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Journal of Physical Chemistry. B

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https://www.readbyqxmd.com/read/28448145/coarse-grained-molecular-dynamics-model-of-double-stranded-dna-for-dna-nanostructure-design
#1
Hiromasa Yagyu, Jae-Young Lee, Do-Nyun Kim, Osamu Tabata
A new coarse-grained molecular dynamics double-stranded DNA model (nCG-dsDNA model) using an improved beads-spring model was proposed. In this model, nucleotide comprising phosphate, sugar, and base group were replaced by a single bead. The double stranded model with 202 base pairs was created to tune the parameters of the bond, the non-bond, stack, angle bending, and electrostatic interaction. The average twisted angle and the persistence length of the model without electrostatic interaction were calculated at 35...
April 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28447461/diffusion-controlled-recrystallization-of-water-sorbed-into-poly-meth-acrylates-revealed-by-variable-temperature-mid-infrared-spectroscopy-and-molecular-dynamics-simulation
#2
Nobuhiro Yasoshima, Mizuki Fukuoka, Hiromi Kitano, Shigehiro Kagaya, Tatsuya Ishiyama, Makoto Gemmei-Ide
Recrystallization behaviors of water sorbed into four poly(meth)acrylates; poly(2-methoxyethyl acrylate) (PMEA), poly(tetrahydrofurfuryl acrylate) (PTHFA), poly(methyl acrylate) (PMA), and poly(methyl methacrylate) (PMMA), are investigated by variable-temperature mid-infrared (VT-MIR) spectroscopy and molecular dynamics (MD) simulation. VT-MIR spectra demonstrate that recrystallization temperatures of water sorbed into the polymers are positively correlated with their glass transition temperatures reported previously...
April 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28447449/molecular-simulations-of-mixed-lipid-bilayers-with-sphingomyelin-glycerophospholipids-and-cholesterol
#3
Indrani Bera, Jeffery B Klauda
The highly-diversified composition of lipid bilayers across living cells is crucial for many biological processes. Lipid bilayers mainly consist of phosphatidylcholines (PC), phosphatidylethanolamines (PE), sphingomyelin (SM) and cholesterol, with eukaryotic membranes containing high percentage of sphingomyelin and cholesterol. In this study, we have modeled bilayers with different concentration of PC, PE and SM to understand the changes in bilayer properties with varied SM concentrations. In addition, membrane models with 33% cholesterol have been simulated to understand the influence of cholesterol...
April 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28445058/non-ideal-behavior-of-glass-and-crystal
#4
Yashika Sharma, Sevi Murugavel
We report deviations from an ideal behavior of binary chalcogenide glass composition Ge20Te80 with respect to its quenching rate on mass density and thermal parameters including glass transition temperature. In an ideal glass, the increase in quenching rate will decrease the characteristic relaxation time and correspondingly shift in the glass transition temperature (Tg) to higher temperature and result in lower density. This, however, holds only when the liquid structure remains same as in equilibrium glass structure independent of their quenching rate...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28443666/correction-to-artifact-free-and-detection-profile-independent-higher-order-fluorescence-correlation-spectroscopy-for-microsecond-resolved-kinetics-2-mixtures-and-reactions
#5
Farshad Abdollah-Nia, Martin P Gelfand, Alan Van Orden
No abstract text is available yet for this article.
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28443664/theory-and-electrochemistry-of-cytochrome-c
#6
Salman S Seyedi, Morteza M M Waskasi, Dmitry V Matyushov
Extensive simulations of cytochrome c in solution are performed to address the apparent contradiction between large reorganization energies of protein electron transfer typically reported by atomistic simulations and much smaller values produced by protein electrochemistry. The two sets of data are reconciled by deriving the activation barrier for electrochemical reaction in terms of an effective reorganization energy composed of half the Stokes shift (characterizing the medium polarization in response to electron transfer) and the variance reorganization energy (characterizing the breadth of electrostatic fluctuations)...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28443331/coupling-between-the-dynamics-of-water-and-surfactants-in-lyotropic-liquid-crystals
#7
Jesse Gatten McDaniel, Arun Yethiraj
Bilayers composed of lipid or surfactant molecules are central to biological membranes and lamellar lyotropic liquid crystalline (LLC) phases. Common to these systems are phases that exhibit either ordered or disordered packing of the hydrophobic tails. In this work, we study the impact of surfactant ordering, i.e., disordered Lα and ordered Lβ LLC phases, on the dynamics of water in the lamellar phases of dicarboxylate gemini surfactants. We study the different phases at identical hydration levels by changing the length of the hydrophobic tails; surfactants with shorter tails form Lα phases and those with longer tails form Lβ phases...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28443330/mechanisms-by-which-salt-concentration-moderates-the-dynamics-of-human-serum-transferrin
#8
Haleh Abdizadeh, Ali Rana Atilgan, Canan Atilgan
The dynamical and thermodynamic behavior of human transferrin (hTf) protein in saline aqueous solution of various concentrations is studied. hTf is an essential transport protein circulating iron in the blood and delivering it to tissues. It displays highly pH dependent cooperativity between the two lobes each carrying an iron, and forms a tight complex with the receptor during endocytosis, eventually recycled to the serum after iron release. Molecular dynamics simulations are used to investigate the effects of the amount of salt on protein conformation and dynamics to analyze the structure-function relationship in free hTf at serum pH...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28430444/molecular-structuring-and-percolation-transition-in-hydrated-sulfonated-poly-ether-ether-ketone-membranes
#9
Madhusmita Tripathy, P B Sunil Kumar, Abhijit P Deshpande
The extent of phase separation and water percolation in sulfonated membranes are the key to their performance in fuel cells. Toward this, the effect of hydration on the morphology and transport characteristics of sulfonated poly(ether ether ketone), sPEEK, membrane is investigated using atomistic molecular dynamics simulation at various hydration levels(λ: number of water molecules per sulfonate group). The evolution of local morphology is investigated using structural correlations and minimum pair distances...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28425710/solvation-structure-of-1-3-butanediol-in-aqueous-binary-solvents-with-acetonitrile-1-4-dioxane-and-dimethyl-sulfoxide-studied-by-ir-nmr-and-molecular-dynamics-simulation
#10
Toshiyuki Takamuku, Yasuhito Higuma, Masaru Matsugami, Takahiro To, Tatsuya Umecky
The solvation structure of 1,3-butanediol (1,3-BD) in aqueous binary solvents of acetonitrile (AN), 1,4-dioxane (DIO), and dimethyl sulfoxide (DMSO) at various mole fractions of organic solvent xOS has been clarified by means of infrared (IR) and (1)H and (13)C NMR. The change in the wavenumber of O-H stretching vibration of 1,3-BD in the three systems suggested that water molecules which are initially hydrogen-bonded with the 1,3-BD hydroxyl groups in the water solvent (xOS = 0) are more significantly replaced by organic solvent molecules in the order of DMSO ≫ DIO > AN...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28418682/mesoscale-simulation-and-machine-learning-of-asphaltene-aggregation-phase-behavior-and-molecular-assembly-landscapes
#11
Jiang Wang, Mohit A Gayatri, Andrew L Ferguson
Asphaltenes constitute the heaviest fraction of the aromatic group in crude oil. Aggregation and precipitation of asphaltenes during petroleum processing costs the petroleum industry billions of dollars each year due to downtime and production inefficiencies. Asphaltene aggregation proceeds via a hierarchical self-assembly process that is well-described by the Yen-Mullins model. Nevertheless, the microscopic details of the emergent cluster morphologies and their relative stability under different processing conditions remain poorly understood...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28414462/pyrene-apelin-conjugation-modulates-fluorophore-and-peptide-micelle-interactions
#12
Robin E Patterson, Nathan Weatherbee-Martin, Jan K Rainey
Bioactive apelin peptide forms ranging in length from 12 to 55 amino acids bind to and activate the apelin receptor (AR or APJ), a class A G-protein coupled receptor. Apelin-12, -17, and -36 isoforms, named according to length, with an additional N-terminal cysteine residue allowed for regiospecific and efficient conjugation of pyrene maleimide. Through steady-state fluorescence spectroscopy, the emission properties of pyrene in aqueous buffer were compared to those of the pyrene-apelin conjugates both without and with zwitterionic or anionic micelles...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28413881/molecular-mechanism-of-stabilizing-the-helical-structure-of-huntingtin-n17-in-a-micellar-environment
#13
Leili Zhang, Hongsuk Kang, Francisco X Vázquez, Leticia Toledo-Sherman, Binquan Luan, Ruhong Zhou
Huntington's disease is a deadly neurodegenerative disease caused by the fibrilization of huntingtin (HTT) exon-1 protein mutants. Despite extensive efforts over the past decade, much remains unknown about the structures of (mutant) HTT exon-1 and their enigmatic roles in aggregation. Particularly, whether the first 17 residues in the N-terminal (HTT-N17) adopt a helical or a coiled structure remains unclear. Here, with the rigorous study of molecular dynamics simulations, we explored the most possible structures of HTT-N17 in both dodecylphosphocholine (DPC) micelles and aqueous solution, using three commonly applied force fields (OPLS-AA/L, CHARMM36, and AMBER99sb*-ILDNP) to examine the underlying molecular mechanisms and rule out potential artifacts...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28402662/dominant-carbons-in-trans-and-cis-resveratrol-isomerization
#14
Feng Wang, Subhojyoti Chatterjee
A comprehensive analysis for isomerization of geometric isomers in the case of resveratrol (R) has been presented. As an important red wine molecule, only one geometric isomer of resveratrol, i.e., trans-R rather than cis-R, is primarily associated with health benefit. In the present study, density function theory (DFT) provides accurate descriptions of isomerization of resveratrol. The nearly planar trans-R forms a relatively rigid and less flexible conjugate network, but the nonplanar cis-R favors a more flexible structure with steric through space interaction...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28399628/examination-of-mixtures-containing-sphingomyelin-and-cholesterol-by-molecular-dynamics-simulations
#15
Eric Wang, Jeffery B Klauda
The all-atom CHARMM36 (C36) force field is used to simulate bilayers of pure palmitoylsphingomyelin (PSM) as well as binary mixtures of PSM and stearoylsphingomyelin (SSM) at various cholesterol concentrations (XC) and temperatures. C36 simulation data is in good agreement with experimental deuterium order parameters and previous computational results, providing evidence of the utility of the force field for potentially studying more complex membranes. The area compressibility modulus is shown to achieve a large value of 2...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28441865/unexpected%C3%A2-effects%C3%A2-of%C3%A2-k-%C3%A2-and%C3%A2-adenosine-triphosphate%C3%A2-on%C3%A2-the-thermal%C3%A2-stability%C3%A2-of%C3%A2-na-k-atpase
#16
M Agueda Placenti, Sergio Benjamín Benjamin Kaufman, F Luis Gonzalez Flecha, Rodolfo Martín González-Lebrero
Na(+),K(+)-ATPase is an integral membrane protein which couples ATP hydrolysis to the transport of three Na(+) out and two K(+) into the cell. The aim of this work is to characterize the effect of K(+), ATP and Mg(2+) (essential activator) on the Na(+),K(+)-ATPase thermal stability. In all conditions tested, thermal inactivation of the enzyme is concomitant with a structural change involving the ATP binding site and membrane-associated regions. Both ligands exert a clear stabilizing effect due to both enthalpic and entropic contributions...
April 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28441485/new-insights-into-the-reaction-paths-of-4-carboxybenzophenone-triplet-with-oligopeptides-containing-n-and-c-terminal-methionine-residues
#17
Piotr Filipiak, Krzysztof Bobrowski, Gordon L Hug, Dariusz Pogocki, Christian Schoneich, Bronislaw Marciniak
The oxidation processes of L-Met-(Pro)n-L-Met peptides that contain two Met residues located on the N and C termini and separated by a defined number (n = 0 - 4) of proline residues were investigated in aqueous solutions using laser flash photolysis. The use of such peptides allowed for distance control between the sulfur atoms located in the side chains of the Met residues. Interactions between side chains of the Met residues were probed by the observation of transients with σ*-type 2c-3e (S∴S)(+), (S∴N)(+) and/or (S∴O)(+)-bonds as well as of α-(alkylthio)alkyl radicals (αS)...
April 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28441023/hydrophobic-nanoparticles-modify-the-thermal-release-behavior-of-liposomes
#18
Matthew Ryan Preiss, Ashley E Hart, Christopher L Kitchens, Geoffrey D Bothun
Understanding the effect of embedded nanoparticles on the characteristics and behavior of lipid bilayers is critical to the development of lipid-nanoparticle assemblies (LNAs) for biomedical applications. In this work we investigate the effect of hydrophobic nanoparticle size and concentration on liposomal thermal release behavior. Decorated LNAs (D-LNAs) were formed by embedding 2 nm (GNP2) and 4 nm (GNP4) dodecanethiol-capped gold nanoparticles into DPPC liposomes at lipid to nanoparticle ratios (L:N) of 25,000:1, 10,000:1, and 5,000:1...
April 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28441017/equilibration-of-micelle-polyelectrolyte-complexes-mechanistic-differences-between-static-and-annealed-charge-distributions
#19
Jennifer E Laaser, Michael McGovern, Yaming Jiang, Elise Lohmann, Theresa M Reineke, David C Morse, Kevin D Dorfman, Timothy P Lodge
The role of charge density and charge annealing in polyelectrolyte complexation was investigated through systematic comparison of two micelle-polyelectrolyte systems. First, poly(dimethylaminoethyl methacrylate)-block-poly(styrene) (PDMAEMA-b-PS) micelles were complexed with poly(styrenesulfonate) (PSS) at pH values above and below the pKa of PDMAEMA to investigate the role of charge annealing in the complexation process. Second, complexes of poly(DMAEMA-stat-oligo(ethylene glycol) methyl ether methacrylate)-block-poly(styrene) (P(DMAEMA-stat-OEGMA)-b-PS) micelles with the same PSS at low pH were used to investigate how the complexation process differs when the charged sites are in fixed positions along the polymer chains...
April 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28440650/comprehensive-computational-and-experimental-analysis-of-biomaterial-towards-the-behavior-of-imidazolium-based-ionic-liquids-an-interplay-between-hydrophilic-and-hydrophobic-interactions
#20
Reddicherla Umapathi, Suresh B Vepuri, Pannuru Venkatesu, Mahmoud E S Soliman
To provide insights into the aggregation behavior, hydration tendency and variation in phase transition temperature produced by the addition of ionic liquids (ILs) to poly(N-isopropylacrylamide) (PNIPAM) aqueous solution, systematic physicochemical studies, and molecular dynamic simulations were carried out. The influence of ILs possessing same [Cl]- anion and a set of cation [Cnmim]+ with increasing alkyl chain length such as 1-ethyl-3-methylimidazolium ([Emim]+), 1-allyl-3-methylimidazolium ([Amim]+), 1-butyl-3-methylimidazolium ([Bmim]+), 1-hexyl-3-methylimidazolium ([Hmim]+), 1-benzyl-3-methylimidazolium ([Bzmim]+), and 1- decyl-3-methylimidazolium ([Dmim] +) on the phase transition of PNIPAM was monitored by the aid of UV-visible absorption spectra, fluorescence intensity spectra, viscosity (ɳ), dynamic light scattering (DLS) and Fourier transform infrared (FTIR) spectroscopy...
April 25, 2017: Journal of Physical Chemistry. B
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