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Journal of Physical Chemistry. B

Linda A Peteanu, Sanchari Chowdhury, Jurjen Wildeman, Matthew Y Sfeir
One measure of exciton mobility in an aggregate is the efficiency of exciton-exciton annihilation (EEA). Both exciton mobilities and EEA are enhanced for aggregate morphologies in which the distances between chromophores and their relative orientations are favorable for Förster energy transfer. Here this principle is applied to gauge the strength of inter-chain interactions in aggregates of two substituted PPV oligomers of 7 (OPPV7) and 13 (OPPV13) phenylene rings. These are models of the semiconducting conjugated polymer MEH-PPV...
January 20, 2017: Journal of Physical Chemistry. B
Nicolas O Johnson, Taylor Patrick Light, Gina MacDonald, Yanjie Zhang
This work investigates the interactions of a series of 11 anions with caffeine by utilizing (13)C and (1)H NMR and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. The aim of this study is to elucidate the molecular mechanisms of ion interactions with caffeine and to study how these interactions affect caffeine aggregation in aqueous solution. The chemical shift changes of caffeine (13)C and (1)H in the presence of salts provide a measure for anions' salting-out/salting-in abilities on individual carbon and hydrogen atoms in caffeine...
January 20, 2017: Journal of Physical Chemistry. B
Hao Jiang, Ioannis George Economou, Athanassios Z Panagiotopoulos
Phase equilibria of water/CO2 and water/n-alkane mixtures over a range of temperatures and pressures were obtained from Monte Carlo simulations in the Gibbs ensemble. Three sets of Drude-type polarizable models for water, namely the BK3, GCP, and HBP models, were combined with a polarizable Gaussian charge CO2 (PGC) model to represent the water/CO2 mixture. The HBP water model describes hydrogen bonds between water and CO2 explicitly. All models underestimate CO2 solubility in water if standard combining rules are used for the dispersion interactions between water and CO2 ...
January 20, 2017: Journal of Physical Chemistry. B
Soichiro Kitazawa, Martin J Fossat, Scott A McCallum, Angel E Garcia, Catherine Ann Royer
Beyond defining the structure and stability of folded states of proteins, primary amino acid sequences determine all of the features of their conformational landscapes. Characterizing how sequence modulates the population of protein excited states or folding pathways requires atomic level detailed structural and energetic information. Such insight is essential for improving protein design strategies, as well as for interpreting protein evolution. Here, high pressure NMR and molecular dynamics simulations were combined to probe the conformational landscape of a small model protein, the tryptophan cage variant, Tc5b...
January 20, 2017: Journal of Physical Chemistry. B
Lin Liu, Andrey G Cherstvy, Ralf Metzler
What are the physical laws of the diffusive search of proteins for their specific binding sites on DNA in the presence of the macromolecular crowding in cells? We performed extensive computer simulations to elucidate the protein target search on DNA. The novel feature is the viscoelastic non-Brownian protein bulk diffusion recently observed experimentally. We examine the influence of the protein-DNA binding affinity and the anomalous diffusion exponent on the target search time. In all cases an optimal search time is found...
January 20, 2017: Journal of Physical Chemistry. B
Anu Kadyan, Siddharth Pandey
Interactions present within the solubilizing media constituted of ionic liquids (ILs) govern the outcomes of chemical processes carried out within such media by controlling the behavior of solutes dissolved therein. Fluidity afforded by IL-based media, in this context, not only reveals interactions present within the system, it also helps decide whether the system is suitable for an application. Response of spectroscopic microviscosity probes dissolved in IL and IL-based solvents, in this regard, reveals information on both solute-solvent and solvent-solvent interactions present within the system...
January 20, 2017: Journal of Physical Chemistry. B
Daniel Kuebler, Anna Bergmann, Lukas Weger, Kim Nadine Ingenbosch, Kerstin Hoffmann-Jacobsen
Detergents are commonly applied in lipase assays to solubilize the sparingly soluble model substrates. However, detergents affect lipases as well as substrates in multiple ways. The effect of detergents on lipase activity is commonly attributed to conformational changes in the lid region. This study deals with the effect of the non-ionic detergent, polyethylene glycol dodecyl ether, on a lipase that does not contain a lid sequence, lipase A from Bacillus subtilis (BSLA). We show that BSLA activity depends strongly on detergent concentration and the dependency profile changes with pH...
January 20, 2017: Journal of Physical Chemistry. B
Liqun Zhang, Matthias Buck
The Plexin family of transmembrane receptors are unique in that their intracellular region interacts directly with small GTPases of the Rho family. The Rho GTPase Binding Domain of plexin (RBD) -that is responsible for these interactions- can bind with Rac1 as well as Rnd1 GTPases. GTPase complexes have been crystallized with the RBDs of plexinA1, -A2 and -B1. The protein association is thought to elicit different functional responses, possibly in a GTPase/plexin isoform specific manner. In this project, we investigated complexes between several RBD and Rac1/Rnd1 GTPases using multi-microsecond length all atom molecular dynamics simulations, also with reference to the free forms of the RBDs and GTPases...
January 19, 2017: Journal of Physical Chemistry. B
Minming Shen, Yuyang Zhang, Kaizhou Chen, Siying Che, Jia Yao, Haoran Li
The ionicity value, which is a key property of protic ionic liquids, was obtained by the attenuated total reflection Fourier transform infrared spectroscopy and nuclear magnetic resonance respectively for a protic ionic liquid: n-propylammonium acetate. The method of potentiometric titration is found not suitable for such kind of ionic liquid as the ∆pKa of the compositing acid and base is relatively small. In the IR spectrum, molecular species can be directly observed in the range 1200-1800 cm-1, and the ratio of ionic and molecular species can be quantitatively calculated by the area of characteristic absorption peaks calibrated by standard curve from NaAc/HAc solutions...
January 19, 2017: Journal of Physical Chemistry. B
Davinder Singh, Shubhrangshu Dasgupta
We show that the coherence between different bacteriochlorophyll-a (BChla) sites in the Fenna-Mathews-Olson complex is an essential ingredient for excitation energy transfer between various sites. The coherence delocalizes the excitation energy, which results in the redistribution of excitation among all the BChla sites in the steady state. We further show that the system remains partially coherent at the steady state. In our numerical simulation of the non-Markovian density matrix equation, we consider both the inhomogeneity of the protein environment and the effect of active vibronic modes...
January 19, 2017: Journal of Physical Chemistry. B
Lennart A I Ramakers, Gordon Hithell, John J May, Gregory M Greetham, Paul M Donaldson, Michael Towrie, Anthony W Parker, Glenn A Burley, Neil T Hunt
The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced non-covalent interactions between ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a sub-optimal alternating A-T sequence. Results from 2-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region...
January 19, 2017: Journal of Physical Chemistry. B
Nikolay V Plotnikov, Satish Kumar Singh, Jason C Rouse, Sandeep Kumar
Early identification of asparagine deamidation and aspartate isomerization degradation sites can facilitate the successful development of biopharmaceuticals. Several knowledge-based models have been proposed to assess these degradation risks. In this study, we propose a physics-based approach to identify the degradation sites on the basis of the free-energy barriers along the prechemical conformational step and the chemical reaction pathway. These contributions are estimated from classical and quantum mechanics/molecular mechanics molecular dynamics simulations...
January 19, 2017: Journal of Physical Chemistry. B
Malika Talantikite, Kahina Aoudia, Lazhar Benyahia, Lila Chaal, Christophe Chassenieux, Claude Deslouis, Cédric Gaillard, Boualem Saidani
Self-assembly in aqueous solutions of an amphiphilic comblike polyelectrolyte (80C12) that consists of a polystyrene (PS) backbone onto which quaternary ammonium pendant moieties have been grafted has been investigated by light scattering and cryo-transmission electron microscopy measurements in the presence of KCl and methylviologen dication (MV(2+)) under conditions mimicking those for electrochemical measurements. Polymer chains self-assemble within branched cylindrical micelles that display viscoelastic properties, characterized by a relaxation time of 4 s...
January 19, 2017: Journal of Physical Chemistry. B
Joshua S Ostrander, Robert Knepper, Alexander S Tappan, Jeffrey J Kay, Martin T Zanni, Darcie A Farrow
Pentaerythritol tetranitrate (PETN) is a common secondary explosive and has been used extensively to study shock initiation and energy propagation in energetic materials. We report 2D IR measurements of PETN thin films that resolve vibrational energy transfer and relaxation mechanisms. Ultrafast anisotropy measurements reveal a sub-500 fs reorientation of transition dipoles in thin films of vapor-deposited PETN that is absent in solution measurements, consistent with intermolecular energy transfer. The anisotropy is frequency dependent, suggesting spectrally heterogeneous vibrational relaxation...
January 18, 2017: Journal of Physical Chemistry. B
Irina Rörich, Oleksandr V Mikhnenko, Dominik W Gehrig, Paul W M Blom, Nicoleta Irina Craciun
Using time-resolved photoluminescence (TRPL) spectroscopy the exciton lifetime in a range of conjugated polymers is investigated. For poly(p-phenylene vinylene) (PPV)-based derivatives and a polyspirobifluorene copolymer (PSBF) we find that the exciton lifetime is correlated with the energetic disorder. Better ordered polymers exhibit a single exponential PL decay with exciton lifetimes of a few hundred picoseconds, whereas polymers with a larger degree of disorder show multi-exponential PL decays with exciton lifetimes in the nanosecond regime...
January 18, 2017: Journal of Physical Chemistry. B
Rivkah Tamar Rogawski, Ivan V Sergeyev, Yongjun Li, Maria Francesca Ottaviani, Virginia W Cornish, Ann E McDermott
Dynamic nuclear polarization is an emerging technique for sensitizing solid state NMR experiments by transferring polarization from electrons to nuclei. Stable biradicals, the polarization source for the cross effect mechanism, are typically co-dissolved at millimolar concentrations with proteins of interest. Here we describe the high-affinity biradical tag TMP-T, created by covalently linking trimethoprim, a nanomolar affinity ligand of dihydrofolate reductase (DHFR), to the biradical polarizing agent TOTAPOL...
January 18, 2017: Journal of Physical Chemistry. B
Nilangshu Mandal, Saied Md Pratik, Ayan Datta
Confined molecular chambers such as macrocycle bridged E1-H···H-E2 (E1(E2) = Si(Si), 1) exhibit rare ultrashort H···H nonbonded contacts (d(H···H) = 1.56 Å). In this article, on the basis of density functional theory and ab initio molecular dynamics simulations, we propose new molecular motifs where d(H···H) can be reduced to 1.44 Å (E1(E2) = Si(Ge), 3). Further tuning the structure of the macrocycle by replacing the bulky phenyl groups by ethylenic spacers and substitution of the H-atoms by -CN groups makes the cavity more compact and furnishes even shorter d(H···H) = 1...
January 18, 2017: Journal of Physical Chemistry. B
Kei Moritsugu, Tohru Terada, Akinori Kidera
Protein-ligand interactions are frequently coupled with protein structural changes. Focusing on the coupling, we present the free-energy surface (FES) of the ligand-binding process for glutamine-binding protein (GlnBP) and its ligand, glutamine, in which glutamine binding accompanies large-scale domain closure. All-atom simulations were performed in explicit solvents by multiscale enhanced sampling (MSES), which adopts a multicopy and multiscale scheme to achieve enhanced sampling of systems with a large number of degrees of freedom...
January 18, 2017: Journal of Physical Chemistry. B
Yizhak Marcus
The cohesive energy densities, ced, and the internal pressures, Pint, of aqueous methanol mixtures are calculated from literature data for the entire composition range over a temperature range of 273-473 K, at saturation pressures up to 373 K and at 7.0 MPa above this temperature. Ratios Pint/ced are measures of the "structuredness" of the studied fluids, and the small values noted signify "tight" structures, due to hydrogen bonding. The "tighter" the structure, the larger is the surface tension of the mixtures (at 298...
January 18, 2017: Journal of Physical Chemistry. B
Ellinor Haglund, Anna Pilko, Roy Wollman, Patricia Ann Jennings, José Nelson Onuchic
Protein engineering is a powerful tool in drug design and therapeutics, where disulphide bridges are commonly introduced to stabilize proteins. However, these bonds also introduce covalent loops, which are often neglected. These loops may entrap the protein backbone on opposite sides, leading to a "knotted" topology, forming a so-called Pierced Lasso (PL). In this elegant system, the "knot" is held together with a single disulphide bridge where part of the polypeptide chain is threaded through. The size and position of these covalent loops can be manipulated through protein design in vitro, whereas nature uses polymorphism to switch the PL topology...
January 18, 2017: Journal of Physical Chemistry. B
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