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Journal of Physical Chemistry. B

Simone L Waite, Hua Li, Alister J Page
Deep eutectic solvents (DESs) are promising candidates as alternate media for industrial gas sequestration processes, such as denitrification via NO2 adsorption. Here, quantum chemical methods are employed to characterise NO2 solvation structure and the adsorption mechanism in choline chloride DES with urea, methylurea and thiourea hydrogen bond donors. Our results show that the solvation structure of NO2 in bulk choline chloride DES is determined by the type of hydrogen bond donor present. Changing the structure of the hydrogen bond donor not only changes its NO2 coordination mechanism, but also the coordination mechanism between NO2 and the choline and chloride ions in the DES as well...
March 22, 2018: Journal of Physical Chemistry. B
Tsuyoshi Yamaguchi, Ryuya Ando, Koji Yoshida, Toshio Yamaguchi, Hiroshi Machida
Shear viscosity of concentrated aqueous solutions of alkylaminoethanols was determined with changing the length of the alkyl chain and the concentration of dissolved CO2 . The viscosity increased with increasing the CO2 loading, reflecting the strengthening of the intermolecular electrostatic interaction. The dependence of the viscosity on both temperature and CO2 loading was described by a modified version of Vogel-Fulchar-Tammann equation. Compared at the same volume concentration of CO2 , the viscosity increased with increasing the alkyl chain lengths, and the dependence on the alkyl chain length increased with the CO2 loading...
March 21, 2018: Journal of Physical Chemistry. B
Ritika S Joshi, Dipanwita Das Mukherjee, Subhendu Chakrabarty, Ansie Martin, Manojkumar Jadhao, Gopal Chakrabarti, Angshuman Sarkar, Sujit Kumar Ghosh
In the development of small molecule drug candidates, naphthalimide based compounds hold a very important position as potent anti-cancer agents with considerable safety in drug discoveries. Being synthetically and readily accessible, naphthalimide compounds with planar architecture have been developed mostly as DNA targeting intercalators. However, in this article, we demonstrate, for the first time, wherein an unfused naphthalimide-benzothiazole bichromophoric compound 2-(6-chlorobenzo[d] thiazol-2-yl)-1H-benzo[de] isoquinoline-1,3(2H)-dione (CBIQD), designed and synthesized by our group, seem to expand the bioactivity of naphthalimide as anti-mitotic agents also...
March 21, 2018: Journal of Physical Chemistry. B
William W Parson
Rate constants for photochemical charge separation and recombination in a zinc-porphyrin-benzoquinone cyclophane are calculated by an approach that was developed recently to include effects of vibrational dephasing and relaxation and to reduce the dependence on freely adjustable parameters. The theory is extended to treat the rate of vibrational relaxation individually for each vibrational sublevel of the initial charge-transfer product. Quantum-mechanical/molecular-mechanical simulations of the reactions in iso-octane, toluene, dichloromethane and acetonitrile suggest that charge separation occurs at conical intersections in the two more polar solvents, but at avoided crossings in the nonpolar solvents...
March 20, 2018: Journal of Physical Chemistry. B
Karina Panczyk, Karolina Gaweda, Mateusz Drach, Wojciech Plazinski
An extension of the GROMOS 56a6CARBO/CARBO_R force field for hexopyranose-based carbohydrates is presented. The additional parameters describe the conformational properties of uronate residues. The three distinct chemical states of the carboxyl group are considered: deprotonated (negatively charged), protonated (neutral) and esterified (neutral). The parameterization procedure was based on quantum-chemical calculations and the resulting parameters were tested in the context of: (i) flexibility of the pyranose rings under different pH conditions; (ii) conformation of the glycosidic linkage of the (1→4)-type for uronates with different chemical states of carboxyl moieties; (iii) conformation of the exocyclic (i...
March 20, 2018: Journal of Physical Chemistry. B
Yuanyuan Tao, Xiaoteng Ma, Yaqian Cai, Li Liu, Hanying Zhao
Synthesis and self-assembly of bioconjugates composed of proteins and synthetic molecules have been widely studied because of the potential applications in medicine, biotechnology and nanotechnology. One of the challenging researches in this area is to develop organic solvent-free approaches to the synthesis and self-assembly of amphiphilic bioconjugates. In this research, dialysis-assisted approach, a method based on unimer-aggregate equilibrium, was applied in the co-assembly of lysozyme and conjugate of cholesterol and glutathione (Ch-GSH)...
March 20, 2018: Journal of Physical Chemistry. B
Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka
In this study, an ab initio fragment molecular orbital (FMO) methodology was developed to evaluate the solvent effects on electrostatic interactions, which make a significant contribution to the physical and chemical processes occurring in biological systems. Here, a fully polarizable solute consisting of the FMO electron density was electrostatically coupled with an implicit solvent based on the Poisson-Boltzmann (PB) equation; in addition, the nonpolar contributions empirically obtained from the molecular surface area (SA) were added...
March 20, 2018: Journal of Physical Chemistry. B
André Luiz Sehnem, Doreen Niether, Simone Wiegand, Antonio Martins Figueiredo Neto
The ionic Soret effect induced by temperature gradients is investigated in organic electrolytes (tetramethylammonium and tetrabutylammonium hydroxides) dispersed in water using a holographic grating experiment. We report the influences of temperature and salt concentrations on the Soret, diffusion and thermal diffusion coefficients. Experimental results to the thermal diffusion coefficient are compared with a theoretical description for thermodiffusion of Brownian particles in liquids based in the thermal expansion of the liquid solution...
March 20, 2018: Journal of Physical Chemistry. B
Catarina S H Jesus, Pedro Fernandes Cruz, Luis G Arnaut, Rui M M Brito, Carlos Serpa
The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution...
March 20, 2018: Journal of Physical Chemistry. B
Anton Khmelnitskiy, Rafael G Saer, Robert E Blankenship, Ryszard J Jankowiak
We report high-resolution (low-temperature) absorption, emission and nonresonant/resonant hole-burned (HB) spectra and results of excitonic calculations using a non-Markovian reduced density matrix theory (with an improved algorithm for parameter optimization in heterogeneous samples) obtained for the Y16F mutant of the Fenna-Matthews-Olson (FMO) trimer from the green sulfur bacterium Chlorobaculum tepidum. We show that the Y16F mutant is a mixture of FMO complexes with three independent low-energy traps (located near 817, 821, and 826 nm), in agreement with measured composite emission and HB spectra...
March 19, 2018: Journal of Physical Chemistry. B
Shalini Awasthi, Shalini Gupta, Ravi Tripathi, Nisanth N Nair
Enhanced sampling of large number of collective variables (CVs) is inevitable in molecular dynamics (MD) simulations of complex chemical processes such as enzymatic reactions. Due to the computational overhead of hybrid quantum mechanical/molecular mechanical (QM/MM) based (MD) simulations, especially together with density functional theory (DFT), predictions of reaction mechanism and estimation of free energy barriers have to be carried out within few tens of picoseconds. We show here that the recently developed Temperature Accelerated Sliced Sampling (TASS) method allows one to sample large number of CVs, thereby enabling us to obtain rapid convergence in free energy estimates in QM/MM MD simulation of enzymatic reactions...
March 19, 2018: Journal of Physical Chemistry. B
Philipp S Orekhov, Ekaterina G Kholina, Marine E Bozdaganyan, Alexey M Nesterenko, Ilya B Kovalenko, Marina G Strakhovskaya
Phthalocyanines are aromatic macrocyclic compounds, which are structurally related to porphyrins. In clinical practice phthalocyanines are used in fluorescence imaging and photodynamic therapy of cancer and non-cancer lesions. Certain forms of the substituted polycationic metallophthalocyanines have been previously shown to be active in photodynamic inactivation of both Gram-negative and Gram-positive bacteria, one of them is zinc octakis(cholinyl)phthalocyanine (ZnPcChol8+ ). However, the molecular details of how these compounds translocate across bacterial membranes still remain unclear...
March 19, 2018: Journal of Physical Chemistry. B
Leena Aggarwal, Parbati Biswas
The distribution and local structural order of hydration water in the proximity of intrinsically disordered proteins/regions are investigated within the frame work of 3D-RISM theory. The hydration water distribution around the protein surface is quantified in terms of the 3D distribution function and the water-protein radial distribution function, while the local ordering of water molecules around the protein surface is measured in terms of the tetrahedral order parameter. To the best of our knowledge, this is the first theoretical study of the 3D hydration water distribution profiles of disordered proteins...
March 19, 2018: Journal of Physical Chemistry. B
Arup Kumar Pathak, Tusar Bandyopadhyay
A well-tempered metadynamics simulation is performed to study the unbinding process of a fluorinated oxime (FHI-6) drug from the active site gorge of acetylcholinesterase enzyme in a polarizable water medium. Cation-π interactions, water bridge, and hydrogen bridge formations between the protein and the drug molecule are found to strongly influence the unbinding process, forming basins and barriers along the gorge pathway. Distinct unbinding pathways are found when compared with its recently reported nonfluorinated analogue, HI-6...
March 19, 2018: Journal of Physical Chemistry. B
Natércia Fernandes Brás, Diogo Santos-Martins, Pedro A Fernandes, Maria João Ramos
The excessive consumption of starch in human diets is associated with highly prevalent chronic metabolic diseases such as type 2 diabetes and obesity. α-glucosidase enzymes contribute for the digestion of starch into glucose and are thus attractive therapeutic targets for diabetes. Given that the active sites of the various families of α-glucosidases have different sizes and structural features, atomistic descriptions of the catalytic mechanisms of these enzymes can support the development of potent and selective new inhibitors...
March 16, 2018: Journal of Physical Chemistry. B
Shushan He, Lutz Maibaum
Understanding the (de)mixing behavior of multicomponent lipid bilayers is an important step towards unraveling the nature of spatial composition heterogeneities in cellular membranes and their role in biological function. We use coarse-grained molecular dynamics simulations to study the composition phase diagram of a quaternary mixture of phospholipids and cholesterol. This mixture is known to exhibit both uniform and coexisting phases. We compare and combine different statistical measures of membrane structure to identify the onset of phase coexistence in composition space...
March 16, 2018: Journal of Physical Chemistry. B
Blake J Bleier, Shelley L Anna, Lynn M Walker
The goal of this work is to develop a simple microfluidic approach to characterizing liquid-liquid phase behavior in complex aqueous mixtures of organics and salts. We take advantage of the permeability of inexpensive microfluidic devices to concentrate aqueous solutions on chip. We demonstrate a technique that allows phase boundaries to be identified with high compositional resolution and small sample volumes. Droplets of single phase samples are produced on-chip and concentrated in the device beyond the phase boundary line to map system phase behavior...
March 16, 2018: Journal of Physical Chemistry. B
Diego Jaramillo-Cano, Maud Formanek, Christos N Likos, Manuel Camargo
Star block-copolymers (SBCs) have been demonstrated to constitute self-assembling building blocks with specific softness, functionalization, shape and flexibility. In this work we study the behaviour of an isolated SBC under shear flow by means of particle-based multi-scale simulations. We systematically analyse the conformational properties of low-functionality stars as well as the formation of attractive patches on their corona as a function of the shear rate. We cover a wide range of system parameters, including functionality, amphiphilicity and solvent quality...
March 16, 2018: Journal of Physical Chemistry. B
Ran Chen, Ying Lu, Zhiyong Jiang, Yongfeng Men
The poly(4-methyl-1-pentene) sample was used to investigate the cavitation induced stress-whitening phenomenon during stretching at different temperatures via the ultra-small-angle X-ray scattering technique. Two modes of cavitation were found that mode I cavitation activated around yield point followed by mode II cavitation generated in highly oriented state. The critical strain for initiating the mode II cavitation increases with the increase of stretching temperature whereas the critical stress grew steadily in the lower temperature regime (30~60oC) and reached a plateau at 70oC...
March 16, 2018: Journal of Physical Chemistry. B
Charles M Luft, Elango Munusamy, Jeanne E Pemberton, Steven D Schwartz
A detailed molecular dynamics simulation study is presented on the behavior of aggre- gates composed of the nonionic monorhamnolipid α-rhamnopyranosyl-β-hydroxydecanoyl- β -hydroxydecanoate (Rha-C10-C10) and decane in bulk water. A graph theoretical approach was utilized to characterize the size and composition of the many aggregates generated in our simulations. Overall we observe that the formation of oil in Rha-C10-C10 aggregates is a fa- vorable process. Detailed analysis on the surfactant/oil aggregate shows that larger aggregates are stable...
March 16, 2018: Journal of Physical Chemistry. B
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