electrical conductivity of the side gates and the semiconductor channel nanoribbons. From the band structure and Mulliken population analysis in the N-doped (B-doped) structures, we found that the N (B) energy levels are located above (below) the conduction band minimum (valence band maximum) and that these impurities are autoionized such that the excess electrons (holes) are transferred to the conduction (valence) band. In the doped devices, the threshold voltage under the forward bias is significantly reduced such that in the 565-B doped and 565-N doped devices, the threshold voltage is approximately zero. In addition, compared with the corresponding undoped devices, the electric current in doped devices under the forward and reverse biases is increased and decreased, respectively. Finally, among all of our structures, in the range of applied bias, the 565-B doped device exhibited the highest rectification ratio of 5.59 × 102, whereas the maximum current value of 12.7 μA under the forward bias conditions was obtained with the 666-B Doped GSSD structure.

GFN2-xTB-An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions.

An extended semiempirical tight-binding model is presented, which is primarily designed for the fast calculation of structures and noncovalent interaction energies for molecular systems with roughly 1000 atoms. The essential novelty in this so-called GFN2-xTB method is the inclusion of anisotropic second order density fluctuation effects via short-range damped interactions of cumulative atomic multipole moments. Without noticeable increase in the computational demands, this results in a less empirical and overall more physically sound method, which does not require any classical halogen or hydrogen bonding corrections and which relies solely on global and element-specific parameters (available up to radon, Z = 86). Moreover, the atomic partial charge dependent D4 London dispersion model is incorporated self-consistently, which can be naturally obtained in a tight-binding picture from second order density fluctuations. Fully analytical and numerically precise gradients (nuclear forces) are implemented. The accuracy of the method is benchmarked for a wide variety of systems and compared with other semiempirical methods. Along with excellent performance for the "target" properties, we also find lower errors for "off-target" properties such as barrier heights and molecular dipole moments. High computational efficiency along with the improved physics compared to its precursor GFN-xTB makes this method well-suited to explore the conformational space of molecular systems. Significant improvements are furthermore observed for various benchmark sets, which are prototypical for biomolecular systems in aqueous solution.

Shock response of condensed-phase RDX: molecular dynamics simulations in conjunction with the MSST method.

We have performed molecular dynamics simulations in conjunction with the multiscale shock technique (MSST) to study the initial chemical processes of condensed-phase RDX under various shock velocities (8 km s−1, 10 km s−1 and 11 km s−1). A self-consistent charge density functional tight-binding (SCC-DFTB) method was used. We find that the N–NO2 bond dissociation is the primary pathway for RDX with the NO2 groups facing (group 1) the shock, whereas the C–N bond scission is the dominant primary channel for RDX with the NO2 groups facing away from (group 2) the shock. In addition, our results present that the NO2 groups facing away from the shock are rather inert to shock loading. Moreover, the reaction pathways of a single RDX molecule under the 11 km s−1 shock velocity have been mapped out in detail, NO2, NO, N2O, CO and N2 were the main products.

Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots?

FtmPT1 is a fungal indole prenyltransferase that affords Tryprostatin B from Brevianamide F and dimethylallyl pyrophosphate; however, when a single residue in the active site is mutated (Gly115Thr), a novel five-membered ring compound is obtained as the major product with Tryprostatin B as the minor product. Herein, we describe detailed studies of the catalysis of the Gly115Thr mutant of FtmPT1 with a focus on the observed regioselectivity of the reaction. We employ one- and two-dimensional potential of mean force simulations to explore the catalytic mechanism, along with molecular dynamics simulations exploring the reaction dynamics of the prenyl transfer reaction. Single-point electronic structure calculations were also used to explore the performance of the self-consistent charge density functional tight-binding method to model specific reaction steps. Importantly, we observe that the two reaction pathways have comparable activation parameters and propose that the origin of the novel product is predicated, at least in part, on the topology of the potential energy surface as revealed by reaction dynamics studies.

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.

Description of non-covalent interactions in SCC-DFTB methods.

We have analyzed the description of non-covalent interactions in multiple variants of the self-consistent charges density functional tight binding (SCC-DFTB) method. While the description of London dispersion can be easily improved by empirical correction, hydrogen bonding poses a much more difficult problem. We have implemented an interaction energy decomposition scheme that allowed us to quantify the error at the level of first-order electrostatic and polarization terms. Both are underestimated because of the monopole approximation used in SCC-DFTB, with the latter being affected also by the use of minimal basis set. Among the methods tested, SCC-DFTB with the empirical D3H4 corrections worked best. To make this correction compatible with the latest development in SCC-DFTB, we have reparameterized it for use with third-order SCC-DFTB with the 3OB parameter set. © 2017 Wiley Periodicals, Inc.

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.

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.

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 ...

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.

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.