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Journal of Physical Chemistry. B

Ali Charkhesht, Chola Regmi, Katie R Mitchell-Koch, Shengfeng Cheng, Nguyen Q Vinh
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here we report dielectric properties of aqueous BSA protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz...
May 23, 2018: Journal of Physical Chemistry. B
Mikko Oskari Salomäki, Lauri Marttila, Henri Kivelä, Tuomo Ouvinen, Jukka Olavi Lukkari
We present a general thermodynamic "top down" analysis of the effect of oxidant and pH on dopamine oxidation and cyclization, supplemented by UV-vis and electrochemical studies. The model is applicable to other catecholamines and various experimental conditions. The results show that the decisive physico-chemical parameters in autoxidation are the pK values of the semiquinone and the amino group in the oxidized quinone. Addition of Ce(IV) or Fe(III) enhances dopamine oxidation in acidic medium in aerobic and anaerobic conditions by direct oxidation of dopamine and, in the presence of oxygen, also by autoxidation of the formed semiquinone...
May 22, 2018: Journal of Physical Chemistry. B
Alessandro Agostini, Daniel M Palm, Harald Paulsen, Donatella Carbonera
Optically detected magnetic resonance (ODMR) of triplet states populated by photoexcitation in the Water-Soluble Chlorophyll Protein (WSCP) from Lepidium virginicum has been performed, using both absorption and fluorescence detection. Well resolved Triplet minus Singlet (T-S) spectra have been obtained, which have been interpreted in terms of electronic interactions among the four chlorophylls (Chls) forming two dimers in WSCP tetramer. Localization of the triplet state on a single Chl leads to a redistribution of the oscillator strenght in the remaining three Chls of the complex...
May 21, 2018: Journal of Physical Chemistry. B
Eric Christopher Novak, Niina Jalarvo, Sudipta Gupta, Kunlun Hong, Stephan Förster, Takeshi Egami, Michael Ohl
Plastic crystals are a promising candidate for solid state ionic conductors. In this work, quasielastic neutron scattering is employed to investigate the center of mass diffusive motions in two types of plastic crystalline cyclic alcohols: cyclohexanol and cyclooctanol. Two separate motions are observed which are attributed to long range translational diffusion (α-process) and cage rattling (fast β-process). Residence times and diffusion coefficients are calculated for both processes, along with the confinement distances for the cage rattling...
May 18, 2018: Journal of Physical Chemistry. B
Takuya Mabuchi, Takashi Tokumasu
A reactive molecular dynamics simulation has been performed for the characterization of the relationship between proton transport and water clustering in polymer electrolyte membranes. We have demonstrated that the anharmonic two-state empirical valence bond ( aTS-EVB) model is capable of describing efficiently excess proton transport through the Grotthuss hopping mechanism within the simplicity of the theoretical framework. In order to explore the long-time diffusion behavior in PFSA membranes with statistical certainty, simulations that are longer than 10 ns are needed...
May 18, 2018: Journal of Physical Chemistry. B
Mariko Okada, Shinji Kajimoto, Takakazu Nakabayashi
Peptide-lipid interactions are widely involved with biologically significant phenomena, including the pathogenic mechanisms of protein misfolding diseases, and transmembrane protein folding. In this paper, the interaction of the cysteine/tryptophan (Cys/Trp) motif, which is a metal binding motif of copper transporter (Ctr) proteins, with a lipid bilayer was studied using fluorescence and circular dichroism (CD) spectroscopy. The binding of Cu(I) to the Cys/Trp motif induced a large red-edge excitation shift (REES) in the Trp fluorescence, indicating that the Trp residue is located inside the lipid bilayer following complexation of Cu(I) with the Cys/Trp motif...
May 18, 2018: Journal of Physical Chemistry. B
Derek Marsh
It is not possible to reproduce simulations of nitroxide spin-label EPR spectra published in J. Phys. Chem. 88, 3454-3465 (1984), when using the motional model and parameters given in that paper. Instead of the apparent two-component line shapes claimed, the spectra resemble single-component powder patterns expected from axially anisotropic, partial motional-averaging (a situation familiar for chain-labelled lipids in nonaligned fluid membranes). This is because: (i) the nitroxide z-axis is inclined at a fixed angle to the principal diffusion axis, and (ii) motion perpendicular to the principal diffusion axis is so slow as to approximate a powder distribution...
May 18, 2018: Journal of Physical Chemistry. B
Erika N Bentz, Rosana Maria Lobayan, Henar Martinez, Pilar Redondo, Antonio Largo
A computational kinetics study of the antioxidant activity of tryptamine toward HO● and HOO● radicals in water at 298 K has been carried out. Density functional methods have been employed for the quantum chemical calculations and conventional transition state theory was used for rate constants evaluation. Different mechanisms have been considered: radical adduct formation (RAF), single electron transfer (SET), and hydrogen atom transfer (HAT). For the reaction of tryptamine with the hydroxyl radical nearly all channels are diffusion controlled, and the overall rate constant is very high, 6...
May 18, 2018: Journal of Physical Chemistry. B
Kazuki Ito, Yuta Ogawa, Keiji Yokota, Sachiko Matsumura, Tamiko Minamisawa, Kanako Suga, Kiyotaka Shiba, Yasuo Kimura, Ayumi Hirano-Iwata, Yuzuru Takamura, Toshio Ogino
Exosomes are extracellular nanovesicles released from any cells and found in any body-fluid. Because exosomes exhibit information of their host cells (secreting cells), their analysis is expected to be a powerful tool for early diagnosis of cancers. To predict the host cells, we extracted multi-dimensional feature data about size, shape, and deformation of exosomes immobilized on solid surfaces by atomic force microscopy (AFM). The key idea is combination of support vector machine (SVM) learning for individual exosome particles and their interpretation by principal component analysis (PCA)...
May 17, 2018: Journal of Physical Chemistry. B
Romina Castañeda-Arriaga, Adriana Pérez-Gonzalez, Miguel Reina, Juan Raul Alvarez-Idaboy, Annia Galano
Oxidative stress (OS) is a health-threatening process that is involved, at least partially, in the development of several diseases. Although antioxidants can be used as a chemical defense against OS, they might also exhibit pro-oxidant effects, depending on environmental conditions. In this work, such a dual behavior was investigated for phenolic compounds (PhCs), within the framework of the density functional theory, and based on kinetic data. Multiple reaction mechanisms were considered in both cases. The presence of redox metals, the pH, and the possibility that PhCs might be transformed into benzoquinones were identified as key aspects in the antioxidant versus pro-oxidant effects of these compounds...
May 17, 2018: Journal of Physical Chemistry. B
Xiongwu Wu, Bernard R Brooks
Internal ionizable groups are known to play important roles in protein functions. A mystery that has attracted decades of extensive experimental and theoretical studies is the apparent dielectric constants experienced by buried ionizable groups, which are much higher than values expected for protein interiors. Many interpretations have been proposed, such as water penetration, conformational relaxation, local unfolding, protein intrinsic backbone fluctuations, etc. However, these interpretations conflict with many experimental observations...
May 17, 2018: Journal of Physical Chemistry. B
Alexander V Levanov, Oksana Ya Isaikina, Ulkar D Gurbanova, Valery V Lunin
The experimental dissociation constants of strong acids are notoriously ill-defined, and it is necessary to rely on theoretical methods for their evaluation. We present a methodology for the theoretical evaluation of the dissociation constants, and the values of Ka for perchloric and sulfuric acids have been estimated. It has been shown that the acid dissociation constant Ka can be expressed as a product of two terms, Ka = K'a × fHA ∞, where K'a is the apparent dissociation constant, and fHA ∞ is the infinite dilution activity coefficient of undissociated molecule of acid in liquid solution...
May 17, 2018: Journal of Physical Chemistry. B
Abdenacer Idrissi, Pal Jedlovszky
The volume, energy, entropy, and Helmholtz free energy of mixing of the seven simplest primary alkanolamine molecules, i.e., MEA, MIPA, 2A1P, ABU, AMP, AMP2, and 1A2B with water is investigated by extensive computer simulations and thermodynamic integration. To check the force field dependence of the results, all calculations are repeated with two commonly used water models, namely SPC/E and TIP4P. The obtained results show that the thermodynamics of mixing of alkanolamines and water is largely independent from the type of the alkanolamine molecule...
May 17, 2018: Journal of Physical Chemistry. B
Olivier Dangles, Pascale Goupy, Michel Carail, Alexandre Giuliani, Denis Duflot, Catherine Caris-Veyrat
Carotenoids are important natural pigments and micronutrients contributing to health prevention by several mechanisms, including their electron-donating (antioxidant) activity. In this work, a large series of carotenoids, including 11 carotenes and 14 xanthophylls, has been investigated by wavelength-resolved atmospheric pressure photoionization mass spectrometry (DISCO line of SOLEIL synchrotron), thus allowing the experimental determination of their ionization energy (IE) for the first time. On the other hand, the carotenoids have been also investigated for their ability to inhibit the heme iron-induced peroxidation of linoleic acid in mildly acidic micelles, a simple but relevant chemical model of oxidative stress in the gastric compartment...
May 17, 2018: Journal of Physical Chemistry. B
Anjela Manandhar, Myungshim Kang, Kaushik Chakraborty, Sharon M Loverde
At the molecular level, the dynamic instability (random growth and shrinkage) of the microtubule (MT) is driven by the nucleotide state (GTP vs. GDP) in the β subunit of the tubulin dimers at the MT cap. Here, we use large-scale molecular dynamics (MD) simulations and normal mode analysis (NMA) to characterize the effect of a single GTP cap layer on tubulin octamers composed by two neighboring protofilaments (PFs). We utilize recently reported high-resolution structures of dynamic MTs to simulate a GDP octamer both with and without a single GTP cap layer...
May 16, 2018: Journal of Physical Chemistry. B
Shaowen Wu, Jianwei Liu, Wenning Wang
Conformational changes of enzyme proteins are often coupled with the catalytic reaction and modulate the enzyme activity. Single molecule technology is a powerful tool to study the mechanism of enzyme catalysis in these complicated cases. However, the chemical reaction cycles and conformational changes could not be monitored simultaneously in a single molecule detection experiment, resulting in some key kinetic parameters unresolved. Here, we describe a method to extract all kinetic parameters from comprehensive single molecule FRET (smFRET) measurements and model analysis...
May 16, 2018: Journal of Physical Chemistry. B
Ang Gao, Liang Tan, Lawrence R Pratt, Mangesh I Chaudhari, Susan B Rempe, Dilipkumar Asthagiri, John D Weeks
The role that van der Waals (vdW) attractive forces play in the hydration and association of atomic hydrophobic solutes like argon (Ar) in water is reanalyzed using the local molecular field (LMF) theory of those interactions. In this problem, solute vdW attractive forces can reduce or mask hydrophobic interactions as measured by contact peak heights of the ArAr correlation function compared to reference results for purely repulsive core solutes. Nevertheless, both systems exhibit characteristic hydrophobic inverse temperature behavior in which hydrophobic association become stronger with increasing temperature through a moderate temperature range...
May 16, 2018: Journal of Physical Chemistry. B
Rodrigo Maghdissian Cordeiro
Phase-separated membrane domains, also known as lipid rafts, are believed to play an important role in cell function. Although most rafts are sterol-enriched membrane regions, evidence suggests that living cells may also contain gel-like rafts. Interactions between gel and fluid domains have a large impact on membrane properties, as is the case with permeability. The membrane permeability may reach a peak at the main phase transition temperature, by far exceeding the values recorded at the fluid phase. It has been proposed that gel-fluid interfaces are leaky, but the effect has not yet been demonstrated at the molecular level...
May 16, 2018: Journal of Physical Chemistry. B
Kristine F Frederiksen, Kacper Januchta, Nerea Mascaraque, Randall E Youngman, Mathieu Bauchy, Sylwester J Rzoska, Michal Bockowski, Morten M Smedskjaer
Alkali aluminoborate glasses have recently been shown to exhibit a very high threshold for indentation cracking compared to other bulk oxide glasses. However, to enable the use of these materials in engineering applications, there is a need to improve their hardness by tuning the chemical composition. In this study, we substitute alkaline earth for alkali network-modifying species at fixed aluminoborate base glass composition and correlate it with changes in structure, mechanical properties, and densification behavior...
May 16, 2018: Journal of Physical Chemistry. B
Wenjing Guo, Prannay Bali, Jeffrey R Errington
We use Monte Carlo simulation to compute the saturation properties of a model octane-water system. The system phase separates into water-rich liquid and vapor phases, octane-rich liquid and vapor phases, and water-rich liquid and octane-rich liquid phases at various conditions. We outline a strategy for determining the saturation properties of the mixture over a wide range of temperatures, pressures, and compositions. The approach begins with direct calculations that enable one to locate a single saturation point...
May 15, 2018: Journal of Physical Chemistry. B
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