Lead selection and characterization of antitubercular compounds using the Nested Chemical Library

Discovering new drugs to treat tuberculosis more efficiently and to overcome multidrug resistance is a world health priority. To find novel antitubercular agents several approaches have been used in various institutions worldwide, including target-based approaches against several validated mycobacterial enzymes and phenotypic screens. We screened more than 17,000 compounds from Vichem's Nested Chemical Library(TM) using an integrated strategy involving whole cell-based assays with Corynebacterium glutamicum and Mycobacterium tuberculosis, and target-based assays with protein kinases PknA, PknB and PknG as well as other targets such as PimA and bacterial topoisomerases simultaneously. With the help of the target-based approach we have found very potent hits inhibiting the selected target enzymes, but good minimal inhibitory concentrations (MIC) against M. tuberculosis were not achieved. Focussing on the whole cell-based approach several potent hits were found which displayed minimal inhibitory concentrations (MIC) against M. tuberculosis below 10 mu M and were non-mutagenic, non-cytotoxic and the targets of some of the hits were also identified. The most active hits represented various scaffolds. Medicinal chemistry-based lead optimization was performed applying various strategies and, as a consequence, a series of novel potent compounds were synthesized. These efforts resulted in some effective potential antitubercular lead compounds which were confirmed in phenotypic assays. (C) 2015 Elsevier Ltd. All rights reserved.

Bolaamphiphiles as carriers for siRNA delivery: From chemical syntheses to practical applications

In this study we have investigated a new class of cationic lipids - ``bolaamphiphiles'' or ``bolas'' - for their ability to efficiently deliver small interfering RNAs (siRNAs) to cancer cells. The bolas of this study consist of a hydrophobic chain with one or more positively charged head groups at each end. Recently, we reported that micelles of the bolas GLH-19 and GLH-20 (derived from vernonia oil) efficiently deliver siRNAs, while having relatively low toxicities in vitro and in vivo. Our previous studies validated that; bolaamphiphiles can be designed to vary the magnitude of siRNA shielding, its delivery, and its subsequent release. To further understand the structural features of bolas critical for siRNAs delivery, new structurally related bolas (GLH-58 and GLH-60) were designed and synthesized from jojoba oil. Both bolas have similar hydrophobic domains and contain either one, in GLH-58, or two, in GLH-60 positively charged head groups at each end of the hydrophobic core. We have computationally predicted and experimentally validated that GLH-58 formed more stable nano sized micelles than GLH-60 and performed significantly better in comparison to GLH-60 for siRNA delivery. GLH-58/siRNA complexes demonstrated better efficiency in silencing the expression of the GFP gene in human breast cancer cells at concentrations of 5 mu g/mL, well below the toxic dose. Moreover, delivery of multiple different siRNAs targeting the HIV genome demonstrated further inhibition of virus production. Published by Elsevier B.V.

Atmospheric pressure plasma chemical vapor deposition reactor for 100 mm wafers, optimized for minimum contamination at low gas flow rates

Gas discharge plasmas used for thinfilm deposition by plasma-enhanced chemical vapor deposition (PECVD) must be devoid of contaminants, like dust or active species which disturb the intended chemical reaction. In atmospheric pressure plasma systems employing an inert gas, the main source of such contamination is the residual air inside the system. To enable the construction of an atmospheric pressure plasma (APP) system with minimal contamination, we have carried out fluid dynamic simulation of the APP chamber into which an inert gas is injected at different mass flow rates. On the basis of the simulation results, we have designed and built a simple, scaled APP system, which is capable of holding a 100 mm substrate wafer, so that the presence of air (contamination) in the APP chamber is minimized with as low a flow rate of argon as possible. This is examined systematically by examining optical emission from the plasma as a function of inert gas flow rate. It is found that optical emission from the plasma shows the presence of atmospheric air, if the inlet argon flow rate is lowered below 300 sccm. That there is minimal contamination of the APP reactor built here, was verified by conducting an atmospheric pressure PECVD process under acetylene flow, combined with argon flow at 100 sccm and 500 sccm. The deposition of a polymer coating is confirmed by infrared spectroscopy. X-ray photoelectron spectroscopy shows that the polymer coating contains only 5% of oxygen, which is comparable to the oxygen content in polymer deposits obtained in low-pressure PECVD systems. (C) 2015 AIP Publishing LLC.

The X-ray photoelectron spectroscopy and high-temperature structural studies of Zn1-xNixO/NiO two-phase composites

Detailed investigation of the chemical states and local atomic environment of Ni and Zn in the two-phase composites of Zn1-xNixO/NiO was reported. The X-ray photoelectron spectra of both Ni-2p and Zn-2p revealed the existence of a doublet with spin-orbit splitting approximate to 17.9 and 23.2eV, respectively confirming the divalent oxidation state of both Ni and Zn. However, the samples fabricated under oxygen-rich conditions exhibit significant difference in the binding energy approximate to 18.75eV between the 2p3/2 and 2p1/2 states of Ni. The shift in the satellite peaks of Ni-2p with increasing the Ni composition x within the Zn1-xNixO/NiO matrix signifies the attenuation of nonlocal screening because of reduced site occupancy of two adjacent Zn ions. The temperature dependence of X-ray diffraction analysis reveals a large distortion in the axial-rhombohedral angle for oxygen-rich NiO. Conversely, no significant distortion was noticed in the NiO system present as a secondary phase within Zn1-xNixO. Nevertheless, the unit-cell volume of both wurtzite h.c.p. Zn1-xNixO and f.c.c. NiO exhibits an anomalous behavior between 150 and 300 degrees C. The origin of such unusual change in the unit-cell volume was discussed in terms of oxygen stoichiometry.

Synthesis of Eu3+-activated ZnO superstructures: Photoluminescence, Judd-Ofelt analysis and Sunlight photocatalytic properties

Photoluminescence and photocatalytic properties of Eu-doped ZnO nanoparticles (NPs) were synthesized by facile phyto route. XPS results demonstrated the existence of Eu3+ as dopant into ZnO. Morphologies of the NPs were mainly dependent on Eu3+ and Aloe vera gel. Red shift of energy band gap was due to the creation of intermediate energy states of Eu3+ and oxygen vacancies in the band gap. PL emission of ZnO:Eu3+ (1-11 mol%, 8 ml and 7 mol%, 2-12 ml) exhibit characteristic peaks of D-5(0) -> F-7(2) transitions. From the Judd-Ofelt analysis, intensities of transitions between different.' levels dependent on the symmetry of the local environment of Eu3+ ions. CIE chromaticity co-ordinates confirm reddish emission of the phosphor. Further, NPs exhibit excellent photocatalytic activity for the degradation of Rhodamine B (94%) under Sunlight was attributed to crystallite size, band gap, morphology and oxygen vacancies. In addition, photocatalyst reusability studies were conducted and found that Eu-doped catalyst could be reused several times with negligible decrease in catalytic activity. The present work directs new possibilities to provide some new insights into the design of new phyto synthesized nanophosphors for display devices, photocatalysts with high activity for environmental clean-up and solar energy conversion. (C) 2015 Elsevier B.V. All rights reserved.

Common effect of chemical and external pressures on the magnetic properties of RCoPO (R = La, Pr, Nd, Sm). II.

We investigate the direct correspondence between Co band ferromagnetism and structural parameters in the pnictide oxides RCoPO for different rare-earth ions (R = La, Pr, Nd, Sm) by means of muon-spin spectroscopy and ab initio calculations, complementing our results published previously G. Prando et al., Common effect of chemical and external pressures on the magnetic properties of RCoPO (R = La, Pr), Phys. Rev. B 87, 064401 (2013)]. We find that both the transition temperature to the ferromagnetic phase T-C and the volume of the crystallographic unit cell V are conveniently tuned by the R ionic radius and/or external pressure. We report a linear correlation between T-C and V and our ab initio calculations unambiguously demonstrate a full equivalence of chemical and external pressures. As such, we show that R ions influence the ferromagnetic phase only via the induced structural shrinkage without involving any active role from the electronic f degrees of freedom, which are only giving a sizable magnetic contribution at much lower temperatures.

Synthesis of 3-dimensional porous graphene nanosheets using electron cyclotron resonance plasma enhanced chemical vapour deposition

Microwave plasma driven chemical vapour deposition was used to synthesize graphene nanosheets from a mixture of acetylene and hydrogen gas molecules. In this plasma, acetylene decomposes to carbon atoms that form nanostructures in the outlet plasma stream and get deposited on the substrate. The GNS consists of a few layers of graphene aligned vertically to the substrate. Graphene layers have been confirmed by high-resolution transmission electron microscopy, and Raman spectral studies were conducted to observe the defective nature of the sample. The growth of nanosheets in a vertical direction is assumed to be due to the effect of electric field and from the difference in the deposition rate in the axial and parallel directions. These vertical graphene sheets are attractive for various applications in energy storage and sensors.

Strain-Induced Hierarchy of Energy Levels in CdS/ZnS Nanocrystals

Aside of size and shape, the strain induced by the mismatch of lattice parameters between core and shell in the nanocrystalline regime is an additional degree of freedom to engineer the electron energy levels. Herein, CdS/ZnS core/shell nanocrystals (NCs) with shell thickness up to four monolayers are studied. As a manifestation of strain, the low temperature radiative lifetime measurements indicate a reduction in Stokes shift from 36 meV for CdS to 5 meV for CdS/ZnS with four monolayers of overcoating. Concomitant crossover of S- and P-symmetric hole levels is observed which can be understood in the framework of theoretical calculations predicting flipping the hierarchy of ground hole state by the strain in CdS NCs. Furthermore, a nonmonotonic variation of higher energy levels in strained CdS NCs is discussed.

Multivariate PLS Modeling of Apicomplexan FabD-Ligand Interaction Space for Mapping Target-Specific Chemical Space and Pharmacophore Fingerprints

Biomolecular recognition underlying drug-target interactions is determined by both binding affinity and specificity. Whilst, quantification of binding efficacy is possible, determining specificity remains a challenge, as it requires affinity data for multiple targets with the same ligand dataset. Thus, understanding the interaction space by mapping the target space to model its complementary chemical space through computational techniques are desirable. In this study, active site architecture of FabD drug target in two apicomplexan parasites viz. Plasmodium falciparum (PfFabD) and Toxoplasma gondii (TgFabD) is explored, followed by consensus docking calculations and identification of fifteen best hit compounds, most of which are found to be derivatives of natural products. Subsequently, machine learning techniques were applied on molecular descriptors of six FabD homologs and sixty ligands to induce distinct multivariate partial-least square models. The biological space of FabD mapped by the various chemical entities explain their interaction space in general. It also highlights the selective variations in FabD of apicomplexan parasites with that of the host. Furthermore, chemometric models revealed the principal chemical scaffolds in PfFabD and TgFabD as pyrrolidines and imidazoles, respectively, which render target specificity and improve binding affinity in combination with other functional descriptors conducive for the design and optimization of the leads.

The electronic, chemical and electrocatalytic processes and intermediates on iron oxide surfaces during photoelectrochemical water splitting

We re-assess experimental soft X-ray absorption spectra of the oxygen K-shell which we recorded operando from iron oxide during photoelectrochemical water splitting in KOH electrolyte. In particular, we refer to recently reported transitional electron hole states which originate within the charge carrier depletion layer of the iron oxide and on the iron oxide surface. For the latter we find that an intermediate oxy-peroxo species is formed on the iron oxide with increasing bias potential, which disappears upon further polarization of the electrode, concomitantly with the evolution and disappearance of the aforementioned surface state. The oxygen spectra contain also the spectroscopic signatures of the electrolyte water, the position of which changes with increasing bias potential towards lower X-ray energies, revealing the breaking and formation of hydrogen bonds in the water during the experiment. Combined with potential dependent impedance spectroscopy data we are able to sketch the molecular structure of chemical intermediates and their charge carrier dynamics. (C) 2015 Elsevier B.V. All rights reserved.

Room temperature ferromagnetism and white light emissive CdS:Cr nanoparticles synthesized by chemical co-precipitation method

Undoped and Cr (3% and 5%) doped CdS nanoparticles were synthesized by chemical co-precipitation method. The synthesized nanocrystalline particles are characterized by energy dispersive X-ray analysis (EDAX), scanning electron microscope (SEM), X-ray Diffraction (XRD), transmission electron microscopy (TEM), diffuse reflectance spectroscopy (DRS), photoluminescence (PL), Electron paramagnetic resonance (EPR), vibrating sample magnetometer (VSM) and Raman spectroscopy. XRD studies indicate that Cr doping in host CdS result a structural change from Cubic phase to mixed (cubic + hexagonal) phase. Due to quantum confinement effect, widening of the band gap is observed for undoped and Cr doped CdS nanoparticles compared to bulk CdS. The average particle size calculated from band gap values is in good agreement with the TEM study calculation and it is around 4-5 nm. A strong violet emission band consisting of two emission peaks is observed for undoped CdS nanoparticles, whereas for CdS:Cr nanoparticles, a broad emission band ranging from 420 nm to 730 nm with a maximum at similar to 587 nm is observed. The broad emission band is due to the overlapped emissions from variety of defects. EPR spectra of CdS:Cr samples reveal resonance signal at g = 2.143 corresponding to interacting Cr3+ ions. VSM studies indicate that the diamagnetic CdS nanoparticles are transform to ferromagnetic for 3% Cr3+ doping and the ferromagnetic nature is diminished with increasing the doping concentration to 5%. (C) 2015 Elsevier B.V. All rights reserved.

Ultrafast Chemical Dynamics in Time Domain Through Fluorescence Spectroscopy

While absorption and emission spectroscopy have always been used to detect and characterize molecules and molecular complexes, the availability of ultrashort laser pulses and associated computer-aided optical detection techniques allowed study of chemical processes directly in the time domain at unprecedented time scales, through appearance and disappearance of fluorescence from participating chemical species. Application of such techniques to chemical dynamics in liquids, where many processes occur with picosecond and femtosecond time scales lead to the discovery of a host of new phenomena that in turn led to the development of many new theories. Experiment and theory together provided new and valuable insight into many fundamental chemical processes, like isomerization dynamics, electron and proton transfer reactions, vibrational energy and phase relaxation, photosynthesis, to name just a few. In this article, we shall review a few of such discoveries in attempt to provide a glimpse of the fascinating research employing fluorescence spectroscopy that changed the field of chemical dynamics forever.

Ab Initio MD Simulations of the Bronsted Acidity of Glutathione in Aqueous Solutions: Predicting pK(a) Shifts of the Cysteine Residue

The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pK(a) value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides shift in the dissociation constant values as compared with the isolated accurate estimates of the pK(a) and correctly predicts the cysteine amino acid.