Rovibrational-Specific QCT and Master Equation Study on N2(X1Σg+) + O(3P) and NO(X2Π) + N(4S) Systems in High-Energy Collisions.

This work presents a detailed investigation of the energy-transfer and dissociation mechanisms in N2(X1Σg+) + O(3P) and NO(X2Π) + N(4S) systems using rovibrational-specific quasiclassical trajectory (QCT) and master equation analyses. The complete set of state-to-state kinetic data, obtained via QCT, allows for an in-depth investigation of the Zel'dovich mechanism leading to the formation of NO molecules at microscopic and macroscopic scales. The master equation analysis demonstrates that the low-lying vibrational states of N2 and NO have dominant contributions to the NO formation and the corresponding extinction of N2 through the exchange process. For the considered temperature range, it is found that nearly 50% of the dissociation processes for N2 and NO molecules occur in the quasi-steady-state (QSS) regime, while for the Zel'dovich reaction, the distribution of the reactants does not reach the QSS conditions. Furthermore, using the QSS approximation to model the Zel'dovich mechanism leads to overestimating NO production by more than a factor of 4 in the high-temperature range. The breakdown of this well-known approximation has profound consequences for the approaches that heavily rely on the validity of QSS assumption in hypersonic applications. Finally, the investigation of the rovibrational state population dynamics reveals substantial similarities among different chemical systems for the energy-transfer and the dissociation processes, providing promising physical foundations for the use of reduced-order strategies in other chemical systems without significant loss of accuracy.

Carbon Clusters: Thermochemistry and Electronic Structure at High Temperatures.

This paper studies the thermochemistry and electronic structure of small carbon clusters and hydrocarbons, which are major constituents of pyrolysis gases released into the boundary layer of ablating heat shields. Our focus lies on clusters of up to four carbon atoms. Among other molecules, thermochemistry data for molecules such as C3H and C4H have been determined using the Weizmann-1 (W1) method. These molecules have very limited thermochemistry data recorded in the literature, thereby necessitating new and accurate computations of required properties such as electronic energies of low-lying states, heats of formation, harmonic frequencies, and rotational constants. A study of electronically excited states of these molecules computed using the equations of motion coupled cluster singles doubles method revealed C4 and C4H to be potential sources of radiation absorption in the boundary layer. The excited electronic states of interest are studied further to obtain their optimum geometries, rotational constants, and vibrational frequencies. Moreover, we also study the effect of low-lying excited electronic states on the partition function to assess their effect on the thermodynamics of these pyrolysis gases in the high-temperature regime. Neglecting the excited electronic states records a maximum difference of 12% in the computed specific heat capacity values, Cp values. Finally, comparisons of the equilibrium mole fractions obtained using the thermodynamics computed in this paper with the existing state-of-the-art tables used for hypersonic applications (e.g., JANAF and Gurvich Tables) show an order of magnitude difference in the mixture compositions. It is shown that the rhombic isomer of C4 (1Ag), which is energetically close to the ground state (3Σg-) and usually neglected in composition calculations, contributes to a 28% increase in the equilibrium mole fraction of the C4 molecule.

Coarse-grained modeling of thermochemical nonequilibrium using the multigroup maximum entropy quadratic formulation.

This work addresses the construction of a reduced-order model based on a multigroup maximum entropy formulation for application to high-enthalpy nonequilibrium flows. The method seeks a piecewise quadratic representation of the internal energy-state populations by lumping internal energy levels into groups and by applying the maximum entropy principle in conjunction with the method of moments. The use of higher-order polynomials allows for an accurate representation of the logarithm of the distribution of the low-lying energy states, while preserving an accurate description of the linear portions of the logarithm of the distribution function that characterize the intermediate- and high-energy states. A comparison of the quadratic and the linear reconstructions clearly demonstrates how the higher-order reconstruction provides a more accurate representation of the internal population distribution function at a modest increase in the computational cost. Numerical simulations carried out under conditions relevant to hypersonic flight reveal that the proposed model is able to capture the dynamics of the nonequilibrium distribution function using as few as three groups, thereby reducing the computational costs for simulations of nonequilibrium flows.

Purification and partial characterization of an anticoagulant PLA2 from the venom of Indian Daboia russelii that induces inflammation through upregulation of proinflammatory mediators.

The present study describes the purification and partial characterization of a basic anticoagulant PLA2 enzyme named as Rv(i) PLA2 from the venom of Indian Daboia russelii. The molecular mass of the protein was found to be 13,659.65 Da, and peptide mass fingerprinting revealed that it belongs to group II PLA2 family. The peptide sequence showed similarity to uncharacterized basic PLA2 enzyme having an accession no. of P86368 reported from Sri Lankan D. russelii. Rv(i) PLA2 exhibited strong phospholipase A2 and anticoagulant activity. It also induced expression of COX-2 and TNF-α mRNA in a dose-dependent manner in phorbol 12-myristate 13-acetate differentiated THP-1 cells, which play a crucial role during inflammation. Chemical modification of His residue in Rv(i) PLA2 with p-bromophenacyl bromide abolished the enzymatic, anticoagulant, and inflammatory activities. The result indicates that the catalytic site of Rv(i) PLA2 might play a vital role in inducing inflammation at the bite site during D. russelii envenomation.

Daboxin P, a Major Phospholipase A2 Enzyme from the Indian Daboia russelii russelii Venom Targets Factor X and Factor Xa for Its Anticoagulant Activity.

In the present study a major protein has been purified from the venom of Indian Daboia russelii russelii using gel filtration, ion exchange and Rp-HPLC techniques. The purified protein, named daboxin P accounts for ~24% of the total protein of the crude venom and has a molecular mass of 13.597 kDa. It exhibits strong anticoagulant and phospholipase A2 activity but is devoid of any cytotoxic effect on the tested normal or cancerous cell lines. Its primary structure was deduced by N-terminal sequencing and chemical cleavage using Edman degradation and tandem mass spectrometry. It is composed of 121 amino acids with 14 cysteine residues and catalytically active His48 -Asp49 pair. The secondary structure of daboxin P constitutes 42.73% of α-helix and 12.36% of ß-sheet. It is found to be stable at acidic (pH 3.0) and neutral pH (pH 7.0) and has a Tm value of 71.59 ± 0.46°C. Daboxin P exhibits anticoagulant effect under in-vitro and in-vivo conditions. It does not inhibit the catalytic activity of the serine proteases but inhibits the activation of factor X to factor Xa by the tenase complexes both in the presence and absence of phospholipids. It also inhibits the tenase complexes when active site residue (His48) was alkylated suggesting its non-enzymatic mode of anticoagulant activity. Moreover, it also inhibits prothrombinase complex when pre-incubated with factor Xa prior to factor Va addition. Fluorescence emission spectroscopy and affinity chromatography suggest the probable interaction of daboxin P with factor X and factor Xa. Molecular docking analysis reveals the interaction of the Ca+2 binding loop; helix C; anticoagulant region and C-terminal region of daboxin P with the heavy chain of factor Xa. This is the first report of a phospholipase A2 enzyme from Indian viper venom which targets both factor X and factor Xa for its anticoagulant activity.

Purification and Characterization of Nk-3FTx: A Three Finger Toxin from the Venom of North East Indian Monocled Cobra.

Snake venom three finger toxins (3FTxs) are a non-enzymatic family of venom proteins abundantly found in elapids. We have purified a 7579.5 ± 0.591 Da 3FTx named as Nk-3FTx from the venom of Naja kaouthia of North East India origin. The primary structure was determined by a combination of N-terminal sequencing and electrospray ionization liquid chromatography-mass spectrometry/mass spectrometry. Biochemical and biological characterization reveal that it is nontoxic to human cell lines and exhibit mild anticoagulant activity when tested on citrated human plasma. Nk-3FTx was found to affect the compound action potential (CAP) and nerve conduction velocity of isolated toad sciatic nerve. This is the first report of a non-conventional 3FTx from Naja kaouthia venom that reduces CAP for its neurotoxic effect. Further studies can be carried out to understand the mechanism of action and to explore its potential therapeutic application.

Unveiling the complexities of Daboia russelii venom, a medically important snake of India, by tandem mass spectrometry.

Composition of Indian Russell's viper (Daboia russelii russelii) venom, a medically important snake and member of "Big Four" snakes of India was done by gel filtration chromatography followed by tandem mass spectrometry. The MS/MS analyses of tryptic digested gel filtration peaks divulged the presence of 63 different proteins belonging to 12 families. Phospholipase A2 (PLA2), serine proteases, metalloproteases, cysteine-rich secretory proteins, l-amino acid oxidase, C-type lectin-like proteins, kunitz-type serine protease inhibitor, disintegrin, nucleotidase, phosphodiesterase, vascular endothelial growth factor and vascular nerve growth factor families were identified. PLA2 enzymes with isoforms of N-, S- and H-type based on their first N-terminal amino acid residue were observed. The venom is also found to be rich in RVV-X, RVV-V and thrombin-like enzymes. Homologues of disintegrins with RGD and RTS motifs were also observed. The high percentage of PLA2 and proteases in the venom proteome could be responsible for the observed coagulopathy, haemorrhage and edema which can be correlated with the clinical manifestations of Russell's viper envenomation. This is the first proteomic analysis of Indian D. russelii venom which might assist in understanding the pathophysiological effects of viper envenomation. Such study will also be important for developing more effective antivenom for viper bite management.