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Journal of Physical Chemistry. B

Jasmin Milzetti, Divya Nayar, Nico F A van der Vegt
The computation of Kirkwood-Buff integrals (KBIs) using molecular simulations of closed systems is challenging due to finite system-size effects. One of the problems involves the incorrect asymptotic behavior of the radial distribution function. Corrections to rectify such effects have been proposed in the literature. This study reports a systematic comparison of the proposed corrections (as given by Ganguly et al. J. Chem. Theory Comput. 2013, 9, 1347-1355 and Krueger et al. J. Phys. Chem. Lett. 2013, 4, 4-7) to assess the asymptotic behavior of the RDFs, the KBIs as well as the estimation of thermodynamic quantities for ideal urea--water and non-ideal modified-urea--water mixtures using molecular dynamics simulations...
January 17, 2018: Journal of Physical Chemistry. B
Saumyak Mukherjee, Sayantan Mondal, Ashish Anilrao Deshmukh, Balasubramanian Gopal, Biman Bagchi
Self-assembly of proteins often gives rise to interesting quasi-stable structures that serve important biological purposes. Insulin hexamer is such an assembly. While monomer is the biologically active form of insulin, hexamer serves as the storehouse of the hormone. The hexamer also prevents the formation of higher order aggregates. While several studies explored the role of bivalent metal ions like Zn2+, Ca2+ etc. in the stabilization of the hexameric form, the role of water molecules has been ignored. We combine molecular dynamics simulations, quantum calculations and X-ray analyses to discover that a team of approximately ten water molecules confined inside a barrel-shaped nano-cavity at the center of insulin hexamer is one of the major causes that account for the unusual stability of the biomolecular assembly...
January 17, 2018: Journal of Physical Chemistry. B
Alpha A Lee, Sarah V Kostinski, Michael P Brenner
Understanding and controlling polyelectrolyte adsorption onto carbon nanotubes is a fundamental challenge in nanotechology. Polyelectrolytes have been shown to stabilise nanotube suspensions through adsorbing onto the nanotube surface, and polyelectrolyte-coated nanotubes are emerging as building blocks for complex and addressable self-assembly. The conventional wisdom suggests that polyelectrolyte adsorption onto nanotubes is driven by specific chemical or van der Waals interactions. We develop a simple mean-field model and show that ion-image attraction is a significant effect for adsorption onto conducting nanotubes at low salt concentrations...
January 17, 2018: Journal of Physical Chemistry. B
Miha Kastelic, Vojko Vlachy
This study presents the theory for liquid--liquid phase separation for systems of molecules modeling monoclonal antibodies. Individual molecule is depicted as an assembly of seven hard spheres, organized to mimic the Y--shaped antibody. We consider the antibody--antibody interactions either through Fab, Fab' (two Fab fragments may be different), or Fc domain. Interaction between these three domains of the molecule (hereafter denoted as A, B, and C, respectively) is modeled by a short--range square--well attraction...
January 16, 2018: Journal of Physical Chemistry. B
David S Goodsell, Ludovic Autin, Arthur J Olson
Mesoscale molecular modeling is providing a new window on the inner workings of living cells. Modeling of genomes, however, remains a technical challenge, due to their large size and complexity. We describe a lattice method for rapid generation of bacterial nucleoid models that integrates experimental data from a variety of biophysical techniques and provides a starting point for simulation and hypothesis generation. The current method builds models of a circular bacterial genome with supercoiled plectonemes, packed within the small space of the bacterial cell...
January 16, 2018: Journal of Physical Chemistry. B
Mithun Biswas, Benjamin Lickert, Gerhard Stock
Enhanced sampling techniques represent a versatile approach to account for rare conformational transitions in biomolecules. A particularly promising strategy is to combine massive parallel computing of short molecular dynamics (MD) trajectories (to sample the free energy landscape of the system) with Markov state modeling (to rebuild the kinetics from the sampled data). To obtain well-distributed initial structures for the short trajectories, it is proposed to employ Metadynamics MD, which quickly sweeps through the entire free energy landscape of interest...
January 16, 2018: Journal of Physical Chemistry. B
Esteban Araya-Hermosilla, José Catalán-Toledo, Fabian Muñoz-Suescun, Felipe Oyarzun-Ampuero, Patrizio Raffa, Lorenzo Massimo Polgar, Francesco Picchioni, Ignacio Moreno-Villoslada
Amphiphilic aromatic polymers have been synthesized by grafting aliphatic polyketones with 4-(aminomethyl)benzoic acid at different molar ratios via the Paal-Knorr reaction. The resulting polymers, showing diketone conversion degree of 16, 37, 53, and 69 %, have been complexed with the redox-active 2,3,5-triphenyl-2H-tetrazolium chloride, precursor molecule with which aromatic-aromatic interactions are held. Upon addition of ascorbic acid to the complexes, in-situ reduction of the tetrazolium salt produced 1,3,5-triphenylformazan nanoparticles stabilized by the amphiphilic polymers...
January 16, 2018: Journal of Physical Chemistry. B
Sarah Loebner, Nino Lomadze, Alexey Kopyshev, Markus Koch, Olga Guskova, Marina Grenzer Saphiannikova, Svetlana A Santer
We report on light induced deformation of colloidal spheres consisting of azobenzene containing polymers. The colloids of the size between 60nm and 2m in diameter were drop casted on a glass surface and irradiated with linearly polarized light. It was found that colloidal particles can be deformed up to ca. 6 times of their initial diameter. The maximum degree of deformation depends on the irradiation wavelength and intensity, as well as on colloidal particles size. Based on recently proposed theory [V. Toshchevikov et al...
January 16, 2018: Journal of Physical Chemistry. B
Jian Tang, Zhou Qu, Jianhui Luo, Lanyan He, Pingmei Wang, Ping Zhang, Xianqiong Tang, Yong Pei, Bin Ding, Baoliang Peng, Yunqing Huang
The detachment process of an oil molecular layer or drop situated above a horizontal substrate was often described by a three-stage process. In this mechanism, the water molecule penetration and diffusion between the oil phase and the solid phase was proposed to be a crucial step to aid in removal of oil drops from solid surfaces. In this work, the detachment process of a two-dimensional alkane molecule layer from a silica surface in aqueous surfactant solutions is studied by means of molecular dynamics (MD) simulations...
January 16, 2018: Journal of Physical Chemistry. B
Gyan P Johari
With the objective of increasing the bioavailability of poorly soluble curative compounds, we describe a thermodynamics-based method for increasing their solubility, σ. It requires forming their pressure-densified glassy (PDG) state by supercooling the melt under a high pressure to form glass, depressurizing, and recovering the glass at a low temperature. First, we formally show that the excess free energy of PDG is higher at ambient pressure than that of a glass (normally) formed by supercooling the melt at ambient pressure (NG), and therefore their σ will be higher...
January 16, 2018: Journal of Physical Chemistry. B
Yasuo Kameda, Shunya Maeda, Yuko Amo, Takeshi Usuki, Kazutaka Ikeda, Toshiya Otomo
Neutron diffraction measurements have been carried out for 6Li/7Li isotopically substituted aqueous 1.0 mol% (0.5 mol/kg) LiCl and 1.1 mol% (0.56 mol/kg) LiClO4 solutions in D2O to obtain structural insight concerning hydration structure of Li+ in more dilute electrolyte solutions. The first-order difference function, ΔLi(Q), was analyzed by means of the least squares fitting procedure to obtain short-range structural parameters around the Li+. It was revealed that the nearest neighbor Li+…O(D2O) distance, rLiO, and the coordination number, nLiO, for the aqueous 1...
January 16, 2018: Journal of Physical Chemistry. B
A Faraone, D V Wagle, G A Baker, E C Novak, M Ohl, D Reuter, P Lunkenheimer, A Loidl, E Mamontov
The deep eutectic solvent glyceline formed by choline chloride and glycerol in 1:2 molar ratio is much less viscous compared to glycerol, which facilitates its use in many applications where high viscosity is undesirable. Despite the large difference in viscosity, we have found that the structural network of glyceline is completely defined by its glycerol constituent, which exhibits complex microscopic dynamic behavior, as expected from a highly correlated hydrogen-bonding network. Choline ions occupy interstitial voids in the glycerol network and show little structural or dynamic correlations with glycerol molecules...
January 16, 2018: Journal of Physical Chemistry. B
Madhulika Gupta, Prabir Khatua, Charusita Chakravarty, Sanjoy Bandyopadhyay
The microscopic properties of water confined within different segments of Trpzip4 (TZ4), Trpzip5 (TZ5) and Trzpip6 (TZ6) have been compared for all the states characterized along their folding pathways. In particular, structural ordering, energetics, and dynamics of water have been examined as the peptide unfolds along the free energy landscape. It is observed that the structuring of tetrahedral network as well as translational and rotational motions of hydration waters confined within the strands and the turn regions are very different, revealing motional heterogeneity in small 16-residue trpzips...
January 15, 2018: Journal of Physical Chemistry. B
Wojciech Radosz, Grzegorz Pawlik, Antoni Mitus
We study theoretically the kinetics of non-interacting photo-switchable guest molecules (model azo-dye) dispersed at low concentration in host (model polymer matrix) in the all-optical poling process close to the glass transition temperature Tg. We modify kinetic Monte Carlo model used in our previous studies of nonlinear optical processes in host-guest systems. The polymer matrix is simulated using the bond-fluctuation model. The kinetics of multiple trans-cis-trans cycles is formulated in terms of transition probabilities which depend on local free volume in the matrix and its dynamics...
January 15, 2018: Journal of Physical Chemistry. B
Zhaoyang Wang, Xiao Cheng, Anjun Qin, Haoke Zhang, Jing Zhi Sun, Ben Zhong Tang
Luminescent molecules with aggregation-induced emission (AIE) property, or AIE-gens are typical stimuli-responsive materials and many AIE-gens have shown luminescent responses to mechano-, thermo-, electro-, vapo- and/or solvato-stimulus, but the detailed structure-property relationship has been addressed for only few of them. Here, we report a tetraphenylethene (TPE) derivative with pyridyl modifiers and ethynylene bridges. The (Z)- and (E)-isomers are clearly purified and both of them are AIE-active and demonstrate multiple luminescent responses to external stimuli...
January 15, 2018: Journal of Physical Chemistry. B
Antoine Brehault, Deepak Patil, Hrishikesh Kamat, Randall E Youngman, Lynn M Thirion, John C Mauro, Claire Corkhill, John Stuart McCloy, Ashutosh Goel
Molybdenum oxides are an integral component of the high-level waste streams being generated from the nuclear reactors in several countries. Although borosilicate glass has been chosen as the baseline waste form by most of the countries to immobilize these waste streams, molybdate oxyanions (MoO42-) exhibit very low solubility (~ 1 mol.%) in these glass matrices. In the past 3-4 decades, several studies describing the compositional and structural dependence of molybdate anions in borosilicate and aluminoborosilicate glasses have been reported in the literature, providing a basis for our understanding of fundamental science that governs the solubility and retention of these species in the nuclear waste glasses...
January 14, 2018: Journal of Physical Chemistry. B
Jasmine Viger-Gravel, Anna Schantz, Arthur C Pinon, Aaron J Rossini, Staffan Schantz, Lyndon Emsley
Here we show how dynamic nuclear polarization (DNP) nuclear magnetic resonance (NMR) spectroscopy experiments permit the atomic level structural characterization of loaded and empty lipid nanoparticles (LNPs). The LNPs used here were synthesized by microfluidic mixing technique and are composed of ionizable cationic lipid (DLin-MC3-DMA), a phospholipid (DSPC), cholesterol and PEG (DMPE-PEG 2000), as well as encapsulated cargoes which are either phosphorothioated-siRNA (50 or 100%) or mRNA. We show that LNPs form physically stable complexes with bioactive drug siRNA for a period of 94 days...
January 14, 2018: Journal of Physical Chemistry. B
Fabio Sterpone, Philippe Derreumaux, Simone Melchionna
Proteins are marginally stable soft-matter entities that can be disrupted using a variety of perturbative stresses, including thermal, chemicals or mechanical ones. Fluid under extreme flow conditions is a possible route to probe the weakness of biomolecules and collect information on the molecular cohesive interactions that secure their stability. Moreover, in many cases, physiological flow triggers the functional response of specialised proteins as occurring in blood coagulation or cell adhesion. In this paper, we deploy the Lattice Boltzmann Molecular Dynamics technique based on the coarse grained model for protein OPEP, to study the mechanism of protein unfolding under Couette flow...
January 12, 2018: Journal of Physical Chemistry. B
Olga A Zakurdaeva, Sergey V Nesterov, Natalya A Sokolova, Pavel V Dorovatovskii, Yan V Zubavichus, Victor N Khrustalev, Andrey F Asachenko, Gleb A Chesnokov, Mikhail Sergeevich Nechaev, Vladimir I Feldman
Ionic Liquid/Crown Ether compositions are an attractive alternative to traditional extractants in the processes for spent nuclear fuel and liquid radioactive wastes reprocessing. These compositions are exposed to ionizing radiation, and their radiation stability, especially in the presence of metal salts, is a crucial issue. In the present study, the macrocyclic 18C6·Sr(BF4)2 and 18C6·Sr(PF6)2 complexes simulating the components of metal loaded Ionic Liquid/Crown Ether extractants were synthesized and their structures were characterized by FTIR spectroscopy and single-crystal X-ray diffraction analysis...
January 12, 2018: Journal of Physical Chemistry. B
Alan J Situ, So-Min Kang, Benjamin B Frey, Woojin An, Chungho Kim, Tobias S Ulmer
The function of membrane proteins relies on a defined orientation of protein relative to lipid. In apparent correlation to protein anchoring, tryptophan residues are enriched in the lipid headgroup region. To characterize the thermodynamic and structural basis of this relationship in α-helical membrane proteins, we examined the role of three conserved tryptophans in the folding of the heterodimeric integrin αIIbβ3 transmembrane (TM) complex in phospholipid bicelles and mammalian membranes. In the homogenous lipid environment of bicelles, tryptophan was replaceable by residues of distinct polarities...
January 11, 2018: Journal of Physical Chemistry. B
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