Hydration dynamics of protein molecules in aqueous solution: Unity among diversity

Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account for the large amplitude of the fast component. Solvation dynamics experiments and also computer simulation studies, on the other hand, repeatedly observed the presence of a non-negligible slow component. Here we show, by considering three well-known proteins (lysozyme, myoglobin and adelynate kinase), that the fast component arises partly from the response of those water molecules that are hydrogen bonded with the backbone oxygen (BBO) atoms. These are structurally and energetically less stable than those with the side chain oxygen (SCO) atoms. In addition, the electrostatic interaction energy distribution (EIED) of individual water molecules (hydrogen bonded to SCO) with side chain oxygen atoms shows a surprising two peak character with the lower energy peak almost coincident with the energy distribution of water hydrogen bonded to backbone oxygen atoms (BBO). This two peak contribution appears to be quite general as we find it for lysozyme, myoglobin and adenylate kinase (ADK). The sharp peak of EIED at small energy (at less than 2 k(B)T) for the BBO atoms, together with the first peak of EIED of SCO and the HBRs on the protein surface, explain why a large fraction (similar to 80%) of water in the protein hydration layer remains almost as mobile as bulk water Significant slowness arises only from the hydrogen bonds that populate the second peak of EIED at larger energy (at about 4 k(B)T). Thus, if we consider hydrogen bond interaction alone, only 15-20% of water molecules in the protein hydration layer can exhibit slow dynamics, resulting in an average relaxation time of about 5-10 ps. The latter estimate assumes a time constant of 20-100 ps for the slow component. Interestingly, relaxation of water molecules hydrogen bonded to back bone oxygen exhibit an initial component faster than the bulk, suggesting that hydrogen bonding of these water molecules remains frustrated. This explanation of the heterogeneous and non-exponential dynamics of water in the hydration layer is quantitatively consistent with all the available experimental results, and provides unification among diverse features.

Synthesis and characterization of cobalt(II), nickel(II), copper(II) and zinc(II) complexes of 2-nitrobenzoic acid with methyl carbazate as ancillary ligand. Crystal structure of the copper(II) complex

Divalent metal complexes of general formula M(2-nb)(2)(mc)(2)].2(2-nbH), where M = Co(II), Ni(II), Cu(II) or Zn(II), 2-nbH = 2-nitrobenzoic acid and mc = methyl carbazate (NH2NHCOOCH3), have been prepared and characterized by physicochemical and spectroscopic methods. Single-crystal X-ray study of the Cu(II) complex revealed that the molecule is centrosymmetric, with two N,O-chelating mc ligands in equatorial positions and a pair of monodentate 2-nb anions in the axial positions. The lattice 2-nbH molecules help to establish the packing of monomers through hydrogen-bonding interactions. Thermal stability and reactivity of the complexes were studied by TG-DTA. Emission studies show that these complexes are fluorescent.

Towards a broadband chirped pulse Fourier transform microwave spectrometer

This article gives a brief review of microwave spectroscopy and the experimental techniques used for obtaining microwave spectrum of molecules and complexes since 1950s. It presents a brief summary of the pulsed nozzle Fourier transform microwave (PNFTMW) spectrometer, fabricated in our laboratory, and discusses some of the important results obtained using the spectrometer. The most significant among the results from this spectrometer is the direct structural determination of weakly bound complexes involving H2O/H2S. These have challenged the conventional wisdom on hydrogen bonding leading us to propose a modern definition for the same through IUPAC. The limitations of the PNFTMW spectrometer and the need for the new chirped pulse Fourier transform microwave spectrometer are discussed as well. Moreover, preliminary results from our laboratory on generating a 1 A mu s chirped pulse of 1 GHz bandwidth are given.

Polymorphic Anhydrous Cocrystals of Gallic Acid and Acetamide from Methanol: Pointers toward a Stable Cocrystal Form

Polymorphic anhydrous cocrystals generated from a methanolic solution of gallic acid monohydrate and acetamide are shown to convert to the stable form II on complete drying, and the pathway to the stable form is explained on the basis of the variability in the hydrogen bonding patterns followed by theoretical calculations.

Stabilization of O-Mn-O clusters (Mn-5) in three dimensionally extended MOF structures: synthesis, structure and properties

Four new three-dimensional Mn2+ ion-containing compounds have been prepared by employing a hydrothermal reaction between Mn(CH3COO)(2)center dot 4H(2)O, sulfodibenzoic acid (H(2)SDBA), imidazole, alkali hydroxide and water at 220 degrees C for 1 day. The compounds have Mn-5 (1-4) clusters connected by SDBA, forming the three-dimensional structure. A time and temperature dependent study on the synthesis mixture revealed the formation of a one-dimensional compound, Mn(SDBA)(H2O)(2), at lower temperatures (T <= 180 degrees C). The stabilization of the fcu related topology in the compounds is noteworthy. Magnetic studies indicate strong anti-ferromagnetic interactions between the Mn2+ ions within the clusters in the temperature range 75-300 K. The rare participation of a sulfonyl group in the bonding is important and can pave way for the design of new structures.

A Rhodanine Derivative CCR-11 Inhibits Bacterial Proliferation by Inhibiting the Assembly and GTPase Activity of FtsZ

A perturbation of FtsZ assembly dynamics has been shown to inhibit bacterial cytokinesis. In this study, the antibacterial activity of 151 rhodanine compounds was assayed using Bacillus subtilis cells. Of 151 compounds, eight strongly inhibited bacterial proliferation at 2 mu M. Subsequently, we used the elongation of B. subtilis cells as a secondary screen to identify potential FtsZ-targeted antibacterial agents. We found that three compounds significantly increased bacterial cell length. One of the three compounds, namely, CCR-11 (E)-2-thioxo-5-({3-(trifluoromethyl)phenyl]furan-2-yl}methylene) thiazolidin-4-one], inhibited the assembly and GTPase activity of FtsZ in vitro. CCR-11 bound to FtsZ with a dissociation constant of 1.5 +/- 0.3 mu M. A docking analysis indicated that CCR-11 may bind to FtsZ in a cavity adjacent to the T7 loop and that short halogen oxygen, H-bonding, and hydrophobic interactions might be important for the binding of CCR-11 with FtsZ. CCR-11 inhibited the proliferation of B. subtilis cells with a half-maximal inhibitory concentration (IC50) of 1.2 +/- 0.2 mu M and a minimal inhibitory concentration of 3 mu M. It also potently inhibited proliferation of Mycobacterium smegmatis cells. Further, CCR-11 perturbed Z-ring formation in B. subtilis cells; however, it neither visibly affected nucleoid segregation nor altered the membrane integrity of the cells. CCR-11 inhibited HeLa cell proliferation with an IC50 value of 18.1 +/- 0.2,mu M (similar to 15 x IC50 of B. subtilis cell proliferation). The results suggested that CCR-11 inhibits bacterial cytokinesis by inhibiting FtsZ assembly, and it can be used as a lead molecule to develop FtsZ-targeted antibacterial agents.

Self-Assembly and Catalytic Activity of Metal Nanoparticles Immobilized in Polymer Membrane Prepared via Layer-by-Layer Approach

Densely packed nanoparticles distributed in a stable and robust thin film is a highly preferred system for utilizing the various applications of nanoparticles. Here, we report covalent bond mediated layer-by-layer (LbL) self-assembled thin films of nanoparticles embedded in polymer membrane. Polymer with complementary functional group is utilized for fabrication of thin film via covalent bonding. UV-visible spectroscopy, atomic force microscopy (AFM) and scanning electron microscopy (SEM) were used to monitor the growth of LbL thin film. Subsequently, the composite thin film is used for catalysis of an organic electron transfer reaction of p-nitrophenol to p-aminophenol by sodium borohydride. The catalytic activity of these composite films is assayed multiple times, proving its applicability as a catalyst. The kinetic data obtained by monitoring reduction of p-nitrophenol suggest that the reaction rates are directly related to the sizes of the nanoparticle and porosity of the membrane.

Structural characterization of backbone-expanded helices in hybrid peptides: (αγ) n and (αβ) n sequences with unconstrained β and γ homologues of L-Val

Learning your αβγ's: The diversity of hydrogen-bonding patterns in backbone-expanded hybrid helices is shown by crystal-structure determination of several oligomeric peptides (see scheme; C=gray; H=white; O=red; N=blue). C 12 helices were observed in the αγ peptide series for n=2-8. In comparison, the αα peptide and αβ peptide sequences show C 10 and mixed C 14/C 15 helices, respectively. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First principles calculations of H-storage in sorption materials

A review of various contributions of first principles calculations in the area of hydrogen storage, particularly for the carbon-based sorption materials, is presented. Carbon-based sorption materials are considered as promising hydrogen storage media due to their light weight and large surface area. Depending upon the hybridization state of carbon, these materials can bind the hydrogen via various mechanisms, including physisorption, Kubas and chemical bonding. While attractive binding energy range of Kubas bonding has led to design of several promising storage systems, in reality the experiments remain very few due to materials design challenges that are yet to be overcome. Finally, we will discuss the spillover process, which deals with the catalytic chemisorption of hydrogen, and arguably is the most promising approach for reversibly storing hydrogen under ambient conditions.

Substrate temperature influenced physical properties of silicon MOS devices with TiO2 gate dielectric

DC reactive magnetron sputtering technique was employed for deposition of titanium dioxide (TiO2) films. The films were formed on Corning glass and p-Si (100) substrates by sputtering of titanium target in an oxygen partial pressure of 6x10-2 Pa and at different substrate temperatures in the range 303 673 K. The films formed at 303 K were X-ray amorphous whereas those deposited at substrate temperatures?=?473 K were transformed into polycrystalline nature with anatase phase of TiO2. Fourier transform infrared spectroscopic studies confirmed the presence of characteristic bonding configuration of TiO2. The surface morphology of the films was significantly influenced by the substrate temperature. MOS capacitor with Al/TiO2/p-Si sandwich structure was fabricated and performed currentvoltage and capacitancevoltage characteristics. At an applied gate voltage of 1.5 V, the leakage current density of the device decreased from 1.8?x?10-6 to 5.4?x?10-8 A/cm2 with the increase of substrate temperature from 303 to 673 K. The electrical conduction in the MOS structure was more predominant with Schottky emission and Fowler-Nordheim conduction. The dielectric constant (at 1 MHz) of the films increased from 6 to 20 with increase of substrate temperature. The optical band gap of the films increased from 3.50 to 3.56 eV and refractive index from 2.20 to 2.37 with the increase of substrate temperature from 303 to 673 K. Copyright (c) 2012 John Wiley & Sons, Ltd.

Non-destructive evaluation of porosity and its effect on mechanical properties of carbon fiber reinforced polymer composite materials

Structural adhesive bonding is widely used to execute assemblies in automobile and aerospace structures. The quality and reliability of these bonded joints must be ensured during service. In this context non destructive evaluation of these bonded structures play an important role. Evaluation of adhesively bonded composite single lap shear joints has been attempted through experimental approach. Series of tests, non-destructive as well as destructive were performed on different sets of carbon fiber reinforced polymer (CFRP) composite lap joint specimens with varied bond quality. Details of the experimental investigations carried out and the outcome are presented in this paper.

Anticancer Activity of Hydrogen-Bond-Stabilized Half-Sandwich RuII Complexes with Heterocycles

Neutral half-sandwich organometallic ruthenium(II) complexes of the type (?6-cymene)RuCl2(L)] (H1H10), where L represents a heterocyclic ligand, have been synthesized and characterized spectroscopically. The structures of five complexes were also established by single-crystal X-ray diffraction confirming a piano-stool geometry with ?6 coordination of the arene ligand. Hydrogen bonding between the N?H group of the heterocycle and a chlorine atom attached to Ru stabilizes the metalligand interaction. Complexes coordinated to a mercaptobenzothiazole framework (H1) or mercaptobenzoxazole (H6) showed high cytotoxicity against several cancer cells but not against normal cells. In vitro studies have shown that the inhibition of cancer cell growth involves primarily G1-phase arrest as well as the generation of reactive oxygen species (ROS). The complexes are found to bind DNA in a non-intercalative fashion and cause unwinding of plasmid DNA in a cell-free medium. Surprisingly, the cytotoxic complexes H1 and H6 differ in their interaction with DNA, as observed by biophysical studies, they either cause a biphasic melting of the DNA or the inhibition of topoisomerase IIa activity, respectively. Substitution of the aromatic ring of the heterocycle or adding a second hydrogen-bond donor on the heterocycle reduces the cytotoxicity.

Molecular probe dynamics reveals suppression of ice-like regions in strongly confined supercooled water

The structure of the hydrogen bond network is a key element for understanding water's thermodynamic and kinetic anomalies. While ambient water is strongly believed to be a uniform, continuous hydrogen-bonded liquid, there is growing consensus that supercooled water is better described in terms of distinct domains with either a low-density ice-like structure or a high-density disordered one. We evidenced two distinct rotational mobilities of probe molecules in interstitial supercooled water of polycrystalline ice Banerjee D, et al. (2009) ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water. Proc Natl Acad Sci USA 106: 11448-11453]. Here we show that, by increasing the confinement of interstitial water, the mobility of probe molecules, surprisingly, increases. We argue that loose confinement allows the presence of ice-like regions in supercooled water, whereas a tighter confinement yields the suppression of this ordered fraction and leads to higher fluidity. Compelling evidence of the presence of ice-like regions is provided by the probe orientational entropy barrier which is set, through hydrogen bonding, by the configuration of the surrounding water molecules and yields a direct measure of the configurational entropy of the same. We find that, under loose confinement of supercooled water, the entropy barrier surmounted by the slower probe fraction exceeds that of equilibrium water by the melting entropy of ice, whereas no increase of the barrier is observed under stronger confinement. The lower limit of metastability of supercooled water is discussed.

Reactions of Titanocene Bis(trimethylsilyl)acetylene Complexes with Carbodiimides: An Experimental and Theoretical Study of Complexation versus C-N Bond Activation

The reaction of the low valent metallocene(II) sources Cp'Ti-2(eta(2)-Me3SiC2SiMe3) (Cp' = eta(5)-cyclopentadienyl, 1a or eta(5)-pentamethylcyclopentadienyl, 1b) with different carbodiimide substrates RN=C=NR' 2-R-R' (R = t-Bu; R' = Et; R = R' = i-Pr; t-Bu; SiMe3; 2,4,6-Me-C6H2 and 2,6-i-Pr-C6H3) was investigated to explore the frontiers of ring strained, unusual four-membered heterometallacycles 5-R. The product complexes show dismantlement, isomerization, or C-C coupling of the applied carbodiimide substrates, respectively, to form unusual mono-, di-, and tetranuclear titanium(III) complexes. A detailed theoretical study revealed that the formation of the unusual complexes can be attributed to the biradicaloid nature of the unusual four-membered heterometallacycles 5-R, which presents an intriguing situation of M-C bonding. The combined experimental and theoretical study highlights the delicate interplay of electronic and steric effects in the stabilization of strained four-membered heterometallacycles, accounting for the isolation of the obtained complexes.