Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13.

In this work, the binding mechanism of new Polyketide Synthase 13 (Pks13) inhibitors has been studied through molecular dynamics simulation and free energy calculations. The drug Tam1 and its analogs, belonging to the benzofuran class, were submitted to 100 ns simulations, and according to the results obtained for root mean square deviation, all the simulations converged from approximately 30 ns. For the analysis of backbone flotation, the root mean square fluctuations were plotted for the Cα atoms; analysis revealed that the greatest fluctuation occurred in the residues that are part of the protein lid domain. The binding free energy value (ΔGbind) obtained for the Tam16 lead molecule was of -51.43 kcal/mol. When comparing this result with the ΔGbind values for the remaining analogs, the drug Tam16 was found to be the highest ranked: this result is in agreement with the experimental results obtained by Aggarwal and collaborators, where it was verified that the IC50 for Tam16 is the smallest necessary to inhibit the Pks13 (IC50 = 0.19 µM). The energy decomposition analysis suggested that the residues which most interact with inhibitors are: Ser1636, Tyr1637, Asn1640, Ala1667, Phe1670, and Tyr1674, from which the greatest energy contribution to Phe1670 was particularly notable. For the lead molecule Tam16, a hydrogen bond with the hydroxyl of the phenol not observed in the other analogs induced a more stable molecular structure. Aggarwal and colleagues reported this hydrogen bonding as being responsible for the stability of the molecule, optimizing its physic-chemical, toxicological, and pharmacokinetic properties.

Isomeric effects tuning the electron transport in carotenoid derivatives: from ohmic to rectifier behavior.

Single-molecules have been widely investigated in the last decades due to their promises as devices in molecular electronics. One of the advantages in the use of natural compounds in molecular electronics is the economy of material and molecular synthesis, which makes the process both cheaper and self-sustaining. Although many studies have considered electronic transport in single molecules, there are few studies associated with isomeric effects in biologically appealing systems. In the present work, we have studied ballistic electron transport in two isomeric forms of a retinol molecule: 11-cis and all-trans-retinol. The molecules were connected between two Au(111) electrodes and calculations were performed with the NEGF-DFT methodology. Current-voltage, differential conductance, and rectification curves were obtained and compared for two structures. While 11-cis-retinol shows a more symmetrical current-voltage curve, all-trans-retinol acts as molecular diode for low applied voltages. Our results suggest that a simple isomeric effect modulates the molecular device from nanowires to diodes with potential applications as field-effect transistors.

Single-molecular diodes based on opioid derivatives.

We propose an efficient single-molecule rectifier based on a derivative of opioid. Electron transport properties are investigated within the non-equilibrium Green's function formalism combined with density functional theory. The analysis of the current-voltage characteristics indicates obvious diode-like behavior. While heroin presents rectification coefficient R>1, indicating preferential electronic current from electron-donating to electron-withdrawing, 3 and 6-acetylmorphine and morphine exhibit contrary behavior, R<1. Our calculations indicate that the simple inclusion of acetyl groups modulate a range of devices, which varies from simple rectifying to resonant-tunneling diodes. In particular, the rectification rations for heroin diodes show microampere electron current with a maximum of rectification (R=9.1) at very low bias voltage of ∼0.6 V and (R=14.3)∼1.8 V with resistance varying between 0.4 and 1.5 M Ω. Once most of the current single-molecule diodes usually rectifies in nanoampere, are not stable over 1.0 V and present electrical resistance around 10 M. Molecular devices based on opioid derivatives are promising in molecular electronics.

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.

Thermodynamic analysis of fuels in gas phase: ethanol, gasoline and ethanol - gasoline predicted by DFT method.

This paper presents a theoretical study using density functional theory to calculate thermodynamics properties of major molecules compounds at gas phase of fuels like gasoline, ethanol, and gasoline-ethanol mixture in thermal equilibrium on temperature range up to 1500 K. We simulated a composition of gasoline mixture with ethanol for a thorough study of thermal energy, enthalpy, Gibbs free energy, entropy, heat capacity at constant pressure with respect to temperature in order to study the influence caused by ethanol as an additive to gasoline. We used semi-empirical computational methods as well in order to know the efficiency of other methods to simulate fuels through this methodology. In addition, the ethanol influence through the changes in percentage fractions of chemical energy released in combustion reaction and the variations on thermal properties for autoignition temperatures of fuels was analyzed. We verified how ethanol reduces the chemical energy released by gasoline combustion and how at low temperatures the gas phase fuels in thermal equilibrium have similar thermodynamic behavior. Theoretical results were compared with experimental data, when available, and showed agreement. Graphical Abstract Thermodynamic analysis of fuels in gas phase.

Nanosphere and carbon nanotube as motor and gun controlled by light.

We propose a system like motor and gun molecular that has the open extremities of external nanotube using the internal C60 nanosphere as a probe. The system consists of a rigid and static nanotube opened and the internal C60 probe that allows relaxation between them. The initial position of C60 is out of symmetry that permits the probe to start the system movement due to van der Waals force acting in the probe. The simulation was made by classic molecular dynamics with standard parameterization. We calculated thermodynamics properties of these two devices as molar specific heat and molar entropy variation. Properties as probe speed were obtained like molecular motor and gun versus time. The nanotube has 360 carbon atoms with up to almost 0.7 ns of simulation. These facts can be useful for building new molecular machines.

Nanoscillator and gun under temperature effect.

We propose a system like motor or gun molecular with a nanotube and C60 nanosphere as a probe. The initial position of C60 is out of symmetry that permits the probe to start the system movement due to van der Waals force acting in the probe. For higher initial temperatures there are ejections of the probe like a nanogun. The simulation was made by classic molecular dynamics with standard parameterization. Thermodynamics properties were obtained like molecular motor and gun versus initial temperature. The nanotube has 360 carbon atoms with up to almost 0.7 ns of simulation.