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Journal of Physical Chemistry. B

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https://www.readbyqxmd.com/read/28230994/artifact-free-and-detection-profile-independent-higher-order-fluorescence-correlation-spectroscopy-for-microsecond-resolved-kinetics-1-multi-detector-and-sub-binning-approach
#1
Farshad Abdollah-Nia, Martin P Gelfand, Alan K Van Orden
Fluorescence correlation spectroscopy (FCS) is a powerful tool in the time-resolved analysis of non-reacting or reacting molecules in solution, based on fluorescence intensity fluctuations. However, conventional (second-order) FCS alone is insufficient to measure all parameters needed to describe a reaction or mixture, including concentrations, fluorescence brightnesses, and forward and reverse rate constants. For this purpose, correlations of higher powers of fluorescence intensity fluctuations can be calculated to yield additional information from the single-photon data stream collected in an FCS experiment...
February 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28230358/membrane-independence-of-ultrafast-photochemistry-in-pharaonis-halorhodopsin-testing-the-role-of-bacterioruberin
#2
Itay Gdor, Maya Mani-Hazan, Noga Friedman, Mordechai Sheves, Sanford Ruhman
Ultrafast photochemistry of p-HR in the intact Natronomonas pharaonic membrane has been studied by photoselective femtosecond pump-hyperspectral probe spectroscopy with high time resolution. Two variants of this sample, one with wild type retinal prosthetic groups, and another after shifting retinal absorption deep into the blue by reducing the Schiff base linkage were studied, and compared with previous results on detergent solubilized p-HR. This comparison shows that retinal photo-isomerization dynamics are identical in the membrane and in the solubilized sample...
February 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28225631/conformational-changes-in-c-reactive-protein-affect-binding-to-curved-membranes-in-a-lipid-bilayer-model-of-the-apoptotic-cell-surface
#3
Aml Abd Alnaas, Carrie L Moon, Mitchell Alton, Scott M Reed, Michelle K Knowles
C-reactive protein (CRP) is a serum protein that binds to damaged membranes through a phosphatidylcholine binding site. The membrane binding process can initiate the complement immune response and facilitates the clearance of apoptotic cells, likely aiding in the protection of autoimmunity. The initiation of an immune response relies on a conformation change from a native, pentameric form to a modified form, where the modified form binds complement proteins (i.e. C1q) and regulatory proteins substantially better than the native form...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28225620/solvent-independent-anharmonicity-for-carbonyl-oscillators
#4
Samuel Hayes Schneider, Huong T Kratochvil, Martin T Zanni, Steven G Boxer
The physical origins of vibrational frequency shifts have been extensively studied in order to understand non-covalent intermolecular interactions in the condensed phase. In the case of carbonyls, vibrational solvatochromism, MD simulations, and vibrational Stark spectroscopy suggest that the frequency shifts observed in simple solvents arises predominately from the environment's electric field due to the vibrational Stark effect. This is contrary to many previously invoked descriptions of vibrational frequency shifts, such as bond polarization, whereby the bond's force constant and/or partial nuclear charges are altered due to the environment, often illustrated in terms of favored resonance structures...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28225285/multi-scale-modeling-of-the-effects-of-salt-and-perfume-raw-materials-on-the-rheological-properties-of-commercial-thread-like-micellar-solutions
#5
Xueming Tang, Weizhong Zou, Peter H Koenig, Shawn D McConaughy, Michael R Weaver, David Michael Eike, Michael J Schmidt, Ronald G Larson
We link micellar structures to rheological properties for two surfactant body-wash formulations at various concentrations of salts and perfume raw materials (PRMs) using molecular simulations and micellar-scale modeling as well as traditional surfactant packing arguments. The two body washes, named BW-1EO and BW-3EO, are composed of sodium lauryl ethylene glycol ether sulfate (SLEnS, where n is the average number of ethylene glycol repeat units), cocamidopropyl betaine (CAPB), ACCORD (which is a mixture of six PRMs), and NaCl salt...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28225273/fabric-softener-cellulose-nanocrystal-interaction-a-model-for-assessing-surfactant-deposition-on-cotton
#6
Evdokia K Oikonomou, Fanny Mousseau, Nikolay Christov, Galder Cristobal, Annie Vacher, Marc Airiau, Claudie Bourgaux, Laurent Heux, Jean-François Berret
There is currently a renewed interest for improving household and personal care formulations to provide more environment friendly products. Fabric conditioners used as softeners have to fulfill a number of stability and biodegradability requirements. They should also display significant adsorption on cotton in the conditions of use. The quantification of surfactant adsorption remains however difficult because the fabric woven structure is complex and deposited amounts are generally small. Here we propose a method to evaluate cellulose/surfactant interactions with increased detection sensitivity...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28224794/localized-bond-charge-corrected-cm1a-charges-for-condensed-phase-simulations
#7
Leela S Dodda, Jonah Z Vilseck, Julian Tirado-Rives, William L Jorgensen
The quality of the 1.14*CM1A and 1.20*CM5 charge models was evaluated for calculations of free energies of hydration. For a set of 426 neutral molecules, 1.14*CM1A and 1.20*CM5 yield MADs of 1.26 and 1.20 kcal/mol, respectively. The 1.14*CM1A charges, which can be readily obtained for large systems, exhibit large deviations only for a subset of functional groups. The results for these cases were systematically improved using Localized Bond Charge Corrections (LBCC) by which off-setting adjustments are made to the partial charges for atoms in specified bond types...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28224788/coarse-grained-molecular-modeling-of-solution-structure-ensemble-of-dengue-virus-non-structural-protein-5-with-small-angle-x-ray-scattering-intensity
#8
Guanhua Zhu, Wuan Geok Saw, Anjaiah Nalaparaju, Gerhard Grüber, Lanyuan Lu
An ensemble modeling scheme incorporating coarse-grained simulations with experimental small-angle X-ray scattering (SAXS) data is applied to the dengue virus 2 (DENV2) non-structural protein 5 (NS5). NS5 serves a key role in viral replication through its two domains that are connected by a ten-residue polypeptide segment. A set of representative structures are generated from a simulated structure pool using SAXS data fitting by the non-negativity least squares (NNLS) or the standard Ensemble Optimization Method (EOM) based on a genetic algorithm (GA)...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28195725/theoretical-insight-into-the-conversion-mechanism-of-glucose-to-fructose-catalyzed-by-crcl2-in-imidazolium-chlorine-ionic-liquids
#9
Yaru Jing, Jun Gao, Chengbu Liu, Dongju Zhang
To better understand the efficient transformation of glucose to fructose catalyzed by chromium chlorides in imidazolium-based ionic liquids (ILs), density functional theory calculations have been carried out on a model system which describes the catalytic reaction by CrCl2 in 1,3-dimethylimidazolium chlorine (MMImCl) ionic liquid (IL). The reaction is shown to involve three fundamental processes: ring opening, 1,2-H migration, and ring closure. The reaction is calculated to exergonic by 3.8 kcal/mol with an overall barrier of 37...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28191973/density-functional-study-on-the-intercalation-of-fullerenes-into-ane-pv-copolymer-layers
#10
Chuan-Ding Dong, Wichard J D Beenken
We investigated the intercalation of C60 into poly(p-anthracene-ethynylene)-alt-poly(p-phenylene-vinylene) copolymers layers by density functional theory calculations in respect of crystal structures and electronic band structures. Based on the experimental observations, we found that the copolymer with branched side chains substituted next to the anthracene units and the linear side chains substituted to the vinylene units has a better tendency to intercalate with C60 than the reversely substituted copolymer...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28186760/estimating-the-lipophobic-contributions-in-model-membranes
#11
Vikas Dubey, Xavier Prasanna, Durba Sengupta
The insertion and association of membrane proteins is critical in several cellular processes. These processes were thought to be protein-driven, but increasing evidence points toward an important role of the lipid bilayer. The lipid-mediated contribution has been shown to be important in the association of membrane peptides, but the corresponding "lipophobic" component has not been directly estimated. Here, we calculate the free energy of insertion for transmembrane peptides and estimate the lipophobic component from the cost of cavity formation...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28222598/drastic-compensation-of-the-electronic-and-solvation-effects-on-the-atp-hydrolysis-revealed-through-a-large-scale-qm-mm-simulations-combined-with-a-theory-of-solutions
#12
Hideaki Takahashi, Satoru Umino, Yuji Miki, Ryosuke Ishizuka, Shu Maeda, Akihiro Morita, Makoto Suzuki, Nobuyuki Matubayasi
Hydrolysis of adenosine triphosphate (ATP) is the "energy source" for a variety of biochemical processes. In the present work, we address key features of ATP hydrolysis: the relatively moderate value (about -10 kcal/mol) of the standard free energy ΔGhyd of reaction and the insensitivity of ΔGhyd to the number of excess electrons on ATP. We conducted quantum mechanical/molecular mechanical (QM/MM) simulation combined with the energy-representation theory of solutions to analyze the electronic-state and solvation contributions to ΔGhyd...
February 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28222597/mechanochemical-kinetics-in-elastomeric-polymer-networks-heterogeneity-of-local-forces-results-in-nonexponential-kinetics
#13
Ramesh Adhikari, Dmitrii E Makarov
A common approach to inducing selective mechanochemical transformations relies on embedding the target molecules (called mechanophores) within elastomeric polymer networks. Mechanical properties of such elastomers can also be modulated through the mechanochemical response of the constituent polymer chains. The inherent randomness in the molecular structure of such materials leads to heterogeneity of the local forces exerted on individual mechanophores. Here we use coarse-grained simulations to study the force distributions within random elastomeric networks and show that those distributions are close to exponential regardless of the applied macroscopic load, entanglement effects and/or network parameters...
February 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28221799/insoluble-off-pathway-aggregates-as-crowding-agents-during-amyloid-fibril-formation
#14
Rosa Crespo, Eva M Villar-Alvarez, Pablo Taboada, Fernando A Rocha, Ana M Damas, Pedro M Martins
The study of drug candidates for the treatment of amyloidosis and neurodegenerative diseases frequently involves in vitro measurements of amyloid fibril formation. Macromolecular crowding and off-pathway aggregation (OPA) are, by different reasons, two important phenomena affecting the scalability of amyloid inhibitors and their successful application in vivo. On the one hand, the cellular milieu is crowded with macromolecules that drastically increase the effective (thermodynamic) concentration of the amyloidogenic protein...
February 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28221796/translational-entropy-and-dispersion-energy-jointly-drive-the-adsorption-of-urea-to-cellulose
#15
Pan Chen, Yoshiharu Nishiyama, Jakob Wohlert, Ang Lu, Karim Mazeau, Ahmed E Ismail
The adsorption of urea on cellulose at room temperature has been studied using adsorption isotherm experiments and molecular dynamics (MD) simulations. Immer5sion of cotton cellulose into bulk urea solutions with concentrations between 0.01 g/mL and 0.30 g/mL led to a decrease of urea concentration in all solutions, allowing the adsorption of urea on the cellulose surface to be measured quantitatively. MD sim8ulations suggest that urea molecules form sorption layers on both hydrophobic and hydrophilic surfaces...
February 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28221047/excited-state-proton-transfer-in-indigo
#16
Joao Pina, Daniela Santos Sarmento, Marco Accoto, Pier Luigi Gentili, Luigi Vaccaro, Adelino M Galvão, J Sérgio Seixas de Melo
Excited state proton transfer (ESPT) in Indigo (Ind) and its mono hexyl-substituted derivative (NHxInd) in solution was investigated experimentally as a function of solvent viscosity, polarity and temperature, and theoretically by time-dependent DFT (TDDFT) calculations. Although a single emission band is observed, the fluorescence decays (collected at different wavelengths along the emission band using time-correlated single photon counting (TCSPC)) are bi-exponential, with two identical decay times but different pre-exponential factors, consistent with the existence of excited state keto and enol species...
February 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28219010/dynamics-of-polarons-in-organic-conjugated-polymers-with-side-radicals
#17
Junjuan Liu, Zengjiang Wei, Yalin Zhang, Yan Meng, Bing Di
Based on the one-dimensional tight-binding Su-Schrieffer-Heeger (SSH) model, and us- ing the molecular dynamics method, we discuss the dynamics of electron and hole polarons propagating along a polymer chain, as a function of the distance between side radicals and the magnitude of the transfer integrals between the main chain and the side radicals. We first dis- cuss the average velocities of electron and hole polarons as a function of the distance between side radicals. It is found that the average velocities of the electron polarons remain almost un- changed, while the average velocities of hole polarons decrease significantly when the radical distance is comparable to the polaron width...
February 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28218856/influence-of-hydrogen-bonding-on-the-kinetic-stability-of-vapor-deposited-glasses-of-triazine-derivatives
#18
Audrey Laventure, Ankit Gujral, Olivier Lebel, Christian Pellerin, Mark D Ediger
It has recently been established that physical vapor deposition (PVD) can produce organic glasses with enhanced kinetic stability, high density, and anisotropic packing, with the substrate temperature during deposition (Tsubstrate) as the key control parameter. The influence of hydrogen bonding on the formation of PVD glasses has not been fully explored. Herein, we use a high-throughput preparation method to vapor-deposit three triazine derivatives over a wide range of Tsubstrate, from 0.69 to 1.08Tg, where Tg is the glass transition temperature...
February 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28218854/long-range-dispersion-effects-on-the-water-vapor-interface-simulated-using-the-most-common-models
#19
Marcello Sega, Christoph Dellago
The long-range contribution to dispersion forces is known to have a major impact on the properties of inhomogeneous fluids, and its correct treatment is increasingly recognized as being a necessary requirement to avoid cutoff-related artefacts. Although analytical corrections for quantities like the surface tension are known, these can not take into account the structural changes induced by the long-range contributions. Here, we analyze the interfacial properties of seven popular water models, comparing the results with the cut-off version of the dispersion potential...
February 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28218850/impact-of-phosphorylation-and-pseudo-phosphorylation-on-the-early-stages-of-aggregation-of-the-microtubule-associated-protein-tau
#20
Dmitriy V Prokopovich, John W Whittaker, Micaiah M Muthee, Azka Ahmed, Luca Larini
The microtubule associated protein tau regulates the stability of microtubules within neurons in the central nervous system. In turn, microtubules are responsible for the remodeling of the cytoskeleton that ultimately leads to the formation or pruning of new connections among neurons. As a consequence, dysfunction of tau is associated with many forms of dementia as well as Alzheimer's disease. In the brain, tau activity is regulated by its phosphorylation state. Phosphorylation is a post-translational modification of proteins that adds a phosphate group to the side chain of an amino acid...
February 20, 2017: Journal of Physical Chemistry. B
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