Computational Methods for Ab Initio Molecular Dynamics

Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.

Antimicrobial Photodynamic Activity of Phthalocyanine Derivatives

Microbial pathogens have increasingly shown multidrug resistance posing a serious threat to the public health. Advances in technology are opening novel avenues for discovery of compounds that will mitigate the ever-increasing drug-resistant microbes. Use of photodynamic photosensitizer is one of the promising alternative approaches since they offer low risk of bacteria resistance as they use generated reactive oxygen species to kill the microbes. Phthalocyanine (Pc) is one such photosensitizer which has already shown promising antimicrobial photodynamic therapeutic properties. Previous studies have shown effectiveness of the Pc against Gram-positive bacteria. However, its effectiveness toward Gram-negative bacteria is limited by the impermeability of the bacteria’s outer membrane which is made up of lipopolysaccharides layer. The effectiveness of this photosensitizer is determined by its photophysical and photochemical properties such as singlet/triplet lifetimes, singlet oxygen quantum yields, and fluorescence quantum yield. Therefore, this review focuses on the recent significance advances on designing Pc that have this improved property by either conjugating with nanoparticles, quantum dots, functional groups in peripheral position, considering effect of cationic charge, and its position on the macrocycle.

QSAR Study of Anthra[1,9-cd]pyrazol-6(2H)-one Derivatives as Potential Anticancer Agents Using Statistical Methods

In this study, the anticancer activity of a series of 32 molecules based on anthra[1,9-cd]pyrazol-6(2H)-one was studied by three-dimensional quantitative structure-activity relationship (QSAR) analyses: multiple linear regression (MLR), partial least squares (PLS), multiple nonlinear regression (MNLR), cross-validation analyses, and Y-randomization. A theoretical study of series was firstly studied using density functional theory (DFT) calculations at B3LYP/6-31 level of theory for employing to determine the structural parameters and electronic properties. Then the topological descriptors were computed using ACD/ChemSketch and ChemDraw 8.0 programs. The RNLM, given the descriptors obtained from the MLR and PLS, exhibited a correlation coefficient close to 0.91. The prediction models collected were confirmed by two methods of cross-validation and scrambling (or Y-randomization). The strong correlation between experimental and predicted activity values was observed, indicating the validation and good quality of the derived QSAR model.

Review on Carbon Dioxide Absorption by Choline Chloride/Urea Deep Eutectic Solvents

In the recent past few years, deep eutectic solvents (DESs) were developed sharing similar characteristics to ionic liquids but with more advantageous features related to preparation cost, environmental impact, and efficiency for gas separation processes. Amongst many combinations of DES solvents that have been prepared, reline (choline chloride as the hydrogen bond acceptor mixed with urea as the hydrogen bond donor) was the first DES synthesized and is still the one with the lowest melting point. Choline chloride/urea DES has proven to be a promising solvent as an efficient medium for carbon dioxide capture when compared with amine alone or ionic liquids under the same conditions. This review sheds light on the preparation method, physical and chemical characteristics, and the CO2 absorption capacity of choline chloride/urea DES under different temperatures and pressures reported up to date.

Inhibition of Aluminium Corrosion in 1.0 M HCl by Caffeine: Experimental and DFT Studies

Aluminium corrosion inhibition in 1.0 M hydrochloric acid solution by caffeine has been studied using mass loss technique and quantum chemical calculations based on DFT. The inhibition efficiency was found to increase with increasing concentration of caffeine but decreases with a rise in temperature. The molecule shows the highest inhibition efficiency of 74% at 10−2 M for T=303 K. The experimental data were used to fit isotherms including Langmuir, Temkin, Freundlich, and El-Awady. The best fits were obtained with the Langmuir model and the kinetic-thermodynamic adsorption model of El-Awady. However, it was found that the adsorption parameters suit well with the isotherm of El-Awady which was chosen as the appropriate isotherm. To distinguish between physisorption and chemisorption, the Dubinin-Radushkevich adsorption model was used. The thermodynamic parameters governing the adsorption of caffeine onto aluminium and that of the metal dissolution were calculated and discussed. DFT study gave further insight into the mechanism of the inhibiting action of caffeine.

Flow and Microwave Induced Pellizzari Reactions: Synthesis of Heterocyclic Analogues of the Benzoxazepine Antipsychotic Agents Loxapine and JL-13

An expeditious route to fused triazolo-pyrido benzoxazepines has been developed using flow and microwave-mediated cyclization chemistry. A range of substituted aryl hydrazides are coupled with a core chloroimine in good to excellent yield via a Pellizzari type process, producing 1,2,4-triazolo-pyrido [2,3-b] [1,5] benzoxazepines with structural similarity to known antipsychotic agents. Modifications allow for strategically functionalized derivatives, and installation of a fluoro group for use in PET imaging is also demonstrated. Given the affinity of the tricyclic core for 5-HT and dopamine receptors, the derivatives are expected to find utility in CNS research.

Determination of Total Chromium and Chromium Species in Kombolcha Tannery Wastewater, Surrounding Soil, and Lettuce Plant Samples, South Wollo, Ethiopia

This research paper deals with the determination of total chromium (total Cr), Cr(III), and Cr(VI) in Kombolcha leather industrial wastewater and the surrounding (soil and lettuce plant) samples where the wastewater flows. The levels of total Cr, Cr(VI), and Cr(III) in wastewater, soil, and lettuce plant samples were determined by FAAS, UV/Vis spectrophotometer, and difference (Cr(VI) from total Cr), respectively. Among all samples taken, the maximum amounts of total Cr, Cr(III), and Cr(VI) were obtained at the discharging point and the minimum amounts of total Cr and Cr(III) were found downstream (400 m from the junction) of Kombolcha leather industrial wastewater. On the other hand, the minimum concentration of Cr(VI) was obtained in lettuce plant sample. The amounts of total Cr in all samples except soil sample were above the permissible limit as set by WHO/FAO. The concentrations of Cr(III) in all wastewater samples were above the permissible level, whereas the concentration of Cr(VI) in wastewater was above the permissible level except 400 m from the junction. The result showed that a remarkable elimination of total Cr and Cr species has not been achieved by this leather industry as its level was not much decreased when entered into the water systems. Therefore, effective treatment methods should be applied to the wastewater for the wellbeing of the surroundings.

Short Jute Fiber Reinforced Polypropylene Composites: Effect of Nonhalogenated Fire Retardants

Short jute fiber reinforced polypropylene (PP) composites were prepared using a single screw extrusion moulding. Jute fiber content in the composites is optimized with the extent of mechanical properties, and composites with 20% jute show higher mechanical properties. Dissimilar concentrations of several fire retardants (FRs), such as magnesium oxide (MO), aluminum oxide (AO), and phosphoric acid (PA), were used in the composites. The addition of MO, AO, and PA improved the fire retardancy properties (ignition time, flame height, and total firing time) of the composites. Ignition time for 30% MO, flame height for 30% PA, and total firing time for 20% MO content composites showed good results which were 8 sec, 1 inch, and 268 sec, respectively. Mechanical properties (tensile strength, tensile modulus, bending strength, bending modulus, and elongation at break), degradation properties (soil test, weathering test, and percentage of weight loss), and water uptake were studied.

Identification and Structural Characterization of Unidentified Impurity in Bisoprolol Film-Coated Tablets

The aim of this study is the identification, structural characterization, and qualification of a degradation impurity of bisoprolol labeled as Impurity RRT 0.95. This degradation product is considered as a principal thermal degradation impurity identified in bisoprolol film-coated tablets. The impurity has been observed in the stress thermal degradation study of the drug product. Using HPLC/DAD/ESI-MS method, a tentative structure was assigned and afterwards confirmed by detailed structural characterization using NMR spectroscopy. The structure of the target Impurity RRT 0.95 was elucidated as phosphomonoester of bisoprolol, having relative molecular mass of 406 (positive ionization mode). The structural characterization was followed by qualification of Impurity RRT 0.95 using several different in silico methodologies. From the results obtained, it can be concluded that no new structural alerts have been generated for Impurity RRT 0.95 relative to the parent compound bisoprolol. The current study presents an in-depth analysis of the full characterization and qualification of an unidentified impurity in a drug product with the purpose of properly defining the quality specification of the product.

In Silico Molecular Docking Analysis of Natural Pyridoacridines as Anticancer Agents

Docking studies are proved to be an essential tool that facilitates the structural diversity of natural products to be harnessed in an organized manner. In this study, pyridoacridines containing natural anticancer pigments were subjected to docking studies using Glide (Schrodinger). Investigations were carried out to find out the potential molecular targets for these selected pigments. The docking was carried out on different cancer macromolecules involved in different cell cycle pathways, that is, CDK-2, CDK-6, Bcl-2, VEGFR-2, IGF-1R kinase, and G-Quadruplexes. CDK-6 was found to be the most suitable anticancer target for the pyridoacridines. In addition, effectiveness of the study was further evaluated by performing docking of known inhibitors against their respective selected macromolecules. However, the results are preliminary and experimental evaluation will be carried out in near future.