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Journal of Physical Chemistry. B

Mohammad Muneeb Sultan, Vijay S Pande
We recently showed that the time-structure based independent component analysis method from Markov state model literature provided a set of variationally optimal slow collective variables for Metadynamics (tICA-Metadynamics). In this paper, we extend the methodology towards efficient sampling of related mutants by borrowing ideas from transfer learning methods in machine learning. Our method explicitly assumes that a similar set of slow modes and metastable states are found in both the wild type (base line) and its mutants...
September 22, 2017: Journal of Physical Chemistry. B
Mehdi Karzar Jeddi, Santiago Romero-Vargas Castrillón
Water present in confining geometries plays key roles in many systems of scientific and technological relevance. Prominent examples are living cells and nanofluidic devices. Despite its importance, a complete understanding of the dynamics of water in nanoscale confinement remains elusive. In this work, we use molecular dynamics (MD) simulation to investigate the diffusive dynamics of water monolayers confined in chemically heterogeneous silica slit pores. The effect of chemical heterogeneity is systematically investigated through the fraction f_SiOH of randomly distributed surface sites that possess hydroxyl functional groups...
September 22, 2017: Journal of Physical Chemistry. B
Duy Quang Dao, Thi Chinh Ngo, Nguyen Minh Thong, Pham Cam Nam
Antioxidant efficiency of all-trans-retinol has been studied on the basis of characteristic thermochemical properties using density functional theory. The influence of the solvent polarity has also been evaluated. It is found that retinol may act in parallel as an effective antioxidant via H-atom donating as well as a prooxidant in yielding reactive hydroxyl radical. In fact, the lowest values of bond dissociation enthalpy were found at C18-H and C18-OH positions. Retinol was also determined as good electron donor but bad acceptor in the single electron transfer (ET) reaction with hydroperoxyl (HOO●) radical...
September 22, 2017: Journal of Physical Chemistry. B
Ryo Kanzaki, Shuma Uchida, Hitoshi Kodamatani, Takashi Tomiyasu
Metal ions in ionic liquids are laid under an unprecedented reaction field. In order to assess the reaction thermodynamics of metal ions in such a situation, Cu(2+)-chloro complex formation was examined with spectroscopic and calorimetric titrations in an ionic liquid, 1-buthyl-3-methylimidazolium trifluoromethanesulfonate (C4mimTfO). In addition, the effect of the structure of the solvated complexes on the complexation mechanism was investigated with the aid of DFT calculations. Chloro complexation successively proceeded and finally provided a [CuCl4](2‒) species, which is also the final product in conventional molecular solvents...
September 22, 2017: Journal of Physical Chemistry. B
Marianne Grognot, Guilhem Gallot
The properties of the solvation shell surrounding biomolecules in solution are fundamental to understand the modifications of the dynamics of the water molecules by peptides and proteins. The dynamics of the hydrogen bonding network typically occurs at the picosecond time scale, then terahertz spectroscopy is a unique tool to investigate the solvation shell. Here, we present terahertz measurements of the refractive index and extinction coefficient of solutions of biomolecules of various molecular weights. We observe a clear correlation between the terahertz dielectric properties and the weight of the molecules...
September 22, 2017: Journal of Physical Chemistry. B
Yu Zou, Zhenyu Qian, Yunxiang Sun, Guanghong Wei, Qingwen Zhang
The accumulation of the human islet amyloid polypeptide (hIAPP) deposits in the pancreas is regarded as an important factor that leads to the depletion of islet β-cells and islet transplantation failure. In recent experiments, it was reported that a small organic molecule O4 inhibits the formation of hIAPP1-37 oligomers and fibrils. However, the interaction between O4 molecules and hIAPP oligomers is largely unknown on the atomic level. In this work, we studied the influence of O4 molecules on fibril-like hIAPP pentamer and decamer by performing atomistic molecular dynamics simulations...
September 22, 2017: Journal of Physical Chemistry. B
Jan Hulva, Zdeněk Jakub, Zbynek Novotny, Niclas Johansson, Jan Knudsen, Joachim Schnadt, Michael Schmid, Ulrike Diebold, Gareth S Parkinson
The interaction of CO with the Fe3O4(001)-(√2 × √2)R45° surface was studied using temperature-programmed desorption (TPD), scanning tunneling microscopy (STM), and X-ray photoelectron spectroscopy (XPS), the latter both under ultrahigh vacuum (UHV) conditions and in CO pressures up to 1 mbar. In general, the CO-Fe3O4 interaction is found to be weak. The strongest adsorption occurs at surface defects, leading to small TPD peaks at 115, 130, and 190 K. Desorption from the regular surface occurs in two distinct regimes...
September 22, 2017: Journal of Physical Chemistry. B
Hideto Tsuji, Ryota Ozawa, Yuki Arakawa
Star-shaped four-armed stereo diblock poly(lactide) (4-LD) and linear one-armed PLLA or PDLA (1-L or 1-D) having the molecular weight similar to that of 4-LD [higher molecular weight 1-L(H) or 1-D(H)] and that of one block of 4-LD [lower molecular weight 1-L(L) or 1-D(L)] were synthesized and the effects of incorporated 1-L or 1-D on the isothermal and non-isothermal crystallization of 4-LD blends from the melt were investigated. Solely stereocomplex crystallites were formed in unblended 4-LD and 4-LD blends incorporated with 1-L or 1-D during isothermal and non-isothermal crystallization...
September 21, 2017: Journal of Physical Chemistry. B
Shu-Fang Yao, Xiao-Tong Chen, Hai-Mu Ye
The detailed structure and crystallization behavior of poly(butylene succinate) (PBS) have been investigated by Fourier transform infrared (FTIR) and other methods systematically. For the first time, we confirmed that the C=O stretching modes of PBS can respond to three distinguish absorption bands in the FTIR spectrum, at around 1736, 1720 and 1714 cm-1 respectively. The 1736 cm-1 band is adopted as the stretching mode of C=O groups in free amorphous fraction (MAF); the 1714 cm-1 band which is relevant to more stable structure, displays more anisotropic in polarized FTIR spectra, and has been confirmed as stretching vibrations of hydrogen-bonded C=O groups in the crystalline phase...
September 21, 2017: Journal of Physical Chemistry. B
Olof Engström, Hani Mobarak, Jonas Ståhle, Göran Widmalm
Three dimensional shape and conformation of carbohydrates are important factors in molecular recognition events and the N-acetyl group of a monosaccharide residue can function as a conformational gatekeeper whereby it influences the overall shape of the oligosaccharide. NMR spectroscopy and quantum mechanics (QM) calculations are used herein to investigate both the conformational preferences and the dynamic behavior of N-acetyl and N-formyl substituents of 3-amino-3,6-dideoxy-α-D-galactopyranose, a sugar and substitution patterns found in bacterial O-antigen polysaccharides...
September 21, 2017: Journal of Physical Chemistry. B
Hari Pandey, David M Leitner
We investigate by molecular simulations thermodynamic properties of hydration water and protein, the sensitivity of hydrogen bonds to change in temperature, and hydration water distribution at varying levels of hydration of a hyperactive antifreeze protein, DAFP-1. Hydration water coverage of the protein and partial thermodynamic properties of the hydration water are heterogeneous, different for the water near the ice-binding site (IBS) and the rest of the protein, particularly at low levels of hydration. Overall, we find the partial specific heat of water to be larger at low hydration levels than in the fully hydrated limit, with the separation corresponding roughly to one hydration layer...
September 21, 2017: Journal of Physical Chemistry. B
Richard Lipkin, Almudena Pino-Angeles, Themis Lazaridis
Protegrin-1 is an 18-residue β-hairpin antimicrobial peptide (AMP) that has been suggested to form transmembrane β-barrels in biological membranes. However, alternative structures have also been proposed. Here, we performed multimicrosecond, all-atom molecular dynamics simulations of various protegrin-1 oligomers on the membrane surface and in transmembrane topologies. The membrane surface simulations indicated that protegrin dimers are stable, whereas trimers and tetramers break down. Tetrameric arcs remained stably inserted in lipid membranes, but the pore water was displaced by lipid molecules...
September 21, 2017: Journal of Physical Chemistry. B
Ryan Gordon, Spencer T Stober, Cameron F Abrams
12-Hydroxystearic acid (12HSA) and its derivatives are well-known organogelators, and they play critical roles in a variety of applications. The overall aggregate structure of 12HSA is sensitive to the chirality at the 12th carbon, but a fundamental understanding of this dependence is lacking. In this study, molecular dynamics simulations were conducted on microsecond long time scales for (1) (R)-12HSA, (2) (S)-12HSA, and (3) a 50/50 racemic mixture, each solvated at 12.5 wt % in explicit hexane. Self-assembly was accelerated by turning off alkyl chain dihedral gauche states and forcing the molecules to adopt an all-trans conformation...
September 21, 2017: Journal of Physical Chemistry. B
Palraj Kalimuthu, Abdel A Belaidi, Guenter Schwarz, Paul V Bernhardt
Direct electrochemistry of human sulfite oxidase (HSO) has been achieved on carboxylate-terminated self-assembled monolayers cast on a Au working electrode in the presence of the promoter chitosan. The modified electrode facilitates a well-defined nonturnover redox response from the heme cofactor (Fe(III/II)) in 750 mM Tris, MOPS, and bicine buffer solutions. The formal redox potential of the nonturnover response varies slightly depending on the nature of the thiol monolayer on the Au electrode. Upon addition of sulfite to the cell a pronounced catalytic current from HSO-facilitated sulfite oxidation is observed...
September 21, 2017: Journal of Physical Chemistry. B
Kara Elizabeth Ranaghan, William G Morris, Laura Masgrau, Kittusamy Senthilkumar, Linus O Johannissen, Nigel S Scrutton, Jeremy N Harvey, Frederick R Manby, Adrian J Mulholland
Aromatic amine dehydrogenase (AADH) and related enzymes are at the heart of debates on the roles of quantum tunnelling and protein dynamics in catalysis. The reaction of tryptamine in AADH involves significant quantum tunnelling in the rate-limiting proton transfer step, shown e.g. by large H/D primary kinetic isotope effects (KIEs), with unusual temperature dependence. We apply correlated ab initio combined quantum mechanics/molecular mechanics (QM/MM) methods, at levels up to local coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), to calculate accurate potential energy surfaces for this reaction, which are necessary for quantitative analysis of tunnelling contributions and reaction dynamics...
September 20, 2017: Journal of Physical Chemistry. B
Caroline Duc, Alexis Vlandas, George G Malliaras, Vincent Senez
Conducting polymers demonstrate an interesting ability to change their wettability at ultra-low voltage (<1V). While the conducting hydrogel poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) is increasingly used as an interface with biology partly thanks to its mechanical properties, little is known about the electrical control of its wettability. We rely on the captive bubble technique to study this hydrogel property in relevant conditions (fully immerged) We here report that the wettability variations of PEDOT:PSS are driven by an electrowetting phenomenon in contrast to other conducting polymers which are thought to undergo wettability changes due to oxido-reduction reactions...
September 20, 2017: Journal of Physical Chemistry. B
Erika Aloi, Maria Oranges, Rita Guzzi, Rosa Bartucci
Continuous wave electron paramagnetic resonance spectroscopy and two-pulse echo detected spectra of chain-labeled lipids are used to study the dynamics of frozen lipid membranes over the temperature range 77-260 K. Bilayers of ester-linked dihexadecanoylphosphatidylcholine (DPPC) with noninterdigitated chains and ether-linked dihexadecyl phosphatidylcholine (DHPC) with interdigitated chains are considered. Rapid stochastic librations of small angular amplitude are found in both lipid matrices. In noninterdigitated DPPC bilayers, the mean-square angular amplitude, [Formula: see text], of the motion increases with temperature and it is larger close to the chain termini than close to the polar/apolar interface...
September 20, 2017: Journal of Physical Chemistry. B
Murat Atiş, Kenneth A Johnson, Ron Elber
Enzymatic reactions usually occur in several steps: A step of substrate binding to the surface of the protein, a step of protein re-organization around the substrate and conduction of a chemical reaction, and a step of product release. The release of inorganic phosphate - PPi - from the matrix of the protein HIV reverse transcriptase is investigated computationally. Atomically detailed simulations with explicit solvent are analyzed to obtain the free energy profile, mean first passage time, and detailed molecular mechanisms of PPi escape...
September 19, 2017: Journal of Physical Chemistry. B
Michael Bley, Magali Duvail, Philippe Guilbaud, Jean-Francois Dufrêche
Herein, a new theoretical method simulating osmotic equilibria and activities is presented, where a bulk liquid and its corresponding vapor phase are simulated with molecular dynamics using polarizable force fields. Time-averaged number density profiles based on the resulting trajectories provide the amount of evaporated molecules present in the vapor phase and consequently the vapor phase density. The activity of the solvent and the corresponding osmotic coefficient are determined by the vapor density at a certain solute concentration with respect to the reference vapor density of the pure solvent...
September 19, 2017: Journal of Physical Chemistry. B
Mattia Bernetti, Matteo Masetti, Fabio Pietrucci, Martin Blackledge, Malene Ringkjøbing Jensen, Maurizio Recanatini, Luca Mollica, Andrea Cavalli
Intrinsically disordered proteins (IDPs) are emerging as an important class of the proteome. Being able to interact with different molecular targets, they participate in many physiological and pathological activities. However, due to their intrinsically heterogeneous nature, determining the equilibrium properties of IDPs is still a challenge for biophysics. Herein, we applied state-of-the-art enhanced sampling methods to Sev NTAIL, a test case of IDPs, and constructed a bin-based kinetic model to unveil the underlying kinetics...
September 19, 2017: Journal of Physical Chemistry. B
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