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Journal of Physical Chemistry. B

Toshiki Yamada, Yukihiro Tominari, Shukichi Tanaka, Maya Mizuno
Infrared spectroscopy was performed on ionic liquids (ILs) that had imidazolium cations with different alkyl chain lengths and various halogen or molecular anions with and without a small amount of water. The molar concentration normalized absorbance due to +C-H vibrational modes in the range of 3000 to 3200 cm-1 was nearly identical for ILs that had imidazolium cations with different alkyl chain lengths and the same anions. A close correlation was found between the red-shifted +C-H vibrational modes, the chemical shift of +C(2)-H proton, and the energy stabilization of hydrogen-bonding interaction...
March 27, 2017: Journal of Physical Chemistry. B
Lukasz Skorka, Piotr Kurzep, Timothée Chauviré, Lionel Dubois, Jean-Marie Mouesca, Vincent Maurel, Irena Kulszewicz-Bajer
Triarylamines oxidized to radical cations can be used as stable spins sources for the design of high-spin compounds. Here, we present the synthesis of the polyarylamine containing hexaazacyclophanes linked via meta-terphenyl bridges. Spins, created after the oxidation of the polymer, can be coupled magnetically in cyclophane moieties via meta-phenyl and along the polymer chain via meta-terphenyl units. The formation of quintet spin state was evidenced by pulsed-EPR nutation spectroscopy. Two exchange coupling constants via both couplers were determined experimentally and corresponded to J/k = 89 K in cyclophane moiety and j/k = 17 K via meta-terphenyl...
March 27, 2017: Journal of Physical Chemistry. B
Leah Marie Heist, Chi-Duen Poon, Edward Thaddeus Samulski, Demetri J Photinos
High field deuterium NMR spectroscopy is used to characterize a number of molecular liquids and their mixtures in order to probe the directional part of the intermolecular interactions through the orientational ordering induced in the isotropic liquid phase by the spectrometer magnetic field. The systems studied include benzene, chloroform, hexafluorobenzene and thiophene at various concentrations and in mixtures. Dilution with the magnetically isotropic tetramethylsilane provides quantification of ordering at "infinite magnetic dilution", i...
March 27, 2017: Journal of Physical Chemistry. B
Daria L Melnikova, Vladimir Dmitrievich Skirda, Irina V Nesmelova
Translational diffusion is the major mode of macromolecular transport in leaving organisms and therefore it is vital to many biological and biotechnological processes. Although translational diffusion of proteins has received considerable theoretical and experimental scrutiny, much of that attention has been directed towards the description of globular proteins. The translational diffusion of intrinsically disordered proteins (IDPs), however, is much less studied. Here, we use a pulsed-gradient nuclear magnetic resonance technique (PFG NMR) to investigate the translational diffusion of a disordered protein in a wide range of concentrations using α-casein that belongs to the class of natively disordered proteins as an example...
March 27, 2017: Journal of Physical Chemistry. B
Akira Sakaguchi, Kenji Higashiguchi, Hajime Yotsuji, Kenji Matsuda
Photoinduced clustering of polystyrene microbeads and photocontrol of their diffusion was achieved in water with the assistance of photoinduced transformation of supramolecular architecture of amphiphilic diarylethene between sphere and fiber states. When a suspension of polystyrene beads containing the sphere state of diarylethene was UV-irradiated from beneath, clustering of the polystyrene beads by thermal convection was observed. The velocity of clustering was dependent on the amount of photogenerated nanofibers that determines the viscosity of the water...
March 27, 2017: Journal of Physical Chemistry. B
Navjeet Ahalawat, Rajesh Kumar Murarka
The AMP-activated protein kinase (AMPK), a central enzyme in the regulation of energy homeostasis, is an important drug target for type 2 diabetes, obesity and cancer. Binding of adenosine nucleotides to the regulatory γ-subunit tightly regulates the activity of this enzyme. Though recent crystal structures of AMPK have provided important insights into the allosteric activation of AMPK, molecular details of the regulatory mechanism of AMPK activation is still elusive. Here, we have performed extensive all-atom molecular dynamics (MD) simulations and shown that the kinase domain (KD) and γ-subunit comes closer resulting in a more compact heterotrimeric AMPK complex in AMP-bound state compared to the ATP-bound state...
March 27, 2017: Journal of Physical Chemistry. B
Jianguo Li, Zhongqiao Hu, Roger Beuerman, Chandra Verma
Human β-defensin 2 is a cysteine-rich antimicrobial peptide. In the crystal state, the N-terminal segment (residues 1-11) exhibits a helical conformation. However, a truncated form, with four amino acids removed from the N-terminus, adopts nonhelical conformations in solution, as shown by NMR. To explore the molecular origins of these different conformations, we performed Hamiltonian replica exchange molecular dynamics simulations of the peptide in solution and in the crystal state. It is found that backbone hydration and specific protein-protein interactions are key parameters that determine the peptide conformation...
March 27, 2017: Journal of Physical Chemistry. B
Balázs Fábián, Marcello Sega, Vladimir P Voloshin, Nikolai N Medvedev, Pál Jedlovszky
The effect of four general anesthetics, namely chloroform, halothane, diethyl ether, and enflurane on the free volume fraction and lateral pressure profiles in a fully hydrated dipalmitoylphosphatidylcholime (DPPC) membrane is investigated by means of computer simulation. In order to find changes that can be related to the molecular mechanism of anesthesia as well as its pressure reversal, the simulations are performed both at atmospheric and high (1000 bar) pressures. The obtained results show that the additional free volume occurring in the membrane is localized around the anesthetic molecules themselves...
March 27, 2017: Journal of Physical Chemistry. B
Lauren Bottorf, Sophia Rafferty, Indra Dev Sahu, Robert M McCarrick, Gary A Lorigan
Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy was used to distinguish between the local secondary structures of an α-helix and a 310-helix. Previously, we have shown that ESEEM spectroscopy in combination with site-directed spin labeling (SDSL) and 2H-labeled amino acids (i) can probe the local secondary structure of α-helices, resulting in an obvious deuterium modulation pattern, where i+4 positions generally show larger 2H ESEEM peak intensities than i+3 positions. Here, we have hypothesized that due to the unique turn periodicities of an α-helix (3...
March 24, 2017: Journal of Physical Chemistry. B
E K Lenzi, R S Zola, H V Ribeiro, Denner S Vieira, F Ciuchi, A Mazzulla, N Scaramuzza, L R Evangelista
In this study, we argue that ion motion in electrolytic cells containing Milli-Q water, weak electrolytes, or liquid crystals may exhibit unusual diffusive regimes that deviate from the expected behavior, leading the system to present an anomalous diffusion. Our arguments lie on the investigation of the electrical conductivity and its relationship with the mean square displacement, which may be used to characterize the ionic motion. In our analysis, the Poisson-Nernst-Planck diffusional model is used with extended boundary conditions to simulate the charge transfer, accumulation, and/or adsorption-desorption at the electrode surfaces...
March 24, 2017: Journal of Physical Chemistry. B
Charles W Bauschlicher, Eric W Bucholz, Justin B Haskins, Joshua D Monk, John W Lawson
Ab initio techniques are used to study the interaction of ethylene glycol and water with a phenolic polymer. The water bonds more strongly with the phenolic OH than with the ring. The phenolic OH groups can form hydrogen bonds between themselves. For more than one water molecule, there is a competition between water-water and water-phenolic interactions. Ethylene glycol shows the same effects as those of water, but the potential energy surface is further complicated by CH2-phenolic interactions, different conformers of ethylene glycol, and two OH groups on each molecule...
March 24, 2017: Journal of Physical Chemistry. B
Halil I Okur, Yixing Chen, Nikolay Smolentsev, Evangelia Zdrali, Sylvie Roke
Three-dimensional (3D) phospholipid monolayers at hydrophobic surfaces are ubiquitous and found in nature as adiposome organelles or in man-made materials such as drug delivery systems. However, the molecular level understanding of such monolayers remains elusive. Here, we investigate the molecular structure of phosphatidylcholine (PC) lipids forming 3D monolayers on the surface of hexadecane nanodroplets. The effects of acyl chain length, saturation, and number of acyl tails per lipid were studied with vibrational sum frequency and second harmonic scattering techniques...
March 24, 2017: Journal of Physical Chemistry. B
Majid Shahbabaei, Daejoong Kim
In this study, molecular dynamics simulations are used to investigate water transport mechanisms through hourglass-shaped pore structure in nanoporous boron nitride (BN) and graphene multilayers. An increase in water flux is evidenced as the gap between the layers increases, reaching a maximum of 41 and 43 at d=6 Å in BN and graphene multilayers, respectively. Moreover, the BN multilayer exhibits less flux compared to graphene due to large friction force and energy barrier. In BN, the friction force dramatically increases when the layers are strongly stacked (d=3...
March 23, 2017: Journal of Physical Chemistry. B
Antonio De Nicola, Andrea Correa, Giuseppe Milano, Pietro La Manna, Pellegrino Musto, Giuseppe Mensitieri, Giuseppe Scherillo
Hydrogen Bonding (HB) interactions play a major role in determining the behavior of macromolecular systems absorbing water. In fact, functional and structural properties of polymer-water mixtures are affected by the amount and type of these interactions. This contribution aims at a molecular level understanding of the interactional scenario for the technologically relevant case of the polyetherimide-water system. The problem has been tackled by combining different experimental and theoretical approaches which, taken together, provide a comprehensive physical picture...
March 23, 2017: Journal of Physical Chemistry. B
Nikhil R Jana, Chumki Dalal
Although trans-activating transcription (TAT)-peptide functionalized nanoparticle/polymer/liposome is widely used for cellular transfection applications, the multivalency (number of attached peptide per particle) effect on cell uptake mechanism and subcellular targeting performance is largely unexplored. Here we show that multivalency of nanoparticle controls the cellular interaction, cellular entry/exit mechanism and subcellular targeting performance. We have synthesized TAT peptide functionalized quantum dot (QD) of 30-35 nm hydrodynamic diameter with varied multivalency from 10 to 75 (e...
March 23, 2017: Journal of Physical Chemistry. B
Nikhil Aggarwal, Archita Patnaik
Structure - property correlations in Rubrene (RB) colloidal J-aggregates were unravelled by steady state and time resolved spectroscopy in conjunction with excited state density functional calculations. The RB J-aggregate with a slippage angle θ = 30.4(0), estimated from the monomeric transition dipole moment directions, exhibited a broad FWHM of 1073 cm(-1) and a 5 nm red shifted absorption band carrying a transition dipole moment (M ⃗_(λagg )= 1.80 D) almost equivalent to the monomeric dye (M ⃗_(λmon )=1...
March 23, 2017: Journal of Physical Chemistry. B
Ariel Antonio Campos Toledo Hijo, Guilherme José Maximo, Mariana Conceição Costa, Rosiane Lopes Cunha, Jorge Fernando Brandão Pereira, Kiki Adi Kurnia, Eduardo A Caldas Batista, Antonio J A Meirelles
Protic ionic liquids (PILs) have emerged as promising compounds and attracted the interest of the industry and the academy community, due to their easy preparation and unique properties. In the context of green chemistry, the use of biocompounds, such as fatty acids for their synthesis could disclose a possible alternative way to produce ILs with low or non-toxic effect and consequently, expanding their applicability in bio-based processes or in the development of bioproducts. This work addressed efforts to a better comprehension of the complex Solid-Liquid-Crystal-Liquid thermodynamic equilibrium of twenty new PILs synthesized by using fatty acids commonly found in vegetable oils, as well as their rheological profile and self-assembling ability...
March 23, 2017: Journal of Physical Chemistry. B
Tao Su, Ming-De Li, Jiani Ma, David Lee Phillips
The mechanism of the defluorination reaction(s) of lomefloxacin (LF) upon light illumination was investigated by using ultrafast laser flash photolysis combined with transient resonance Raman spectroscopy in near neutral water solution. The zwitterionic configuration of LF was determined to be the main species present in the near neutral water solution and was the species that was photoexcited to initiate the photochemical reaction. Femtosecond transient absorption revealed that the first excited singlet state (S1) of LF did not appreciably undergo intersystem crossing (ISC) and instead partially decayed to the ground state via fluorescence emission and partially underwent the cleavage of the carbon-fluorine bond at position 8 to produce a singlet LF aryl cation intermediate...
March 23, 2017: Journal of Physical Chemistry. B
Takahito Yasuda, Kaito Sasaki, Rio Kita, Naoki Shinyashiki, Shin Yagihara
Broadband dielectric spectroscopy measurements were performed on partially crystallized gelatin-water mixtures with gelatin concentrations of 1-5 wt % for temperatures between 123 and 298 K to study the dynamics of ice. These systems contain only hexagonal ice. Nevertheless, four dielectric relaxation processes of ice were observed. At temperatures below the crystallization temperature, a loss peak was observed, and it separated into four loss peaks at around 225 K. Using the temperature and concentration dependencies of these relaxation processes, we confirmed that these four processes originated from ice...
March 23, 2017: Journal of Physical Chemistry. B
Paweł Bilski, Kacper Drużbicki, Jacek Jenczyk, Jadwiga Mielcarek, Jan Wąsicki
Molecular and vibrational dynamics of a widely used cholesterol-lowering agent, lovastatin, have been studied by combining nuclear magnetic resonance relaxation experiments ((1)H NMR) with inelastic neutron scattering (INS) and periodic density functional theory modeling (plane-wave DFT). According to a complementary experimental study, lovastatin shows no phase transitions down to cryogenic conditions, while a progressive, stepwise activation of several molecular motions is observed below room temperature...
March 23, 2017: Journal of Physical Chemistry. B
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