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Journal of Physical Chemistry. B

Toshifumi Mori, Shinji Saito
Proteins involve motions over a wide range of spatial and temporal scales. While the large conformational changes such as folding and functioning are slow and appear to occur in a highly cooperative manner, how the hierarchical dynamics over different timescales play a role during these slow transitions has been of great interest over the decades. Here we study the folding mechanism of the villin headpiece subdomain (HP35) to understand the molecular mechanism behind this prototypical fast-folding protein. The ~ 400 µs molecular dynamics (MD) trajectories obtained by Piana et al...
October 21, 2016: Journal of Physical Chemistry. B
Giuseppe Lanza, Maria A Chiacchio
Exploration of interfacial hydration networks of zwitterion and non-ionized trialanine has been performed using DFT-M062X quantum chemical computations explicitly considering up to 41 water molecules. The step-by-step water molecules peptide surrounding, carried out for unfolded extended (β), polyproline II (PPII) conformations reveals the crucial importance of explicit solvent effects in stabilizing the zwitterion form and the left-handed PPII-helix ubiquitously found at room temperature for short polyalanines...
October 21, 2016: Journal of Physical Chemistry. B
Giorgio Lanzani, Ari P Seitsonen, Marcella Iannuzzi, Kari Laasonen, Simo Olavi Pehkonen
The chemistry of aluminium or oxo-aluminium in water is still relatively unknown, although it is the basis for many chemical and industrial processes, including floc- culation in water treatment plants. Trimeric species have a predominant role in the formation of the Keggin cations, which are the basic building block of aluminium- based chemicals. Despite this, the details of the structural evolution of these small solvated clusters and how this is related to the processes leading to the formation of larger aggregates is still an open issue...
October 21, 2016: Journal of Physical Chemistry. B
Ivan Ljubic, Aleksandar Sabljic, Marija Bonifacic
The reactions of α-hydroxyalkyl radicals in aqueous medium are of interest because they exhibit a rich variety of fundamentally important competing mechanisms, such as proton-coupled electron transfer (PCET), hydrogen atom transfer, free radical substitutions, abstractions and additions etc. We present a theoretical study of the mechanism and kinetics of the aqueous reactions of α-hydroxyisopropyl (2-propanol) radical with four halogenated organic substrates: iodoacetate (IAc), iodoacetamide (IAm), 5-bromouracil (5-BrU), and carbon tetrachloride (CCl4)...
October 21, 2016: Journal of Physical Chemistry. B
Zhimin Xie, Dongliang Chai, Youshan Wang, Huifeng Tan
The effective potentials are of great importance for the coarse-grained (CG) simulations, which can be obtained by the structure-based iterative Boltzmann inversion (IBI) method. However, the standard IBI method is incapable of keeping the mechanical and thermodynamic properties of the CG model in consistence with those of the all-atom model. Unlike the existed techniques, such as introducing the friction force as the dissipative force to drop the superatom motion while the conservative force arising from the CG potential was kept intact, we directly modified the standard IBI nonbonded potential by adding an empirical function...
October 21, 2016: Journal of Physical Chemistry. B
Michael Thomas Ruggiero, J Axel Zeitler
Anharmonicity has been shown to be an important piece of the fundamental framework that dictates numerous observable phenomena. In particular, anharmonicity is the driving force of vibrational relaxation processes, mechanisms that are integral to the proper function of numerous chemical processes. However, elucidating its origins has proven difficult due to experimental and theoretical challenges, specifically related to separating the anharmonic contributions from other unrelated effects. While no one technique is particularly suited for providing a complete picture of anharmonicity, by combining multiple complementary methods such a characterisation can be made...
October 21, 2016: Journal of Physical Chemistry. B
Chao-Chen Lin, Hsin-Fang Hsu, Peter Jomo Walla
The fusion of two opposing membranes is essential in biological functions such as fertilization, viral entry, membrane trafficking and synaptic transmission. Before the membrane bilayers are fully connected, at some stage a hemifusion intermediate-when the outer leaflets are merged but not the inner leaflets-is formed. However, the position of hemifusion in the energy landscape and the duration of it vary and have not been fully mapped out. To date, there has not been a way to differentiate lipid mixing of the two leaflets directly in a single experiment...
October 20, 2016: Journal of Physical Chemistry. B
Justin A Lemkul, Alexander D MacKerell
Mg2+ ions are important in biological systems, particularly in stabilizing compact RNA folds. Mg2+ is strongly polarizing, and representing its interactions in heterogeneous environments is a challenge for empirical force field development. To date, the most commonly used force fields in molecular dynamics simulations utilize a pairwise-additive approximation for electrostatic interactions, which cannot account for the significant polarization response in systems containing Mg2+. In the present work, we refine the interactions of Mg2+ with water, Cl- ions, and nucleic acid moieties using a polarizable force field based on the classical Drude oscillator model...
October 19, 2016: Journal of Physical Chemistry. B
Pengyun Yu, Yan Zhao, Fan Yang, Huifen Pan, Jianru Wang, Juan Zhao, Wenming Wang, Hongfei Wang, Jianping Wang
The [Ru(II)-NO(+)] group affects the structure and chemical reactivity of nitrosylruthenium(II) complexes. A characteristic infrared absorption band due to the nitrosyl (NO) stretching motion is shown in the frequency region of 1800-1900 cm(-1). In this work, linear infrared (IR) and nonlinear IR methods, including pump-probe and two-dimensional (2D) IR, were utilized to study the structures and dynamics of two isomeric nitrosylruthenium complexes [Ru(OAc)(2mqn)2NO] (H2mqn= 2-methyl-8-quinolinol) in cis and trans isomeric configurations in a weak polar solvent (CDCl3)...
October 18, 2016: Journal of Physical Chemistry. B
William W Parson
The rates of nonadiabatic electron-transfer reactions depend on four main factors: the probability of finding the system in a conformation in which the reactant and product states have the same energy, the electronic coupling that drives oscillations between the two diabatic states, the dephasing that damps these oscillations, and the vibrational or electronic relaxations that trap the product state by transferring energy to the surroundings. This paper develops a simple expression that combines these factors in a relatively realistic manner...
October 18, 2016: Journal of Physical Chemistry. B
Gabriel L S Rodrigues, Willian Ricardo Rocha
In this article Density Functional Theory in conjunction with Monte Carlo statistical mechanical simulation were used to investigate the electronic structure, reduction potential, solvation and solvent effects on the electronic spectra of nitrosyl ammine complexes, using [Ru(NH3)5(NO)]2+/3+ as model compounds. In addition, ligand exchange reactions with solvent water molecules were also investigated. It is shown that the complexes are involved in strong hydrogen bonds in aqueous solution, with mean average energies of (-13...
October 18, 2016: Journal of Physical Chemistry. B
Luigi Leonardo Palese
In the last years there has been a huge progress of knowledge in protein folding. However, some aspects of the problem still need further attention. One of these is the exact relationship between the folded and unfolded states and their differences. While the folded state is well knowable at least from a structural point of view (just think of the thousands of structures in on-line databases), the unfolded state is more elusive. Also these are dynamic states of matter and this aspect can not be overlooked. The study of the molecular dynamics derived correlation matrices is an invaluable source of information on the protein dynamics...
October 18, 2016: Journal of Physical Chemistry. B
Hweiyan Tsai, Zihkai Chen, Huiwen Deng, Sinmei Tsai, C Bor Fuh
We report a method that involves using atomic force microscopy to estimate molecular interaction forces for bioapplications. Experimental parameters, comprising the labeling concentrations of tips and substrates and the loading rates of tips, were optimized for estimating molecular interaction forces for three pairs of model molecules (IgG/anti-IgG, BSA/anti-BSA, streptavidin/biotin). The estimated molecular interaction forces of IgG/anti-IgG, BSA/anti-BSA, and streptavidin/biotin were 121 ± 3, 185 ± 4, and 241 ± 4 pN, respectively...
October 18, 2016: Journal of Physical Chemistry. B
Zhenyu Deng, Yangwei Jiang, Linli He, Linxi Zhang
By employing molecular dynamics simulations, we explored the conformation transition of nanoparticles (NPs) in semiflexible ring polymer nanocomposite melts. A novel aggregation- dispersion transition for NPs in ring polymer nanocomposites occurs when the bending energy of ring chains increases. The conformations of flexible ring chains near NPs are radial distribution, and the entropic depletion interactions between a pair of NPs in flexible ring polymer nanocomposite melts are attractive, however, the rod-like ring chains are wrapped around the NPs and the entropic depletion interactions between NPs in rod-like ring polymer melts are repulsive...
October 18, 2016: Journal of Physical Chemistry. B
Hu Shi, Baotao Kang, Jin Yong Lee
Histidine state (deprotonated, neutral, and protonated) is considered an important factor influencing the structural properties and aggregation mechanisms in amyloid β-peptides which are associated with the pathogenesis of Alzheimer's disease. Understanding the structural properties and aggregation mechanisms is a great challenge because two forms (the Nε-H or Nδ-H tautomer) can exist in the free neutral state of histidine. Here, replica exchange molecular dynamics simulation was performed to elucidate the changes of structure and mechanism of aggregation influenced by tautomeric behaviors of histidine in Aβ (1-40)...
October 17, 2016: Journal of Physical Chemistry. B
David Sean Boucher, Jason S Howell
Empirical data indicates that several good solvents for C60 and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) have substantial polar and hydrogen-bonding components, which are not intrinsic to the structure of the molecules themselves. Functional solubility parameter (FSP) and convex solubility parameter (CSP) computations are performed on C60 and PCBM using solubility data available in the literature. The CSP and FSP results are compared to previously reported Hansen solubility parameters (HSPs) and to the parameters calculated using additive functional group contribution methods...
October 17, 2016: Journal of Physical Chemistry. B
Peng Wei Zhu, Luguang Chen
A persistence length is a key parameter for the quantitative interpretation of the flexibility of polymers. We have studied the complexes composed of spherical poly(N-isopropylacrylamide) (PNIPAM) brush and sodium dodecyl sulfate (SDS) micelle in efforts to characterize the flexibility of tethered PNIPAM below the lower critical solution temperature TLCST. An analytical mean-field model is utilized to describe the persistence length Lp in a broad range of ψ, the number of bound micelles per chain. The persistence length of the micelle-constrained PNIPAM is quantitatively correlated with the thermal energy kBT, electrostatic repulsion fC, and effective excluded volume parameter νeff...
October 17, 2016: Journal of Physical Chemistry. B
Kyaw Hpone Myint, Jonathan R Brown, Anne R Shim, Barbara E Wyslouzil, Lisa Michelle Hall
The formation of block copolymer micelles with and without hydrophobic nanoparticles is simulated using dissipative particle dynamics. We use the model developed by Spaeth et al. [J. Chem. Phys. 134, 164902 (2011)], and drive micelle formation by adjusting the interaction parameters linearly over time to represent a rapid change from organic solvent to water. For different concentrations of added nanoparticles, we determine characteristic times for micelle formation and coagulation, and characterize micelles with respect to size, polydispersity, and nanoparticle loading...
October 17, 2016: Journal of Physical Chemistry. B
Kai Song, Shuming Bai, Qiang Shi
Recent experimental and theoretical studies have revealed that quantum coherence plays an important role in the excitation energy transfer in photosynthetic light harvesting complexes. Inspired by the recent single molecule two-color double-pump experiment, we investigate theoretically the effect of pulse shaping on observing coherent energy transfer in the single bacterial light harvesting 2 (LH2) complex. It is found that, quantum coherent energy transfer can be observed when the time delay and phase difference between the two laser pulses are controlled independently...
October 17, 2016: Journal of Physical Chemistry. B
Yilong Tu, Shuai Ma, Fufeng Liu, Yan Sun, Xiaoyan Dong
Accumulation and aggregation of amyloid β-protein (Aβ) play an important role in the pathogenesis of Alzheimer's disease. There has been increased interest in finding new anti-amyloidogenic compounds to inhibit Aβ aggregation. Herein, thioflavin T fluorescent assay and transmission electron microscopy results showed that hematoxylin, a natural organic molecule extracted from caesalpinia sappan, was a powerful inhibitor of Aβ42 fibrillogenesis. Circular dichroism studies revealed hematoxylin reduced the β-sheet content of Aβ42 and made it assemble into antiparallel arrangement, which induced Aβ42 to form off-pathway aggregates...
October 17, 2016: Journal of Physical Chemistry. B
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