Augusto F. Oliveira

Density-functional based tight-binding: an approximate DFT method

The DFTB method, as well as its self-consistent charge corrected variant SCC-DFTB, has widened the range of applications of fundamentally well established theoretical tools. As an approximate density-functional method, DFTB holds nearly the same accuracy, but at much lower computational costs, allowing investigation of the electronic structure of large systems which can not be exploited with conventional ab initio methods. In the present paper the fundaments of DFTB and SCC-DFTB and inclusion of London dispersion forces are reviewed. In order to show an example of the DFTB applicability, the zwitterionic equilibrium of glycine in aqueous solution is investigated by molecular-dynamics simulation using a dispersion-corrected SCC-DFTB Hamiltonian and a periodic box containing 129 water molecules, in a purely quantum-mechanical approach.

Electromechanics in MoS2 and WS2: nanotubes vs. monolayers

The transition-metal dichalcogenides (TMD) MoS2 and WS2 show remarkable electromechanical properties. Strain modifies the direct band gap into an indirect one, and substantial strain even induces an semiconductor-metal transition. Providing strain through mechanical contacts is difficult for TMD monolayers, but state-of-the-art for TMD nanotubes. We show using density-functional theory that similar electromechanical properties as in monolayer and bulk TMDs are found for large diameter TMD single- (SWNT) and multi-walled nanotubes (MWNTs). The semiconductor-metal transition occurs at elongations of 16%. We show that Raman signals of the in-plane and out-of-plane lattice vibrations depend significantly and linearly on the strain, showing that Raman spectroscopy is an excellent tool to determine the strain of the individual nanotubes and hence monitor the progress of nanoelectromechanical experiments in situ. TMD MWNTs show twice the electric conductance compared to SWNTs, and each wall of the MWNTs contributes to the conductance proportional to its diameter.

Electromechanics in MoS 2 and WS 2 : nanotubes vs. monolayers

The transition-metal dichalcogenides (TMD) MoS2 and WS2 show remarkable electromechanical properties. Strain modifies the direct band gap into an indirect one, and substantial strain even induces an semiconductor-metal transition. Providing strain through mechanical contacts is difficult for TMD monolayers, but state-of-the-art for TMD nanotubes. We show using density-functional theory that similar electromechanical properties as in monolayer and bulk TMDs are found for large diameter TMD single- (SWNT) and multi-walled nanotubes (MWNTs). The semiconductor-metal transition occurs at elongations of 16%. We show that Raman signals of the in-plane and out-of-plane lattice vibrations depend significantly and linearly on the strain, showing that Raman spectroscopy is an excellent tool to determine the strain of the individual nanotubes and hence monitor the progress of nanoelectromechanical experiments in situ. TMD MWNTs show twice the electric conductance compared to SWNTs, and each wall of the MWNTs contributes to the conductance proportional to its diameter.

DFTB Parameters for the Periodic Table: Part 1, Electronic Structure

A parametrization scheme for the electronic part of the density-functional based tight-binding (DFTB) method that covers the periodic table is presented. A semiautomatic parametrization scheme has been developed that uses Kohn-Sham energies and band structure curvatures of real and fictitious homoatomic crystal structures as reference data. A confinement potential is used to tighten the Kohn-Sham orbitals, which includes two free parameters that are used to optimize the performance of the method. The method is tested on more than 100 systems and shows excellent overall performance.

Conformational analysis of aqueous BMP-2 using atomistic molecular dynamics simulations.

BMP-2 is an osteoinductive protein, involved in the differentiation and proliferation of osteoblasts, with potential application as bioactive agent in bone implants and scaffolds. Since the three-dimensional structure of a protein usually determines its bioactivity, in order to efficiently design bone implants activated with BMP-2 it is essential to identify the factors influencing the protein conformation. In the present work, atomistic molecular dynamics simulations are employed to investigate the BMP-2 monomer and homodimer in vacuum and water. The influence of each environment on the BMP-2 structure is analyzed regarding protein structural changes and energy contributions driving the BMP-2 conformation.

DFTB Parameters for the Periodic Table, Part 2: Energies and Energy Gradients from Hydrogen to Calcium

In the first part of this series, we presented a parametrization strategy to obtain high-quality electronic band structures on the basis of density-functional-based tight-binding (DFTB) calculations and published a parameter set called QUASINANO2013.1. Here, we extend our parametrization effort to include the remaining terms that are needed to compute the total energy and its gradient, commonly referred to as repulsive potential. Instead of parametrizing these terms as a two-body potential, we calculate them explicitly from the DFTB analogues of the Kohn-Sham total energy expression. This strategy requires only two further numerical parameters per element. Thus, the atomic configuration and four real numbers per element are sufficient to define the DFTB model at this level of parametrization. The QUASINANO2015 parameter set allows the calculation of energy, structure, and electronic structure of all systems composed of elements ranging from H to Ca. Extensive benchmarks show that the overall accuracy of QUASINANO2015 is comparable to that of well-established methods, including PM7 and hand-tuned DFTB parameter sets, while coverage of a much larger range of chemical systems is available.

Inventory of benthic macroinvertebrates diversity in the Peti Environmental Station Reservoir of Minas Gerais, Brazil

The aim of this study was to inventory the diversity of benthic macroinvertebrates of the reservoir of the Peti Environmental Station in Minas Gerais State through the evaluation of these communities in space and temporal scales during the rainy and dry periods from June - 2002 up to June - 2004. The Peti reservoir has almost 50 years and is used for hydropower generation. The benthic macroinvertebrates are an important tool for the evaluation of water quality and environment monitoring through inventories of diversity and data on community structure. A total of 16 taxa was found and the most abundant groups were Chaoboridae (47,51 %), the Chironomidae genera Coelotanypus (15,1%) and Chironomus (2,77%), Bivalvia (19,11%) and Oligochaeta (9,54%). There were no signifi cant variations (R = 0,1927; p >0,05) for the biotic data among the sampling stations during the studied periods. The evaluation of the distribution and structure of the benthic community showed that the quality of the reservoir’s water is preserved, because there was no predominance of bad quality indicator organisms. This situation is due to the constant oxygenation of the hypolimnion which is probably related with the reservoir operation. Key words: benthic communities, reservoir, inventory.

High-Performance 2D p-Type Transistors Based on GaSe Layers: An Ab Initio Study

Ultrascaled GaSe field effect transistors are investigated through ab initio calculations. GaSe monolayers, 3 nm long, exhibit excellent performance with reduced short-channel effects and considerable high ON-current. Such device characteristics are due to the valence band edge shape, which leads to very heavy holes in the transport direction and eventually suppresses intraband tunneling, detrimental for correct operation in the OFF state.

Spin polarization in SCC-DFTB

We evaluate the performance of spin-polarized DFTB within the SCC-DFTB (also known as DFTB2) model. The method has been implemented in the ADF modeling suite. We briefly review how spin polarization is incorporated into the DFTB2 method and validate the method in terms of structural parameters and energies using the GMTKN30 test set, from which we used 288 spin-polarized systems.

FASP: a framework for automation of Slater–Koster file parameterization

The self-consistent-charge density-functional tight-binding method (SCC-DFTB) is largely used for investigating systems of increasing complexity. However, the SCC-DFTB parameters are not available for the whole periodic table and some issues related to its transferability can limit its usefulness. The framework for automating the repulsion energy (Erep) parameterization uses reference chemical models to parameterize the repulsion term of the SCC-DFTB. The aim is to provide a straightforward and accessible manner to obtain accurate SCC-DFTB Erep parameters automatically. Large number of reference chemical models can be simultaneously used to increase the accuracy and transferability of the parameters with respect to the total energies and derived properties. SCC-DFTB parameters for the C, O, N, H set were obtained. The results are in good agreement with the well-established SCC-DFTB parameters available for this test case. Extensions to include other properties such as reaction energies in the Erep parameterization are briefly discussed.