Charge Density-functional Tight-binding Method Research Articles

Toward an efficient f-in-core/f-in-valence switchable description for DFTB calculations of Ce 4f states in ceria.

A computational protocol is developed for efficient studies of partially reduced redox-active oxides using the self-consistent charge density functional tight-binding method. The protocol is demonstrated for ceria, which is a prototypical reducible oxide material. The underlying idea is to achieve a consistent (and harmonized) set of Slater-Koster (SK) tables with connected repulsive potentials that enable switching on and off the in-valence description of the Ce 4f states without serious loss of accuracy in structure and energetics. The implicit treatment of the Ce 4f states, with the use of f-in-core SK-tables, is found to lead to a significant decrease in computational time. More importantly, it allows for explicit control of the oxidation states of individual Ce atoms. This makes it possible to "freeze" the electronic configuration, thereby allowing the exploration of the energetics for various meta-stable configurations. We anticipate that the outlined strategy can help to shed light on the interplay between the size, shape, and redox activity for nanoceria and other related materials.

Influence of stretching and compression deformations on the electrical conductive properties of graphene-nanotube composites with an island-type topology

Within the framework of the self--consistent--charge density functional tight-binding method, we study the features of the atomic structure and electrical conductive properties of a hybrid graphene-nanotube film with an island topology under uniaxial stretching and compression. The hybrid film is a composite structure formed by AB-stacked bilayer graphene and horizontally oriented chiral single-walled carbon nanotubes of 1.2 nm in diameter. The regularities of the deformation behavior of the investigated hybrid structure are revealed and the limits of its strength are established. It is shown how the electrical resistance and the current-voltage characteristic of the film change under stretching/compression deformations. Keywords: island-type graphene-nanotube films, uniaxial stretching/compression, resistance, current-voltage characteristic.

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.

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.

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.

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.

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.

Fusion reaction dynamics of fullerene molecules

SynopsisSystematic molecular dynamics simulations based on the self-consistent charge density functional tight-binding method have been performed for the molecular collisions inside clusters of fullerene molecules, after prompt atom knockouts by the keV ions. The thermodynamic and kinetic stabilities, as well as the bonding features, have been investigated for the most stable dumbbell dimers C+18, C+19 and C+20.

Formation dynamics of fullerene dimersC118+,C119+, andC120+

Dumbbell-shaped fullerene dimers ${C}_{118}^{+}$ and ${C}_{119}^{+}$ have recently been observed in mass spectra resulting from collisions between clusters of C${}_{60}$ molecules and keV He${}^{2+}$ or Ar${}^{2+}$ ions [H. Zettergren et al., Phys. Rev. Lett. 110, 185501 (2013) and F. Seitz et al., J. Chem. Phys. 139, 034309 (2013)]. To unveil the formation mechanisms of these fullerene dimers, systematic molecular dynamics (MD) simulations based on the self-consistent charge density functional tight-binding method have been performed for C${}_{n}^{+}$ + C${}_{60}$ ($n=58,59,60$) collisions following prompt atom knockouts by the fast ions. The statistics from the MD simulations indicate a much higher reactivity of ${C}_{59}^{+}$ and ${C}_{58}^{+}$ fragments compared to that of ${C}_{60}^{+}$. It is found that the covalently bonded dumbbell-shaped fullerene dimers ${C}_{118}^{+}$ and ${C}_{119}^{+}$ can be formed at very low-collision energies within 1 ps and are stable enough to survive on the microsecond time scale of the experiment. The thermodynamic and kinetic stabilities, as well as the bonding features, have been investigated for the most stable dumbbell dimers ${C}_{118}^{+}$, ${C}_{119}^{+}$, and ${C}_{120}^{+}$.

Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method.

An important element determining the time requirements of Born-Oppenheimer molecular dynamics (BOMD) is the convergence rate of the self-consistent solution of Roothaan equations (SCF). We show here that improved convergence and dynamics stability can be achieved by use of a Lagrangian formalism of BOMD with dissipation (DXL-BOMD). In the DXL-BOMD algorithm, an auxiliary electronic variable (e.g., the electron density or Fock matrix) is propagated and a dissipative force is added in the propagation to maintain the stability of the dynamics. Implementation of the approach in the self-consistent charge density functional tight-binding method makes possible simulations that are several hundred picoseconds in lengths, in contrast to earlier DFT-based BOMD calculations, which have been limited to tens of picoseconds or less. The increase in the simulation time results in a more meaningful evaluation of the DXL-BOMD method. A comparison is made of the number of iterations (and time) required for convergence of the SCF with DXL-BOMD and a standard method (starting with a zero charge guess for all atoms at each step), which gives accurate propagation with reasonable SCF convergence criteria. From tests using NVE simulations of C(2)F(4) and 20 neutral amino acid molecules in the gas phase, it is found that DXL-BOMD can improve SCF convergence by up to a factor of two over the standard method. Corresponding results are obtained in simulations of 32 water molecules in a periodic box. Linear response theory is used to analyze the relationship between the energy drift and the correlation of geometry propagation errors.

Electronic Transport Properties of Graphitic Ribbons under Finite Bias Voltages

We present a theoretical study of the electronic transport through finite-sized nano-scale graphitic ribbon under the finite bias voltage. By making use of the self-consistent charge density functional tight-binding method along with the Keldysh nonequilibrium Green's function formalism, we obtain remarkable nonlinear behaviors of the current-voltage characteristics of graphitic ribbons, which are found to be attributed to their unique electronic structures by analyzing the energy distribution of the transmission probabilities. [DOI: 10.1380/ejssnt.2006.78]

Electron-spin-resonance studies of HMX pyrolysis products

Chemical transformations that occur at the reactive shock front of energetic materials determine many aspects of material properties and performance. One major shortcoming of current explosive models is the lack of chemical kinetics data of the reacting explosive at the high pressures and temperatures experienced under detonation conditions. In the absence of experimental data, long time-scale atomistic molecular dynamics simulations with reactive chemistry provide insight into the decomposition mechanisms of explosives and allow us to obtain effective reaction rates. These rates can then be incorporated into a thermochemical continuum code for accurate and predictive description of grain- and continuum-scale dynamics of reacting explosives. During the course of the past decade, we have examined the chemistry of several reacting explosive materials, such as the high-performing HMX and the very insensitive TATB explosives, both of which are organic molecular solids at ambient conditions. We have used quantum-based, self-consistent charge density functional tight-binding method to calculate the interatomic forces in molecular dynamics simulations either for thermal decomposition studies (constant volume–temperature) or dynamical shock studies using the multiscale shock simulation technique (MSST). These studies allow us to investigate the chemical reactivity of explosives and to examine electronic properties at extreme conditions of temperature and pressure for a relatively long timescale on the order of several hundreds of picoseconds. In this chapter, we discuss challenges in simulating the reactions of shocked energetic materials and review specific examples of our recent simulations on HMX, PETN, and shocked TATB. Each of these studies revealed interesting aspects associated with known macroscopic properties of these materials. We also discuss simulations on nonenergetic materials such as shocked carbon and methane.