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Journal of Physical Chemistry. B

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https://www.readbyqxmd.com/read/30004696/exploiting-fluorescence-spectroscopy-to-identify-magnetic-ionic-liquids-suitable-for-the-isolation-of-oligonucleotides
#1
Kalyan Santra, Kevin D Clark, Nishith Maity, Jacob W Petrich, Jared L Anderson
Magnetic ionic liquids (MILs), which incorporate paramagnetic ions, promise to minimize manual user intervention, decrease extraction times, and facilitate rapid recovery of the analyte-enriched extraction solvent. If, however, fluorescence is employed in the downstream analysis of an analyte tagged with a fluorophore, the paramagnetic ion may quench fluorescence by introducing new nonradiative processes. Thus, it is necessary to employ a paramagnetic ion that offers a compromise between possessing a high magnetic moment and not introducing new nonradiative channels...
July 13, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30004229/testing-kinetic-identities-involving-transition-path-properties-using-single-molecule-folding-trajectories
#2
Krishna Neupane, Noel Q Hoffer, Michael T Woodside
Recent advances in single-molecule assays have allowed individual transition paths during the folding of single molecules to be observed directly. We used transition paths of DNA hairpins having different sequences, measured with high-resolution optical tweezers, to test theoretical relations between the properties of the transition paths and the folding kinetics. We showed that folding and unfolding rates were related to the average transition-path times, as expected from theory, for all hairpins studied. We also found that the probability distribution of transition path occupancies agreed with the profile of the average velocity along the transition paths for each of the hairpins, as expected theoretically...
July 13, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30003785/photoinduced-shape-changes-of-mixed-molecular-glass-particles-containing-azobenzene-based-photochromic-amorphous-molecular-materials-fixed-in-agar-gel
#3
Hideyuki Nakano, Ryota Ichikawa, Hiroyasu Ukai, Ayame Kitano
As well as single molecular glass particles of azobenzene-based photochromic amorphous molecular materials, mixed molecular glass particles were found to exhibit photoinduced shape changes, elongating their shapes to form string-like structures, and interestingly the addition of 15 mol% of photochemically inert 4,4',4"-tris[3-methylphenyl(phenyl)amino]triphenylamine enhanced the phenomenon relative to single particles of 4-[bis(4-methylphenyl)amino]azobenzene. Present mixed systems allowed to elucidate the effects of Tg and of the apparent photochromic reactivity independently by changing the mixing ratio of suitable materials...
July 13, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30001623/kinetic-trapping-of-folded-proteins-relative-to-aggregates-under-physiologically-relevant-conditions
#4
Angela Elizabeth Varela, Jonathan Frederick Lang, Yufan Wu, Matthew David Dalphin, Andrew James Stangl, Yusuke Okuno, Silvia Cavagnero
Anfinsen's thermodynamic hypothesis does not explicitly take into account the possibility of protein aggregation. Here, we introduce a cyclic-perturbation approach to prove that not only the native state but also soluble aggregates of most proteins can be highly populated under mild, physiologically relevant conditions, even at very low concentration. Surprisingly, these aggregates are not necessarily amyloid in nature, and are usually not observed in bioactive proteins due to the extremely low kinetic flux from the native state towards a region of the chemical-potential landscape encoding aggregates...
July 12, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30001131/importance-of-solvents-translational-rotational-coupling-for-translational-jump-of-a-small-hydrophobic-solute-in-supercooled-water
#5
Vikas Dubey, Nitesh Kumar, Snehasis Daschakraborty
Despite clear evidence of sudden translational jump occurrence of a solute in supercooled water, a detailed mechanism of this jump is still lacking. A previous work (Indra, S.; Daschakraborty, S. Chem. Phys. Lett. 2017, 685, 322-327) put forward a mechanism of this jump from an initial solvent cage to a final one. The proposed mechanism is astoundingly similar to that of the electron/proton transfer reaction in aqueous solution. The above study identified the spatial prearrangement (rearrangement before the jump occurrence) of cage forming water solvent molecules as the actual reaction coordinate...
July 12, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30001130/molecular-mobility-effect-on-magnetic-interactions-in-all-organic-paramagnetic-liquid-crystal-with-nitroxide-radical-as-a-hydrogen-bonding-acceptor
#6
Sho Nakagami, Takuya Akita, Daichi Kiyohara, Yoshiaki Uchida, Rui Tamura, Norikazu Nishiyama
We synthesized new chiral all-organic liquid crystalline (LC) compounds with nitroxide (NO) and hydroxy (OH) groups, which form intermolecular hydrogen bonds between the NO and OH groups. The LC compounds show hexagonal columnar phases at room temperature, which solidify as LC glasses at low temperature. The experimental magnetic susceptibility of each of the compounds in the LC and isotropic phases is larger than that theoretically estimated on the simple assumption about the amount of the spins, whereas it accords with the theoretical one in the LC glass state...
July 12, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29999329/puzzling-aqueous-solubility-of-guanine-obscured-by-the-formation-of-nanoparticles
#7
Termeh Darvishzad, Tomasz Lubera, Stefan S Kurek
Dissolution of guanine in neutral solutions was obscured by peculiar behavior of guanine, indicating an apparent dependence of solubility on the amount of solid guanine used. Here, we demonstrate that the problem is caused by formation of tiny guanine nanoparticles that tend to grow forming stable particles of ca. 800 nm size. This effect can be minimalized by using small quantities of guanine powder for dissolution. We show also that assuming a constant, independent of pH, concentration of neutral form of guanine, at 25 °C equal 25...
July 12, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29996651/a-theoretical-model-of-the-protochlorophyllide-oxidoreductase-from-a-hierarchy-of-protocols
#8
Samira Gholami, Artur Nenov, Ivan Rivalta, Marco Bocola, Abdol Khalegh Bordbar, Ulrich Schwaneberg, Mehdi D Davari, Marco Garavelli
The enzyme protochlorophyllide oxidoreductase (LPOR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), a crucial step in chlorophyll biosynthesis. Molecular understanding of the photocatalytic mechanism of LPOR is essential for harnessing light energy to mediate enzymatic reactions. The absence of X-ray crystal structure has promoted development of LPOR homology models that however lack of a catalytically competent active site and could not explain the variously reported spectroscopic evidences, including time-resolved optical spectroscopy data...
July 11, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29996049/cooling-of-pure-water-at-room-temperature-by-weak-electric-currents
#9
Iman Rad, Gerald H Pollack
Flow of electrical current through water is expected to increase water temperature. We passed low-frequency alternating electric current through distilled, deionized water using platinum electrodes and found, instead, a diminution of temperature. The diminution was observed using both an infrared camera and a spectro-radiometer, the latter allowing us to obtain spectral information. The diminished temperature persisted for at least half an hour following cessation of current flow. Diminished radiant energy implies reduced charge displacements, which in turn implies increased structural order...
July 11, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29995415/the-effect-of-imidazolium-based-ionic-liquids-on-structure-and-stability-of-stem-bromelain-concentration-and-alkyl-chain-length-effect
#10
Indrani Jha, Meena Bisht, Navin Kumar Mogha, Pannuru Venkatesu
In the present work, changes in the structure and stability of stem bromelain (BM) are observed in the presence of a set of four imidazolium-based ionic liquids (ILs) such as 1-ethyl-3-methylimidazolium chloride ([Emim][Cl]), 1-butyl-3-methylimidazolium chloride ([Bmim][Cl]), 1-hexyl-3-methylimidazolium chloride ([Hmim][Cl]) and 1-decyl-3-methylimidazolium chloride ([Dmim][Cl]) utilizing various biophysical techniques. Fluorescence spectroscopy is utilized to observe changes taking place in microenvironment around tryptophan (Trp) residues of BM and its thermal stability due to interactions with the ILs at different concentrations...
July 11, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29995414/predicting-q-speciation-in-binary-phosphate-glasses-using-statistical-mechanics
#11
Mikkel S Bødker, John C Mauro, Sushmit Goyal, Randall E Youngman, Morten M Smedskjaer
Predicting the compositional evolution of the atomic-scale structure of oxide glasses is important for developing quantitative composition-property models. In binary phosphate glasses, the addition of network modifiers generally leads to depolymerization of the networks as described by the Q-speciation, where Qn denotes PO4 tetrahedra with n number (between 0 and 3) of bridging P-O-P linkages per tetrahedron. Upon the initial creation of non-bridging oxygens and thus partly depolymerized Q species, a variety of network former/modifier interactions exists...
July 11, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29995413/correction-to-theoretical-investigations-of-the-role-of-mutations-in-dynamics-of-kinesin-motor-proteins
#12
Mikita Misiura, Qian Wang, Margaret S Cheung, Anatoly B Kolomeisky
No abstract text is available yet for this article.
July 11, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29995412/on-the-binding-free-energy-and-molecular-origin-of-sickle-cell-hemoglobin-aggregation
#13
Nuno Galamba, Silvio Pipolo
Protein aggregation is associated with various diseases, including Alzheimer and Parkinson as well as sickle cell disease (SCD). From a molecular point of view protein aggregation depend on a complex balance of electrostatic and hydrophobic interactions mediated by water. An impressive manifestation of the importance of this balance concerns the human hemoglobin (HbA) mutant, HbS (sickle cell Hb), where a single substitution at the 6th position of HbA β-chains, from glutamic acid to valine, causes the polymerization of deoxygenated HbS (deoxy-HbS), responsible for SCD...
July 11, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29993246/frustration-vs-prenucleation-understanding-the-surprising-stability-of-supersaturated-sodium-thiosulfate-solutions
#14
Judith Reichenbach, Klaas Wynne
Gibbs classical nucleation theory predicts that a supersaturated solution will have transient nuclei that flitter in and out of existence. Only when one of these nuclei becomes larger than a critical size, will the solution crystalize. Recently, non-classical nucleation theories have invoked the presence of pre-nuclei possibly associated with a liquid-liquid phase separation. However, there are few experimental observations of such pre-nuclei. Here we use ultrafast optical Kerr-effect spectroscopy to measure the temperature-dependent low-frequency (sub-gigahertz to terahertz) anisotropic Raman spectra of supersaturated aqueous sodium thiosulfate solutions...
July 11, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29993242/coldock-concentrated-ligand-docking-with-all-atom-molecular-dynamics-simulation
#15
Kazuhiro Takemura, Chika Sato, Akio Kitao
We propose a simple but efficient and accurate method to generate protein-ligand complex structures, called Concentrated ligand Docking (ColDock). This method consists of multiple independent molecular dynamics simulations in which ligands are initially distributed randomly around a protein at relatively high concentration (∼100 mM). This condition significantly increases the probability of the ligand exploring the protein surface, which induces spontaneous ligand binding to the correct binding sites within a 100 ns MD...
July 11, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29991263/impedance-analysis-of-polyaniline-in-comparison-with-some-conventional-solid-electrolytes
#16
Serguei D Mikhailenko, Marco Antônio Siqueira Rodrigues, Fabricio Celso, Franciélli Muller, Carlos Arthur Ferreira, Serge Kaliaguine
Doped polyaniline (PANI) is well known as an electronic (polaronic) conductor and mostly is used as semiconductor in various applications. However in the literature there are examples of employment of acid doped form of PANI as electrolytic filler in proton exchange membranes. In order to distinguish between two type of conduction in the present study powdered samples of polyaniline, either in form of emeraldine base (PANI-EB) or doped with camphorsulphonic acid (PANI-CSA), were investigated using impedance spectroscopy both in dry state and in contact with liquid water...
July 10, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29991255/decoding-oxyanion-aqueous-solvation-structure-a-potassium-nitrate-example-at-saturation
#17
Hsiu-Wen Wang, Lukas Vlcek, Joerg C Neuefeind, Katharine Page, Stephan Irle, John Michael Simonson, Andrew G Stack
The ability to probe the structure of a salt solution at the atomic scale is fundamentally important for our understanding of many chemical reactions and their mechanisms. The capability of neutron diffraction to "see" hydrogen (or deuterium) and other light isotopes is exceptional for resolving the structural complexity around the dissolved solutes in aqueous electrolytes. We have made measurements using oxygen isotopes on aqueous nitrate to reveal a small hydrogen-bonded water coordination number (3...
July 10, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29989815/effects-of-hydration-on-structure-and-phase-behavior-of-pig-gastric-mucin-elucidated-by-saxs
#18
Yana Znamenskaya Falk, Johan Engblom, Jan Skov Pedersen, Thomas Arnebrant, Vitaly Kocherbitov
In this work small angle X-ray scattering (SAXS) was used to study hydration and temperature-induced changes of pig gastric mucin (PGM) within the entire concentration range. The scattering is interpreted as originating from PGM fiber-like structures that adopt rod-like bottle-brush conformation in dilute solutions. Based on the knowledge about molecular structure of mucins and SAXS data for dilute solutions, we propose a theoretical model for predicting mucin conformation in solution and calculate the corresponding scattering profile...
July 10, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29986138/on-the-scavenging-ability-of-homogentisic-acid-and-ergosterol-towards-free-radicals-derived-from-ethanol-consumption
#19
Manuel Eusebio Medina, Annia Galano, Angel Trigos
Acute, or chronic, ethanol consumption leads to the formation of free radicals in the liver, which is related to hepatic damage. Among these radicals 1-hydroxyethyl, •CH(OH)CH3, is the most abundant one. Thus, efficient •CH(OH)CH3 scavengers are likely candidates to offer liver protection after ethanol consumption. In the present work ergosterol and homogentisic acid (HGA), which are found in edible mushrooms, were investigated as potential candidates to that purpose. The investigation was carried out following the QM-ORSA protocol, and using the density functional theory (DFT)...
July 9, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29985628/protein-folding-cooperativity-and-thermodynamic-barriers-of-the-simplest-%C3%AE-sheet-fold-a-survey-on-ww-domains
#20
Manuel Iglesias-Bexiga, Malwina Szczepaniak, Celia Sanchez-Medina, Eva S Cobos, Raquel Godoy-Ruiz, Jose Cristobal Martinez, Victor Munoz, Irene Luque
Theory and experiments have shown that microsecond folding proteins exhibit characteristic thermodynamic properties that reflect the limited cooperativity of folding over marginal barriers (downhill folding). Those studies have mostly focused on proteins with large α-helical contents and small size, which tend to be the fastest folders. A key open question is whether such properties are also present in the fastest all-beta proteins. We address this issue investigating the unfolding thermodynamics of a collection of WW domains as representatives of the simplest β-sheet fold...
July 9, 2018: Journal of Physical Chemistry. B
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