@article { ISI:000255704100017, title = {Density functional investigations of electronics structure and dehydrogenation reactions of Al- and Si-substituted magnesium hydride}, journal = {ChemPhysChem }, volume = {9}, number = {6}, year = {2008}, month = {APR}, pages = {928-934}, publisher = {WILEY-V C H VERLAG GMBH}, type = {Article}, address = {PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY}, abstract = {

{The effect on the hydrogen storage attributes of magnesium hydride (MgH2) of the substitution of Mg by varying fractions of Al and Si is investigated by an ab initio plane-wave pseuodopotential method based on density functional theory. Three supercells, namely, 2 x 2 x x 3 x 1 x 1 and 5 x 1 x 1 are used for generating configurations with varying amounts (fractions x=0.0625, 0.1, and 0.167) of impurities. The analyses of band structure and density of states (DOS) show that, when a Mg atom is replaced by Al, the band gap vanishes as the extra electron occupies the conduction band minimum. In the case of Si-substitution, additional states are generated within the band gap of pure MgH2-significontly reducing the gap in the process. The reduced band gaps cause the Mg-H bond to become more susceptible to dissociation. For all the fractions, the calculated reaction energies for the stepwise removal of H-2 molecules from Al- and Si-substituted MgH2 ore much lower than for H-2 removal from pure MgH2. The reduced stability is also reflected in the comparatively smaller heats of formation (Delta H-f) of the substituted MgH2 systems. Si causes greater destabilization of MgH2 than Al for each x. For fractions x = 0.167 of Al

}, keywords = {band structure, Density functional calculations, hydrides, Hydrogen storage, Thermodynamics}, issn = {1439-4235}, doi = {10.1002/cphc.200700860}, author = {Kelkar, Tuhina and Pal, Sourav and Kanhere, Dilip G.} } @article { ISI:000305295000014, title = {Design, synthesis and evaluation of unique 2,4,5-triaryl imidazole derivatives as novel potent aspartic protease inhibitors}, journal = {Medicinal Chemistry}, volume = {8}, number = {3}, year = {2012}, month = {MAY}, pages = {428-435}, publisher = {BENTHAM SCIENCE PUBL LTD}, address = {EXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES}, abstract = {

The 2,4,5-triaryl imidazole derivatives (API) were designed, screened and characterized kinetically \& thermo-dynamically against Pepsin and their activity was also tested on the in silico platform. The docking studies of API with Pepsin show that these are novel and unique inhibitors of Aspartic protease. Drug like properties of these compounds were validated in silico based on Lipinski{\textquoteright}s rule of Five by calculating ClogP, LogS, H-bond acceptors, H-Bond donors, rotational bonds, PSA, PB and BBB values. The Et/Ki and Et/Km values of API show that they follow the Michaelis-Menten kinetics. The binding of inhibitors with proteases was explained by using Van{\textquoteright}t Hoff plot and thermodynamic parameters viz. free energy (Delta G), Entropy (Delta S) and Enthalpy (Delta H). The Van{\textquoteright}t Hoff analysis showed that the value of K-i decreases with increase in temperature and the binding of the inhibitor are entropically driven. API act as new potent aspartic protease inhibitors with K-i, for Pepsin, ranges from 3.7 mu M to 16.7 mu M. Strong hydrophobic groups at C-4 \& C-5 position in API favor binding of inhibitors with Pepsin. Experiments also showed that among C-2 aryl substituted imidazole, a 4-substitution on aryl ring is preferred and less polar substituent makes the molecule more active whereas polar substituents at 2-position on C-2 aryl ring makes the molecule less active. The docking studies of API with Pepsin further intensify and validate our results.

}, keywords = {2, 4, 5-triaryl imidazole derivatives, docking, Lipinski{\textquoteright}s rule of Five, Protease inhibitors, Thermodynamics}, issn = {1573-4064}, author = {Khan, Mohd Sajid and Akhtar, Salman and Siddiqui, S. A. and Siddiqui, M. S. and Srinivasan, K. V. and Arif, J. M.} } @article { ISI:000320836600009, title = {Effect of different arginine methylations on the thermodynamics of tat peptide binding to HIV-1 TAR RNA}, journal = {Biochimie}, volume = {95}, number = {7}, year = {2013}, month = {JUL}, pages = {1422-1431}, publisher = {ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER}, address = {23 RUE LINOIS, 75724 PARIS, FRANCE}, abstract = {

RNA-binding proteins are an important class of mediators that regulate cell function and differentiation. Methylation of arginine, a post-translational modification (PTM) found in these proteins, can modulate their function. Arginine can be monomethylated or dimethylated, depending on the type of methyl transferases involved. This paper describes a comparative study of the thermodynamics of unmodified and modified Tat peptide interaction with TAR RNA, where the peptide is methylated at epsilon (epsilon) and eta (eta) nitrogen atoms of guanidinium group of arginine side chain at position 52 or 53. The results indicate that monomethylation of arginine at epsilon (epsilon) nitrogen atom enhances binding affinity, owing to a more favourable enthalpy component which overrides the less favourable entropy change. In contrast, monomethylation of arginine residue at eta nitrogen results in reduced binding affinity originating exclusively from a less favourable enthalpy change leaving entropic component unaffected. However, in case of simultaneous methylation at epsilon and eta positions, the binding parameters remain almost unaffected, when compared to the unmodified peptide. In case of symmetric dimethylation at eta position the observed enthalpy change of the binding was found to be smaller than the values obtained for the unmodified peptide. Asymmetric dimethylation at eta position showed the most reduced binding affinities owing to less favourable enthalpy changes. These results provide insights that enable elucidation of the biological outcome of arginine methylation as PTMs that regulate protein function, and will contribute to our understanding of how these PTMs are established in vitro and in vivo. (C) 2013 Elsevier Masson SAS. All rights reserved.

}, keywords = {HIV-1, Post-translational modification, Protein methylation, RNA-protein interaction, Thermodynamics}, issn = {0300-9084}, doi = {10.1016/j.biochi.2013.03.008}, author = {Kumar, Santosh and Maiti, Souvik} } @article { ISI:000317352000009, title = {Hydrate phase equilibrium of ternary gas mixtures containing carbon dioxide, hydrogen and propane}, journal = {Journal of Chemical Thermodynamics}, volume = {61}, year = {2013}, month = {JUN}, pages = {58-63}, publisher = {ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD}, address = {24-28 OVAL RD, LONDON NW1 7DX, ENGLAND}, abstract = {

Hydrate phase equilibrium of the ternary guest mixtures containing carbon dioxide, hydrogen and propane at two different compositions were determined. Addition of mole composition of 2.5\% propane to the fuel gas (CO2 (40\%)/H-2 (60\%)) mixture reduces the hydrate formation conditions by 66\% at the temperature of 278.4 K. A Clausius-Clapeyron plot for the experimental results was plotted and from the slope, the enthalpy of hydrate dissociation was calculated. The enthalpy of dissociation of the mixed hydrate formed from a ternary gas mixture containing mole composition 38.1\% CO2, 59.4\% H-2 and 2.5\% C3H8 was found to be 110 kJ.mol(-1) and hence it was concluded that the mixed hydrate formed structure II (sII) hydrates. Whereas for the ternary gas mixture containing mole composition 80.0\% CO2, 18.8\% H-2, and 1.2\% C3H8, the enthalpy of dissociation of the mixed hydrate was found to be 78 kJ.mol(-1) and hence we believe the mixed hydrate formed structure I (sI) hydrate. (C) 2013 Elsevier Ltd. All rights reserved.

}, keywords = {Carbon dioxide capture, Gas hydrates, Global warming, Phase equilibrium, Pre-combustion, Thermodynamics}, issn = {0021-9614}, doi = {10.1016/j.jct.2013.02.003}, author = {Babu, Ponnivalavan and Yang, Ting and Veluswamy, Hari Prakash and Kumar, Rajnish and Linga, Praveen} } @article { ISI:000370464800023, title = {Complexation key to a pH locked redox reaction}, journal = {Journal of Chemical Education}, volume = {93}, number = {2}, year = {2016}, month = {FEB}, pages = {355-361}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

An unfavorable pH can block a feasible electron transfer for a pH dependent redox reaction. In this experiment, a series of potentiometric titrations demonstrate the sequential loss in feasibility of iron(II) dichromate redox reaction over a pH range of 0-4. The pH at which this reaction failed to occur was termed as a pH locked reaction. The comparative ability of 10 selected iron binding ligands with varied propensity for the redox potential modification of Fe(III)/Fe(II) redox couple to restore/unlock the pH locked redox reaction is shown using potentiometric titrations. The spectrophotometric speciation analysis of Fe(III) Tiron complexation with pH was carried out to explain the differing ability of EDTA and Tiron to unlock the reaction under different pH Conditions. The experiment illustrates how environmental, biological redox reactions avoid severe laboratory conditions to occur and can be explored in the design of novel redox systems for natural attenuation of environmental toxins to their non- or lesser-toxic forms. The experiment also demonstrates prudent laboratory practice for safe waste disposal.

}, keywords = {Analytical Chemistry, Aqueous Solution Chemistry, Coordination Compounds, Oxidation/Reduction, pH, Physical Chemistry, Potentiometry, Second-Year Undergraduate, Thermodynamics, Titration/Volumetric Analysis, Upper-Division Undergraduate}, issn = {0021-9584}, doi = {10.1021/acs.jchemed.5b00499}, author = {Rizvi, Masood Ahmad and Dangat, Yuvraj B. and Shams, Tahir and Khan, Khaliquz Zaman} } @article {47168, title = {Molecular dynamics study on growth of carbon dioxide and methane hydrate from a seed crystal}, journal = {Chinese Journal of Chemical Engineering}, volume = {27}, year = {2019}, month = {SEP}, pages = {2074-2080}, type = {Article}, abstract = {

In the current work, molecular dynamics simulation is employed to understand the intrinsic growth of carbon dioxide and methane hydrate starting from a seed crystal of methane and carbon dioxide respectively. This comparison was carried out because it has relevance to the recovery of methane gas from natural gas hydrate reservoirs by simultaneously sequestering a greenhouse gas like CO2. The seed crystal of carbon dioxide and methane hydrate was allowed to grow from a super-saturated mixture of carbon dioxide or methane molecules in water respectively. Two different concentrations (1:6 and 1:8.5) of CO2/CH4 molecules per water molecule were chosen based on gas-water composition in hydrate phase. The molecular level growth as a function of time was investigated by all atomistic molecular dynamics simulation under suitable temperature and pressure range which was well above the hydrate stability zone to ensure significantly faster growth kinetics. The concentration of CO2 molecules in water played a significant role in growth kinetics, and it was observed that maximizing the CO2 concentration in the aqueous phase may not result in faster growth of CO2 hydrate. On the contrary, methane hydrate growth was independent of methane molecule concentration in the aqueous phase. We have validated our results by performing experimental work on carbon dioxide hydrate where it was seen that under conditions appropriate for liquid CO2, the growth for carbon dioxide hydrate was very slow in the beginning. (C) 2019 The Chemical Industry and Engineering Society of China, and Chemical Industry Press Co., Ltd. All rights reserved.

}, keywords = {Cage dynamics, CH4 recovery, CO2 sequestration, F-4 order parameter, kinetics, Natural gas hydrate, Thermodynamics}, issn = {1004-9541}, doi = {10.1016/j.cjche.2019.02.006}, author = {Nakate, Prajakta and Ghosh, Bappa and Das, Subhadip and Roy, Sudip and Kumar, Rajnish} }