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

DFTB Simulation of Charged Clusters Using Machine Learning Charge Inference.

We present a modification to self-consistent charge density functional-based tight binding (SCC-DFTB), which allows computation based on approximate atomic charges. We obtain these charges by means of a machine learning (ML) process that combines a Coulomb model with a neural network. This allows us to avoid the SCC cycles in the SCC-DFTB calculation while maintaining its accuracy. The main input of the model is the atomic positions characterized by a set of atom-centered symmetry functions. The charge inference from our ML algorithm is as close as 10-2 units of charge from the exact SCC solution. Our ML-DFTB approach provides a good approximation of the density matrix and of the energy and forces with only a single diagonalization. This is a significant computational saving with respect to the complete SCC algorithm, which allows us to investigate a bigger ensemble of atoms. We show the quality of our approach in the case of charged silicon carbide (SiC) clusters. The ML-DFTB potential energy surface (PES) mimics the SCC-DFTB PES rather well, despite its simplicity. This allows us to obtain the same geometric structure ordering with respect to energy for small clusters. The dissociation barriers for ion emission are well-reproduced, which opens the way to investigating ion field emission and charged cluster stability. The ML-DFTB approach is obviously not limited to charged clusters or SiC materials. It opens a new route to investigate larger clusters than those investigated by standard SCC-DFTB, as well as surface and solid-state chemistry at the atomic level.

Effect of temperature on the emission properties of quasi 2D glass-like carbon placed on silicon and silicon dioxide substrates

In this work, in silico methods are used to study the temperature effect of the emission properties, including the electron work function, of quasi 2D glass-like carbon (GLC) films deposited on few/multi-layer Si/SiO2 substrates of two types. The equilibrium configuration of the structures under study at different temperatures is established by molecular dynamics (MD) method using reactive force field (ReaxFF) due to the polyatomic nature of supercells. The electronic structure is determined using the self-consistent charge density-functional based tight-binding (SCC-DFTB) method. The temperature range under consideration is 50–1000 K. The effect of one substrate layer and several substrate layers on the electronic structure and emission properties of GLC is considered. In the case of one layer of Si and SiO2, in fact, the functionalization of the GLC film occurs. This leads to a decrease in the work function by ∼ 6 % and ∼ 21 %, respectively, at a temperature of 300 K. As the temperature increased to 1000 K, the work function of the GLC with one SiO2 layer further decreased by ∼ 7 %. An increase in the substrate thickness to five Si layers and two SiO2 layers leads to a decrease in the work function by 7.3 % and 20.5 %, respectively. An increase in temperature leads to a change in the work function of the GLC with five Si substrate layers and two SiO2 layers by 0.2 % and 3.8 %, respectively.

Theoretical Investigations of the Crystal Structures and Molecular Energetics of High Quality Silicon Carbide (β-SiC) Precursor Compound 1,4-bis(trimethylsilyl)benzene

Over the last decades, the rapidly growing theoretical methods have revolutionized whole scientific paradigm, developed state-of-art analyses, and created substantial computational platforms through the huge support of outstanding mathematical algorithms. The self-consistent-charge density-functional based tight-binding (SCC-DFTB) scheme is one of them that offers versatile and efficient quantum mechanical calculations with some unique features compatible especially to the crystalline solid even at low computational resources. Its effective parametrizations and computational implementations under the Gaussian standardized interface as an "External program" via the users' script (Gaussian- External methodology; GEM) has added an additional value because of which various in-built high-level Gaussian computations are directly accessible. Herewith, the Gaussian offered geometry optimization algorithms and convergence criteria plus the ModRedundant type relaxed potential energy surface (PES) scanning techniques are assessed through the GEM, and characterized the crystal structures with concerned molecular energetics and PES of the experimentally synthesized 1,4-bis (trimethylsilyl) benzene (1,4-BTMSB) compound; a potential precursor for the high quality Silicon Carbide (β-SiC) coating particles, and an ideal "Internal Standard" for the quantitative spectroscopic analyses. The general results reveal that the 1,4- BTMSB molecules in its unit-cell and crystal lattice experience significant non-bonding interactions that induces them to attain the definite molecular geometry with recognizable ring, angle, torsional, and steric strains. The quantitative analyses of its PES depict that the phenylene ring has to overcome multiple yet unidentical energy barriers with the tallest Ea1= 5.3 kcal/mol in order to undergo internal 2π angular rotation around the 1,4-(C-Si) axes. And, exhibiting such type internal rotation of its phenylene ring is energetically highly probable as this compound is widely employed in coating high temperature reactors, and in quantizing analyte in high energy run spectroscopic facilities. The same quantification is referred here in order to underscore the significance of adopting perfectly closed topological molecular architectures while designing/synthesizing amphidynamic type crystalline free molecular gyrotops and their prototypes.

Electronic and Electrical Properties of Island-Type Hybrid Structures Based on Bi-Layer Graphene and Chiral Nanotubes: Predictive Analysis by Quantum Simulation Methods

Hybrid structures based on graphene and carbon nanotubes (CNTs) are one of the most relevant modern nanomaterials for applications in various fields, including electronics. The variety of topological architectures of graphene/CNT hybrids requires a preliminary study of their physical properties by in silico methods. This paper is devoted to the study of the electronic and electrical properties of graphene/CNT hybrid 2D structures with an island topology using the self-consistent charge density functional-based tight-binding (SCC-DFTB) formalism and the Landauer–Buttiker formalism. The island-type topology is understood as the atomic configuration of a graphene/CNT hybrid film, in which the structural fragments of graphene and nanotubes form “islands” (regions of the atomic structure) with an increased density of carbon atoms. The island-type graphene/CNT hybrid structures are formed by AB-stacked bilayer graphene and (6,3)/(12,8) chiral single-walled carbon nanotubes (SWCNT). The bilayer graphene is located above the nanotube perpendicular to its axis. Based on the binding energy calculations, it is found that the atomistic models of the studied graphene/SWCNT hybrid structures are thermodynamically stable. The peculiarities of the band structure of graphene/SWCNT (6,3) and graphene/SWCNT (12,8) hybrid structures are analyzed. It is shown that the electronic properties of graphene/SWCNT hybrid structures are sensitive to the orientation and size of the graphene layers with respect to the nanotube surface. It is found that an energy gap of ~0.1 eV opens in the band structure of only the graphene/SWCNT (6,3) hybrid structure, in which the graphene layers of the same length are arranged horizontally above the nanotube surface. We revealed the electrical conductivity anisotropy for all considered atomistic models of the graphene/SWCNT (12,8) hybrid structure when bilayer graphene sheets with different sizes along the zigzag and armchair directions are located at an angle with respect to the nanotube surface. The obtained knowledge is important to evaluate the prospects for the potential application of the considered atomic configurations of graphene/SWCNT hybrid structures with island-type topology as connecting conductors and electrodes in electronic devices.

Structural Characterization of Isolated Siloxaalkane Molecular Gyroscopes via DFTB-based Quantum Mechanical Model

Despite many more improvements in the mathematical formalisms of the DFT model, it is still unable to compute ground state electronic structure of the crystalline macrocyclic molecular compounds (CMMCs) with closed topology at low computational cost. In the recent years, a less computationally complex and relatively fast plus efficient self-consistent-charge density functional based tight binding (SCC-DFTB) scheme has been heavily extended to CMMCs under both periodic and isolated molecular conditions mainly for computing as reliable molecular structures as standard time-dependent DFT. In this study, the SCC-DFTB method is employed to characterize the molecular structures of three different molecular gyroscopes (MGs) encapsulating dihalogen substituted (e.g. ROT-2F and ROT-2Cl) and non-substituted (e.g. ROT-2H) phenylene segments under isolated condition. We realized the SCC-DFTB method a cheap yet decent quantum mechanical model in reproducing one or more X-ray observed equilibrium structures of all these three MGs as well as in deriving as consistently good structural information as DFT method. While elucidating experimentally observed structural deformation mainly in the ROT-2F and ROT-2Cl, the SCC-DFTB computed free-volume units present around their central phenylene segments are also found to be in quantitatively good agreement with those derived by the X-ray and DFT. The results presented here enlighten us about the SCC-DFTB method for adopting it directly in crystalline condition to predict crystal structures and rotational dynamics of these MGs. This theoretical insight will promote SCC-DFTB studies on gyroscopic nanostructures and giant molecular assemblies that attract increasing attention for molecular machinery world.

Carbon nanotubes functionalized with Zinc(II) phthalocyanines: Effect of the expanded aromatic system and aromatic substituents on the binding energy

As a result of quantum chemical calculations performed using the Self-consistent-charge Density Functional based Tight Binding (SCC-DFTB) method, it was found that the expansion of the aromatic system of zinc phthalocyanine (ZnPc) to the corresponding naphthalocyanine, as well as the introduction of an oxypyrene substituent into the ZnPc molecule, lead to an increase in the binding energy with carbon nanotubes due to additional π-π interaction. Calculations of changes in the quantum conductance of these hybrid compounds during the adsorption of NH3 molecules, performed within the non-equilibrium Green's function (NEGF) approach, showed that such structural changes not only do not lead to a decrease in the sensor response to ammonia, but in many cases contribute to its increase.

Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems

ABSTRACTThis review is dedicated to the application of the self-consistent-charge density-functional-based tight-binding (SCC-DFTB) approach to describe the structures, energetics, thermodynamic and spectral properties of water clusters, in the context of both fundamental and applied studies. We first present modifications implemented in the parametrisation of the potential that is mandatory to describe molecular aggregates as well as methods for global optimisation and determination of macroscopic properties. Then a number of applications of atmospherical and astrophysical interest, involving collaborations between theoreticians and experimentalists, are discussed to exemplify past and present contributions of SCC-DFTB to those two domains. Most applications presented in this review take advantage of the computational efficiency of SCC-DFTB to conduct extensive molecular dynamics simulations to obtain spectral and thermodynamic properties of water clusters. We also show some new results related to ongoing studies on both water clusters with impurities and liquid water.

Phosphorene quantum dot-fullerene nanocomposites for solar energy conversion: An unexplored inorganic-organic nanohybrid with novel photovoltaic properties

Using the self-consistent charge density-functional based tight-binding (SCC-DFTB) method, coupled with time-dependent density functional theory (TDDFT) calculations, for the first time we explore the possibility of use of phosphorene quantum dots in solar energy harvesting devices. The phosphorene quantum dots-fullerene (PQDs-PCBA) nanocomposites show type-II band alignment indicating spatial separation of charge carriers. The TDDFT calculations also show that the PQD-fullerene nanocomposites seem to be exciting material for future generation solar energy harvester, with extremely fast charge transfer and very poor recombination rate.

Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies.

We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC-DFTB) level of theory. The SCC-DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene [Formula: see text], pyrene [Formula: see text] and coronene [Formula: see text] at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C2H2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C2H2 ratio was found to increase with PAH size and to decrease with energy. For [Formula: see text], which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Structural Characterization of Sulfur-Containing Water Clusters Using a Density-Functional Based Tight-Binding Approach.

A global optimization search of low-energy isomers is carried out to investigate the structural and stability properties of sulfur-containing water clusters, including both (H2O)nSO42- and (H2O)nH2SO4 aggregates. The systematic optimization algorithm involves a combination of parallel-tempering molecular dynamics and periodic gradient-driven quenches with energy and energy-gradient calculations performed using the Self-Consistent-Charge Density-Functional based Tight-Binding (SCC-DFTB) scheme. Comparisons with new MP2 and DFT calculations on the smallest systems and previous ab initio investigations of the literature show that the SCC-DFTB approach provides a fairly accurate description of both neutral and ionic species, comparable to that of DFT. Structural and stability features of larger sulfur-containing clusters, with up to 20 water molecules, are also determined using the SCC-DFTB scheme. The interest of this work is 2-fold: (i) the benchmark on small species demonstrates the ability of SCC-DFTB to describe complex potential energy landscapes involving hydrogen-bonds and proton transfers; (ii) it opens the way to the study of large clusters that can hardly be performed within ab initio approaches.

Benchmarking Density Functional Based Tight-Binding for Silver and Gold Materials: From Small Clusters to Bulk.

We benchmark existing and improved self-consistent-charge density functional based tight-binding (SCC-DFTB) parameters for silver and gold clusters as well as for bulk materials. In the former case, our benchmarks focus on both the structural and energetic properties of small-size AgN and AuN clusters (N from 2 to 13), medium-size clusters with N = 20 and 55, and finally larger nanoparticles with N = 147, 309, and 561. For bulk materials, structural, energetics and elastic properties are discussed. We show that SCC-DFTB is quite satisfactory in reproducing essential differences between silver and gold aggregates, in particular their 2D-3D structural transitions, and their dependency upon cluster charge. SCC-DFTB is also in agreement with DFT and experiments in the medium-size regime regarding the energetic ordering of the different low-energy isomers and allows for an overall satisfactory treatment of bulk properties. A consistent convergence between the cohesive energies of the largest investigated nanoparticles and the bulk's is obtained. On the basis of our results for nanoparticles of increasing size, a two-parameter analytical extrapolation of the cohesive energy is proposed. This formula takes into account the reduction of the cohesive energy for undercoordinated surface sites and converges properly to the bulk cohesive energy. Values for the surface sites cohesive energies are also proposed.

Femtosecond charge and molecular dynamics of I-containing organic molecules induced by intense X-ray free-electron laser pulses.

We studied the electronic and nuclear dynamics of I-containing organic molecules induced by intense hard X-ray pulses at the XFEL facility SACLA in Japan. The interaction with the intense XFEL pulse causes absorption of multiple X-ray photons by the iodine atom, which results in the creation of many electronic vacancies (positive charges) via the sequential electronic relaxation in the iodine, followed by intramolecular charge redistribution. In a previous study we investigated the subsequent fragmentation by Coulomb explosion of the simplest I-substituted hydrocarbon, iodomethane (CH3I). We carried out three-dimensional momentum correlation measurements of the atomic ions created via Coulomb explosion of the molecule and found that a classical Coulomb explosion model including charge evolution (CCE-CE model), which accounts for the concerted dynamics of nuclear motion and charge creation/charge redistribution, reproduces well the observed momentum correlation maps of fragment ions emitted after XFEL irradiation. Then we extended the study to 5-iodouracil (C4H3IN2O2, 5-IU), which is a more complex molecule of biological relevance, and confirmed that, in both CH3I and 5-IU, the charge build-up takes about 10 fs, while the charge is redistributed among atoms within only a few fs. We also adopted a self-consistent charge density-functional based tight-binding (SCC-DFTB) method to treat the fragmentations of highly charged 5-IU ions created by XFEL pulses. Our SCC-DFTB modeling reproduces well the experimental and CCE-CE results. We have also investigated the influence of the nuclear dynamics on the charge redistribution (charge transfer) using nonadiabatic quantum-mechanical molecular dynamics (NAQMD) simulation. The time scale of the charge transfer from the iodine atomic site to the uracil ring induced by nuclear motion turned out to be only ∼5 fs, indicating that, besides the molecular Auger decay in which molecular orbitals delocalized over the iodine site and the uracil ring are involved, the nuclear dynamics also play a role for ultrafast charge redistribution. The present study illustrates that the CCE-CE model as well as the SCC-DFTB method can be used for reconstructing the positions of atoms in motion, in combination with the momentum correlation measurement of the atomic ions created via XFEL-induced Coulomb explosion of molecules.

SCC-DFTB Parametrization for Boron and Boranes.

We present the results of our recent parametrization of the boron-boron and boron-hydrogen interactions for the self-consistent charge density-functional-based tight-binding (SCC-DFTB) method. To evaluate the performance, we compare SCC-DFTB to full density functional theory (DFT) and wave-function-based semiempirical methods (AM1 and MNDO). Since the advantages of SCC-DFTB emerge especially for large systems, we calculated molecular systems of boranes and pure boron nanostructures. Computed bond lengths, bond angles, and vibrational frequencies are close to DFT predictions. We find that the proposed parametrization provides a transferable and balanced description of both finite and periodic systems.

Vibrational spectroscopy and molecular dynamics of water monomers and dimers adsorbed on polycyclic aromatic hydrocarbons

This paper reports structures, energetics, dynamics and spectroscopy of H2O and (H2O)2 systems adsorbed on coronene (C24H12), a compact polycyclic aromatic hydrocarbon (PAH). On-the-fly Born-Oppenheimer molecular dynamics simulations are performed for temperatures T varying from 10 to 300 K, on a potential energy surface obtained within the self-consistent-charge density-functional based tight-binding (SCC-DFTB) approach. Anharmonic infrared (IR) spectra are extracted from these simulations. We first benchmark the SCC-DFTB semi-empirical hamiltonian vs. DFT (Density Functional Theory) calculations that include dispersion, on (C6H6)(H2O)1,2 small complexes. We find that charge corrections and inclusion of dispersion contributions in DFTB are necessary to obtain consistent structures, energetics and IR spectra. Using this Hamiltonian, the structures, energetics and IR features of the low-energy isomers of (C24H12)(H2O)1,2 are found to be similar to the DFT ones, with evidence for a stabilizing edge-coordination. The temperature dependence of the motions of H2O and (H2O)2 on the surface of C24H12 is analysed, revealing ultra-fast periodic motion. The water dimer starts diffusing at a higher temperature than the water monomer (150 K vs. 10 K respectively), which appears to be consistent with the binding energies. Qualitative and quantitative analyses of the effects of T on the IR spectra are performed. Anharmonic factors in particular are derived and it is shown that they can be used as signatures for the presence of PAH-water complexes. Finally, this paper lays the foundations for the studies of larger (PAH)m(H2O)n clusters, that can be treated with the efficient computational approach benchmarked in this paper.

Glycine Adsorption on (101̅0) ZnO Surfaces

The structural and electronic properties of glycine adsorbed on nonpolar (1010) ZnO surfaces have been investigated by using the self-consistent-charge density-functional-based tight-binding (SCC-DFTB) method. A coverage range from 0.25 to 1 monolayer (ML) was considered. We found that the molecule prefers to adsorb dissociatively for all coverages and adsorption modes. For 1 ML coverage, the molecule binds to the surface through either the carboxyl or the amine group with similar adsorption energies. In particular, adsorption through the amine group has a strong influence on the surface electronic properties. For coverages of 0.5 and 0.25 ML, glycine binds to the surface through both functional groups. Additionally, we studied the adsorption of glycine on oxygen-reduced surfaces. Our results show that the presence of oxygen vacancies slightly enhances the molecular adsorption energy compared to the adsorption on the defect-free surface.

Modeling Charge Resonance in Cationic Molecular Clusters: Combining DFT-Tight Binding with Configuration Interaction.

In order to investigate charge resonance situations in molecular complexes, Wu et al. (J. Chem. Phys. 2007, 127, 164119) recently proposed a configuration interaction method with a valence bond-like multiconfigurational basis obtained from constrained DFT calculations. We adapt this method to the Self-Consistent Charge Density-Functional-based Tight Binding (SCC-DFTB) approach and provide expressions for the gradients of the energy with respect to the nuclear coordinates. It is shown that the method corrects the wrong SCC-DFTB behavior of the potential energy surface in the dissociation regions. This scheme is applied to determine the structural and stability properties of positively charged molecular dimers with full structural optimization, namely, the benzene dimer cation and the water dimer cation. The method yields binding energies in good agreement with experimental data and high-level reference calculations.

Density‐functional based tight‐binding modelling of ZnO structures

AbstractA self‐consistent charge density‐functional based tight‐binding (SCC‐DFTB) parametrisation for structural optimization and electronic properties of zinc oxide is presented. Repulsive potentials are obtained from the ZnO wurtzite geometry and a thin nanowire and applied to the bulk rock salt phase, a (0001) oriented slab and nanowires of different sizes. The parametrisation is shown to reproduce geometries in agreement with DFT calculations.A different set of parameters is generated for electronic calculations giving band structures with a bulk band gap of 3.3 eV and a strong split‐off of the d‐bands in agreement with experiments. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Supramolecular Nanopatterns Self-Assembled by Adenine−Thymine Quartets at the Liquid/Solid Interface

By means of scanning tunneling microscopy (STM), we have observed for the first time well-ordered supramolecular nanopatterns formed by mixing two complementary DNA bases: adenine (A) and thymine (T), respectively, at the liquid/solid interface. By mixing A and T at a specific mixing molar ratio, cyclic structures that were distinctly different from the structures observed by the individual base molecules separately were formed. From an interplay between the STM findings and self-consistent charge density-functional based tight-binding (SCC-DFTB) calculation method, we suggest formation of A-T-A-T quartets constructed on the basis of A-T base pairing. The formation of the A-T-A-T quartets opens new avenues to use DNA base pairing as a way to form nanoscale surface architecture and biocompatible patterned surfaces particularly via host-guest complexation that might be suitable for drug design, where the target can be trapped inside the cavities of the molecular containers.

Coadsorption of Guanine and Cytosine on Graphite: Ordered Structure Based on GC Pairing

Nanostructures formed by coadsorption of the complementary DNA bases guanine (G) and cytosine (C) at a graphite surface in 1-octanol solvent were investigated by in situ scanning tunneling microscopy. The high-resolution observations showed for the first time a well-ordered coadsorption structure, attributed to rows formed from Watson-Crick G-C pairs, which was distinctly different from the structures observed for the individual G/C components. The observed coadsorption structure has been modeled by self-consistent charge density-functional-based tight-binding (SCC-DFTB) calculations, providing information on the intermolecular interactions underlying its formation.

Elastic properties of single amylose chains in water: a quantum mechanical and AFM study.

Recent single-molecule atomic force microscopy (AFM) experiments have revealed that some polysaccharides display large deviations from force-extension relationships of other polymers which typically behave as simple entropic springs. However, the mechanism of these deviations has not been fully elucidated. Here we report the use of novel quantum mechanical methodologies, the divide-and-conquer linear scaling approach and the self-consistent charge density functional-based tight binding (SCC-DFTB) method, to unravel the mechanism of the extensibility of the polysaccharide amylose, which in water displays particularly large deviations from the simple entropic elasticity. We studied the deformations of maltose, a building block of amylose, both in a vacuum and in solution. To simulate the deformations in solution, the TIP3P molecular mechanical model is used to model the solvent water, and the SCC-DFTB method is used to model the solute. The interactions between the solute and water are treated by the combined quantum mechanical and molecular mechanical approach. We find that water significantly affects the mechanical properties of maltose. Furthermore, we performed two nanosecond-scale steered molecular dynamics simulations for single amylose chains composed of 10 glucopyranose rings in solution. Our SCC-DFTB/MM simulations reproduce the experimentally measured force-extension curve, and we find that the force-induced chair-to-boat transitions of glucopyranose rings are responsible for the characteristic plateau in the force-extension curve of amylose. In addition, we performed single-molecule AFM measurements on carboxymethyl amylose, and we found that, in contrast to the results of an earlier work by others, these side groups do not significantly affect amylose elasticity. By combining our experimental and modeling results, we conclude that the nonentropic elastic behavior of amylose is governed by the mechanics of pyranose rings themselves and their force-induced conformational transitions.