Oxidation pathways and kinetics of the 1,1,2,3-tetrafluoropropene (CF2CF-CH2F) reaction with Cl-atoms and subsequent aerial degradation of its product radicals in the presence of NO.

To give a comprehensive account of the environmental acceptability of 1,1,2,3-tetrafluoropropene (CF2CF-CH2F) in the troposphere, we have examined the oxidation reaction pathways and kinetics of CF2CF-CH2F initiated by Cl-atoms using the second-order Møller-Plesset perturbation (MP2) theory along with the 6-31+G(d,p) basis set. We also performed single-point energy calculations to further refine the energies at the CCSD(T) level along with the basis sets 6-31+G(d,p) and 6-311++G(d,p). The estimation of the relative energies and thermodynamic parameters of the CF2CF-CH2F + Cl reaction clearly shows that Cl-atom addition reaction pathways are more dominant compared to H-abstraction reaction pathways. The value of the rate coefficient for each reaction channel is calculated using the conventional transition state theory (TST) over the temperature range of 200-1000 K at 1 atm. The estimated overall rate coefficients for the title reaction are found to be 1.10 × 10-12, 1.21 × 10-10, and 1.13 × 10-8 cm3 per molecule per s via the respective calculation methods viz. MP2/6-31+G(d,p), CCSD(T)//MP2/6-31+G(d,p), and CCSD(T)/6-311++G(d,p)//MP2/6-31+G(d,p), at 298.15 K. Moreover, the calculated rate coefficients and percentage branching ratio values suggest that the Cl-atom addition reaction at the ß-carbon atom is more preferable to that of the α-carbon addition to CF2CF-CH2F. Based on the rate coefficient values calculated by the three different methods, the atmospheric lifetime for the title reaction at 298.15 K is estimated. The radiative efficiency (RE) and Global Warming Potential (GWP) results of the title molecule show that its GWP would be negligible. Further, we have explored the degradation of its product radicals in the presence of O2 and NO. From the degradation results, we have found that CF2(Cl)COF, FCOCH2F, FCFO and FCOCl are formed as stable end products along with various radicals such as ˙CF2Cl and ˙CH2F. Therefore, these findings of kinetic and mechanistic data can be applied to the development and implementation of a novel CFC replacement.

Reverse vaccinology and immunoinformatics approach to design a chimeric epitope vaccine against Orientia tsutsugamushi.

Scrub typhus is a vector-borne infectious disease caused by Orientia tsutsugamushi and it is reportedly associated with up to 20 % of hospitalized cases of febrile illnesses. The major challenge of vaccine development is the lack of identified antigens that can induce both heterotypic and homotypic immunity including the production of antibodies, cytotoxic T lymphocyte, and helper T lymphocytes. We employed a comprehensive immunoinformatic prediction algorithm to identify immunogenic epitopes of the 56-kDa type-specific cell membrane surface antigen and surface cell antigen A of O. tsutsugamushi to select potential candidates for developing vaccines and diagnostic assays. We identified 35 linear and 29 continuous immunogenic B-cell epitopes and 51 and 27 strong-binding T-cell epitopes of major histocompatibility complex class I and class II molecules, respectively, in the conserved and variable regions of the 56-kDa type-specific surface antigen. The predicted B- and T-cell epitopes were used to develop immunogenic multi-epitope candidate vaccines and showed to elicit a broad-range of immune protection. A stable interactions between the multi-epitope vaccines and the host fibronectin protein were observed using docking and simulation methods. Molecular dynamics simulation studies demonstrated that the multi-epitope vaccine constructs and fibronectin docked models were stable during simulation time. Furthermore, the multi-epitope vaccine exhibited properties such as antigenicity, non-allergenicity and ability to induce interferon gamma production and had strong associations with their respective human leukocyte antigen alleles of world-wide population coverage. A correlation of immune simulations and the in-silico predicted immunogenic potential of multi-epitope vaccines implicate for further investigations to accelerate designing of epitope-based vaccine candidates and chimeric antigens for development of serological diagnostic assays for scrub typhus.

Inhibitory potential of furanocoumarins against cyclin dependent kinase 4 using integrated docking, molecular dynamics and ONIOM methods.

Cyclin Dependent Kinase 4 (CDK4) is vital in the process of cell-cycle and serves as a G1 phase checkpoint in cell division. Selective antagonists of CDK4 which are in use as clinical chemotherapeutics cause various side-effects in patients. Furanocoumarins induce anti-cancerous effects in a range of human tumours. Therefore, targeting these compounds against CDK4 is anticipated to enhance therapeutic effectiveness. This work intended to explore the CDK4 inhibitory potential of 50 furanocoumarin molecules, using a comprehensive approach that integrates the processes of docking, drug-likeness, pharmacokinetic analysis, molecular dynamics simulations and ONIOM (Our own N-layered Integrated molecular Orbital and Molecular mechanics) methods. The top five best docked compounds obtained from docking studies were screened for subsequent analysis. The molecules displayed good pharmacokinetic properties and no toxicity. Epoxybergamottin, dihydroxybergamottin and notopterol were found to inhabit the ATP-binding zone of CDK4 with substantial stability and negative binding free energy forming hydrogen bonds with key catalytic residues of the protein. Notopterol exhibiting the highest binding energy was subjected to ONIOM calculations wherein the hydrogen bonding interactions were retained with significant negative interaction energy. Hence, through these series of computerised methods, notopterol was screened as a potent CDK4 inhibitor and can act as a starting point in successive processes of drug design.Communicated by Ramaswamy H. Sarma.

Reaction Mechanism and Kinetics for the Selective Hydrogenation of Carbon Dioxide to Formic Acid and Methanol over the [Cu2]0,±1 Dimer.

With the rapid growth of industrialization, deforestation, and burning of fossil fuels, undeniably there has been an incredible escalation of the CO2 concentration in the atmosphere. In order to mitigate the problem, the capture and utilization of CO2 in different value-added chemicals have thus remained topics of concerned research for more than a decade. Accordingly, we have performed molecular -level catalytic hydrogenation of CO2 to formic acid using bare [Cu2]0,±1 dimers as catalysts. The entire investigation has been performed using a density functional theory (DFT) method employing the Perdew-Burke-Ernzerhof (PBE) functional with the def2TZVPP basis set to explore the different possible routes and efficiency of the catalysts. Results reveal the feasibility of H2 dissociation on all three Cu2, Cu2+, and Cu2- dimers. The negatively charged hydride formed during H2 dissociation on Cu2 and Cu2+ dimers facilitates the formation of the HCOO* intermediate over COOH*, thereby providing product selectivity for HCOOH above CO. However, the reaction on the Cu2- dimer forms both HCOO* and COOH* intermediates, but HCOO*, being kinetically more favorable, results in HCOOH production. The free-energy change suggests that the complete reaction on Cu2 and Cu2+ dimers forms a stable product compared to the Cu2- dimer. Furthermore, H3COH production is studied using the title catalysts via the obtained HCOOH* intermediate from the reaction channel. Transition state theory (TST) has been considered to evaluate the rate constants for each step of the reaction. Overall results suggest Cu2 to be better compared to Cu2+ and Cu2- dimers for HCOOH formation and Cu2+ over Cu2 and Cu2- dimers to be more efficient for H3COH formation. This work opens the way for further investigation of the reaction mechanism and development of an efficient catalyst for CO2 hydrogenation.

Design of LNA Analogues Using a Combined Density Functional Theory and Molecular Dynamics Approach for RNA Therapeutics.

Antisense therapeutics treat a wide spectrum of diseases, many of which cannot be addressed with the current drug technologies. In the quest to design better antisense oligonucleotide drugs, we propose five novel LNA analogues (A1-A5) for modifying antisense oligonucleotides and establishing each with the five standard nucleic acids: adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U). Monomer nucleotides of these modifications were considered for a detailed Density Functional Theory (DFT)-based quantum chemical analysis to determine their molecular-level structural and electronic properties. A detailed MD simulation study was done on a 14-mer ASO (5'-CTTAGCACTGGCCT-3') containing these modifications targeting PTEN mRNA. Results from both molecular- and oligomer-level analysis clearly depicted LNA-level stability of the modifications, the ASO/RNA duplexes maintaining stable Watson-Crick base pairing preferring RNA-mimicking A-form duplexes. Notably, monomer MO isosurfaces for both purines and pyrimidines were majorly distributed on the nucleobase region in modifications A1 and A2 and in the bridging unit in modifications A3, A4, and A5, suggesting that A3/RNA, A4/RNA, and A5/RNA duplexes interact more with the RNase H and solvent environment. Accordingly, solvation of A3/RNA, A4/RNA, and A5/RNA duplexes was higher compared to that of LNA/RNA, A1/RNA, and A2/RNA duplexes. This study has resulted in a successful archetype for creating advantageous nucleic acid modifications tailored for particular needs, fulfilling a useful purpose of designing novel antisense modifications, which may overcome the drawbacks and improve the pharmacokinetics of existing LNA antisense modifications.

Oxido- and mixed-ligand peroxido complexes of niobium(V) as potent phosphatase inhibitors and efficient catalysts for eco-friendly styrene epoxidation.

The present study describes the facile synthesis and comprehensive characterization of new oxido and peroxidoniobium(V) complexes with biogenic ligands, maltol (malt) and deferiprone (def) in their co-ordination sphere, viz., [NbO(malt)3]2·9H2O (1), Na2[Nb(O2)3(malt)]·H2O (2) and Na2[Nb(O2)3(def)]·2H2O (3). The complexes were characterized using various analytical and spectroscopic techniques (FTIR, Raman, NMR, UV-visible, TGA, ICP-OES and elemental analysis). The charge neutral complex 1 was further characterized by single crystal XRD analysis, and the proposed structures of the peroxidoniobium (pNb) complexes 2 and 3 were validated by density functional theory (DFT) studies. A comparative investigation on the in vitro effect of the title compounds and a set of previously reported polymer-anchored peroxidoniobium complexes, [Nb(O2)3(sulfonate)2]3--PSS [PSS = poly(sodium 4-styrene sulfonate)] (5), [Nb2(O2)6(carboxylate)2]4--PA [PA = poly(sodium acrylate)] (6) and [Nb(O2)3(carboxylate)]2--PMA [PMA = poly(sodium methacrylate)] (7), on the activity of the model enzyme wheat thylakoid acid phosphatase has revealed that each of the compounds is an effective inhibitor of the enzyme (IC50 values varying within the range 1-64 µM). The results of the detailed enzyme kinetic study demonstrated that the compounds induce their inhibitory effect via distinct pathways. The oxidoniobium complex 1 as well as polymer-anchored pNb complexes acted as classical non-competitive inhibitors of ACP, whereas the monomeric pNb complexes emerged as mixed inhibitors of the enzyme (Kii > Ki). Notably, the complexes serve as excellent recyclable catalysts for selective styrene epoxidation with H2O2, affording 99% styrene conversion, ≥98% epoxide selectivity and a high turnover number of 1740 under eco-friendly solventless conditions.

Immunoinformatics mapping of potential epitopes in SARS-CoV-2 structural proteins.

All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2. Employing a comprehensive immunoinformatic prediction algorithm and leveraging the genetic closeness with SARS-CoV, we have predicted potential immune epitopes in the structural proteins of SARS-CoV-2. The S and N proteins of SARS-CoV-2 and SARS-CoVs are main targets of antibody detection and have motivated us to design four multi-epitope vaccines which were based on our predicted B- and T-cell epitopes of SARS-CoV-2 structural proteins. The cardinal epitopes selected for the vaccine constructs are predicted to possess antigenic, non-allergenic, and cytokine-inducing properties. Additionally, some of the predicted epitopes have been experimentally validated in published papers. Furthermore, we used the C-ImmSim server to predict effective immune responses induced by the epitope-based vaccines. Taken together, the immune epitopes predicted in this study provide a platform for future experimental validations which may facilitate the development of effective vaccine candidates and epitope-based serological diagnostic assays.

Structural insight into locked nucleic acid based novel antisense modifications: A DFT calculations at monomer and MD simulations at oligomer level.

In the present study, five novel LNA based antisense modifications have been proposed. A conformational search was carried out using TANGO, followed by geometry optimization using MOPAC. Based on their electronic energies the most stable conformation for each modification was identified. Further, DFT based full geometry optimization on the most stable conformations at the gas phase B3LYP/6-31G(d,p) using a Gaussian03 and single point energy calculations on the optimized structures at the solvent phase B3LYP/6-311G(d,p) level of theory were done to derive their quantum chemical descriptors using the Gaussian09. A comparison of global reactivity descriptors confirmed that the LNA based modifications were the most reactive. Base-pair stability was recorded by observing the binding energies and base-pairing conformations of modified GC base pairs at the B3LYP/6-311G(d,p) level of theory. Molecular dynamics simulations have been performed at the oligomer duplex level by incorporating individual modifications on 20-mer RNA-RNA duplexes using AMBER16. Free energy calculations of duplex structures suggested that incorporation of A2 modification into the RNA-RNA duplex increased the duplex binding affinity similar to LNA. Whereas, the A3 modification showed less binding compared to LNA but improved binding compared to MOE. This computational approach using quantum chemical methods may be very useful to propose better modifications than the existing ones before performing the experiments in the area of antisense technology.

Tuning the transition barrier of H2 dissociation in the hydrogenation of CO2 to formic acid on Ti-doped Sn2O4 clusters.

A density functional theory study has been performed to investigate cation-doped Sn2O4 clusters for selective catalytic reduction of CO2. We study the influence of Si and Ti dopants on the height of the H2 dissociation barrier for the doped systems, and then the subsequent mechanism for the conversion of CO2 into formic acid (FA) via a hydride pinning pathway. The lowest barrier height for H2 dissociation is observed across the 'Ti-O' bond of the Ti-doped Sn2O4 cluster, with a negatively charged hydride (Ti-H) formed during the heterolytic H2 dissociation, bringing selectivity towards the desired FA product. The formation of a formate intermediate is identified as the rate-determining step (RDS) for the whole pathway, but the barrier height is substantially reduced for the Ti-doped system when compared to the same steps on the undoped Sn2O4 cluster. The free energy of formate formation in the RDS is calculated to be negative, which reveals that the hydride transfer would occur spontaneously. Overall, our results show that the small-sized Ti-doped Sn2O4 clusters exhibit better catalytic activity than undoped clusters in the important process of reducing CO2 to FA when proceeding via the hydride pinning pathway.

Unveiling the Role of Hydrogen Bonding and g-Tensor in the Interaction of Ru-Bis-DMSO with Amino Acid Residue and Human Serum Albumin.

Density functional theory calculations have been carried out to observe the role of hydrogen bonding in hydrolysis and the coordination mechanism of three amino acid residues (histidine, cysteine, and alanine) with Ru-bis-DMSO complex via which the complex tends to interact with the HSA protein receptor. The interaction mechanism shows that ruthenium complexes prefer to bind protein receptor through cysteine and histidine residues rather than through alanine, which has been confirmed by DFT evaluated H-bonding and g-tensor analysis. The number of H-bonds plays a major role in stabilizing the intermediates and transition states involved in the Ru-bis-DMSO and amino acid residue interactions. Our theoretical g-tensor values are in good agreement with the available experimental results. Further QM/MM calculation on the Ru-bis-DMSO-HSA adducts reveals that the adduct is more stable when Ru gets coordinated with histidine imidazole rather than cysteine. These investigations helped us in understanding the type of amino acid residue responsible for binding the metal complex Ru-bis-DMSO with the carrier protein HSA.