Orientation dependent electrocatalysis using self-assembled molecular films

Surface orientation of self-assembled molecular films of 2,9,6,23-tetraamino cobalt phthalocyanine on gold and silver is shown to determine the nature and the products of the electrocatalytic reduction of oxygen.

Self-assembled molecular films of tetraamino metal (Co, Cu, Fe) phthalocyanines on gold and silver. Electrochemical and spectroscopic characterization

The formation of molecular films of 2,9,16,23-tetraamino metal phthalocyanines [TAM(II)Pc; M (II) = Co, Cu, and TAM(III)Pc; M = Fe] by spontaneous adsorption on gold and silver surfaces is described. The properties of these films have been investigated by cyclic voltammetry, impedance, and FT-Raman spectroscopy. The charge associated with Co(II) and Co(I) redox couple in voltammetric data leads to a coverage of (0.35+/-0.05) x 10(-10) mol cm(-2), suggesting that the tetraamino cobalt phthalocyanine is adsorbed as a monolayer with an almost complete coverage. The blocking behavior of the films toward oxygen and Fe(CN)(6)(3-/4-) redox couple have been followed by cyclic voltammetry and impedance measurements. This leads to an estimate of the coverage of about 85 % in the case of copper and the iron analogs. FT-Raman studies show characteristic bands around 236 cm(-1) revealing the interaction between the metal substrate and the nitrogen of the -NH2 group on the phthalocyanine molecules.

Synthesis, crystal structure and catalytic properties of (p-cymene)ruthenium(II) azophenol complexes: azophenyl to azophenol conversion by oxygen insertion to a ruthenium---carbon bond

Azophenol complexes of formulation [(η6-p-cymene)RuCl(Ln)] (1–6, n=1–6) were prepared by two synthetic methods involving either an oxygen insertion to the Ru---C bond in cycloruthenated precursors forming complexes 1 and 2 or from the reaction of [{(η6-p-cymene)RuCl}2(μ-Cl)2] with azophenol ligands (HL3–HL6) in the presence of sodium carbonate in CH2Cl2. The molecular structure of the 1-(phenylazo)-2-naphthol complex has been determined by X-ray crystallography. The complex has a η6-p-cymene group, a chloride and a bidentate N,O-donor azophenol ligand. The complexes have been characterized from NMR spectral data. The catalytic activity of the complexes has been studied for the conversion of acetophenone to the corresponding alcohol in the presence of KOH and isopropanol. Complexes 4 and 6 having a methoxy group attached to the ortho-position of the phenylazo moiety and 2 with a methyl group in the meta-position of the phenolic moiety show high percentage conversion (>84%).

Quasichemical equations for oxygen and sulphur in liquid binary alloys

An equation has been derived for predicting the activity coefficient of oxygen or sulphur in dilute solution in binary alloys, based on the quasichemical approach, where the metal atoms and the oxygen atoms are assigned different bond numbers. This equation is an advance on Alcock and Richardson's earlier treatment where all the three types of atoms were assigned the same coordination number. However, the activity coefficients predicted by this new equation appear to be very similar to those obtained through Alcock and Richardson's equation for a number of alloy systems, when the coordination number of oxygen in the new model is the same as the average coordination number used in the earlier equation. A second equation based on the formation of “molecular species” of the type XnO and YnO in solution is also derived, where X and Y atoms attached to oxygen are assumed not to make any other bonds. This equation does not fit experimental data in all the systems considered for a fixed value of n. Howover, if the strong oxygen-metal bonds are assumed to distort the electronic configuation around the metal atoms bonded to oxygen and thus reduce the strength of the bonds formed by these atoms with neighbouring metal atoms by approximately a factor of two, the resulting equation is found to predict the activity coefficients of oxygen that are in good agreement with experimental data in a number of binary alloys.

Metal based photosensitizers of tetradentate Schiff base: Promising role in anti-tumor activity through singlet oxygen generation mechanism

In the present investigation, a Schiff base N'(1),N'(3)-bis(Z)-(2-hydroxynapthyl)methylidene]benzene-1,3-dicarbod ihydrazide (L-1) and its Co(II), Ni(II) and Cu(II) complexes have been synthesized and characterized as novel photosensitizing agents for photodynamic therapy (PDT). The interaction of these complexes with calf thymus DNA (CT DNA) has been explored using absorption, thermal denaturation and viscometric studies. The experimental results revealed that Co(II) and Ni(II) complexes on binding to CT DNA imply a covalent mode, most possibly involving guanine N7 nitrogen of DNA, with an intrinsic binding constant K-b of 4.5 x 10(4) M-1 and 4.2 x 10(4) M-1, respectively. However, interestingly, the Cu(II) complex is involved in the surface binding to minor groove via phosphate backbone of DNA double helix with an intrinsic binding constant K-b of 5.7 x 10(4) M-1. The Co(II), Ni(II) and Cu(II) complexes are active in cleaving supercoiled (SC) pUC19 DNA on photoexposure to UV-visible light of 365 nm, through O-1(2) generation with quantum yields of 0.28, 0.25 and 0.30, respectively. Further, these complexes are cytotoxic in A549 lung cancer cells, showing an enhancement of cytotoxicity upon light irradiation. (C) 2013 Elsevier B.V. All rights reserved.

Gas Phase Oxygen Quenching Studies of Ketone Tracers for Laser-Induced Fluorescence Applications in Nitrogen Bath Gas

In this paper we report the quantitative oxygen quenching effect on laser-induced fluorescence of acetone, methyl ethyl ketone, and 3-pentanone at low pressures (approximate to 700torr) with oxygen partial pressures up to 450torr. Nitrogen was used as a bath gas in which these molecular tracers were added in different quantities according to their vapor pressure at room temperature. These tracers were excited by using a frequency-quadrupled, Q-switched, Nd:YAG laser (266nm). Stern-Volmer plots were found to be linear for all the tracers, suggesting that quenching is collisional in nature. Stern-Volmer coefficients (k(sv)) and quenching rate constants (k(q)) were calculated from Stern-Volmer plots. The effects of oxygen on the laser-induced fluorescence of acetone, methyl ethyl ketone, and 3-pentanone were compared with each other. Further, the Smoluchowski theory was used to calculate the quenching parameters and compared with the experimental results.

Interferon-gamma induced cell death: Regulation and contributions of nitric oxide, cJun N-terminal kinase, reactive oxygen species and peroxynitrite

Interferon-gamma (Ifn gamma), a known immunomodulatory cytokine, regulates cell proliferation and survival. In this study, the mechanisms leading to the selective susceptibility of some tumor cells to Ifn gamma were deciphered. Seven different mouse tumor cell lines tested demonstrated upregulation of MHC class I to variable extents with Ifn gamma; however, only the cell lines, H6 hepatoma and L929 fibrosarcoma, that produce higher amounts of nitric oxide (NO) and reactive oxygen species (ROS) are sensitive to Ifn gamma-induced cell death. NO inhibitors greatly reduce Ifn gamma-induced ROS; however, ROS inhibitors did not affect the levels of Ifn gamma-induced NO, demonstrating that NO regulates ROS. Consequently, NO inhibitors are more effective, compared to ROS inhibitors, in reducing Ifn gamma-induced cell death. Further analysis revealed that Ifn gamma induces peroxynitrite and 3-nitrotyrosine amounts and a peroxynitrite scavenger, FeTPPS, reduces cell death. Ifn gamma treatment induces the phosphorylation of c-jun N-terminal kinase (Jnk) in H6 and L929 but not CT26, a colon carcinoma cell line, which is resistant to Ifn gamma-mediated death. Jnk activation downstream to NO leads to induction of ROS, peroxynitrite and cell death in response to Ifn gamma. Importantly, three cell lines tested, i.e. CT26, EL4 and Neuro2a, that are resistant to cell death with Ifn gamma alone become sensitive to the combination of Ifn gamma and NO donor or ROS inducer in a peroxynitrite-dependent manner. Overall, this study delineates the key roles of NO as the initiator and Jnk, ROS, and peroxynitrite as the effectors during Ifn gamma-mediated cell death. The implications of these findings in the Ifn gamma-mediated treatment of malignancies are discussed. (C) 2014 Elsevier B.V. All rights reserved.

Interferon-gamma induced cell death: Regulation and contributions of nitric oxide, cJun N-terminal kinase, reactive oxygen species and peroxynitrite

Interferon-gamma (Ifn gamma), a known immunomodulatory cytokine, regulates cell proliferation and survival. In this study, the mechanisms leading to the selective susceptibility of some tumor cells to Ifn gamma were deciphered. Seven different mouse tumor cell lines tested demonstrated upregulation of MHC class I to variable extents with Ifn gamma; however, only the cell lines, H6 hepatoma and L929 fibrosarcoma, that produce higher amounts of nitric oxide (NO) and reactive oxygen species (ROS) are sensitive to Ifn gamma-induced cell death. NO inhibitors greatly reduce Ifn gamma-induced ROS; however, ROS inhibitors did not affect the levels of Ifn gamma-induced NO, demonstrating that NO regulates ROS. Consequently, NO inhibitors are more effective, compared to ROS inhibitors, in reducing Ifn gamma-induced cell death. Further analysis revealed that Ifn gamma induces peroxynitrite and 3-nitrotyrosine amounts and a peroxynitrite scavenger, FeTPPS, reduces cell death. Ifn gamma treatment induces the phosphorylation of c-jun N-terminal kinase (Jnk) in H6 and L929 but not CT26, a colon carcinoma cell line, which is resistant to Ifn gamma-mediated death. Jnk activation downstream to NO leads to induction of ROS, peroxynitrite and cell death in response to Ifn gamma. Importantly, three cell lines tested, i.e. CT26, EL4 and Neuro2a, that are resistant to cell death with Ifn gamma alone become sensitive to the combination of Ifn gamma and NO donor or ROS inducer in a peroxynitrite-dependent manner. Overall, this study delineates the key roles of NO as the initiator and Jnk, ROS, and peroxynitrite as the effectors during Ifn gamma-mediated cell death. The implications of these findings in the Ifn gamma-mediated treatment of malignancies are discussed. (C) 2014 Elsevier B.V. All rights reserved.

Estimating successive pK(a) values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers

Estimation of the dissociation constant, or pK(a), of weak acids continues to be a central goal in theoretical chemistry. Here we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free energy profile of the dissociation reaction can provide reasonable estimates of the successive pK(a) values of polyprotic acids. We use the distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic group as the collective variable to explore the free energy profile of the dissociation process. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. Two distinct minima corresponding to the dissociated and un-dissociated states of the acid are observed and the difference in their free energy values provides the estimate for pK(a), the acid dissociation constant. We show that the method predicts the pK(a) value of benzoic acid in good agreement with experiment and then show using phthalic acid (benzene dicarboxylic acid) as a test system that both the first and second pK(a) values as well, as the subtle difference in their values for different isomers can be predicted in reasonable agreement with experimental data.

The influence of reduced oxygen availability on gene expression in laboratory (H37Rv) and clinical strains (S7 and S10) of Mycobacterium tuberculosis

Mycobacterium tuberculosis has the ability to persist within the host in a dormant stage. One important condition believed to contribute to dormancy is reduced access to oxygen known as hypoxia. However, the response of M. tuberculosis to such hypoxia condition is not fully characterized. Virtually all dormant models against tuberculosis tested in animals used laboratory strain H37Rv or Erdman strain. But major outbreaks of tuberculosis (TB) occur with the strains that have widely different genotypes and phenotypes compared to H37Rv. In this study, we used a custom oligonucleotide microarray to determine the overall transcriptional response of laboratory strain (H37Rv) and most prevalent clinical strains (S7 and S10) of M. tuberculosis from South India to hypoxia. Analysis of microarray results revealed that a total of 1161 genes were differentially regulated (>= 1.5 fold change) in H37Rv, among them 659 genes upregulated and 502 genes down regulated. Microarray data of clinical isolates showed that a total of 790 genes were differentially regulated in S7 among which 453 genes were upregulated and 337 down regulated. Interestingly, numerous genes were also differentially regulated in S10 (total 2805 genes) of which 1463 genes upregulated and 1342 genes down regulated during reduced oxygen condition (Wayne's model). One hundred and thirty-four genes were found common and upregulated among all three strains (H37Rv, S7, and S10) and can be targeted for drug/vaccine development against TB. (C) 2015 Published by Elsevier B.V.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.

Polyketide Quinones Are Alternate Intermediate Electron Carriers during Mycobacterial Respiration in Oxygen-Deficient Niches

Mycobacterium tuberculosis (Mtb) adaptation to hypoxia is considered crucial to its prolonged latent persistence in humans. Mtb lesions are known to contain physiologically heterogeneous microenvironments that bring about differential responses from bacteria. Here we exploit metabolic variability within biofilm cells to identify alternate respiratory polyketide quinones (PkQs) from both Mycobacterium smegmatis (Msmeg) and Mtb. PkQs are specifically expressed in biofilms and other oxygen-deficient niches to maintain cellular bioenergetics. Under such conditions, these metabolites function as mobile electron carriers in the respiratory electron transport chain. In the absence of PkQs, mycobacteria escape from the hypoxic core of biofilms and prefer oxygenrich conditions. Unlike the ubiquitous isoprenoid pathway for the biosynthesis of respiratory quinones, PkQs are produced by type III polyketide synthases using fatty acyl-CoA precursors. The biosynthetic pathway is conserved in several other bacterial genomes, and our study reveals a redox-balancing chemicocellular process in microbial physiology.

Numerical analysis of spatial evolution of the small signal gain in a chemical oxygen-iodine laser operating without primary buffer gas

A chemical oxygen iodine laser (COIL) that operates without primary buffer gas has become a new way of facilitating the compact integration of laser systems. To clarify the properties of spatial gain distribution, three-dimensional (3-D) computational fluid dynamics (CFD) technology was used to study the mixing and reactive flow in a COIL nozzle with an interleaving jet configuration in the supersonic section. The results show that the molecular iodine fraction in the secondary flow has a notable effect on the spatial distribution of the small signal gain. The rich iodine condition produces some negative gain regions along the jet trajectory, while the lean iodine condition slows down the development of the gain in the streamwise direction. It is also found that the new configuration of an interleaving jet helps form a reasonable gain field under appropriate operation conditions. (c) 2007 Elsevier Ltd. All rights reserved.

Studies of molecular bonding, interactions and decomposition reactions on the (001) surface of ruthenium

The interactions of N₂, formic acid and acetone on the Ru(001) surface are studied using thermal desorption mass spectrometry (TDMS), electron energy loss spectroscopy (EELS), and computer modeling.

Low energy electron diffraction (LEED), EELS and TDMS were used to study chemisorption of N₂ on Ru(001). Adsorption at 75 K produces two desorption states. Adsorption at 95 K fills only the higher energy desorption state and produces a (√3 x √3)R30° LEED pattern. EEL spectra indicate both desorption states are populated by N₂ molecules bonded "on-top" of Ru atoms.

Monte Carlo simulation results are presented on Ru(001) using a kinetic lattice gas model with precursor mediated adsorption, desorption and migration. The model gives good agreement with experimental data. The island growth rate was computed using the same model and is well fit by R(t)^m - R(t₀)^m = At, with m approximately 8. The island size was determined from the width of the superlattice diffraction feature.

The techniques, algorithms and computer programs used for simulations are documented. Coordinate schemes for indexing sites on a 2-D hexagonal lattice, programs for simulation of adsorption and desorption, techniques for analysis of ordering, and computer graphics routines are discussed.

The adsorption of formic acid on Ru(001) has been studied by EELS and TDMS. Large exposures produce a molecular multilayer species. A monodentate formate, bidentate formate, and a hydroxyl species are stable intermediates in formic acid decomposition. The monodentate formate species is converted to the bidentate species by heating. Formic acid decomposition products are CO₂, CO, H₂, H₂O and oxygen adatoms. The ratio of desorbed CO with respect to CO₂ increases both with slower heating rates and with lower coverages.

The existence of two different forms of adsorbed acetone, side-on, bonded through the oxygen and acyl carbon, and end-on, bonded through the oxygen, have been verified by EELS. On Pt(111), only the end-on species is observed. On dean Ru(001) and p(2 x 2)O precovered Ru(001), both forms coexist. The side-on species is dominant on clean Ru(001), while O stabilizes the end-on form. The end-on form desorbs molecularly. Bonding geometry stability is explained by surface Lewis acidity and by comparison to organometallic coordination complexes.

Wastewater Electrolysis Cell for Environmental Pollutants Degradation and Molecular Hydrogen Generation

This study proposes a wastewater electrolysis cell (WEC) for on-site treatment of human waste coupled with decentralized molecular H₂ production. The core of the WEC includes mixed metal oxides anodes functionalized with bismuth doped TiO₂ (BiO_x/TiO₂). The BiO_x/TiO₂ anode shows reliable electro-catalytic activity to oxidize Cl- to reactive chlorine species (RCS), which degrades environmental pollutants including chemical oxygen demand (COD), protein, NH4⁺, urea, and total coliforms. The WEC experiments for treatment of various kinds of synthetic and real wastewater demonstrate sufficient water quality of effluent for reuse for toilet flushing and environmental purposes. Cathodic reduction of water and proton on stainless steel cathodes produced molecular H2 with moderate levels of current and energy efficiency. This thesis presents a comprehensive environmental analysis together with kinetic models to provide an in-depth understanding of reaction pathways mediated by the RCS and the effects of key operating parameters. The latter part of this thesis is dedicated to bilayer hetero-junction anodes which show enhanced generation efficiency of RCS and long-term stability.

Chapter 2 describes the reaction pathway and kinetics of urea degradation mediated by electrochemically generated RCS. The urea oxidation involves chloramines and chlorinated urea as reaction intermediates, for which the mass/charge balance analysis reveals that N₂ and CO₂ are the primary products. Chapter 3 investigates direct-current and photovoltaic powered WEC for domestic wastewater treatment, while Chapter 4 demonstrates the feasibility of the WEC to treat model septic tank effluents. The results in Chapter 2 and 3 corroborate the active roles of chlorine radicals (Cl•/Cl₂^-•) based on iR-compensated anodic potential (thermodynamic basis) and enhanced pseudo-first-order rate constants (kinetic basis). The effects of operating parameters (anodic potential and [Cl^-] in Chapter 3; influent dilution and anaerobic pretreatment in Chapter 4) on the rate and current/energy efficiency of pollutants degradation and H₂ production are thoroughly discussed based on robust kinetic models. Chapter 5 reports the generation of RCS on Ir_0.7Ta_0.3O_y/Bi_xTi_1-xO_z hetero-junction anodes with enhanced rate, current efficiency, and long-term stability compared to the Ir_0.7Ta_0.3O_y anode. The effects of surficial Bi concentration are interrogated, focusing on relative distributions between surface-bound hydroxyl radical and higher oxide.