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Journal of Chemical Physics

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https://www.readbyqxmd.com/read/28456151/cheap-but-accurate-calculation-of-chemical-reaction-rate-constants-from-ab-initio-data-via-system-specific-black-box-force-fields
#1
Julien Steffen, Bernd Hartke
Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections...
October 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915765/the-parameter-uncertainty-inflation-fallacy
#2
Pascal Pernot
Statistical estimation of the prediction uncertainty of physical models is typically hindered by the inadequacy of these models due to various approximations they are built upon. The prediction errors caused by model inadequacy can be handled either by correcting the model's results or by adapting the model's parameter uncertainty to generate prediction uncertainties representative, in a way to be defined, of model inadequacy errors. The main advantage of the latter approach (thereafter called PUI, for Parameter Uncertainty Inflation) is its transferability to the prediction of other quantities of interest based on the same parameters...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915764/sequence-dependent-aggregation-of-peptides-and-fibril-formation
#3
Nguyen Ba Hung, Duy-Manh Le, Trinh X Hoang
Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915763/extended-screened-exchange-functional-derived-from-transcorrelated-density-functional-theory
#4
Naoto Umezawa
We propose a new formulation of the correlation energy functional derived from the transcorrelated method in use in density functional theory (TC-DFT). An effective Hamiltonian, HTC, is introduced by a similarity transformation of a many-body Hamiltonian, H, with respect to a complex function F: HTC=1FHF. It is proved that an expectation value of HTC for a normalized single Slater determinant, D(n), corresponds to the total energy: E[n] = ⟨Ψ(n)|H|Ψ(n)⟩/⟨Ψ(n)|Ψ(n)⟩ = ⟨D(n)|HTC|D(n)⟩ under the two assumptions: (1) The electron density nr associated with a trial wave function Ψ(n) = D(n)F is v-representable and (2) Ψ(n) and D(n) give rise to the same electron density nr...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915762/on-the-relationship-between-the-local-segmental-dynamics-and-the-tagged-monomer-dynamics-in-lamellar-phases-of-diblock-copolymers
#5
Vaidyanathan Sethuraman, Venkat Ganesan
In this brief article, we present results from coarse-grained molecular dynamics simulations which probed the relationship between the local segmental dynamics and the tagged monomer dynamics in lamellar phases of diblock copolymers. Our results demonstrate that monomer relaxation times do not provide directly a quantitatively accurate measure of the spatial variations in segmental dynamics. However, a convolution of the monomer density distributions with their corresponding relaxation times is shown to provide an approximate, but accurate, quantitative characterization of the average local segmental dynamics...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915761/a-potential-model-for-sodium-chloride-solutions-based-on-the-tip4p-2005-water-model
#6
A L Benavides, M A Portillo, V C Chamorro, J R Espinosa, J L F Abascal, C Vega
Despite considerable efforts over more than two decades, our knowledge of the interactions in electrolyte solutions is not yet satisfactory. Not even one of the most simple and important aqueous solutions, NaCl(aq), escapes this assertion. A requisite for the development of a force field for any water solution is the availability of a good model for water. Despite the fact that TIP4P/2005 seems to fulfill the requirement, little work has been devoted to build a force field based on TIP4P/2005. In this work, we try to fill this gap for NaCl(aq)...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915760/molybdenum-disulfide-and-water-interaction-parameters
#7
Mohammad Heiranian, Yanbin Wu, Narayana R Aluru
Understanding the interaction between water and molybdenum disulfide (MoS2) is of crucial importance to investigate the physics of various applications involving MoS2 and water interfaces. An accurate force field is required to describe water and MoS2 interactions. In this work, water-MoS2 force field parameters are derived using the high-accuracy random phase approximation (RPA) method and validated by comparing to experiments. The parameters obtained from the RPA method result in water-MoS2 interface properties (solid-liquid work of adhesion) in good comparison to the experimental measurements...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915759/an-ab-initio-study-of-hydroxylated-graphane
#8
Francesco Buonocore, Andrea Capasso, Nicola Lisi
Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915758/co-adsorption-of-water-and-oxygen-on-gan-effects-of-charge-transfer-and-formation-of-electron-depletion-layer
#9
Qi Wang, Ajinkya Puntambekar, Vidhya Chakrapani
Species from ambient atmosphere such as water and oxygen are known to affect electronic and optical properties of GaN, but the underlying mechanism is not clearly known. In this work, we show through careful measurement of electrical resistivity and photoluminescence intensity under various adsorbates that the presence of oxygen or water vapor alone is not sufficient to induce electron transfer to these species. Rather, the presence of both water and oxygen is necessary to induce electron transfer from GaN that leads to the formation of an electron depletion region on the surface...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915757/liquid-bridging-of-cylindrical-colloids-in-near-critical-solvents
#10
M Labbé-Laurent, A D Law, S Dietrich
Within mean field theory, we investigate the bridging transition between a pair of parallel cylindrical colloids immersed in a binary liquid mixture as a solvent that is close to its critical consolute point Tc. We determine the universal scaling functions of the effective potential and of the force between the colloids. For a solvent that is at the critical concentration and close to Tc, we find that the critical Casimir force is the dominant interaction at close separations. This agrees very well with the corresponding Derjaguin approximation for the effective interaction between the two cylinders, while capillary forces originating from the extension of the liquid bridge turn out to be more important at large separations...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915756/a-thermally-driven-differential-mutation-approach-for-the-structural-optimization-of-large-atomic-systems
#11
Katja Biswas
A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating a thermal selection criterion, which makes it possible to reliably obtain low lying minima with just a small population size and is suitable for multimodal structural optimization. The method is tested on the structural optimization of amorphous graphene from unbiased atomic starting configurations...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915755/defects-and-oxidation-of-group-iii-monochalcogenide-monolayers
#12
Yu Guo, Si Zhou, Yizhen Bai, Jijun Zhao
Among various two-dimensional (2D) materials, monolayer group-III monochalcogenides (GaS, GaSe, InS, and InSe) stand out owing to their potential applications in microelectronics and optoelectronics. Devices made of these novel 2D materials are sensitive to environmental gases, especially O2 molecules. To address this critical issue, here we systematically investigate the oxidization behaviors of perfect and defective group-III monochalcogenide monolayers by first-principles calculations. The perfect monolayers show superior oxidation resistance with large barriers of 3...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915754/modeling-the-mechanism-of-cln025-beta-hairpin-formation
#13
Keri A McKiernan, Brooke E Husic, Vijay S Pande
Beta-hairpins are substructures found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915753/non-renewal-statistics-for-electron-transport-in-a-molecular-junction-with-electron-vibration-interaction
#14
Daniel S Kosov
Quantum transport of electrons through a molecule is a series of individual electron tunneling events separated by stochastic waiting time intervals. We study the emergence of temporal correlations between successive waiting times for the electron transport in a vibrating molecular junction. Using the master equation approach, we compute the joint probability distribution for waiting times of two successive tunneling events. We show that the probability distribution is completely reset after each tunneling event if molecular vibrations are thermally equilibrated...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915752/a-new-insight-into-diffusional-escape-from-a-biased-cylindrical-trap
#15
Alexander M Berezhkovskii, Leonardo Dagdug, Sergey M Bezrukov
Recent experiments with single biological nanopores, as well as single-molecule fluorescence spectroscopy and pulling studies of protein and nucleic acid folding raised a number of questions that stimulated theoretical and computational investigations of barrier crossing dynamics. The present paper addresses a closely related problem focusing on trajectories of Brownian particles that escape from a cylindrical trap in the presence of a force F parallel to the cylinder axis. To gain new insights into the escape dynamics, we analyze the "fine structure" of these trajectories...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915751/photobleaching-of-randomly-rotating-fluorescently-decorated-particles
#16
Swadhin Taneja, Andrew D Rutenberg
Randomly rotating particles that have been isotropically labeled with rigidly linked fluorophores will undergo non-isotropic (patchy) photobleaching under illumination due to the dipole coupling of fluorophores with light. For a rotational diffusion rate D of the particle and a photobleaching time scale τ of the fluorophores, the dynamics of this process are characterized by the dimensionless combination Dτ. We find significant interparticle fluctuations at intermediate Dτ. These fluctuations vanish at both large and small Dτ or at small or large elapsed times t...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915750/near-infrared-spectroscopy-and-anharmonic-theory-of-the-h2o-ar1-2-cation-complexes
#17
J Philipp Wagner, David C McDonald, Michael A Duncan
Weakly bound complexes of the water radical cation with argon (H2O(+)Arn, n = 1,2) were generated by an electrical discharge/supersonic expansion and probed with mid- and near-infrared photodissociation spectroscopy in the 2050-4550 and 4850-7350 cm(-1) regions. To elucidate these spectra, these complexes were studied computationally at the CCSD(T) level including anharmonicity with the VPT2 method. The comparison between experiment and predicted spectra demonstrates that the VPT2 method is adequate to capture most of the vibrational band positions and their intensities...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915749/note-effect-of-a-small-surface-defect-on-the-smoluchowski-rate-constant-and-capacitance-of-a-spherical-capacitor
#18
Leonardo Dagdug, Alexander M Berezhkovskii, Vladimir Yu Zitserman
No abstract text is available yet for this article.
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915748/magnetic-two-dimensional-organic-topological-insulator-au-1-3-5-triethynylbenzene-framework
#19
Yu Chen, Qiang Sun
Based on first-principles calculations, we demonstrate that the recently-synthesized 2D organometallic framework consisting of Au atoms and 1,3,5-triethynylbenzene (Au-TEB) is a magnetic 2D organic topological insulator (OTI). The charge transfer and covalent bonding character lead to ferromagnetism and half-metallicity in the framework, and the weak spin-orbit coupling (SOC) of C pz orbitals mediated by Au d orbitals opens modest bandgaps in the vicinity of the Fermi level. Moreover, using tight-binding model simulations, we further characterize the nonzero Chern number and edge states of Au-TEB to confirm its topological nontriviality that remains intact when the framework is supported on an insulating substrate, and applying an external strain can increase the magnitude of SOC gaps, leading to an enhanced topological nontriviality...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915747/mechanisms-and-rates-of-nucleation-of-amyloid-fibrils
#20
Cheng-Tai Lee, Eugene M Terentjev
The classical nucleation theory finds the rate of nucleation proportional to the monomer concentration raised to the power, which is the "critical nucleus size," nc. The implicit assumption, that amyloids nucleate in the same way, has been recently challenged by an alternative two-step mechanism, when the soluble monomers first form a metastable aggregate (micelle) and then undergo conversion into the conformation rich in β-strands that are able to form a stable growing nucleus for the protofilament. Here we put together the elements of extensive knowledge about aggregation and nucleation kinetics, using a specific case of Aβ1-42 amyloidogenic peptide for illustration, to find theoretical expressions for the effective rate of amyloid nucleation...
September 14, 2017: Journal of Chemical Physics
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