Comparative Study of Protein Unfolding in Aqueous Urea and Dimethyl Sulfoxide Solutions: Surface Polarity, Solvent Specificity, and Sequence of Secondary Structure Melting

Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here, we alter the solvent environment in a controlled manner by choosing two different cosolvents of water, urea, and dimethyl sulfoxide (DMSO) and study unfolding of four different proteins to understand the respective sequence of melting by computer simulation methods. We indeed find interesting differences in the sequence of melting of alpha helices and beta sheets in these two solvents. For example, in 8 M urea solution, beta-sheet parts of a protein are found to unfold preferentially, followed by the unfolding of alpha helices. In contrast, 8 M DMSO solution unfolds alpha helices first, followed by the separation of beta sheets for the majority of proteins. Sequence of unfolding events in four different alpha/beta proteins and also in chicken villin head piece (HP-36) both in urea and DMSO solutions demonstrate that the unfolding pathways are determined jointly by relative exposure of polar and nonpolar residues of a protein and the mode of molecular action of a solvent on that protein.

Enhancement in Bath Mixing and Plume area in a New Degassing Process - A Computational Fluid Dynamic Study

Reaction between the various species in slag and metal phase is usually mass transfer controlled. There have been continuous efforts to increase the reaction efficiency in slag-metal system, especially during decarburization of steel to produce the ultra low carbon steel (ULCS) in secondary steelmaking. It has been found that the surface reaction is a dominant factor in the final stage of decarburization. In the initial stage, the inner site reaction is major factor in the refining process. The mixing of bath affects the later reaction. However, the former reaction (surface reaction) is affected by the plume size area at the top of the metal surface. Therefore, a computational study has been made to understand the fluid dynamics of a new secondary steelmaking process called Revolutionary Degasser Activator (REDA) to study the bath mixing and plume area. REDA process has been considered as it is claimed that this process can reduce the carbon content in steel below 10ppm in a less time than the other existing processes such as RH and Tank degasser. This study shows that both bath mixing and plume area are increased in REDA process facilitating it to give the desired carbon content in less time. Qualitative comments are made on slag-metal reaction system based on this finding.

A comparison of the molecular orbital (ab initio, CNDO and EHT) methods applied to the conformational study of thiocarbonohydrazide in its basic and diprotonated forms

Conformational preferences of thiocarbonohydrazide (H2NNHCSNHNH2) in its basic and N,N′-diprotonated forms are examined by calculating the barrier to internal rotation around the C---N bonds, using the theoretical LCAO—MO (ab initio and semiempirical CNDO and EHT) methods. The calculated and experimental results are compared with each other and also with values for N,N′-dimethylthiourea which is isoelectronic with thiocarbonohydrazide. The suitability of these methods for studying rotational isomerism seems suspect when lone pair interactions are present.

Phase transition in ammonium aluminium and ammonium chromium alums-A high pressure EPR study

An investigation of the phase transitions at high pressures in the alums mentioned in the title has been carried out using EPR of the Cr3+ ion (at the trivalent metal ion site). It is observed that at ambient as well as at high pressures there is a change of slope in the linear variations of the zero field splitting with temperature and that the low temperature phase is characterised by a large number of lines in the EPR spectra. The transition temperature shows a large positive shift with pressure, for both the alums. All these facts are explained in terms of our model of the origin of the trigonal field at the trivalent metal ion site as well as the details of the motion of NH4+ ion.

Study of switching characteristics and thermal noise in ferroelectric crystals both in the pure and radiation damaged state

The phase transition in gamma-irradiated triglycine sulphate (TGS) has been investigated by using a method based on the measurement of thermal noise. The results of a study of the polarization switching characteristics of gamma irradiated TGS and sodium nitrite (NaNO2) have also been presented. The effect of irradiation on the phase transition and the switching processes has been discussed.

A Comparative Study of Aromaticity in Substituted Tetracyclic and Hexacyclic Thiophenes

We have studied the nature of aromaticity in expanded porphyrinic analogues of thiophenes formed by four and six thiophenes. Using density functional theory (DFT) we have analyzed the aromaticity of both the macrocycle and individual molecular fragments. We find paramagnetic annulenic ring currents in the case of tetracyclic molecules and diamagnetic annulenic ring currents for hexacyclic molecules. We have also studied the effect of substitution of benzene rings within the macrocycle. We find that as the number of benzene rings is increased the aromaticity increases for tetracyclic systems and decreases for hexacyclic systems. All the results have been analyzed with various microscopic parameters, including geometry, excitation gap, and NMR criteria.

Sign Of The Order Parameter In Oriented Systems And Its Utility In The Study Of The Dynamic Properties Of Molecules

Novel one and two dimensional NMR techniques are proposed and utilized for the determination of the signs of the order parameters used for the study of the mobility of the fatty acid chains. The experiments designed to extract this information involve the use of the intensities of the side bands in the spectra of oriented systems spinning at the magic angle. Advantages of the two dimensional technique over the one dimensional method are discussed. The utility of the method in the study of the dynamic properties of membranes and model systems is pointed out.

Infrared spectroscopic study of the phase transitions in CsNO3, RbNO3 and NH4NO3

Phase transitions of CsNO3 (II-I), RbNO3 (IV-III-II) and NH4NO3 (V-IV-III-II-I) have been studied by i.r. spectroscopy. The study has provided useful information on the changes in the dispositions of the ions during the phase transitions.

On the gluing and ungluing of strange attractors in the study of the Lorenz system

The ungluing of a strange attractor, gluing of strange attractors, and the coexistence of strange attractors, not reported earlier in the study of the Lorenz system, are discovered numerically.

Mutagenic significance of proton acidities in methylated guanine and thymine bases and deoxynucleosides: A theoretical study

Proton changes have been advanced as being the key molecular basis for the mutagenecity of alkylated DNA bases and nucleosides, leading to questions as to which protons are involved and whether the protic changes are tautomeric shifts or abstractions. This semiempirical molecular orbital study seeks to clarify the issue by examining the various possibilities open for these protic changes in a number of methylated guanines and thymines and their deoxynucleosides. Proton shifts leading to tautomer formation are not predicted as being thermodynamically favourable in most cases. The most feasible proton abstractions are predicted to involve the Watson-Crick protons in all cases, which corroborates Watson-Crick proton loss as providing the key molecular basis for the induction of point mutations. The calculated proton acidities correlate well with experimental data. The gas-phase deprotonation enthalpies for a number of alkylated nucleosides are found to correlate linearly with the solvent-phase pK(a) values. The theoretically calculated enthalpies in a simulated aqueous solvent phase of the deprotonation reactions of various nucleic acid bases are also found to have good linear correlations with experimental pK(a) values. The consensus of these calculations is that O-6-alkyldeoxyguanosines, and O-2- and O-4-alkyldeoxythymidines would be mutagenic while N-7-alkyldeoxyguanosines would not be mutagenic (as experiment indicates). The untested N-3-methyldeoxyguanosine is predicted to be mutagenic. (C) 1997 Elsevier Science B.V.

A molecular dynamics study and molecular level explanation of pressure dependence of ionic conductivity of potassium chloride in water

Experimental ionic conductivity of different alkali ions in water shows markedly different dependences on pressure. Existing theories such as that of Hubbard-Onsager are unable to explain these dependences on pressure of the ionic conductivity for all ions. We report molecular dynamics investigation of potassium chloride solution at low dilution in water at several pressures between 1 bar and 2 kbar. Two different potential models have been employed. One of the models successfully reproduces the experimentally observed trend in ionic conductivity of K+ ions in water over the 0.001-2 kbar range. We also propose a theoretical explanation, albeit at a qualitative level, to account for the dependence of ionic conductivity on pressure in terms of the previously studied Levitation Effect. It also provides a microscopic picture in terms of the pore network in liquid water.

The molecular dynamics study of lithium ion conduction in phosphate glasses and the role of non-bridging oxygen

Molecular dynamics (MD) simulation of lithium phosphate (Li2O-P2O5) glasses with varying Li2O content has been carried out. Two different P-O distances corresponding to phosphorus coordination with bridging oxygen (BO) and non-bridging oxygen (NBO) were identified in the simulated glasses. NBO-BO interconversion or bond switching was noted, which results in a dynamic equilibration of the tetrahedral phosphate units (P-n, n = 1,3 indicates the number of bridging oxygen atoms in the coordination of phosphorus). The NBO-BO bond switching is mildly activated with an effective activation barrier of 0.03-0.05 eV. Lithium ion jumps do not appear to be strongly coupled to bond switching. But the number of Li+ ions coordinated to an optimum number of NBOs and the number of Li+ ions jumping out of their sites appear to be correlated. Detailed analysis was made of the dynamics of P-n species and new insights have been obtained regarding ion migration in network-modified phosphate glasses.

An ab-initio study of the role of lone pairs in the structure and insulator-metal transition in SnO and PbO

We have performed density functional calculations on tetragonal SnO and PbO (litharge) in the space group P4/nmm with the specific intention of examining the role played by Sn 5s and Pb 6s lone pairs in stabilizing the structure, and in giving rise to semi-metallic behavior (of SnO at ambient pressure and of PbO in the gamma phase). Use of the electron localization function has permitted real-space visualization of the lone pair in these structures. We also discuss the electronic structure of the orthorhombic PbO (massicot, space group Pbma) which again has localized lone pairs, contrary to some earlier expectation. (C) 2002 Editions scientifiques et medicales Elsevier SAS. All rights reserved.

Experimental study and optimization of Plasma Actuators for Flow control in subsonic regime

Experimental study and optimization of Plasma Ac- tuators for Flow control in subsonic regime PRADEEP MOISE, JOSEPH MATHEW, KARTIK VENKATRAMAN, JOY THOMAS, Indian Institute of Science, FLOW CONTROL TEAM | The induced jet produced by a dielectric barrier discharge (DBD) setup is capable of preventing °ow separation on airfoils at high angles of attack. The ef-fect of various parameters on the velocity of this induced jet was studied experimentally. The glow discharge was created at atmospheric con-ditions by using a high voltage RF power supply. Flow visualization,photographic studies of the plasma, and hot-wire measurements on the induced jet were performed. The parametric investigation of the charac- teristics of the plasma show that the width of the plasma in the uniform glow discharge regime was an indication of the velocity induced. It was observed that the spanwise and streamwise overlap of the two electrodes,dielectric thickness, voltage and frequency of the applied voltage are the major parameters that govern the velocity and the extent of plasma.e®ect of the optimized con¯guration on the performance characteristics of an airfoil was studied experimentally.