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Journal of Physical Chemistry. B

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https://read.qxmd.com/read/30779573/proton-transfer-and-ionicity-an-15-n-nmr-study-of-pyridine-base-protonation
#1
Mohammad Hasani, Samrat A Amin, Jeffery L Yarger, Stephen K Davidowski, C Austen Angell
Protic ionic liquids (PILs) are made by proton transfer from a Brønsted acid to a base and are of interest for their solvent and electrolyte properties such as high ionic conductivity. Unfortunately, many PILs have been misnamed, because their ionic content is minimal due to an insufficient driving force for the proton transfer. Here we review this problem and introduce a new method, using 15 N NMR spectroscopy, of characterizing the relation between the extent of proton transfer to a given base and the strength of the proton-donating acid...
February 19, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30779571/in-silico-evolution-of-biochemical-log-response
#2
Mathieu Hemery, Paul Francois
Numerous biological systems are known to harbour a form of logarithmic behaviour, from Weber's law to bacterial chemotaxis. Such log-response allows for sensitivity to small relative variations of biochemical inputs over a large range of concentration values. Here we use a genetic algorithm to evolve biochemical networks displaying a logarithmic response. A quasi-perfect log-response implemented by the same core network evolves in a convergent way across our different \textit{in silico} replications. The best network is able to fit a logarithm over 4 orders of magnitude with an accuracy of the order of $1\%$...
February 19, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30779570/vibrational-relaxation-in-carotenoids-as-an-explanation-for-their-rapid-optical-properties
#3
Jan Philipp Götze
We propose the ultrafast S2 (1Bu) to S1 (2Ag) "electronic internal conversion" observed in carotenoids to be a vibrational relaxation of the 1Bu state. This suggestion arises from comparing excited state geometries computed with the CAM-B3LYP density functional to the ground states; it is found that each conjugated atom moves less than 5 pm for, e.g., violaxanthin. However, the changes of excitation energies are large, ranging from 0.4 to 1.2 eV. This is connected to the size of the conjugated system: While each atom only contributes 0...
February 19, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30779569/molecular-mobility-in-a-set-of-imidazolium-based-ionic-liquids-bmim-sup-sup-a-sup-sup-by-nmr-relaxation-method
#4
Sergei Sergeevich Bystrov, Vladimir Victorovich Matveev, Yuri S Chernyshev, Vytautas Balevicius, Vladimir Ivanovich Chizhik
The detailed investigation of the local mobility in a set of dried imidazolium-based ionic liquids (1-butyl-3-methylimidazolium) in a wide temperature range and varying anions (BF<sub>4</sub>-, I-, Cl-, Br-, NO<sub>3</sub>-, TfO-) is presented. The measurements of temperature dependencies of the spin-lattice relaxation times of <sup>1</sup>H and <sup>13</sup>C nuclei are motivated by the need to obtain a fundamental characterization of molecular mobility of the substances under study, namely, to estimate the correlation times, τ</sub>c<sub>, for the motion of individual molecular groups...
February 19, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30777763/bayesian-estimation-for-stochastic-gene-expression-using-multifidelity-models
#5
Huy D Vo, Zachary R Fox, Ania Baetica, Brian Munsky
The finite state projection (FSP) approach to solving the chemical master equation has enabled successful inference of discrete stochastic models to predict single-cell gene regulation dynamics. Unfortunately, the FSP approach is highly computationally intensive for all but the simplest models, an issue that is highly problematic when parameter inference and uncertainty quantification takes enormous numbers of parameter evaluations. To address this issue, we propose two new computational methods for the Bayesian inference of stochastic gene expression parameters given single-cell experiments...
February 19, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30777756/spontaneous-dispersion-and-large-scale-deformation-of-liquid-metal-induced-by-ferric-ions
#6
Sen Chen, Jing Liu
Gallium-based liquid metal owns the largest interfacial tension among all the room temperature liquid, which gives it strong deformability and promises its role in the field of soft machines. Paradoxically, such a material always remains nearly spherical in solution due to large interfacial tension, which in turn hinders the construction of liquid metal-based soft machines. Consequently, it is of significant theoretical and practical value to regulate the interfacial tension of liquid metal in order to carry out richer deformation...
February 19, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30777437/reply-to-comments-on-the-quest-to-demystify-water-ideal-solution-behaviors-are-obtained-by-adhering-to-the-equilibrium-mass-action-law
#7
Andreas A Zavitsas
Not required for Comment.
February 19, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30777433/comments-on-the-quest-to-demystify-water-ideal-solution-behaviors-are-obtained-by-adhering-to-the-equilibrium-mass-action-law
#8
Zhong-Hua Yang
In the comment, we fully demonstrated the so-called numbers of waters bound strongly to each mole of solute H_d and of particles formed per mole of the solute i_e by Zavitsas are only parameters without the special physical meaning.
February 19, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30776235/correction-to-atomistic-simulation-of-gas-uptake-and-interface-induced-disordering-in-solid-phases-of-an-organic-ionic-plastic-crystal
#9
Vinay S Kandagal, Fangfang Chen, Jennifer M Pringle, Maria Forsyth
No abstract text is available yet for this article.
February 18, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30776233/catalytic-mechanism-for-2-3-dihydroxybiphenyl-ring-cleavage-by-non-heme-extradiol-dioxygenases-bphc-insights-from-qm-mm-analysis
#10
Junjie Wang, Jinfeng Chen, Xiaowen Tang, Yanwei Li, Ruiming Zhang, Ledong Zhu, Yanhui Sun, Qingzhu Zhang, Wenxing Wang
An extradiol-cleaving catecholic dioxygenase, BphC, plays important roles in catabolism of biphenyl/polychlorinated biphenyls (PCBs) aromatic contaminants in the environment. To better elucidate the biodegradable pathway, a theoretical investigation of the ring-open degradation for 2,3-dihydroxybiphenyl (DHBP) was performed with the aid of quantum mechanical/molecular mechanical (QM/MM) calculations. A quintet state of the DHBP-iron-dioxygen group adducts was found to be reactive ground state with a substrate radical-FeII-superoxo (DHBP• ↑-FeII-O2• ‾↓) character...
February 18, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30775921/a-spectroscopic-insight-on-ethanol-induced-aggregation-of-papain
#11
Vaisakh Mohan, Nilimesh Das, Aritra Das, Vipin Mishra, Pratik Sen
In this contribution, the structural and dynamical changes occurring to papain molecules in ethanol-water binary solvent mixture have been investigated and compared with its denatured state induced by guanidine hydrochloride. Steady-state fluorescence, solvation dynamics, time-resolved rotational anisotropy, circular dichroism and single molecular level fluorescence correlation spectroscopic studies were carried out for this purpose. In ethanol-water mixture with XEtOH = 0.6, DACIA-tagged papain was found to undergo a blue shift of 12 nm, while in presence of 5 M GnHCl, a red shift of 5 nm was observed...
February 18, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30775920/raman-spectroscopic-study-of-the-effect-of-aqueous-salt-solutions-on-the-inhibition-of-carbon-dioxide-gas-hydrates
#12
Christine Carola Holzammer, Andreas Siegfried Braeuer
We present an experimental Raman study on the thermodynamic inhibition effect of different salts (NaCl, KCl, MgCl2 and CaCl2 from 2.5 - 11 wt-%) on the formation of carbon dioxide gas hydrates. We performed the experiments in a high pressure vessel with two phases: A water-rich phase and a CO2 -rich phase. We investigated the changes the inhibitors induce in the water-rich phase before the onset of hydrate formation. This includes a study of the change in molar reaction enthalpy between strongly and weakly hydrogen bonded water and the decrease in solubility of carbon dioxide in water...
February 18, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30768906/combinatorial-control-through-allostery
#13
Vahe Galstyan, Luke Funk, Tal Einav, Rob Phillips
Many instances of cellular signaling and transcriptional regulation involve switch-like molecular responses to the presence or absence of input ligands. To understand how these responses come about and how they can be harnessed, we develop a statistical mechanical model to characterize the types of Boolean logic that can arise from allosteric molecules following the Monod-Wyman-Changeux (MWC) model. Building upon previous work, we show how an allosteric molecule regulated by two inputs can elicit AND, OR, NAND and NOR responses, but is unable to realize XOR or XNOR gates...
February 15, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30768899/on-the-mechanism-of-phenolate-photo-oxidation-in-aqueous-solution
#14
Alexandra L Tyson, Jan R R Verlet
The photo-oxidation dynamics following UV (257 nm) excitation of the phenolate anion in aqueous solution is studied using broadband (550 to 950 nm) transient absorption spectroscopy. A clear signature from electron ejection is observed on a sub-picosecond timescale, followed by cooling dynamics and the decay of the signal to a constant offset that is assigned to the hydrated electron. The dynamics are compared to the charge-transfer-to-solvent dynamics from iodide at the same excitation wavelength and are shown to be very similar to these...
February 15, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30768898/molecular-dynamics-investigation-of-poly-lysine-peptide-translocation-through-mos-2-nanopores
#15
Adrien Nicolaï, Maria Daniela Barrios Perez, Patrice Delarue, Vincent Meunier, Marija Drndic, Patrick Senet
Solid-state nanopores (SSN) made of 2D materials such as molybdenum disulfide (MoS2) have emerged as candidate devices for biomolecules sequencing. SSN sequencing is based on measuring the variations in ionic conductance as charged biomolecules translocate through nanometer-sized channels, in response to an external voltage applied across the membrane. Although several experiments on DNA translocation through SSN have been performed in the past decade, translocation of proteins has been less studied, partly due to small protein size and detection limits...
February 15, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30768279/a-phage-display-derived-peptide-binds-to-human-cd206-and-modeling-reveals-a-new-binding-site-in-the-receptor
#16
Eliana Karina Asciutto, Sergei Kopanchuk, Anni Lepland, Lorena Simón-Gracia, Carlos Alemán, Tambet Teesalu, Pablo Scodeller
We recently identified a tumor homing peptide (mUNO, sequence: "CSPGAK") that specifically interacts with mouse CD206 to target CD206/MRC1-expressing tumor-associated macrophages in mice. Here, we report studies on the binding of mUNO to human recombinant CD206 (hCD206) and on modeling the mUNO/hCD206 interaction by computational analysis. Fluorescence anisotropy analysis demonstrated that fluorophore-labeled mUNO interacts with hCD206. Microsecond timescale molecular dynamic simulations and docking predictions showed that mUNO binds to a newly identified epitope between C-type lectin domains 1 and 2...
February 15, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30768271/reply-to-comment-on-distinct-populations-in-spin-label-epr-spectra-from-nitroxides
#17
Derek Marsh
The reader can be excused for not recognizing, in the Comment by Meirovitch et al., the paper that I wrote. Much of the emphasis is on topics not touched upon by me, and attributes to me statements that I did not make; and never would make. In view of this misrepresentation, it is useful first to describe what my paper actually is about. I identify a very clear and serious error in the paper entitled "Analysis of Protein-Lipid Interactions Based on Model Simulations of ESR." by Meirovitch et al. (referred to as MNF)...
February 15, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30768266/comment-on-distinct-populations-in-spin-label-epr-spectra-from-nitroxides
#18
Eva Meirovitch, Boris Dzikovski, Jack H Freed
n/a.
February 15, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30767526/interfacial-water-features-at-the-air-water-interface-as-influenced-by-charged-surfactants
#19
Vu N T Truong, Xuming Wang, Liem Xuan Dang, Jan D Miller
The features of interfacial water at air-water interfaces of anionic sodium dodecyl sulfate (SDS) and cationic dodecyl amine hydrochloride (DDA) solutions were examined by combining sum frequency generation (SFG) vibrational spectroscopy measurements and molecular dynamics simulations (MDS). The SFG spectra revealed that interfacial water molecules for SDS solutions were highly-ordered compared with those for DDA solutions. To elucidate this observation, in addition to agreement with the literature in regards to the interfacial electric field at the interfaces, we investigated the features of interfacial water molecules with respect to their network and their interaction with surfactant head groups...
February 15, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30767501/photolytic-cleavage-of-co-c-bond-in-coenzyme-b-12-dependent-glutamate-mutase
#20
Abdullah Al Mamun, Megan J Toda, Piotr Lodowski, Pawel M Kozlowski
Glutamate mutase (GLM) is a coenzyme B12-dependent enzyme which catalyzes the conversion of S-glutamate to (2S,3S)-3-methyl aspartate. The initial step in the catalytic process is the homolytic cleavage of the coenzyme's Co-C bond upon binding of a substrate. Alternatively, the Co-C bond can be cleaved using light. To investigate the photolytic cleavage of the Co-C bond in GLM, we applied a combined DFT/MM and TD-DFT/MM methods to scrutinize the ground and the low-lying excited states. Potential energy surfaces were generated as a function of axial bond lengths to describe the photodissociation mechanism...
February 15, 2019: Journal of Physical Chemistry. B
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