Extending the Supramolecular Synthon Based Fragment Approach (SBFA) for Transferability of Multipole Charge Density Parameters to Monofluorobenzoic Acids and their Cocrystals with Isonicotinamide: Importance of C-H center dot center dot center dot O, C-H center dot center dot center dot F, and F center dot center dot center dot F Intermolecular Regions

An extension of the supramolecular synthon-based fragment approach (SBFA) method for transferability of multipole charge density parameters to include weak supramolecular synthons is proposed. In particular, the SBFA method is applied to C-H center dot center dot center dot O, C-H center dot center dot center dot F, and F center dot center dot center dot F containing synthons. A high resolution charge density study has been performed on 4-fluorobenzoic acid to build a synthon library for C-H center dot center dot center dot F infinite chain interactions. Libraries for C-H center dot center dot center dot O and F center dot center dot center dot F synthons were taken from earlier work. The SBFA methodology was applied successfully to 2- and 3-fluorobenzoic acids, data sets for which were collected in a routine manner at 100 K, and the modularity of the synthons was demonstrated. Cocrystals of isonicotinamide with all three fluorobenzoic acids were also studied with the SBFA method. The topological analysis of inter- and intramolecular interaction regions was performed using Bader's AIM approach. This study shows that the SBFA method is generally applicable to generate charge density maps using information from multiple intermolecular regions.

The generalized Onsager model for the secondary flow in a high-speed rotating cylinder

The generalizations of the Onsager model for the radial boundary layer and the Carrier-Maslen model for the end-cap axial boundary layer in a high-speed rotating cylinder are formulated for studying the secondary gas flow due to wall heating and due to insertion of mass, momentum and energy into the cylinder. The generalizations have wider applicability than the original Onsager and Carrier-Maslen models, because they are not restricted to the limit A >> 1, though they are restricted to the limit R e >> 1 and a high-aspect-ratio cylinder whose length/diameter ratio is large. Here, the stratification parameter A = root m Omega(2)R(2)/2k(B)T). This parameter A is the ratio of the peripheral speed, Omega R, to the most probable molecular speed, root 2k(B)T/m, the Reynolds number Re = rho w Omega R(2)/mu, where m is the molecular mass, Omega and R are the rotational speed and radius of the cylinder, k(B) is the Boltzmann constant, T is the gas temperature, rho(w) is the gas density at wall, and mu is the gas viscosity. In the case of wall forcing, analytical solutions are obtained for the sixth-order generalized Onsager equations for the master potential, and for the fourth-order generalized Carrier-Maslen equation for the velocity potential. For the case of mass/momentum/energy insertion into the flow, the separation-of-variables procedure is used, and the appropriate homogeneous boundary conditions are specified so that the linear operators in the axial and radial directions are self-adjoint. The discrete eigenvalues and eigenfunctions of the linear operators (sixth-order and second-order in the radial and axial directions for the Onsager equation, and fourth-order and second-order in the axial and radial directions for the Carrier-Maslen equation) are determined. These solutions are compared with direct simulation Monte Carlo (DSMC) simulations. The comparison reveals that the boundary conditions in the simulations and analysis have to be matched with care. The commonly used `diffuse reflection' boundary conditions at solid walls in DSMC simulations result in a non-zero slip velocity as well as a `temperature slip' (gas temperature at the wall is different from wall temperature). These have to be incorporated in the analysis in order to make quantitative predictions. In the case of mass/momentum/energy sources within the flow, it is necessary to ensure that the homogeneous boundary conditions are accurately satisfied in the simulations. When these precautions are taken, there is excellent agreement between analysis and simulations, to within 10 %, even when the stratification parameter is as low as 0.707, the Reynolds number is as low as 100 and the aspect ratio (length/diameter) of the cylinder is as low as 2, and the secondary flow velocity is as high as 0.2 times the maximum base flow velocity. The predictions of the generalized models are also significantly better than those of the original Onsager and Carrier-Maslen models, which are restricted to thin boundary layers in the limit of high stratification parameter.

Interaction of G-Quadruplexes with Nonintercalating Duplex-DNA Minor Groove Binding Ligands

The enzyme telomerase synthesizes the G-rich DNA strands of the telomere and its activity is often associated with cancer. The telomerase may be therefore responsible for the ability of a cancer cell-to escape apoptosis. The G-rich DNA sequences often adopt tetra-stranded structure, known as the G-quadruplex DNA (G4-DNA). The stabilization of the telomeric DNA into the G4-DNA structures by small molecules has been the focus of many researchers for the design and development of new anticancer agents. The compounds which stabilize the G-quadruplex in the telomere inhibit the telomerase activity. Besides telomeres, the G4-DNA forming sequences are present in the genomic regions of biological significance including the transcriptional regulatory and promoter regions of several oncogenes. Inducing a G-quadruplex structure within the G-rich promoter sequences is a potential way of achieving selective gene regulation. Several G-quadruplex stabilizing ligands are known. Minor groove binding ligands (MGBLs) interact with the double-helical DNA through the minor grooves sequence-specifically and interfere with several DNA associated processes. These MGBLs when suitably modified switch their preference sometimes from the duplex DNA to G4-DNA and stabilize the G4-DNA as well. Herein, we focus on the recent advances in understanding the G-quadruplex structures, particularly made by the human telomeric ends, and review the results of various investigations of the interaction of designed organic ligands with the G-quadruplex DNA while highlighting the importance of MGBL-G-quadruplex interactions.

A resistometric study of solute–solute interaction in dilute aluminium–silver alloys

The experimentally determined apparent vacancy formation energy values in dilute aluminium—silver alloys showed a divergence from calculated values at higher solute fractions. This is explained in terms of a solute—solute interaction energy of the order of 0.10 ev which exists when the binding energy between a vacancy and a solute atom pair is reduced to zero.

Nonspecific Interaction between DNA and Protein allows for Cooperativity: A Case Study with Mycobacterium DNA Binding Protein

Different DNA-binding proteins have different interaction modes with DNA. Sequence-specific DNA protein interaction has been mostly associated with regulatory processes inside a cell, and as such extensive studies have been made. Adequate data is also available on nonspecific DNA protein interaction, as an intermediate to protein's search for its cognate partner. Multidomain nonspecific DNA protein interaction involving physical sequestering of DNA has often been implicated to regulate gene expression indirectly. However, data available on this type of interaction is limited. One such interaction is the binding of DNA with mycobacterium DNA binding proteins. We have used the Langmuir-Blodgett technique to evaluate for the first time the kinetics and thermodynamics of Mycobacterium smegmatis Dps 1 binding to DNA. By immobilizing one of the interacting partners, we have shown that, when a kinetic bottleneck is applied, the binding mechanism showed cooperative binding (n = 2.72) at lower temperatures, but the degree of cooperativity gradually reduces (n = 1.38) as the temperature was increased We have also compared the kinetics and thermodynamics of sequence-specific and nonspecific DNA protein interactions under the same set of conditions.

The interaction of halogen molecules with SWNTs and graphene

The interaction of halogen molecules of varying electron affinity, such as iodine monochloride (ICl), bromine (Br(2)), iodine monobromide (IBr) and iodine (I(2)) with single-walled carbon nanotubes (SWNTs) and graphene has been investigated in detail. Halogen doping of the two nanocarbons has been examined using Raman spectroscopy in conjunction with electronic absorption spectroscopy and extensive theoretical calculations. The halogen molecules, being electron withdrawing in nature, induce distinct changes in the electronic states of both the SWNTs and graphene, which manifests with a change in the spectroscopic signatures. Stiffening of the Raman G-bands of the nanocarbons upon treatment with the different halogen molecules and the emergence of new bands in the electronic absorption spectra, both point to the fact that the halogen molecules are involved in molecular charge-transfer with the nanocarbons. The experimental findings have been explained through density functional theory (DFT) calculations, which suggest that the extent of charge-transfer depends on the electron affinities of the different halogens, which determines the overall spectroscopic properties. The magnitude of the molecular charge-transfer between the halogens and the nanocarbons generally varies in the order ICl > Br(2) > IBr > I(2), which is consistent with the expected order of electron affinities.

Functional regulation of PVBV Nuclear Inclusion protein-a protease activity upon interaction with Viral Protein genome-linked and phosphorylation

Regulation of NIa-Pro is crucial for polyprotein processing and hence, for successful infection of potyviruses. We have examined two novel mechanisms that could regulate NIa-Pro activity. Firstly, the influence of VPg domain on the proteolytic activity of NIa-Pro was investigated. It was shown that the turnover number of the protease increases when these two domains interact (as: two-fold; trans: seven-fold) with each other. Secondly, the protease activity of NIa-Pro could also be modulated by phosphorylation at Ser129. A mutation of this residue either to aspartate (phosphorylation-mimic) or alanine (phosphorylation-deficient) drastically reduces the protease activity. Based on these observations and molecular modeling studies, we propose that interaction with VPg as well as phosphorylation of Ser129 could relay a signal through Trp143 present at the protein surface to the active site pocket by subtle conformational changes, thus modulating protease activity of NIa-Pro. (C) 2011 Elsevier Inc. All rights reserved.

15-deoxyspergualin hinders physical interaction between basic residues of transit peptide in PfENR and Hsp70-1

The apicoplast of Plasmodium harbors several metabolic pathways. The enzymes required to perform these reactions are all nuclearly encoded and apicoplast targeted (NEAT) proteins. Plasmodium falciparum Enoyl-ACP Reductase (PfENR) is one such NEAT protein. The NEAT proteins have a transit peptide which is required for crossing the membranes of apicoplast. We studied the importance of basic residues like Arginine and Lysine within the transit peptide. Previous studies have suggested that all basic residues are essential for apicoplast trafficking. In this study, we demonstrate that only some of these residues are essential (K44, R48, K51, and R52), whereas others are dispensable (R40, K42, and K49). On mutating these specific residues, PfENR is not imported into the apicoplast and is mislocalized to the cytoplasm. We also demonstrate that these residues are also crucial for interaction with Hsp70-1, implying that interactions of Lysine 44, Arginine 48, Lysine 51, and Arginine 52 of the transit peptide with PfHsp70-1 are required for apicoplast trafficking. 15-Deoxyspergualin, which has earlier been proposed to interact with EEVD motif of PfHsp70-1 hinders the physical interaction between these cationic residues of PfENR and Hsp70-1. Hence, we propose that in the transport competent state of NEAT proteins some specific positively charged amino acids in the transit peptide interact with PfHsp70-1, and this interaction is essential for apicoplast targeting.

Thermally induced secondary atomization of droplet in an acoustic field

We study the thermal effects that lead to instability and break up in acoustically levitated vaporizing fuel droplets. For selective liquids, atomization occurs at the droplet equator under external heating. Short wavelength [Kelvin-Helmholtz (KH)] instability for diesel and bio-diesel droplets triggers this secondary atomization. Vapor pressure, latent heat, and specific heat govern the vaporization rate and temperature history, which affect the surface tension gradient and gas phase density, ultimately dictating the onset of KH instability. We develop a criterion based on Weber number to define a condition for the inception of secondary atomization. (C) 2012 American Institute of Physics. [doi:10.1063/1.3680257]

Interaction of guar gum with hydrophobic solids

The interaction of guar gum with the hydrophobic solids namely talc, mica and graphite has been investigated through adsorption, electrokinetic and flotation experiments. The adsorption densities of guar gum onto the above hydrophobic minerals show that they are more or less independent of pH. The adsorption isotherms of guar gum onto talc, mica and graphite indicate that the adsorption densities increase with increase in guar gum concentration and all the isotherms follow the as L1 type according to Giles classification. The magnitude of the adsorption density of guar gum onto the above minerals may be arranged in the following sequence: talc > graphite > mica The effect of particle size on the adsorption density of guar gum onto these minerals has indicated that higher adsorption takes place in the coarser size fraction, consequent to an increase in the surface face-to-edge ratio. In the case of the talc and mica samples pretreated with EDTA and the leached graphite sample, a decrease in the adsorption density of guar gum is observed, due to a reduction in the metallic adsorption sites. The adsorption densities of guar gum increase with decrease in sample weight for all the three minerals. Electrokinetic measurements have indicated that the isoelectric points (iep) of these minerals lie between pH 2-3, Addition of guar gum decreases the negative electrophoretic mobility values in proportion to the guar gum concentration without any observable shift in the iep values, resembling the influence of an indifferent electrolyte. The flotation recovery is diminished in the presence of guar gum for all the three minerals, The magnitude of depression follows the same sequence as observed in the adsorption studies. The floatability of EDTA treated talc and mica samples as well as the leached graphite sample is enhanced, complementing the adsorption data, Possible mechanisms of interaction between the hydrophobic minerals and guar gum are discussed.