Enzyme-substrate interactions in orotate-mimetic OPRT inhibitor complexes: a QM/MM analysis.

Orotate phosphoribosyltransferase (OPRT) catalyses the reversible phosphoribosyl transfer from α-D-5-phosphoribosyl-1-pyrophosphate (PRPP) to orotic acid (OA) to yield orotidine 5'-monophosphate (OMP) during the de novo synthesis of nucleotides. Numerous studies have reported the inhibition of this reaction as a strategy to check diseases like tuberculosis, malaria and cancer. Insight into the inhibition of this reaction is, therefore, of urgent interest. In this study, we implemented a QM/MM framework on OPRT derived from Saccharomyces cerevisiae to obtain insights into the competitive binding of OA and OA-mimetic inhibitors by quantifying their interactions with OPRT. 4-Hydroxy-6-methylpyridin-2(1H) one showed the best inhibiting activity among the structurally similar OA-mimetic inhibitors, as quantified from the binding energetics. Our analysis of protein-ligand interactions unveiled the association of this inhibitory ligand with a strong network of hydrogen bonds, a large contribution of hydrophobic contacts, and bridging water molecules in the binding site. The ortho-substituted CH3 group in the compound resulted in a large population of π-electrons in the aromatic ring of this inhibitor, supporting the ligand binding further.

Biomimetic CO2 hydration activity of boronic acids.

Inspired by the recent experimental reports on boron containing compounds to be active and biomimetic for carbon capture, we report the mechanistic details of CO2 hydration activities of boronic acids using density functional theory calculations. Four boronic acids were analyzed, viz., [3-methyl-6-(1H-pyrazol-1-yl)phenyl]boronic acid, 3-aminophenylboronic acid, 2,6-dibromophenylboronic acid and 2,6-bis(trifluoromethyl)phenylboronic acid. Free energy landscapes were developed for the hydration reaction. 2,6-Dibromophenylboronic acid showed the highest turnover frequency. Computational NMR and FTIR spectra for various intermediates of the reaction were analyzed and compared with experimental spectra. The energetics as well as the spectral analyses confirmed the biomimetic mechanism for CO2 hydration over all the boronic acid catalysts under investigation.

On the stability of hydroxyl groups on substituted titania.

The present study reports the stability of hydroxyl groups involving the surface coordinated oxygens of Pd,C,N-doped, and Pd/C and Pd/N-codoped anatase TiO2, probed using DFT calculations. Two unique surface planes, (001) and (100), were chosen for the analysis of the stability of hydroxyl groups and their activities were studied by net oxygen activation analysis. The hydroxyl group formation energies ranged between -6.16 and -7.88 eV for the C,N-doped, and Pd/C and Pd/N-codoped TiO2(001) and (100) planes. The order of hydroxyl stability was observed to be TiO2(001) > TiO2(100) > Pd/C-codoped (001) > Pd/N-codoped (100) > Pd/C-codoped (100) > N-doped (001) > C-doped (100) > N-doped (100) > Pd/N-codoped (001) > C-doped (001) planes of TiO2. Although the formation energies of Pd/C and Pd/N-codoped TiO2 were marginally higher compared to those of the pure TiO2(001) and (100) planes, they exhibited a higher net oxygen activation of 32.1% and 28.9% over the surface exposed (100) plane, which indicated the better feasibility of reversible exchange of lattice oxygen. Electron density maps displayed the surface reconstruction phenomenon corresponding to the rearrangement of surface atoms and the transfer of electrons between O-H over the (001) and (100) planes of C,N-doped, and Pd/C and Pd/N-codoped TiO2.

On the ligand-free palladium cluster catalysed Suzuki-Miyaura reaction.

C-C cross coupling reactions have been widely used for developing synthesis protocols for pharmaceuticals and agricultural products in the past few decades. Of all the reported C-C cross coupling reactions, the Suzuki-Miyaura reaction is preferred because of its mild reaction conditions, the commercial availability of associated reagents and the ease of removal of boron containing by-products. Recently, Corma and co-workers [Leyva-Perez et al., Angew. Chem., 2013, 125, 11768] reported water-stabilized three- and four-atom Pd clusters as highly active catalytic species for C-C coupling reactions. The present work focuses on developing detailed mechanistic insights into the Suzuki-Miyaura reaction with Pd3 and Pd4 clusters utilizing density functional theory calculations. The role of the base in the reaction was analysed in this study, which was found to lower the activation barriers of transmetalation over both Pd3 and Pd4. Free energy landscapes for Suzuki-Miyaura coupling of bromobenzene and phenylboronic acid over Pd3 and Pd4 clusters were developed. The highest free energy barriers of 34.7 and 30.4 kcal mol-1 were observed for the oxidative addition over Pd3 and Pd4, respectively, indicating the oxidative addition as the rate limiting step. Detailed energetics conclusively proved the active nature of small-atom Pd clusters for catalyzing the Suzuki-Miyaura reaction.

Dry reforming activity due to ionic Ru in La1.99Ru0.01O3: the role of specific carbonates.

Dry reforming of methane was carried out over La2-2xRu2xO3 (x = 0.005, 0.01). Substitution of just 0.5 atom% of Ru in La2O3 enhanced the activity by 20 times in terms of conversion when compared to the activity exhibited by La2O3. The oxygen storage capacity of the Ru doped sample was considerably higher than undoped La2O3, which resulted in higher conversions of CH4 and CO2. The measured conversion of CH4 and CO2 was 72 and 80%, respectively, at 850 °C. The same was merely 4% with La2O3 under the same experimental conditions. DRIFTS studies demonstrated the role of a specific type of carbonates in promoting the activity of the catalyst. DFT calculations provided the rationale behind the selection of the Ru-in-La2O3 methane dry reforming catalyst. The surface structures of the pure and Ru-substituted compounds were determined, corroborating the experimental observation of enhanced oxygen storage capacity on Ru substitution. Different active surface oxygen species were identified and their roles in improving reducibilities and improving reactivities were established. The experimentally observed surface carbonate species were also identified using calculations. The combined experiment + calculation approach proved ionic Ru in La2-2xRu2xO3 to be a novel and efficient dry reforming catalyst.

Mechanistic insights into biomimetic carbonic anhydrase action catalyzed by doped carbon nanotubes and graphene.

Electronic structural analyses of hydrogen terminated metal doped carbon nanotube/graphene (M-CNT/Gr, MN3-CNT/Gr, M = Ru/Rh) and ruthenium cluster decorated carbon nanotube/graphene (Ru4-CNT/Gr) were carried out for examining the biomimetic catalytic activity towards CO2 hydration reaction. The carbonic anhydrase action was followed for the reaction of CO2 with H2O resulting in a bicarbonate ion and a proton. All the catalysts were found to be active for CO2 hydration and the mechanism proved them to be biomimetic. Interconversion of CO2 to a HCO3- ion took place with five elementary steps viz. OH- formation by H2O dissociation, linear CO2 complexation, CO2 bending by nucleophilic attack of an OH- ion over CO2, HCO3- ion formation by intramolecular proton migration and HCO3- ion displacement by H2O addition. Free energy landscapes over the catalysts were developed for CO2 hydration reaction. The activation energies of H2O dissociation and CO2 bending were observed to be substantially smaller over Ru4-CNT when compared to those over the other catalysts. Ru4-CNT was found to be the best catalyst for CO2 hydration with the rate limiting step being HCO3- ion formation.

Computational insights into crystal plane dependence of thermal activity of anion (C and N)-substituted titania.

Geometry optimizations of anion (C and N) doped anatase TiO2 were carried out by using DFT+U calculations. Various anion vacancy sites were examined to study the synergistic effects of anion doping accompanied with anion vacancy formation on lattice oxygen activation. Two non-identical crystal planes (0 0 1) and (1 0 0) were chosen for C and N substitutions. Energetically favoured N-vacancy pairs were identified on TiO2 surfaces. Substitution of N along with anion vacancies at various sites was energetically more favoured than that of C-doping in bulk TiO2 while the energies were comparable for surface substitutions. Bond length distributions due to the formation of differential bonds were determined. Net oxygen activation and accompanying reversible oxygen exchange capacities were compared for TiO2-2xCx and TiO2-3xN2x. Substitution of C in the surface exposed (1 0 0) plane of TiO2 resulted in 47.6% and 23.8% of bond elongation and compression, respectively, resulting in 23.8% of net oxygen activation which was higher when compared to N substitution in the (1 0 0) plane of TiO2 resulting in a net oxygen activation of 17%.

Adsorption of C2 gases over CeO2-based catalysts: synergism of cationic sites and anionic vacancies.

The synthesis of novel and efficient catalysts for acetylene hydrogenation exhibiting high selectivity towards ethylene is important due to the presence of selective acetylene hydrogenation reaction in petrochemical processing. Since adsorption of C2 gases constitutes the primary step in catalytic hydrogenation and governs the selectivity of the catalysts, we have explored the C2-adsorption potential of reducible CeO2-based systems. The adsorption of C2-gases over CeO2-based materials was assessed using experimental in situ spectroscopic techniques and in silico theoretical studies based on density functional theory. The effect of Pd2+ substitution on adsorption was studied. The addition of Pd2+-ions was found to enhance the adsorption of the gases. Theoretical calculations provided insights into the modes of adsorption, adsorption energetics and reactant-catalyst interactions. The role of the presence of cationic substitution and anionic vacancies in strengthening the adsorption of gases was established. Pd-substituted reduced CeO2 showed activity for the adsorption of all C2 gases. On the basis of the aforementioned experimental and theoretical observations, the catalysts were tested for acetylene hydrogenation, and Pd-substituted CeO2 was found to be a good catalyst for the reaction with complete acetylene conversion observed below 100 °C.

Computational Design of New Heterofullerene-Based Biomimetic α-Carbonic Anhydrase Analogues.

The biomimetic CO2 hydration activity of Ru/Rh-doped fullerenes was revealed by using density functional theory calculations. The mechanism of CO2 hydration on the proposed heterofullerenes followed the mechanistic action of α-carbonic anhydrases, and consisted of the adsorption and deprotonation of H2 O, CO2 interaction with hydroxyl groups, CO2 bending, and proton transfer to give the HCO-3 product. Free-energy landscapes for the reaction showed the catalysts to be active for the reaction. H2 O adsorption over the catalysts was exergonic whereas CO2 adsorption over the catalyst-OH complex was observed to be an endergonic process. Intramolecular proton transfer resulting in the final product, HCO-3 , was found to be the rate-limiting step for the reaction on C56 N3 M (M=Ru/Rh), whereas H2 O dissociation was found to be the rate-limiting step for the reaction on C59 M (M=Ru/Rh). C56 N3 M catalysts were found to be superior to C59 M catalysts for biomimetic CO2 hydration, as indicated by the free-energy landscapes and energy requirements.

Efficient proton shuttle makes SazCA an excellent CO2 hydration enzyme.

The fastest member of the carbonic anhydrase family catalysing the reversible hydration of carbon dioxide to bicarbonate ions has been recently reported to be SazCA. While thermostable, this enzyme shows exceptional activity at 353 K for the reaction. This study explores the molecular basis for the exceptional activity of SazCA, in contrast to SspCA, probed using molecular dynamics simulations. Our simulations, carried out at different temperatures, indicate the presence of efficient proton shuttle between the active zinc centre and His64 residue in the two enzymes. The proton accepting His64 residue was identified to have in and out conformations with the in conformations being supportive to proton acceptance. Our simulations show a large population of in conformations in SazCA making the enzyme exhibit an exceptional activity. The RMSF and H-bonds analysis confirmed the role of His2 and His207 in supporting the attainment of in conformations in SazCA resulting in exceptional activity.Communicated by Ramaswamy H. Sarma.

Computational analysis of the effect of Gly100Ala mutation on the thermostability of SazCA.

Maintaining the protein stability upon mutation is a challenging task in protein engineering. In the present computational study, we induced a single point Gly100Ala mutation in SazCA and examined the factors governing the stability and flexibility of the mutated form, and compared it to that of the wildtype using molecular dynamics simulations. We observed higher structural stability and lesser residual mobility in the mutated SazCA. Improved H-bonding due to Gly100Ala was observed. Ala100 was responsible for the increased helical contents in the mutated SazCA while Gly100 compromised the secondary structure contents in the wildtype. A strong network of salt bridges and high local ordering of the solvent molecules at the protein surface contributed to the enhanced stability of the mutated protein. Our simulations conclusively highlight Gly100Ala mutation as a step towards designing a more robust and thermostable SazCA.Communicated by Ramaswamy H. Sarma.

Rapid synthesis of ultrahigh adsorption capacity zirconia by a solution combustion technique.

Tetragonal ZrO(2) was synthesized by the solution combustion technique using glycine as the fuel. The compound was characterized by X-ray diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy, infrared spectroscopy, and BET surface area analysis. The ability of this compound to adsorb dyes was investigated, and the compound had a higher adsorption capacity than commercially activated carbon. Infrared spectroscopic observations were used to determine the various interactions and the groups responsible for the adsorption activity of the compound. The effects of the initial concentration of the dye, temperature, adsorbent concentration, and pH of the solution were studied. The kinetics of adsorption was described as a first-order process, and the relative magnitudes of internal and external mass transfer processes were determined. The equilibrium adsorption was also determined and modeled by a composite Langmuir-Freundlich isotherm.

Noble metal ionic sites for catalytic hydrogen combustion: spectroscopic insights.

A catalytic hydrogen combustion reaction was carried out over noble metal catalysts substituted in ZrO(2) and TiO(2) in ionic form. The catalysts were synthesized by the solution combustion technique. The compounds showed high activity and CO tolerance for the reaction. The activity of Pd and Pt ion substituted TiO(2) was comparable and was higher than Pd and Pt ion substituted ZrO(2). The mechanisms of the reaction over the two supports were proposed by making use of the X-ray photoelectron spectroscopy and FT infrared spectroscopic observations. The reaction over ZrO(2) supported catalysts was proposed to take place by the utilization of the surface hydroxyl groups while the reaction over TiO(2) supported catalysts was hypothesized to be a hybrid mechanism utilizing surface hydroxyl groups and the lattice oxygen.

Structural and thermodynamic analysis of factors governing the stability and thermal folding/unfolding of SazCA.

Molecular basis of protein stability at different temperatures is a fundamental problem in protein science that is substantially far from being accurately and quantitatively solved as it requires an explicit knowledge of the temperature dependence of folding free energy of amino acid residues. In the present study, we attempted to gain insights into the thermodynamic stability of SazCA and its implications on protein folding/unfolding. We report molecular dynamics simulations of water solvated SazCA in a temperature range of 293-393 K to study the relationship between the thermostability and flexibility. Our structural analysis shows that the protein maintains the highest structural stability at 353 K and the protein conformations are highly flexible at temperatures above 353 K. Larger exposure of hydrophobic surface residues to the solvent medium for conformations beyond 353 K were identified from H-bond analysis. Higher number of secondary structure contents exhibited by SazCA at 353 K corroborated the conformations at 353 K to exhibit the highest thermal stability. The analysis of thermodynamics of protein stability revealed that the conformations that denature at higher melting temperatures tend to have greater maximum thermal stability. Our analysis shows that 353 K conformations have the highest melting temperature, which was found to be close to the experimental optimum temperature. The enhanced protein stability at 353 K due the least value of heat capacity at unfolding suggested an increase in folding. Comparative Gibbs free energy analysis and funnel shaped energy landscape confirmed a transition in folding/unfolding pathway of SazCA at 353 K.

On interaction of arginine, cysteine and guanine with a nano-TiO2 cluster.

Nanoscopic properties of TiO2 augmented with its physicochemical properties and biocompatibility make it a material interest in the biomedical field. Efficient methods to design of such materials require a thorough understanding of associated nano-bio interfaces. In the present study, density functional theory calculations were performed to study the interactions of arginine, cysteine and guanine with a nano-TiO2 cluster. Different configurations were sampled for the adsorption of arginine, cysteine and guanine to probe the nano-bio interface via the interaction of various functional groups present on biomolecules. Adsorption energies for arginine, cysteine and guanine were in a range of -25.0 to -57.6, -12.1 to -29.6 and -45.6 to -58.7 kcal/mol, respectively. From the change in adsorption energies and free energies, interaction of amino acids with carboxylic (COOH), thiol (SH) and amine (NH2) groups while the interaction of the nucleobase via O bonded to C and N of purine ring was found to be essential for thermodynamically stable and energetically favorable states. Density of states analysis also disclosed the prominent interactions of the biomolecules with the nano-TiO2 cluster. Decrease in band gaps on adsorption of the biomolecules was a pertinent phenomenon indicating the strong chemical interactions of the biomolecules with the nanoscopic TiO2 chosen for analysis in this study.

QM/MM reveals the sequence of substrate binding during OPRT action.

Computational investigation of orotate phosphoribosyltransferase (OPRT) action, an enzymatic reaction between phosphoribosyl pyrophosphate (PRPP) and orotic acid (OA) to yield orotidine 5'-monophosphate (OMP), was carried out. Insights into the pathways of the substrate attack step of the reaction were developed under the quantum mechanics/molecular mechanics framework with S. cerevisiae strain as the representative enzyme bearer. Four pathways were proposed for PRPP and OA binding differing in the sequence of PRPP, OA and Mg2+ ion complexation with OPRT. The formation of Mg2+-OPRT complex was accompanied by a small energy change while the largest stabilization was observed for the formation of Mg2+-PRPP complex supporting the experimental observation of Mg2+-PRPP complex as the true substrate for the reaction. Formation of PRPP-OPRT complex was found to be energetically not probable rendering the pathway requiring Mg2+-OA complex not probable. Further, PRPP migration towards the active site was found to be energetically not favoured rendering the pathway involving Mg2+-OA complexation improbable. Migration of OA and Mg2+-PRPP complex towards the active site was found to be energetically probable with a large stabilization of the system when Mg2+-PRPP complex bound to the OA-OPRT complex. This conclusively proved the sequential binding of OA and Mg2+-PRPP complexes during OPRT action.

QM/MM analysis of effect of divalent metal ions on OPRT action.

The role of Mg2+ cofactor in orotate phosphoribosyltransferase (OPRT) catalyzed synthesis of orotidine monophosphate (OMP) from phosphoribosyl pyrophosphate (PRPP) and orotate (OA) in substrate binding and the influence of the identity of the divalent metal ion on the reaction mechanism were addressed in this study using quantum mechanics/molecular mechanics framework. Energetics of migration and binding of different substrate complexes in the active site cavity was established. A quantitative analysis of various processes indicated the reaction pathway to consist of complexation of Mg2+ with PRPP, migration of Mg2+-PRPP and OA towards the active site, binding of OA to OPRT, and binding of Mg2+-PRPP complex to OA-OPRT complex. The mechanism of the reaction was unaltered by the change in the identity of divalent metal ion. Experimentally reported inhibiting character of Co2+ was explained on the basis of large Co2+-PRPP binding and migration energies. Mg2+, Ca2+, Mn2+, Co2+ and Zn2+ ions were screened computationally to assess their inhibiting/activating characteristics. Trends obtained by our computational investigations were in correspondence with experimentally reported trends.

Enhancing the performance of single-chambered microbial fuel cell using manganese/palladium and zirconium/palladium composite cathode catalysts.

Application of ZrO2, MnO2, palladium, palladium-substituted-zirconium oxide (Zr0.98Pd0.02O2) and palladium-substituted-manganese oxide (Mn0.98Pd0.02O2) cathode catalysts in a single-chambered microbial fuel cell (MFC) was explored. The highest power generation (1.28W/m3) was achieved in MFC with Mn0.98Pd0.02O2 catalyst, which was higher than that with MnO2 (0.58W/m3) alone; whereas, MFC having Zr0.98Pd0.02O2 catalyzed cathode and non-catalyzed cathode produced powers of 1.02 and 0.23W/m3, respectively. Also, low-cost zirconium-palladium-composite showed better catalytic activity and capacitance over ZrO2 with 20A/m3 current production and demonstrated its suitability for MFC applications. Cyclic voltammetry analyses showed higher well-defined redox peaks in composite catalysts (Mn/Zr-Pd-C) over other catalyzed MFCs containing MnO2 or ZrO2. Electrochemical behaviour of composite catalysts on cathode showed higher availability of adsorption sites for oxygen reduction and, hence, enhanced the rate of cathodic reactions. Thus, Mn/Zr-Pd-C-based composite catalysts exhibited superior cathodic performance and could be proposed as alternatives to costly Pd-catalyst for field applications.

Highly Active Tungsten Oxide Nanoplate Electrocatalysts for the Hydrogen Evolution Reaction in Acidic and Near Neutral Electrolytes.

An efficient, cost-effective, and earth-abundant catalyst that could drive the production of hydrogen from water without or with little external energy is the ultimate goal toward hydrogen economy. Herein, nanoplates of tungsten oxide and its hydrates (WO3·H2O) as promising electrocatalysts for the hydrogen evolution reaction (HER) are reported. The square-shaped and stacked WO3·H2O nanoplates are synthesized at room temperature under air in ethanol only, making it as a promising green synthesis strategy. The repeated electrochemical cyclic voltammetry cycles modified the surface of WO3·H2O nanoplates to WO3 as confirmed by X-ray photoelectron and Auger spectroscopy, which leads to an improved HER activity. Hydrogen evolution is further achieved from distilled water (pH 5.67) producing 1 mA cm-2 at an overpotential of 15 mV versus the reversible hydrogen electrode. Moreover, WO3·H2O and WO3 nanoplates demonstrate excellent durability in acidic and neutral media, which is highly desirable for practical application. Improved hydrogen evolution by WO3(200) when compared to that by Pt(111) is further substantiated by the density functional theory calculations.

On origin and evolution of carbonic anhydrase isozymes: A phylogenetic analysis from whole-enzyme to active site.

Genetic evolution of carbonic anhydrase enzyme provides an interesting instance of functional similarity in spite of structural diversity of the members of a given family of enzymes. Phylogenetic analysis of α-, ß- and γ-carbonic anhydrase was carried out to determine the evolutionary relationships among various members of the family with the enzyme marking its presence in a wide range of cellular and chromosomal locations. The presence of more than one class of enzymes in a particular organism was revealed by phylogenetic time tree. The evolutionary relationships among the members of animal, plant and microbial kingdom were developed. The study revises a long-established notion of kingdom-specificity of the different classes of carbonic anhydrases and provides a new version of the presence of multiple classes of carbonic anhydrases in a single organism and the presence of a given class of carbonic anhydrase across different kingdoms.