Density functional theory for the thermodynamic gas-phase investigation of butanol biofuel and its isomers mixed with gasoline and ethanol.

Herein, we present the results of our study on the thermodynamic properties of the isomers of butanol (n-butanol, 2-butanol, i-butanol, and t-butanol) to evaluate their thermodynamic potential as a complementary biofuel and/or substitute for ethanol and gasoline. The Gaussian09W software was used to perform molecular geometry optimization calculations using density functional theory with the B3lyp hybrid function using the base set 6-311++g(d,p) and the compound methods G3, G4, and CBS-QB3. Calculations of the fundamental frequency of the molecules were performed to obtain the molecular vibration modes for the respective frequencies. These calculations provided thermodynamic parameters such as the entropy, enthalpy, and specific molar heat at constant pressure, all as a function of the temperature. The parameter values obtained by each method were compared to the experimental values available in the literature. The results showed good accuracy, especially those obtained at the B3lyp/6-311++g(d,p) level for n-butanol. The error between the theoretical and experimental values for the combustion enthalpy of n-butanol was less than 4% at 298.15 K; due to the good prediction of its thermodynamic properties, we used n-butanol as a model for the prediction of other thermodynamic properties. We started a molecular docking study of four ligands, namely, n-butanol, ethanol, propanol, heptane, isooctane, and methanol interacting with butanol isomers. The highest values of affinity energy found were for N-butanol. The possible formation of hydrogen bonds, associations by means of London forces, hydrogen, and alkyl interactions were analyzed. n-Butanol was added to ethanol-gasoline mixtures in the temperature range of 298.15 to 600 K and the results suggest that n-butanol has a higher calorific value than gasoline-ethanol mixtures in G30E, G40E, G50E, G60E, G70E, G80E, G90E, and E100 blends. As such, n-butanol releases greater amounts of heat during combustion and is thus a viable alternative to biofuels.

Pharmacophore-based virtual screening and molecular docking to identify promising dual inhibitors of human acetylcholinesterase and butyrylcholinesterase.

The dual inhibition of human acetylcholinesterase (hAChE) and butyrylcholinesterase (hBuChE) plays an important role in Alzheimer's disease treatment. Thus, this study aims identify promising dual inhibitors against hAChE and hBuChE by in silico approaches (pharmacophore-based virtual screening and molecular docking). Ten 3 D pharmacophore models for dual inhibitors using default genetic parameters were built by GALAHAD™ available on SYBYL-X 2.0. Validation steps were carried out according to Energy (<100.0 kcal/mol), Pareto = 0, Area under the ROC Curve (>0.70), Boltzmann-Enhanced Discrimination of ROC curve (BEDROC >0.50) and structure-activity relationship (SAR) for known inhibitors. The best dual pharmacophore model based on internal/external statistical parameters and SAR data (one hydrogen bond acceptor, two hydrogen bond donors and four hydrophobic centers) was employed in virtual screening at Sigma-Aldrich® subset (n = 214,446) of ZINC database by UNITY module of SYBYL-X 2.0. According to superposition values (QFIT), the best ranked compounds were prioritized for molecular docking and partition coefficient analysis (clog p < 5.0). 37 top-ranked compounds (QFIT > 64.22) from pharmacophore model showed affinity in hAChE (-10.2 < Affinity energy < -6.3 kcal/mol) and hBuChE (-10.9 < Affinity energy < -2.3 kcal/mol) binding sites. Next, liposolubity prediction and commercially available showed that ZINC43198636, ZINC43198637 and ZINC00390718 can be potential dual inhibitors against hAChE and hBuChE.Communicated by Ramaswamy H. Sarma.

Chemical Composition, Antimicrobial Properties of Siparuna guianensis Essential Oil and a Molecular Docking and Dynamics Molecular Study of its Major Chemical Constituent.

The essential oil of Siparuna guianensis was obtained by hydrodistillation. The identification of the chemical compounds was performed by gas chromatography coupled with mass spectrometry (GC/MS). Antimicrobial activity was investigated for four microorganisms: Streptococcus mutans (ATCC 3440), Enterococcus faecalis (ATCC 4083), Escherichia coli (ATCC 25922), and Candida albicans (ATCC-10231). The studies of doping and molecular dynamics were performed with the molecule that presented the highest concentration of drug-target proteins, 1IYL (C. albicans), 1C14 (E. coli), 2WE5 (E. faecalis), and 4TQX (S. mutans). The main compounds identified were: Curzerene (7.1%), γ-Elemene (7.04%), Germacrene D (7.61%), trans-ß-Elemenone (11.78%), and Atractylone (18.65%). Gram positive bacteria and fungi were the most susceptible to the effects of the essential oil. The results obtained in the simulation showed that the major compound atractylone interacts with the catalytic sites of the target proteins, forming energetically favourable systems and remaining stable during the period of molecular dynamics.

First Report on Yield and Chemical Composition of Essential Oil Extracted from Myrcia eximia DC (Myrtaceae) from the Brazilian Amazon.

The essential oil (EO) of plants of the Myrtaceae family has diverse chemical composition and several applications. However, data on the oil yield, its composition, and its complete chemistry are still unavailable for some species belonging to this family, such as Myrcia eximia DC. In this study, the chemical compositions of the EOs of Myrcia eximia were evaluated by using gas chromatography (GC) alone and gas chromatography coupled with mass spectrometry (GC-MS). Samples for both evaluations were collected from the city of Magalhães Barata, State of Pará, Brazil, in 2017 and 2018. For the plant material collected in 2017, EO was obtained by hydrodistillation (HD) only, while, for the material collected in 2018, EO was obtained by hydrodistillation and steam distillation (SD), in order to evaluate the differences in chemical composition and mass yield of the EO. The yields of (E)-caryophyllene were 15.71% and 20.0% for the samples collected by HD in 2017 and 2018, respectively, while the yield was 15.0% for the sample collected by SD in 2018. Hexanal was found to be the major constituent in the EO obtained by HD, with yield of up to 26.09%. The oil yields reached 0.08% by using SD, and 0.01% and 0.36% for the samples collected in 2017 and 2018, respectively, using HD. The results of this study provide new information about the mass yield and chemical composition of Myrcia eximia DC, and they can add value and income to traditional populations, as well as facilitate the preservation of this species.

Potential inhibitors of the enzyme acetylcholinesterase and juvenile hormone with insecticidal activity: study of the binding mode via docking and molecular dynamics simulations.

Models validation in QSAR, pharmacophore, docking and others can ensure the accuracy and reliability of future predictions in design and selection of molecules with biological activity. In this study, pyriproxyfen was used as a pivot/template to search the database of the Maybridge Database for potential inhibitors of the enzymes acetylcholinesterase and juvenile hormone as well. The initial virtual screening based on the 3D shape resulted in 2000 molecules with Tanimoto index ranging from 0.58 to 0.88. A new reclassification was performed on the overlapping of positive and negative charges, which resulted in 100 molecules with Tanimoto's electrostatic score ranging from 0.627 to 0.87. Using parameters related to absorption, distribution, metabolism and excretion and the pivot molecule, the molecules selected in the previous stage were evaluated regarding these criteria, and 21 were then selected. The pharmacokinetic and toxicological properties were considered and for 12 molecules, the DEREK software not fired any alert of toxicity, which were thus considered satisfactory for prediction of biological activity using the Web server PASS. In the molecular docking with insect acetylcholinesterase, the Maybridge3_002654 molecule had binding affinity of -11.1 kcal/mol, whereas in human acetylcholinesterase, the Maybridge4_001571molecule show in silico affinity of -10.2 kcal/mol, and in the juvenile hormone, the molecule MCULE-8839595892 show in silico affinity value of -11.6 kcal/mol. Subsequent long-trajectory molecular dynamics studies indicated considerable stability of the novel molecules compared to the controls.AbbreviationsQSARquantitative structure-activity relationshipsPASSprediction of activity spectra for substancesCommunicated by Ramaswamy H. Sarma.

Chemical profile of Lippia thymoides, evaluation of the acetylcholinesterase inhibitory activity of its essential oil, and molecular docking and molecular dynamics simulations.

The essential oils of the fresh and dry flowers, leaves, branches, and roots of Lippia thymoides were obtained by hydrodistillation and analyzed using gas chromatography (GC) and GC-mass spectrometry (MS). The acetylcholinesterase inhibitory activity of the essential oil of fresh leaves was investigated on silica gel plates. The interactions of the key compounds with acetylcholinesterase were simulated by molecular docking and molecular dynamics studies. In total, 75 compounds were identified, and oxygenated monoterpenes were the dominant components of all the plant parts, ranging from 19.48% to 84.99%. In the roots, the main compounds were saturated and unsaturated fatty acids, having contents varying from 39.5% to 32.17%, respectively. In the evaluation of the anticholinesterase activity, the essential oils (detection limit (DL) = 0.1 ng/spot) were found to be about ten times less active than that of physostigmine (DL = 0.01ng/spot), whereas thymol and thymol acetate presented DL values each of 0.01 ng/spot, equivalent to that of the positive control. Based on the docking and molecular dynamics studies, thymol and thymol acetate interact with the catalytic residues Ser203 and His447 of the active site of acetylcholinesterase. The binding free energies (ΔGbind) for these ligands were -18.49 and -26.88 kcal/mol, demonstrating that the ligands are able to interact with the protein and inhibit their catalytic activity.