Analysing oxygen reduction electrocatalysis on transition metal doped niobium oxide(110).

A good oxygen reduction reaction (ORR) catalyst should be stable and active under electrochemical reaction conditions. Niobium pentaoxide (Nb2O5) is known to be stable under ORR conditions. However it has a large band gap, which makes conductivity a challenge during the reaction. In this work, we aim to understand if surface modification of the 110 facet of niobium pentaoxide with transition metal doping has any effect on its ORR activity and conductivity. While the problem of conductivity in the case of transition metal oxides (TMOs) can be partially rectified by transition metal doping, it has negligible influence on the ORR activity of the doped systems.

Opportunities and Challenges in Electrolytic Propylene Epoxidation.

Propylene oxide (PO) is an important chemical. So far, its synthesis protocol relies on expensive oxidants. In contrast, direct epoxidation of propylene (DEP) using molecular oxygen is considered ideal for PO synthesis. Unfortunately, DEP has not met industrial demands due to the low propylene conversion and high side-product selectivity for known catalysts. Instead of a thermal process using molecular oxygen, electrolytic propylene oxidation can synthesize PO at room temperature, using the atomic oxygen generated from water-splitting. Herein, using density functional theory, surface Pourbaix analysis, scaling relation analysis, and microkinetic modeling, we show that (i) propylene epoxidation is facile on weak-binding catalysts if reactive atomic oxygen preexists; (ii) electrolytic epoxidation is facile to provide atomic oxygen for epoxidation, while hydroperoxyl formation does not overwhelm the epoxidation process at the potential of interest; (iii) propylene dehydrogenation is a competing step that forms side products. Finally, we discuss the opportunities and challenges of this green PO synthesis method.

Fullerene C24 as a potential carrier of ephedrine drug - a computational study of interactions and influence of temperature.

Interactions between fullerene C24 and a frequently used supplement for sport activities, ephedrine (EPH), have been studied in detail by a combination of density functional theory (DFT), time dependent DFT (TD-DFT) calculations, the symmetry-adapted perturbation theory (SAPT) approach and molecular dynamics (MD) simulations. Information about interaction energies and non-covalent interactions formed between C24 and EPH have been obtained by DFT calculations. TD-DFT calculations have been used in order to obtain UV/vis spectra and to check whether the presence of the EPH molecule produces significant changes in the spectrum. The SAPT approach has been employed in order to decompose the interaction energy into components and therefore to better understand the physical origins of interaction between C24 and EPH. Last, but not least, MD simulations have been used in order to track the influence of temperature on the interactions between C24 and EPH.

Computational evaluation of the reactivity and pharmaceutical potential of an organic amine: A DFT, molecular dynamics simulations and molecular docking approach.

2-[N-(carboxymethyl)anilino] acetic acid (PIDAA) molecule has been spectroscopically characterized and computationally investigated for its fundamental reactive properties by a combination of density functional theory (DFT) calculations, molecular dynamics (MD) simulations and molecular docking procedure. A comparison drawn between the simulated and experimentally attained spectra by FT-Raman and FT-IR showed concurrence. The natural bond orbital (NBO) analysis enabled in comprehending the stability and charge delocalization in the title molecule. The first hyperpolarizability which is an important parameter for future studies of nonlinear optics (NLO) was calculated to check the potential of the molecule to be an NLO material. Besides, frontier molecular orbitals (FMO), electron localization function (ELF) and localized orbital locator (LOL) analysis were performed. Energy gap (ΔE), electronegativity (χ), chemical potential (µ), global hardness (η), softness (S), Mulliken population analysis on atomic charges and thermodynamic properties of the title compound at different temperatures have been calculated. The local reactive properties of PIDAA have been addressed by MEP and ALIE surfaces, together with bond dissociation energy for hydrogen abstraction (H-BDE). MD simulations have been used in order to identify atoms with pronounced interactions with water molecules. The pharmaceutical potential of PIDAA has been considered by the analysis of drug likeness parameters and molecular docking procedure. The biological activity of the molecule in terms of molecular docking has been analyzed theoretically for the treatment of SARS and minimum binding energy calculated. The Ramachandran plot was used to check the stereochemistry of the protein structure. In addition, a comparison of the physiochemical parameters of PIDAA and commercially available drugs (Yu et al., 2004; Tan et al., 2004; Elshabrawy et al., 2014; Chu et al., 2004; Gopal Samy and Xavier, 2015) were carried out.

Spectroscopic and quantum/classical mechanics based computational studies to compare the ability of Andrographolide and its derivative to inhibit Nitric Oxide Synthase.

The inhibition of the enzyme Nitric Oxide Synthase by a bioactive compounds results in it possessing anti-inflammatory property. The ability of Andrographolide and its derivative Isoandrographolide to inhibit Nitric Oxide Synthase was studied using computational and experimental techniques. A combination of UV Spectroscopic and DFT computational techniques were used to calculate the molecular descriptors of the title compounds which were used to establish relationship with its biological activity. The drug-likeness of the compounds was estimated using Lipinski's rule. Molecular dynamics and docking studies were carried out to test for the structural and energetic favourability of the title compounds(ligand) being bound to Nitric Oxide Synthase(Protein) to induce inhibition. The force constant data obtained from IR spectroscopy was used in aid to parametrize force fields used in molecular dynamics simulation. The DFT method was used to perform NBO analysis that revealed the charge transfer interactions responsible for its biological properties. The Molecular Electrostatic Potential (MEP) plot revealed the regions of electrophilic and nucleophilic reactivity of the title compounds. MTT (3-(4, 5-dimethyl thiazolyl-2)-2, 5-diphenyltetrazolium bromide) assay was carried out which revealed the cytotoxicity at different concentrations of the title compounds by which means the biologically safe concentration was determined and therefore at this biologically safe concentration the ability of the compounds to inhibit Nitric Oxide formation was determined. Quantitative Structure-Activity Studies (QSAR) were used to furnish relationship between molecular descriptors and the Nitric Oxide Synthase inhibition activity resulting in anti-inflammatory property, based on the chosen molecular descriptors suggestions were made for the search of more potent Nitric Oxide Synthase inhibitors in the Andrographolide derivative family of compounds.

Molecular docking studies, charge transfer excitation and wave function analyses (ESP, ELF, LOL) on valacyclovir : A potential antiviral drug.

Valacyclovir is the l-valyl ester prodrug of the antiviral drug acyclovir that exhibits activity against Herpes simplex virus types and varicella zoster virus. An explicit surface analysis on the title compound was carried out theoretically using the wavefunction analyser multiwfn software, inorder to study the reactivity of the compound. The input wavefunction files were generated by Gaussian 09W software using B3LYP/6-311++G(d,p) as the basis set. The structure of the title compound was optimized; wave function analyses and the molecular docking studies were completed. The UV spectrum was experimentally recorded in solvent phase and in addition to it the electronic absorption spectrum of the compound was evaluated by TD-DFT in the gas and solvent phase. The ESP (Electrostatic potential) map points out the surface extremas where the global surface minimum is seen at the oxygen atom with the value -61.5675 and global surface maximum near the hydrogen atom with the value 67.862. The energy band gap obtained from the HOMO-LUMO gap (E = 3.6023 eV) were found to be in agreement with the energy gap (E = 3.6174 eV) calculated using λmax from the UV spectrum. The electron-hole distribution of the molecule indicated a charge transfer within the molecule. Electron Localization Function, Local Orbital Localizer, Thermodynamic functions were discussed. The reactive sites of the compound were studied from the fukui function calculations and chemical descriptors define the reactivity of the molecule on the whole. The antiviral activities of the title compound against various viral proteins (VZV, HSV, Dengue) were studied using molecular docking.

Spectroscopic profiling (FT-IR, FT-Raman, NMR and UV-Vis), autoxidation mechanism (H-BDE) and molecular docking investigation of 3-(4-chlorophenyl)-N,N-dimethyl-3-pyridin-2-ylpropan-1-amine by DFT/TD-DFT and molecular dynamics: A potential SSRI drug.

Spectroscopic profiling in terms of FT-IR, FT-Raman, UV-vis and NMR in addition to reactivity study by density functional theory (DFT) and molecular dynamics (MD) simulations of 3-(4-chlorophenyl)-N,N-dimethyl-3-pyridin-2-ylpropan-1-amine (C16H19ClN2) have been discussed. In order to assign principal vibrational numbers, the Potential energy distribution (PED) analysis has been executed. Frontier molecular orbitals (FMOs) analysis in addition to the stabilization energy and natural hybrid orbital analysis has been done. Local reactivity properties of this compound have been addressed through molecular electrostatic potential (MEP) and average local ionization energy (ALIE) surfaces. The bond dissociation energy for hydrogen abstraction (H-BDE) and chemical bonding analysis in terms of electron localization function gave details regarding the Pauli exchange repulsion effect in the electrons of the molecule. Molecular dynamics simulation has been performed in order to understand reactivity of title molecule with water. Molecular docking study was executed to evaluate the potential of the title molecule to bind with 5-HT1 A serotonin receptor and thus can be a lead compound for developing new SSRI (Selective serotonin reuptake inhibitor) drug. Aside from molecular docking, drug likeness parameters have been also considered and by QSAR modeling the comparison of physiochemical parameters of commercially available SSRI drugs and title molecule is carried out.

Quantum mechanical, spectroscopic and docking studies of 2-Amino-3-bromo-5-nitropyridine by Density Functional Method.

Experimental and theoretical investigations on the molecular structure, electronic and vibrational characteristics of 2-Amino-3-bromo-5-nitropyridine are presented. The vibrational frequencies were obtained by DFT/B3LYP calculations employing 6-311++G (d, p) basis set. This was compared with experimental FT-IR and FT-Raman spectral data. Simulated FT-IR (4000-400cm-1) and FT-Raman spectra (4000-100cm-1) showed good agreement with the observed spectra. The molecular equilibrium geometry of the title compound was fully optimized. Quantum chemical calculations of the equilibrium geometry and the complete vibrational assignments of wavenumbers using potential energy distribution (PED) were calculated with scaled quantum mechanics. HOMO-LUMO energies, energy gap (ΔE), electronegativity (χ), chemical potential (µ), global hardness (η), softness (S) and the Fukui function were calculated for the title molecule. The title compound has a low softness value (0.239) and the calculated value of electrophilicity index (5.905) describes the biological activity. The stability and charge delocalization of the title molecule were studied by Natural Bond Orbital (NBO) analysis, Non-Linear Optical (NLO) behaviour in terms of first order hyperpolarizability, dipole moment and anisotropy of polarizability and Molecular Electrostatic Potential (MEP) were accounted. The computed values of µ, α and ß for the title molecule are 1.851 Debye, 1.723×10-23esu and 7.428×10-30esu respectively. The high ß value and non-zero value of µ indicate that the title compound might be a good candidate for NLO material. Thermodynamic properties of the title molecule were studied for different temperatures thereby revealing the correlations between heat capacity (C), entropy (S) and enthalpy changes (H) with temperatures. Docking studies of the title compound were scrutinized to predict the preferred binding orientation, affinity and activity of the given compound. The title compound was docked into the active site of the protein 5FCT which belongs to the class of proteins exhibiting the property as a Dihydrofolate synthase inhibitor. A minimum binding energy of -5.9kcal/mol and intermolecular energy of -6.5kcal/mol is seen in the interaction.