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Corrine A Kumar, Arjun Saha, Krishnan Raghavachari
Transition metal sulfides (TMS) are being investigated with increased frequency because of their ability to efficiently catalyze the hydrogen evolution reaction. We have studied the trimetallic TMS cluster ions, Mo3S4(-), W3S4(-), and W3S3(-), and probed their efficiency for bond activation and hydrogen evolution from water. These clusters have geometries that are related to the edge sites on bulk MoS2 surfaces that are known to play a role in hydrogen evolution. Using density functional theory, the electronic structures of these clusters and their chemical reactivity with water have been investigated...
February 17, 2017: Journal of Physical Chemistry. A
Li-Qiang Xie, Liang Chen, Zi-Ang Nan, Hai-Xin Lin, Tan Wang, Dongping Zhan, Jia-Wei Yan, Bing-Wei Mao, Zhong-Qun Tian
The spontaneous α-to-δ phase transition of the Formamidinium-based (FA) lead halide perovskite hinders its large scale application in solar cells. Though this phase transition can be inhibited by alloying with Methylammonium-based (MA) perovskite, the underlying mechanism is largely unexplored. In this communication, we grow high quality mixed cations and halides perovskite single crystals (FAPbI3)1-x(MAPbBr3)x to understand the principles for maintaining pure perovskite phase, which is essential to device optimization...
February 17, 2017: Journal of the American Chemical Society
Duc D Nguyen, Bao Wang, Guo-Wei Wei
Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with solvent excluded surfaces for estimating both electrostatic solvation free energies and electrostatic binding free energies...
February 16, 2017: Journal of Computational Chemistry
Greg Starek, J Alfredo Freites, Simon Bernèche, Douglas J Tobias
We used targeted molecular dynamics, informed by experimentally determined inter-atomic distances defining the pore region of open and closed states of the KvAP voltage-gated potassium channel, to generate a gating pathway of the pore domain in the absence of the voltage-sensing domains. We then performed umbrella sampling simulations along this pathway to calculate a potential of mean force that describes the free energy landscape connecting the closed and open conformations of the pore domain. The resulting energetic landscape displays three minima, corresponding to stable open, closed, and intermediate conformations with roughly similar stabilities...
February 16, 2017: Journal of Computational Chemistry
Roobee Garla, Narinder Kaur, Mohinder Pal Bansal, Mohan Lal Garg, Biraja Prasad Mohanty
Exposure to inorganic arsenic (As) is one of the major health concerns in several regions around the world. Binding of As(III) with thiols is central to the mechanisms related to its toxicity, detoxification, and therapeutic effects. Due to its high thiol content, metallothionein (MT) is presumed to play an important role in case of arsenic toxicity. Consequences of these As-thiol interactions are not yet clear due to various difficulties in the characterization of arsenic bound proteins by spectroscopic techniques...
March 2017: Journal of Molecular Modeling
Meng-Xu Jiang, Chun-Guang Liu
Although epoxidation of alkenes by N2O catalyzed by Mn-substituted polyoxometalates (POMs) has been studied both experimental and theoretical methods, a complete catalytic cycle has not been established currently. In the present paper, density functional theory (DFT) calculations were employed to explore possible reaction mechanism about this catalytic cycle. Our DFT studies reveal that the reaction pathway starts from a low-valent Keggin-type POM aquametal derivative [PW11O39Mn(III)H2O](4-). In the presence of N2O pressure, the formation of the active catalytic species [PW11O39Mn(V)O](4-) involves a ligand-substituted reaction about replacement of the aqua ligand with N2O to generation of POM/N2O adduct [PW11O39Mn(III)ON2](4-) and dissociation of N2 from this adduct...
December 21, 2016: Journal of Molecular Graphics & Modelling
Nuno M Silvestre, M Tasinkevych
The Landau-de Gennes free energy is used to study theoretically the effective interaction of spherical "key" and anisotropic "lock" colloidal particles. We assume identical anchoring properties of the surfaces of the key and of the lock particles, and we consider planar degenerate and perpendicular anchoring conditions separately. The lock particle is modeled as a spherical particle with a spherical dimple. When such a particle is introduced into a nematic liquid crystal, it orients its dimple at an oblique angle θ_{eq} with respect to the far field director n_{∞}...
January 2017: Physical Review. E
Jiawen Deng, Alvis Mazon Tan, Peter Hänggi, Jiangbin Gong
Work is one of the most basic notions in statistical mechanics, with work fluctuation theorems being one central topic in nanoscale thermodynamics. With Hamiltonian chaos commonly thought to provide a foundation for classical statistical mechanics, here we present general salient results regarding how (classical) Hamiltonian chaos generically impacts on nonequilibrium work fluctuations. For isolated chaotic systems prepared with a microcanonical distribution, work fluctuations are minimized and vanish altogether in adiabatic work protocols...
January 2017: Physical Review. E
Mathias Hayn, Tobias Brandes
We analyze the thermodynamic properties of a generalized Dicke model, i.e., a collection of three-level systems interacting with two bosonic modes. We show that at finite temperatures the system undergoes first-order phase transitions only, which is in contrast to the zero-temperature case where a second-order phase transition exists as well. We discuss the free energy and prominent expectation values. The limit of vanishing temperature is discussed as well.
January 2017: Physical Review. E
José Antonio Vélez-Pérez, Luis Olivares-Quiroz
In this work we analyze the translocation of homopolymer chains poly-X, where X represents any of the 20 naturally occurring amino acid residues, in terms of size N and single-helical propensity ω. We provide an analytical framework to calculate both the free energy F of translocation and the translocation time τ as a function of chain size N, energies U and ε of the unfolded and folded states, respectively. Our results show that free energy F has a characteristic bell-shaped barrier as function of the percentage of monomers translocated...
January 2017: Physical Review. E
José A Carrasco, Federico Finkel, Artemio González-López, Miguel A Rodríguez
We study the critical behavior and the ground-state entanglement of a large class of su(1|1) supersymmetric spin chains with a general (not necessarily monotonic) dispersion relation. We show that this class includes several relevant models, with both short- and long-range interactions of a simple form. We determine the low temperature behavior of the free energy per spin, and deduce that the models considered have a critical phase in the same universality class as a (1+1)-dimensional conformal field theory (CFT) with central charge equal to the number of connected components of the Fermi sea...
January 2017: Physical Review. E
Ivan Latella, Agustín Pérez-Madrid, Alessandro Campa, Lapo Casetti, Stefano Ruffo
Completely open systems can exchange heat, work, and matter with the environment. While energy, volume, and number of particles fluctuate under completely open conditions, the equilibrium states of the system, if they exist, can be specified using the temperature, pressure, and chemical potential as control parameters. The unconstrained ensemble is the statistical ensemble describing completely open systems and the replica energy is the appropriate free energy for these control parameters from which the thermodynamics must be derived...
January 2017: Physical Review. E
Yang Su, Hongfei Li, Hanbin Ma, John Robertson, Arokia Nathan
Cu2O nanoparticles with controllable facets are of great significance for photocatalysis. In this work, the surface termination and facet orientation of Cu2O nanoparticles are accurately tuned by adjusting the amount of hydroxylamine hydrochloride and surfactant. It is found that Cu2O nanoparticles with Cu-terminated (110) or (111) surfaces show high photocatalytic activity, while other exposed facets show poor reactivity. DFT simulations confirm that the SDS surfactant can lower the surface free energy of Cu-terminated surfaces, increasing the density of exposed Cu atoms at the surfaces, and thus benefiting the photocatalytic activity...
February 16, 2017: ACS Applied Materials & Interfaces
Mauricio Cattaneo, Scott A Ryken, James M Mayer
A diverse set of 2 e(-) /2 H(+) reactions are described that interconvert [Ru(II) (bpy)(en*)2 ](2+) and [Ru(IV) (bpy)(en-H*)2 ](2+) (bpy=2,2'-bipyridine, en*=H2 NCMe2 CMe2 NH2 , en*-H=H2 NCMe2 CMe2 NH(-) ), forming or cleaving different O-H, N-H, S-H, and C-H bonds. The reactions involve quinones, hydrazines, thiols, and 1,3-cyclohexadiene. These proton-coupled electron transfer reactions occur without substrate binding to the ruthenium center, but instead with precursor complex formation by hydrogen bonding...
February 16, 2017: Angewandte Chemie
Yan-Jun Zhang, Jing-Na Ding, Hui Zhong, Ju-Guang Han
Multifunctional viral protein (VP35) encoded by the highly pathogenic Ebola viruses (EBOVs) can antagonize host double-stranded RNA (dsRNA) sensors and immune response because of the simultaneous recognition of dsRNA backbone and blunt ends. Mutation of select hydrophobic conserved basic residues within the VP35 inhibitory domain (IID) abrogates its dsRNA-binding activity, and impairs VP35-mediated interferon (IFN) antagonism. Herein the detailed binding mechanism between dsRNA and WT, single mutant, and double mutant were investigated by all-atom molecular dynamics (MD) simulation and binding energy calculation...
February 16, 2017: Proteins
Jerome Cuny, Kseniia Korchagina, Chemseddine Menakbi, Tzonka Mineva
Application of ab initio molecular dynamics to study free energy surfaces (FES) is still not commonly performed because of the extensive sampling required. Indeed, it generally necessitates computationally costly simulations of more than several hundreds of picoseconds. To achieve such studies, efficient density functional theory (DFT) formalisms, based on various levels of approximate computational schemes, have been developed, and provide a good alternative to commonly used DFT implementations. We report benchmark results on the conformational change FES of alanine dipeptide obtained with auxiliary density functional theory (ADFT) and second- and third-order density functional tight-binding (DFTB) methods coupled to metadynamics simulations...
March 2017: Journal of Molecular Modeling
Vojtech Mlynsky, Giovanni Bussi
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a variety of RNAs and are used to characterize conformational changes in riboswitches. However, the structural determinants that lead to differential reactivities in unpaired nucleotides have not been investigated yet. In this work we used a combination of theoretical approaches, i...
February 15, 2017: RNA
Davit Hakobyan, Andreas Heuer
Based on all-atom Molecular Dynamics (MD) simulations of a lipid bilayer we present a systematic mapping on a 2D lattice model. Keeping the lipid type and the chain order parameter as key variables we derive a free energy functional, containing the enthalpic interaction of adjacent lipids as well as the tail entropy. The functional form of both functions is explicitly determined for saturated and polyunsaturated lipids. By studying the lattice model via Monte Carlo simulations it is possible to reproduce the temperature dependence of the distribution of order parameters of the pure lipids, including the prediction of the gel transition...
February 14, 2017: Journal of Chemical Physics
Mohammadhasan Dinpajooh, Marshall D Newton, Dmitry V Matyushov
The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation...
February 14, 2017: Journal of Chemical Physics
Adam P Hughes, Uwe Thiele, Andrew J Archer
For a film of liquid on a solid surface, the binding potential g(h) gives the free energy as a function of the film thickness h and also the closely related (structural) disjoining pressure Π=-∂g/∂h. The wetting behaviour of the liquid is encoded in the binding potential and the equilibrium film thickness corresponds to the value at the minimum of g(h). Here, the method we developed in the work of Hughes et al. [J. Chem. Phys. 142, 074702 (2015)], and applied with a simple discrete lattice-gas model, is used with continuum density functional theory (DFT) to calculate the binding potential for a Lennard-Jones fluid and other simple liquids...
February 14, 2017: Journal of Chemical Physics
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