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Journal of Physical Chemistry. B

Stanislav Anatolievich Pshenichnyuk, Alberto Modelli, Eleonora F Lazneva, Alexei S Komolov
This study is aimed to point out the important role played by resonance electron attachment in reductive dehalogenation, in particular in phytoremediation of organic pollutants under conditions of excess negative charge. To model enzymatic reactions occurring in reductive conditions, low-energy electron capture by the halogenated herbicides atrazine and bromoxynil was studied in vacuo using electron transmission spectroscopy. A variety of decay channels of the temporary molecular negative ions was discovered by means of dissociative electron attachment spectroscopy...
November 4, 2016: Journal of Physical Chemistry. B
Malgorzata Jasiurkowska-Delaporte, Simone Napolitano, Jan Leys, Ewa Juszyńska-Gałązka, Michael Wübbenhorst, Maria Massalska-Arodź
The molecular dynamics of butyloxybenzylidine octylaniline (BBOA, abbreviated also as 4O.8) was studied by broadband dielectric spectroscopy (BDS) for samples that were exposed to various thermal treatments. Phase transitions between liquid crystalline phases (N, SmA, SmBhex and SmBCr) were evidenced by abrupt changes in the temperature dependence of the dielectric permittivity spectra and dielectric relaxation times. A particularly complex dynamic behaviour was revealed for the highly ordered SmBCr phase that showed clear evidence for cooperative dynamics of a glass forming liquid as manifested by a Vogel-Fulcher-Tammann (VFT) type temperature dependence of its structural relaxation time τ(T)...
November 3, 2016: Journal of Physical Chemistry. B
Alexander S Côté, Alastair N Cormack, Antonio Tilocca
Understanding how calcium interacts with silica sources and influences their polycondensation in aqueous solutions is of central importance for the development of more effective biomaterials by sol-gel approaches. For this purpose, the atomic-scale evolutions of a calcium-containing precursor solution corresponding to a typical sol-gel bioactive glass and of a corresponding Ca-free solution were compared using reactive molecular dynamics simulations. The simulations highlight a significantly faster rate of condensation when calcium is present in the initial solution, resulting in the formation of large and ramified silica clusters within 5 ns, which are absent in the Ca-free system...
November 3, 2016: Journal of Physical Chemistry. B
Vance W Jaeger, Jim Pfaendtner
Ionic liquid (IL) containing solvents can change the structure, dynamics, function, and stability of proteins. In order to investigate the mechanisms by which ILs induce structural changes in a large multi-domain protein, we study the interactions of human serum albumin (HSA) with two different ILs, 1-butyl-3-methylimidazolium tetrafluoroborate and choline dihydrogenphosphate. Root mean square deviation and fluctuation calculations indicate that high concentrations of ILs in mixtures with water lead to protein structures that remain close to their crystallographic structures on timescales of hundreds of nanoseconds...
November 3, 2016: Journal of Physical Chemistry. B
Tatyana Vladimirovna Mikhailova, Valentina A Mikhailova, Anatoly Ivanovich Ivanov
Manifestation of the dynamic solvent effect on charge recombination kinetics of photoexcited donor-acceptor complexes in polar solvents has been investigated within the framework of the multichannel stochastic model. The model takes into account the reorganization of both the solvent and a number of the intramolecular high-frequency vibration modes as well as their relaxation. The non-Markovian solvent dynamics are described in the terms of two relaxation modes. The similarities and differences inherent to ultrafast charge transfer reactions occurring in the nonequilibrium and thermal regimes have been identified...
November 3, 2016: Journal of Physical Chemistry. B
Jan Domanski, George Hedger, Robert B Best, Phillip James Stansfeld, Mark S P Sansom
Potential of mean force (PMF) calculations are used to characterize the free energy landscape of protein-lipid and protein-protein association within membranes. Coarse-grained simulations allow binding free energies to be determined with reasonable statistical error. This accuracy relies on defining a good collective variable describing the binding and unbinding transition, and upon criteria for assessing the convergence of the simulation toward representative equilibrium sampling. As examples, we calculate protein-lipid binding PMFs for ANT/cardiolipin and Kir2...
November 3, 2016: Journal of Physical Chemistry. B
Daniel John Saltzberg, Howard B Broughton, Riccardo Pellarin, Michael J Chalmers, Alfonso Espada, Jeffrey A Dodge, Bruce D Pascal, Patrick R Griffin, Christine Humblet, Andrej Sali
Characterization of interactions between proteins and other molecules is crucial for understanding the mechanisms of action of biological systems and, thus, drug discovery. An increasingly useful approach to mapping these interactions is measurement of hydrogen/deuterium exchange (HDX) using mass spectrometry (HDX-MS), which measures the time-resolved deuterium incorporation of peptides obtained by enzymatic digestion of the protein. Comparison of exchange rates between apo- and ligand-bound conditions results in a mapping of the differential HDX (ΔHDX) of the ligand...
November 3, 2016: Journal of Physical Chemistry. B
Hao Jiang, Othonas A Moultos, Ioannis George Economou, Athanassios Z Panagiotopoulos
A polarizable intermolecular potential model with short-range directional hydrogen bonding interactions was developed for water. The model has a rigid geometry with bond lengths and angle set to the experimental gas-phase values. Dispersion interactions are represented by the Buckingham potential assigned to the oxygen atom, while electrostatic interactions are modeled by Gaussian charges. Polarization is handled by a Drude oscillator site, using a negative Gaussian charge attached to the oxygen atom by a harmonic spring...
November 3, 2016: Journal of Physical Chemistry. B
Sukanya Sasmal, Nadine Schwierz, Teresa Head-Gordon
In this work we characterize the nucleation and elongation mechanisms of the "diseased" polymorph of the amyloid-β 40 fibril by using an off-lattice coarse-grained (CG) protein model. After determining the nucleation size and subsequent stable protofibrillar structure from the CG model, validated with all-atom simulations, we consider the "lock and dock" and "activated monomer" fibril elongation mechanisms for the protofibril by the statistical additions of a monomer drawn from four different ensembles of the free amyloid-β 40 peptide to grow the fibril...
November 2, 2016: Journal of Physical Chemistry. B
Anna G Baldwin, Yuan Yang, Nicholas J Bridges, Jenifer Claire Braley
Diffusion nuclear magnetic resonance (NMR) spectroscopy was used to find the inter-aggregate interactions and sizes of tributyl phosphate (TBP) aggregates containing varying concentrations of uranium or zirconium and HNO3 in an n-dodecane diluent. The average diffusion coefficients of TBP species were measured using a pulsed-field gradient stimulated echo experiment with a longitudinal eddy-current delay (STE-LED). Inter-aggregate interactions were determined by measuring the diffusion coefficient of TBP in a sample after a series of dilutions with n-dodecane...
November 2, 2016: Journal of Physical Chemistry. B
Nan Yan, Yutian Zhu, Wei Jiang
The self-assembly of AB-type diblock copolymers confined in a three-dimensional (3D) soft nano-droplet is investigated by the combination of Monte Carlo simulation and experiment. The influences of two critical factors, i.e. confinement degree of the imposed confinement space and the interfacial interaction between each individual block and boundary interface, on the 3D soft confined self-assembly are examined systematically. The simulation results reveal that block copolymer chains become more and more folded as the confinement degree (It can be monitored by the ratio of D/L, where L is the length of polymer chain and D is the reduced diameter of the final polymeric particle...
November 2, 2016: Journal of Physical Chemistry. B
Sharmistha Dutta Choudhury, Haridas Pal
The water-assisted tautomerism of Lumichrome (LC) in binary aqueous-organic solvent mixtures exhibits intriguing spectroscopic features. An especially striking and novel observation is the occurrence of an induction period or lagtime for the evolution of the isoalloxazine form of LC, from the excited alloxazine form. It is inferred that the observed lagtime provides an overview of the changing H-bond network of the surrounding water molecules, at various compositions of the mixed solvent systems. The unique spectral changes for the water-assisted tautomerization of LC, along with the observed lagtimes, can offer exciting prospects for the use of LC as a promising site-specific probe, to examine complex aqueous microenvironments and active biological systems...
November 2, 2016: Journal of Physical Chemistry. B
Mohd Afzal, Saptarshi Ghosh, Sinjan Das, Nitin Chattopadhyay
The photophysics of phenosafranin (PSF), a member of the photosensitizer phenazinium family, has been explored in nonionic Triton X-165 (TX-165) micelle, calf thymus DNA (ctDNA), and a composite environment consisting of both micelle and DNA, using diverse spectroscopic techniques of both steady-state and time-resolved natures, to divulge the binding interactions of the probe with different hosts. The vivid experimental results demonstrate that PSF binds with both micelle and DNA; however, the binding affinity of the probe is much higher toward the DNA...
November 1, 2016: Journal of Physical Chemistry. B
Sunil Kumar Arya, Satwinder Singh Danewalia, Manju Arora, Kulvir Singh
In the present study, the effect of variable vanadium oxidation states on structural, optical and dielectric properties of vanadium oxide containing lithium borate glasses has been investigated. The electron paramagnetic resonance study indicates that vanadium in these glasses is in mostly in V4+ state having tetragonal symmetry. As V2O5 increases in glass composition, the tetragonality also increases in the cost of octahedral symmetry. The photoluminescence (PL) spectra of these glasses are dominated by zinc oxide transition; whereas, the peaks pertaining to vanadyl group are not visible in the PL spectra...
November 1, 2016: Journal of Physical Chemistry. B
Jing Huang, Sirish Kaushik Lakkaraju, Andrew Coop, Alexander D MacKerell
G-protein coupled receptors (GPCRs), including the μ-opioid receptor, interact with G-proteins and other proteins via their intracellular face as required for signal transduction. However, characterization of the structure of the intracellular face of GPCRs is complicated by the experimental methods used for structural characterization. In the present study we undertook a series of long-time molecular dynamics (MD) simulations, ranging from 1 to 5 μs, on the μ-opioid receptor in both the dimeric and monomeric states...
November 1, 2016: Journal of Physical Chemistry. B
Siri Camee van Keulen, Eleonora Gianti, Vincenzo Carnevale, Michael L Klein, Ursula Rothlisberger, Lucie Delemotte
Hv1 are ubiquitous highly selective voltage-gated proton channels involved in male fertility, immunology and the invasiveness of certain forms of breast cancer. The mechanism of proton extrusion in Hv1 is not yet understood while it constitutes the first step towards the design of high-affinity drugs aimed at this important pharmacological target. In this contribution, we explore the details of the mechanism via an integrative approach, using classical and QM/MM molecular dynamics simulations of a monomeric hHv1 model...
November 1, 2016: Journal of Physical Chemistry. B
Udita Brahmachari, Bridgette A Barry
In photosynthesis, the light-driven oxidation of water is a sustainable process, which converts solar to chemical energy and produces protons and oxygen. To enable biomimetic strategies, the mechanism of photosynthetic oxygen evolution must be elucidated. Here, we provide information concerning a critical step in the oxygen-evolving, or S-state, cycle. During this S3-to-S0 transition, oxygen is produced, and substrate water binds to the manganese-calcium catalytic site. Our spectroscopic and H2(18)O labeling experiments show that this S3-to-S0 step is associated with the protonation of an internal water cluster in a hydrogen-bonding network, which contains calcium...
November 1, 2016: Journal of Physical Chemistry. B
Dariusz Kluczyk, Arkadiusz Paweł Matwijczuk, Andrzej Górecki, Monika M Karpińska, Mariusz Szymanek, Andrzej Niewiadomy, Mariusz Gagos
The article presents the results of spectroscopic studies of two compounds from the 1,3,4-thiadiazole group, i.e. 4-(5-methyl-1,3,4-thiadiazole-2-yl)benzene-1,3-diol (C1) and 4-(5-heptyl-1,3,4-thiadiazole-2-yl)benzene-1,3-diol (C7), present at different molar concentrations in DPPC liposome systems. In the case of both investigated compounds, fluorescence measurements revealed the presence of several emission bands, whose appearance is related to the molecular organisation induced by changes in the phase transition in DPPC...
October 31, 2016: Journal of Physical Chemistry. B
Tadashi Ando, Isseki Yu, Michael Feig, Yuji Sugita
The cytoplasm of a cell is crowded with many different kinds of macromolecules. The macromolecular crowding affects the thermodynamics and kinetics of biological reactions in a living cell, such as protein folding, association, and diffusion. Theoretical and simulation studies using simplified models focus on the essential features of the crowding effects and provide a basis for analyzing experimental data. In most of the previous studies on the crowding effects, a uniform crowder size is assumed, which is in contrast to the inhomogeneous size distribution of macromolecules in a living cell...
October 31, 2016: Journal of Physical Chemistry. B
Gang Wang, Congdi Shang, Li Wang, Haonan Peng, Shiwei Yin, Yu Fang
A pyrenyl unit (Py) was chemically connected to a perylene bisimide moiety (PBI) via a long and flexible linker, 4,7,10-trioxa-1,13-tridecanediamine (TOA), resulting in a fluorescent dyad, PBI-TOA-Py. UV-Vis absorption and fluorescence studies revealed that the two fluorescent units of PBI-TOA-Py behave independently. However, efficient Förster Resonance Energy Transfer (FRET) from the Py unit to the PBI moiety in solution state was also observed. Temperature and solvent effect studies demonstrated that the energy transfer efficiency is highly dependent upon solution temperature and solvent nature...
October 31, 2016: Journal of Physical Chemistry. B
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