Antimicrobial effects of vanillin-based pyridyl-benzylidene-5-fluoroindolins

In this study, the antimicrobial effect and DNA gyrase inhibitor potential of vanillin-based pyridyl–substituted fluoro-indolines were evaluated. These compounds are synthesized and established through green-chemistry approaches. The inhibition effect on both DNA gyrase A and B was evaluated in silico and in vitro. Agar well diffusion method–based antimicrobial activity against Gram-ve Pseudomonas aeruginosa (MTCC 424) and Escherichia coli (MTCC 443), Gram+ve Streptococcus pyogenes (MTCC 442) and Staphylococcus aureus (MTCC 96), and a clinical isolate of Candida albicans (Fungi) was evaluated. The cytotoxicity of the compounds was assessed over macrophages using the MTT assay. In the results, the target compounds exhibited a broad-spectrum antimicrobial activity against both bacterial types and fungal.     

Nonlinearity management and diffraction management for the stabilization of two-dimensional spatial solitons

The nonlinear Schrödinger equation which governs the dynamics of two-dimensional spatial solitons in Kerr media with periodically varying diffraction and nonlinearity has been analyzed in this paper using variational approach and numerical studies. Analytical expressions for soliton parameters have been derived using variational analysis. Variational equations and partial differential equation have been simulated numerically. Analytical and numerical studies have shown that nonlinearity management and diffraction management stabilize the pulse against decay or collapse providing undisturbed propagation even for larger energies of the incident beam.     

Ab initio investigation of benzene clusters: molecular tailoring approach

An exhaustive study on the clusters of benzene (Bz)(n), n = 2-8, at MP2/6-31++G(??) level of theory is reported. The relative strengths of CH-π and π-π interactions in these aggregates are examined, which eventually govern the pattern of cluster formation. A linear scaling method, viz., molecular tailoring approach (MTA), is efficiently employed for studying the energetics and growth patterns of benzene clusters consisting up to eight benzene (Bz) units. Accuracy of MTA-based calculations is appraised by performing the corresponding standard calculations wherever possible, i.e., up to tetramers. For benzene tetramers, the error introduced in energy is of the order of 0.1 mH (～0.06 kcal/mol). Although for higher clusters the error may build up, further corrections based on many-body interaction energy analysis substantially reduce the error in the MTA-estimate. This is demonstrated for a prototypical case of benzene hexamer. A systematic way of building up a cluster of n monomers (n-mer) which employs molecular electrostatic potential of an (n-1)-mer is illustrated. The trends obtained using MTA method are essentially identical to those of the standard methods in terms of structure and energy. In summary, this study clearly brings out the possibility of effecting such large calculations, which are not possible conventionally, by the use of MTA without a significant loss of accuracy.     

Spectroscopically determined electronegativity values for heavy elements

A new scale of electronegativity based on X-ray spectroscopic data was earlier presented by Mande and others for the elements₃Li to₅₄Xe. The present paper reports an extension of this scale carried out for most of the heavier elements lying between₅₅Cs and₉₂U. The present approach is based on the physical interpretation of electronegativity of an atom as the attractive electrostatic force it exerts at a distance equal to its covalent radius. To estimate this force, experimental spectroscopic data have been employed. The merits of such an approach have been pointed out recently by Mullay and may be of interest in the context of the intimate relation found between electronegativity and superconducting transition temperature.     

A theoretical study on structural, spectroscopic and energetic properties of acetamide clusters [CH3CONH2] (n=1-15)

Insights into the formation of hydrogen bonded clusters are of outstanding importance and quantum chemical calculations play a pivotal role in achieving this understanding. Structure and energetic comparison of linear, circular and standard forms of (acetamide)(n) clusters (n = 1-15) at the B3LYP/D95** level of theory including empirical dispersion correction reveals significant cooperativity of hydrogen bonding and size dependent structural preference. A substantial amount of impact of BSSE is observed in these calculations as the cluster size increases irrespective of the kind of arrangement. The interaction energy per monomer increases from dimer to 15mer by 90% in the case of the circular arrangement, by 76% in the case of the linear arrangement and by 34% in the case of the standard arrangement respectively. The cooperativity in hydrogen bonding is also manifested by a regular decrease in average OH and C-N bond distances, while average C=O and N-H bond lengths increase with increasing cluster size. Atoms-In-Molecules (AIM) analysis is used to characterize the nature of hydrogen bonding between the acetamide molecules in the cluster on the basis of electron density (ρ) values obtained at the bond critical point. An analysis of N-H bond stretching frequencies as a function of the cluster size shows a marked red shift as the cluster size increases from 1 to 15.     

Characterization of high intensity focused ultrasound transducers using acoustic streaming

A new approach for characterizing high intensity focused ultrasound (HIFU) transducers is presented. The technique is based upon the acoustic streaming field generated by absorption of the HIFU beam in a liquid medium. The streaming field is quantified using digital particle image velocimetry, and a numerical algorithm is employed to compute the acoustic intensity field giving rise to the observed streaming field. The method as presented here is applicable to moderate intensity regimes, above the intensities which may be damaging to conventional hydrophones, but below the levels where nonlinear propagation effects are appreciable. Intensity fields and acoustic powers predicted using the streaming method were found to agree within 10% with measurements obtained using hydrophones and radiation force balances. Besides acoustic intensity fields, the streaming technique may be used to determine other important HIFU parameters, such as beam tilt angle or absorption of the propagation medium.     

Crystallization and thermal characterization of calcium hydrogen phosphate dihydrate crystals

Calcium hydrogen phosphate dihydrate (CHPD) is found quite frequently in urinary calculi (stones). The CHPD crystals were grown by the single diffusion gel growth technique in sodium metasilicate gel. The crystals were found to be having platelet and broad needle type morphologies. The crystals were analyzed by FTIR spectroscopy. The thermal properties were studied by employing the thermogravimetric analysis (TG). Various kinetic and thermodynamic parameters for dehydration were estimated from the TG curve. The selected platelet was studied by scanning electron microscope (SEM) for the growth morphologies indicating that the crystals grew in the form of leaflets having prominent (010) faces. This was in agreement with earlier reported studies.     

Eu(III) and Tb(III) luminescence sensitized by thiophenyl-derivatized nitrobenzoato antennas

Thiophenyl-derivatized nitrobenzoic acid ligands have been evaluated as possible sensitizers of Eu(III) and Tb(III) luminescence. The resulting solution and solid-state species were isolated and characterized by luminescence spectroscopy and X-ray crystallography. The Eu(III) complex with 2-nitro-3-thiophen-3-yl-benzoic acid, 1, crystallizes in the monoclinic space group C2/c with a = 28.569(3) A, b = 17.7726(18) A, c = 17.7073(18) A, beta= 126.849(2) degrees, and V = 7194.6(13) A3. The Tb(III) complex with this ligand, 2, is isostructural, and its cell parameters are a = 29.755(6) A, b = 18.123(4) A, c = 19.519(4) A, beta= 130.35(3) degrees, and V = 8021(3) A3. Eu(III) crystallizes with 3-nitro-2-thiophen-3-yl-benzoic acid as a triclinic complex, 3, in the space group P1 with a = 11.045(2) A, b = 12.547(3) A, c = 15.500(3) A, alpha = 109.06(3)degrees, beta = 94.79(3) degrees, gamma = 107.72(3) degrees. and V = 1893.5(7) A3. With the ligand 5-nitro-2-thiophen-3-yl-benzoic acid, Eu(III) yields another molecular compound, 4, triclinic P1, with a = 10.649(2) A, b = 14.009(3) A, c = 15.205(3) A, alpha= 112.15(3) degrees, beta = 100.25(3) degrees, gamma = 106.96(3) degrees, and V = 1900.5(7) A3. All compounds dissolve in water and methanol, and the methanolic solutions are luminescent. The solution species have a metal ion-to-ligand ratio of 1:1. The quantum yields have been determined to be in the range of 0.9-3.1% for Eu(III) and 4.7-9.8% for Tb(III). The highest values of these correspond to the most intense luminescence reported for Ln(III) solutions with this type of sensitizer. The lifetimes of luminescence are in the range of 248.3-338.9 micros for Eu(III) and 208.6-724.9 micros for Tb(III). The stability constants are in the range of log 11 = 2.73-4.30 for Eu(III) and 3.34-4.18 for Tb(III) and, along with the energy migration pathways, are responsible for the reported efficiency of sensitization.     

Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations

Molecular channel exploration perseveres to be the prominent solution for eliciting structure and accessibility of active site and other internal spaces of macromolecules. The volume and silhouette characterization of these channels provides answers for the issues of substrate access and ligand swapping between the obscured active site and the exterior of the protein. Histone deacetylases (HDACs) are metal-dependent enzymes that are involved in the cell growth, cell cycle regulation, and progression, and their deregulations have been linked with different types of cancers. Hence HDACs, especially the class I family, are widely recognized as the important cancer targets, and the characterizations of their structures and functions have been of special interest in cancer drug discovery. The class I HDACs are known to possess two different protein channels, an 11 ? and a 14 ? (named channels A and B1, respectively), of which the former is a ligand or substrate occupying tunnel that leads to the buried active site zinc ion and the latter is speculated to be involved in product release. In this work, we have carried out random acceleration molecular dynamics (RAMD) simulations coupled with the classical molecular dynamics to explore the release of the ligand, N-(2-aminophenyl) benzamide (LLX) from the active sites of the recently solved X-ray crystal structure of HDAC2 and the computationally modeled HDAC1 proteins. The RAMD simulations identified significant structural and dynamic features of the HDAC channels, especially the key 'gate-keeping' amino acid residues that control these channels and the ligand release events. Further, this study identified a novel and unique channel B2, a subchannel from channel B1, in the HDAC1 protein structure. The roles of water molecules in the LLX release from the HDAC1 and HDAC2 enzymes are also discussed. Such structural and dynamic properties of the HDAC protein channels that govern the ligand escape reactions will provide further mechanistic insights into the HDAC enzymes, which, in the long run, have a potential to bring new ideas for developing more promising HDAC inhibitors as well as extend our atomic level understandings on their mechanisms of action.     

Glycine sodium nitrate

The glycine mol­ecule in the title compound, Na(NO₃)·C₂H₅NO₂, exists in the zwitterionic form. The Na atom exhibits eightfold coordination and the polyhedron may be visualized as a distorted hexagonal bipyramid. The glycine mol­ecules are linked through head-to-tail hydrogen bonds and are found `sandwiched' between the Na(NO₃) layers.