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Journal of Physical Chemistry. B

Solene Bechelli, Brittany Gonzalez, Vincent Piquet, Ilham Essafri, Caroline Desgranges, Jerome Delhommelle
Using molecular simulation, we shed light on the crystal nucleation process in systems of Cu, Ni and their nanoalloy. For each system, we simulate the formation of the crystal nucleus along the entire nucleation pathway and determine the free energy barrier overcome by the system to form a critical nucleus. Comparing the results obtained for the pure metals to those for the nanoalloy, we analyze the impact of alloying on the free energy of nucleation, as well as on the size and structure of the crystal nucleus...
August 16, 2017: Journal of Physical Chemistry. B
Amin Aramoon, Timothy D Breitzman, Christopher F Woodward, Jaafar A El-Awady
A new algorithm is developed to quantify the free-volume hole distribution and its evolution in coarse-grained molecular dynamics simulations of polymeric networks. This is achieved by analyzing the geometry of the network rather than a voxelized image of the structure to accurately and efficiently find and quantify free-volume hole distributions within large scale simulations of polymer networks. The free-volume holes are quantified by fitting the largest ellipsoids and spheres in the free-volumes between polymer chains...
August 16, 2017: Journal of Physical Chemistry. B
Martin Brehm, Ghulam Saddiq, Tobias Watermann, Daniel Sebastiani
In this study, we investigate the effect of a series of additive molecules with different types of philicities on the structure and dynamics of DPPC bilayers. To this aim, we performed extensive force field molecular dynamics simulations of the systems, using our recently developed perfluoroalkane force field. We found that addition of perfluoro-n-decane and fluorotelomer alcohol at 323 K leads to a phase transition of the membrane from liquid crystalline to gel phase, whereas the addition of n-decane and partially fluorinated n-decane leaves the liquid crystalline phase intact...
August 16, 2017: Journal of Physical Chemistry. B
Lars Konermann
Molecular dynamics (MD) simulations have become a key tool for examining the properties of electrosprayed protein ions. Traditional force fields employ static charges on titratable sites, whereas in reality, protons are highly mobile in gas-phase proteins. Earlier studies tackled this problem by adjusting charge patterns during MD runs. Within those algorithms, proton redistribution was subject to energy minimization, taking into account electrostatic and proton affinity contributions. However, those earlier approaches described (de)protonated moieties as point charges, neglecting charge solvation, which is highly prevalent in the gas phase...
August 16, 2017: Journal of Physical Chemistry. B
Heather E Bailey, Yong-Lei Wang, Michael D Fayer
The orientational dynamics and microscopic liquid structure of a protic ionic liquid, 1-ethylimidazolium bis(trifluoromethylsulfonyl)imide (EhimNTf2), and its aprotic analogue, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EmimNTf2), were studied at various water concentrations using optical heterodyne-detected optical Kerr Effect (OHD-OKE) spectroscopy, linear infrared spectroscopy, and atomistic simulations. The OHD-OKE experiments essentially measure the orientational relaxation of the Ehim+ and Emim+ cations...
August 15, 2017: Journal of Physical Chemistry. B
Ranu Satish Dhale, Prabhat Kumar Sahu, Moloy Sarkar
The present study has been undertaken with an aim to find out the suitability of a binary solvent system, comprising an anionic liquid, 1-(2-hydroxyethyl)-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([OHEMIM][NTf2]) and ethylene glycol (EG), toward lithium ion battery applications. For this purpose, the behavior in terms of structure, intermolecular interaction, and dynamics of several solvent systems, [OHEMIM][NTf2], [OHEMIM][NTf2]-LiNTf2(lithium bis(trifluorimethylsulfonyl)imide), [OHEMIM][NTf2]-EG, and [OHEMIM][NTf2]-EG-LiNTf2, is investigated by carrying out steady state and time-resolved fluorescence, nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR) measurements...
August 15, 2017: Journal of Physical Chemistry. B
Sathi Goswami, Anupa Majumdar, Munna Sarkar
The interaction of a painkiller Isoxicam, belonging to the oxicam group of Non Steroidal Anti-Inflammatory Drugs (NSAIDs) and its copper complex with different cyclodextrins (β-CD, γ-CD, HPβCD and HPγCD ) has been investigated in both solution and the solid state. Steady state and time resolved fluorescence spectroscopy, fluorescence anisotropy, 1H NMR and FTIR spectroscopy are used. Both the drug and its copper complex form host-guest inclusion complex with all CDs. Fluorescence spectroscopy is used to determine binding constants and stoichiometries of the host-guest complex...
August 14, 2017: Journal of Physical Chemistry. B
Matthew Douglas Watson, Jeremy Monroe, Daniel P Raleigh
Changes in protein stability are commonly reported as changes in the melting temperature, ΔTM, or as changes in unfolding free energy at a particular temperature, ΔΔG°. Using data for 1124 mutants from 16 proteins we examine the relationship between ΔΔG° and ΔTM. A linear relationship is observed for each protein. The slopes of the plots of ΔTM vs ΔΔG° for different proteins scale as N(-1) where N is the number of residues in the protein. Thus, a given change in ΔG° causes a much larger change in TM for a small protein relative to the effect observed for a large protein...
August 14, 2017: Journal of Physical Chemistry. B
Zhaleh Ghaemi, Irisbel Guzman, David Gnutt, Zaida Luthey-Schulten, Martin Gruebele
U1A protein - stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape towards a specific binding site...
August 14, 2017: Journal of Physical Chemistry. B
Josip Pozar, Ivana Niksic-Franjic, Marija Cvetnic, Katarina Leko, Nikola Cindro, Katarina Piculjan, Ivana Borilovic, Leo Frkanec, Vladislav Tomisic
The medium effect on the complexation of alkali metal cations with a calix[4]arene ketone derivative (L) was systematically examined in methanol, ethanol, N-methylformamide, N,N-dimethylformamide, dimethyl sulfoxide, and acetonitrile. In all solvents the binding of Na+ cation by L was rather efficient, whereas the complexation of other alkali metal cations was observed only in methanol and acetonitrile. Complexation reactions were enthalpically controlled, while ligand dissolution was endothermic in all cases...
August 14, 2017: Journal of Physical Chemistry. B
Baran Eren, Heath Kersell, Robert S Weatherup, Christian Heine, Ethan J Crumlin, Cynthia M Friend, Miquel B Salmeron
Using ambient pressure X-ray photoelectron spectroscopy (APXPS) and high pressure scanning tunneling microscopy (HPSTM), we show that in equilibrium with 0.01-0.2 Torr of methanol vapor, at room temperature, the Cu(100) surface is covered with methoxy species forming a c(2 × 2) overlayer structure. In contrast, no methoxy is formed if the surface is saturated with an ordered oxygen layer, even when the methanol pressure is 0.2 Torr. At oxygen coverages below saturation, methanol dissociates and reacts with the atomic oxygen, producing methoxy and formate on the surface, and formaldehyde that desorbs to the gas phase...
August 14, 2017: Journal of Physical Chemistry. B
Ying Wang, Yue Shen, Bin Li, Shuo Wang, Jinjin Zhang, Yi Zhang, Jun Hu
Nanomanipulation of single DNA molecules has great potential in fundamental genetic research and clinical analysis, and is a good model system for studying the interfacial effects on physiochemical processes, which occur when manipulating the linear DNA molecules with an atomic force microscope (AFM) tip. Here, we demonstrate that AFM nanomanipulation can be carried out on DNA molecules covered by a single-layered reduced graphene oxide sheet. Nanomanipulation, which includes cutting, pushing, and sweeping operations, specific to the covered DNA molecules can be achieved in a well-controlled manner using AFM in the PeakForce Quantitative Nano-Mechanics mode...
August 14, 2017: Journal of Physical Chemistry. B
John T Newberg, Chris Goodwin, Chris Arble, Yehia Khalifa, Jorge Anibal Boscoboinik, Sana Rani
The interaction of water vapor with a single crystal ZnO(101 ̅0) surface was investigated using synchrotron-based ambient pressure X-ray photoelectron spectroscopy (APXPS). Two isobaric experiments were performed at 0.3 and 0.07 Torr water vapor pressure at sample temperatures ranging from 750 K to 295 K up to a maximum of 2 % relative humidity (RH). Below 10-4 % RH the ZnO(101 ̅0) interface is covered with ~0.25 monolayers of OH groups attributed to dissociation at non-stoichiometric defect sites. At ~10-4 % RH there is sharp onset in increased surface hydroxylation attributed to reaction at stoichiometric terrace sites...
August 11, 2017: Journal of Physical Chemistry. B
Yan Zhang, Yun He, Nan Yan, Yutian Zhu, Yuexin Hu
Recently, it has been reported that the incorporation of functional inorganic nanoparticles (NPs) into the three-dimension (3D) confined self-assembly of block copolymers (BCPs) creates the unique nanostructured hybrid composites, which can not only introduce new functions to BCPs but also induce some interesting morphological transitions of BCPs. In the current study, we systematically investigate the cooperative self-assembly of a series of size-controlled and surface chemistry-tunable gold nanoparticles (AuNPs) and polystyrene-b-poly(2-vinyl pyridine) (PS-b-P2VP) diblock copolymer within the emulsion droplets...
August 11, 2017: Journal of Physical Chemistry. B
Jakob Fester, Zhaozong Sun, Jonathan Rodriguez-Fernandez, Alex S Walton, Jeppe V Lauritsen
Well-characterized metal oxides supported on single crystal surfaces serve as valuable model systems to study fundamental chemical properties and reaction mechanisms in heterogeneous catalysis or as new thin film metal oxide catalysts in their own right. Here, we present Scanning Tunneling Microscopy and X-ray Photoelectron Spectroscopy results for cobalt oxide nanoislands that reveal the detailed atomistic mechanisms leading to transitions between Co-O bilayer and O-Co-O trilayer, induced by oxidation in O2 and reductive vacuum annealing treatments, respectively...
August 11, 2017: Journal of Physical Chemistry. B
Mary Jo Weiss-Errico, Ion Ghiviriga, Kevin E O'Shea
Legacy perfluoroalkyl substances (PFASs) are known environmental pollutants with serious adverse health effects. Perfluoroethercarboxylic acids (PFECAs), emerging PFASs now being substituted for legacy PFASs, have recently been detected in the environment. Cyclodextrins (CDs) have been proposed as agents for the remediation of problematic pollutants, including legacy PFASs. The current study uses (19)F NMR spectroscopy to measure the complexation of mono-, di-, and triether PFECAs by CDs for eventual environmental applications...
August 11, 2017: Journal of Physical Chemistry. B
Tiedong Sun, Alexander Mirzoev, Nikolay Korolev, Alexander P Lyubartsev, Lars Nordenskiöld
It is well established that the presence of the trivalent cobalt(III)-hexammine cation (CoHex(3+)) at submillimolar concentrations leads to bundling (condensation) of double-stranded DNA molecules, which is caused by DNA-DNA attraction induced by the multivalent counterions. However, the detailed mechanism of this process is still not fully understood. Furthermore, in all-atom molecular dynamics (MD) simulations, spontaneous aggregation of several DNA oligonucleotides in the presence of CoHex(3+) has previously not been demonstrated...
August 11, 2017: Journal of Physical Chemistry. B
Daniel Corbett, Max Hebditch, Rose Keeling, Peng Ke, Sofia Ekizoglou, Prasad Srinivasan Sarangapani, Jai A Pathak, Christopher F van der Walle, Shahid Uddin, Clair Baldock, Carlos Avendano, Robin A Curtis
Predicting the concentrated solution behaviour for monoclonal antibodies requires developing and using minimal models to describe their shape and interaction potential. Towards this end, the small-angle X-ray scattering (SAXS) profiles for a monoclonal antibody (COE-03) have been measured under solution conditions chosen to produce weak self-association. The experiments are complemented with molecular simulations of a three-bead antibody model with and without inter-bead attraction. The scattering profile is extracted directly from the molecular simulation to avoid using the decoupling approximation...
August 10, 2017: Journal of Physical Chemistry. B
Caizhen Liang, Bin Wang, Jianjun Chen, Qiwen Yong, Yuewen Huang, Bing Liao
The block copolymers poly(4-(N-carbazolyl)methyl styrene-bl-poly (ethylene glycol) methyl ether methacrylate) (PCMSm-b-PAPEGn) and homopolymer PCMS30 synthesized by RAFT polymerization were used to disperse multi-walled carbon nanotubes (MWCNTs). To probe the adsorption and dispersion ability of polymers, characterization analysis of MWCNT dispersions was evaluated by Fourier transform infrared, X-ray photoelectron spectroscopic, transmission electron microscopy, ultraviolet-visible spectroscopic and thermogravimetric analysis...
August 10, 2017: Journal of Physical Chemistry. B
Calvin R Chen, George I Makhatadze
Pressure is well known environmental stressor that can either stabilize or destabilize proteins. The volumetric change upon protein unfolding determines the effect of pressure on protein stability, where negative volume changes destabilize proteins at high pressures. High temperature often accompanies high pressure, for example in the ocean depths near hydrothermal vents or near faults, so it is important to study the effect of temperature on the volumetric change upon unfolding. We previously detailed the magnitude and sign of the molecular determinants of volumetric change, allowing us to quantitatively predict the volumetric change upon protein unfolding...
August 10, 2017: Journal of Physical Chemistry. B
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