Thermodynamics study of biokerosene from coconut and palm kernel oils and JP-8 aircraft fuels in the gas phase by the DFT method.

In this work, we performed a theoretical density functional theory (DFT) and semi-empirical (PM3) analysis to calculate thermodynamic properties of biokerosene from coconut and palm kernel oils, Jet Propulsion Fuel 8 (JP-8), and mixtures of these fuels. All simulations were performed in thermal equilibrium and for a temperature range of 0.5-1500 K, considering the canonical ensemble model. We predicted the thermal properties energy, enthalpy, enthalpy change, Gibbs free energy, entropy, and specific heat at constant pressure with respect to temperature. In addition, we compared the performances of the DFT functional hybrid B3LYP and the basis set 6-311++G(d,p) and PM3 methods, in order to determine their accuracy for thermodynamic predictions relating to the fuels. Calculations for combustion enthalpy were carried out using the following methods: B3LYP/6-311++G(d,p), B3LYP/6-31+G(d), CBS-QB3, G3, G4, and G3/G4. The results showed good agreement with measured values, indicating that DFT may be a good method to calculate and predict thermodynamic properties of the combustion reactions of kerosene and biokerosene.

Effect of the Electric Field on DNA Bases as Pigments for Nanodevices: A First-Principles Study.

In this work we used Density Functional Theory to simulate the molecular electronics behavior of the nitrogenous bases of human DNA under electric field effects. The results can describe some internal effects in the use of DNA-based as photoconductor or semiconductor nanodevices. For this investigation, calculations were performed to predict structural deformations, HOMO and LUMO orbitals, and thermodynamic properties of each one of the following nitrogenous bases: adenine, thymine, guanine and cytosine. All the quantities were calculated as functions of the electric field. This analysis allows us to verify the influence of the electric field in the molecular geometry of nitrogenous bases, enabling us to determine that adenine, thymine and guanine are those bases most susceptible to presenting substantial deformations when DNA is submitted to the action of an external electric field, while the molecular structure of cytosine is highly resistant to this effect.

Molecular Electronics Including Temperature Effects Based on Dyes Pigments.

In this work we used the Density Functional Theory to study the thermodynamic properties from Brazilein (BZE) and Brazilin (BZI) molecules, main pigments responsible for the red color from Brazil wood. We did a comparison between the two dyes to then know which dye has better resistance to temperature (T ) and external electric field (E) values, aiming their potential to possible applications in solar cells, as excitons trainers. We have found that the BZE molecule becomes less stable after a temperature known as degradation temperature, and therefore enters oxidation state. However, BZE is more stable and more resistant to high temperatures. With respect to the applied external electric field, we find that BZE is more reactive to almost all the applied electric fields, thus more easily converted into energy in the form of electrical work.

Time-Dependent Density Functional Theory Analysis of Triphenylamine-Functionalized Graphene Doped with Transition Metals for Photocatalytic Hydrogen Production.

The electronic structures and optical properties of triphenylamine-functionalized graphene (G-TPA) doped with transition metals, using water as a solvent, were theoretically investigated to verify the efficiency of photocatalytic hydrogen production with the use of transition metals. This study was performed by Density Functional Theory and Time-dependent Density Functional Theory through Gaussian 09W software, adopting the B3LYP functional for all structures. The 6-31g(d) basis set was used for H, C and N atoms, and the LANL2DZ basis set for transition metals using the Effective Core Potentials method. Two approaches were adopted: (1) using single metallic dopants (Ni, Pd, Fe, Os and Pt) and (2) using combinations of Ni with the other dopants (NiPd, NiPt, NiFe and NiOs). The DOS spectra reveal an increase of accessible states in the valence shell, in addition to a gap decrease for all dopants. This doping also increases the absorption in the visible region of solar radiation where sunlight is most intense (400 nm to 700 nm), with additional absorption peaks. The results lead us to propose the G-TPA structures doped with Ni, Pd, Pt, NiPt or NiPd to be novel catalysts for the conversion of solar energy for photocatalytic hydrogen production, since they improve the absorption of solar energy in the range of interest for solar radiation; and act as reaction centers, reducing the required overpotential for hydrogen production from water.

Intermolecular interactions between DNA and methamphetamine, amphetamine, ecstasy and their major metabolites.

In this work, we carried out a theoretical investigation regarding amphetamine-type stimulants, which can cause central nervous system degeneration, interacting with human DNA. These include amphetamine, methamphetamine, 3,4-Methylenedioxymethamphetamine (also known as ecstasy), as well as their main metabolites. The studies were performed through molecular docking and molecular dynamics simulations, where molecular interactions of the receptor-ligand systems, along with their physical-chemical energies, were reported. Our results show that 3,4-Methylenedioxymethamphetamine and 3,4-Dihydroxymethamphetamine (ecstasy) present considerable reactivity with the receptor (DNA), suggesting that these molecules may cause damage due to human-DNA. These results were indicated by free Gibbs change of bind (ΔGbind) values referring to intermolecular interactions between the drugs and the minor grooves of DNA, which were predominant for all simulations. In addition, it was observed that 3,4-Dihydroxymethamphetamine (ΔGbind = -13.15 kcal/mol) presented greater spontaneity in establishing interactions with DNA in comparison to 3,4-Methylenedioxymethamphetamine (ΔGbind = -8.61 kcal/mol). Thus, according with the calculations performed our results suggest that the 3,4-Methylenedioxymethamphetamine and 3,4-Dihydroxymethamphetamine have greater probability to provide damage to human DNA fragments.

Thermodynamic DFT analysis of natural gas.

Density functional theory was performed for thermodynamic predictions on natural gas, whose B3LYP/6-311++G(d,p), B3LYP/6-31+G(d), CBS-QB3, G3, and G4 methods were applied. Additionally, we carried out thermodynamic predictions using G3/G4 averaged. The calculations were performed for each major component of seven kinds of natural gas and to their respective air + natural gas mixtures at a thermal equilibrium between room temperature and the initial temperature of a combustion chamber during the injection stage. The following thermodynamic properties were obtained: internal energy, enthalpy, Gibbs free energy and entropy, which enabled us to investigate the thermal resistance of fuels. Also, we estimated an important parameter, namely, the specific heat ratio of each natural gas; this allowed us to compare the results with the empirical functions of these parameters, where the B3LYP/6-311++G(d,p) and G3/G4 methods showed better agreements. In addition, relevant information on the thermal and mechanic resistance of natural gases were investigated, as well as the standard thermodynamic properties for the combustion of natural gas. Thus, we show that density functional theory can be useful for predicting the thermodynamic properties of natural gas, enabling the production of more efficient compositions for the investigated fuels. Graphical abstract Investigation of the thermodynamic properties of natural gas through the canonical ensemble model and the density functional theory.

A Molecular Dynamics of Cold Neutral Atoms Captured by Carbon Nanotube Under Electric Field and Thermal Effect as a Selective Atoms Sensor.

Here we analyzed several physical behaviors through computational simulation of systems consisting of a zig-zag type carbon nanotube and relaxed cold atoms (Rb, Au, Si and Ar). These atoms were chosen due to their different chemical properties. The atoms individually were relaxed on the outside of the nanotube during the simulations. Each system was found under the influence of a uniform electric field parallel to the carbon nanotube and under the thermal effect of the initial temperature at the simulations. Because of the electric field, the cold atoms orbited the carbon nanotube while increasing the initial temperature allowed the variation of the radius of the orbiting atoms. We calculated the following quantities: kinetic energy, potential energy and total energy and in situ temperature, molar entropy variation and average radius of the orbit of the atoms. Our data suggest that only the action of electric field is enough to generate the attractive potential and this system could be used as a selected atoms sensor.

Flagella interacting with a carbon nanowire with the variation of time and initial temperature.

The system proposed consists of a flagellum relaxing around a static carbon nanowire to mimics behavior of a natural flagellum moving with damped harmonic motion along a wire under van der Waals and electrostatic forces. This flagellum is composed of a C20 nanosphere with different sizes of his tail formed by hydrocarbons. The thermodynamic properties such as molar entropy variation, as well as molar heat dissipation, efficiency and speed were obtained to evaluate which system is most stable by using the variable temperature. This system has a number of carbon atoms ranging from 103-110, with a maximum of 300 ps for each simulation. We had simulated molar entropy variation, energies and efficiency changing with time and initial temperature. The results indicate that among the systems studied, the flagellum with five carbon atoms achieved greater stability and better results in this search.

A dynamic molecular study of parallel gold nanowires matrix.

We study the theoretical van der Waals interaction of parallel gold nanowires (GNs) in matrix form with free extremities using molecular mechanics. It was calculated force, velocity, efficiency, thermodynamics properties like molar heat capacity, molar entropy variation and the relation between kinetic energy and temperature in situ of the GNs. We found new information about the nanowire behavior due to the matrix form. Each nanowire has 20 atoms and distant 27.78 angstroms from each one.