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free-energy principle

Wojciech Grochala
In this perspective contribution, we revisit the Maximum Hardness Principle (MHP), formulated by Pearson in 1987, and an equivalent Minimum Polarizability Principle (MPP) from Chattaraj and Parr, with particular emphasis on the cases where nuclear potential acting on electrons does not remain constant, and where substantial modifications of the nuclear geometry take place (Generalized MHP, GMHP). We first bring basic concepts related to electronic hardness, and then we present an overview of important manifestations of the GMHP for molecular systems such as (i) the tendency of two free radicals to couple, (ii) reduced reactivity of noble gases, (iii) symmetry-breaking distortions related to the Jahn-Teller effect, and/or these connected with (anti)aromatic character of certain organic molecules, (iv) enhanced reactivity of excited states, (v) high-low spin transitions, etc...
August 17, 2017: Physical Chemistry Chemical Physics: PCCP
Oleg N Starovoytov, Pengzhi Zhang, Piotr Cieplak, Margaret S Cheung
The light-harvesting molecular triad consisting of carotenoid polyene (C), diaryl-porphyrin (P) and pyrrole-fullerene (C60) is a donor-acceptor molecule capable of absorbing incident light in the visible range. Its ability to convert solar energy to electrical excitation and charge separation energy suggests a great potential in real-world applications. The ensemble of its conformations under ambient conditions varies widely according to its electronic state. In previous work, we applied a non-polarizable model to study the conformational distribution of the molecular triad in the ground and charge separated states...
August 17, 2017: Physical Chemistry Chemical Physics: PCCP
Roohollah Hafizi, S Javad Hashemifar, Mojtaba Alaei, MohammadReza Jangrouei, Hadi Akbarzadeh
In this paper, we employ an evolutionary algorithm along with the full-potential density functional theory (DFT) computations to perform a comprehensive search for the stable structures of stoichiometric (WS2)n nano-clusters (n = 1 - 9), within three different exchange-correlation functionals. Our results suggest that n = 5 and 8 are possible candidates for the low temperature magic sizes of WS2 nano-clusters while at temperatures above 500 Kelvin, n = 7 exhibits a comparable relative stability with n = 8. The electronic properties and energy gap of the lowest energy isomers were computed within several schemes, including semilocal Perdew-Burke-Ernzerhof and Becke-Lee-Yang-Parr functionals, hybrid B3LYP functional, many body based DFT+GW approach, ΔSCF method, and time dependent DFT calculations...
December 7, 2016: Journal of Chemical Physics
Chad Priest, Bo Li, De-En Jiang
Exploring the structural interplay of ligands with uranyl can provide important knowledge for technology advances in uranium extraction from seawater. However, obtaining such chemical information is not an easy endeavor experimentally. From a plethora of computational methods, this work provides both microscopic insights and free-energy profiles of the binding between uranyl and deprotonated glutardiamidoxime (H2B) for which experimental structural information is not available, despite H2B being an important model ligand with an open-chain conformation for understanding aqueous uranium extraction chemistry...
August 7, 2017: Inorganic Chemistry
Marek Trojanowicz, Anna Bojanowska-Czajka, Andrea G Capodaglio
The increasing role of chemistry in industrial production and its direct and indirect impacts in everyday life create the need for continuous search and efficiency improvement of new methods for decomposition/removal of different classes of waterborne anthropogenic pollutants. This review paper addresses a highly promising class of water treatment solutions, aimed at tackling the pressing problem of emerging contaminants in natural and drinking waters and wastewater discharges. Radiation processing, a technology originating from radiation chemistry studies, has shown encouraging results in the treatment of (mainly) organic water pollution...
August 5, 2017: Environmental Science and Pollution Research International
H Shinotsuka, B Da, S Tanuma, H Yoshikawa, C J Powell, D R Penn
We calculated electron inelastic mean free paths (IMFPs) for liquid water from its optical energy-loss function (ELF) for electron energies from 50 eV to 30 keV. These calculations were made with the relativistic full Penn algorithm (FPA) that has been used for previous IMFP and electron stopping-power calculations for many elemental solids. We also calculated IMFPs of water with three additional algorithms: the relativistic single-pole approximation (SPA), the relativistic simplified SPA, and the relativistic extended Mermin method...
April 2017: Surface and Interface Analysis: SIA
Yujin Ji, Huilong Dong, Mingye Yang, Tingjun Hou, Youyong Li
The development of novel cathode catalysts is of great importance to the practical applications of nonaqueous lithium oxygen (Li-O2) batteries. Here by using first-principles calculations, we revealed the catalytic mechanism and evaluated the catalytic activity of monolayer germanium monochalcogenides (2D-GeXs, X = S/Se) as cathode catalytic materials. For 2D-GeXs, Li4O4 with a ring-like structure is the final discharge product. The free energy diagram demonstrates that 2D-GeSe is more energetically favorable than 2D-GeS due to its considerably lower oxygen reduction reaction (ORR) overpotential (0...
August 9, 2017: Physical Chemistry Chemical Physics: PCCP
Billy J Williams-Noonan, Elizabeth Yuriev, David K Chalmers
Underpinning all drug discovery projects is the interaction between a drug and its target, usually a protein. Thus, improved methods for predicting the magnitude of protein-ligand interactions have the potential to improve the efficiency of drug development. In this review, we describe the principles of free energy methods used for the calculation of protein-ligand binding free energies, the challenges associated with these methods, and recent advances developed to address these difficulties. We then present case studies from 2005-2017, each demonstrating that alchemical free energy methods can assist rational drug design projects...
July 26, 2017: Journal of Medicinal Chemistry
Sara Khan, Umar Farooq, Maria Kurnikova
In this study, we explore the structural and dynamic adaptations of the Tryptophan synthase α-subunit in a ligand bound state in psychrophilic, mesophilic and hyperthermophilic organisms at different temperatures by MD simulations. We quantify the global and local fluctuations in the 40 ns time scale by analyzing the root mean square deviation/fluctuations. The distinct behavior of the active site and loop 6 is observed with the elevation of temperature. Protein stability relies more on electrostatic interactions, and these interactions might be responsible for the stability of varying temperature evolved proteins...
July 24, 2017: Molecular BioSystems
Vatsal A Jhalani, Jin-Jian Zhou, Marco Bernardi
GaN is a key material for lighting technology. Yet, the carrier transport and ultrafast dynamics that are central in GaN light-emitting devices are not completely understood. We present first-principles calculations of carrier dynamics in GaN, focusing on electron-phonon (e-ph) scattering and the cooling and nanoscale dynamics of hot carriers. We find that e-ph scattering is significantly faster for holes compared to electrons and that for hot carriers with an initial 0.5-1 eV excess energy, holes take a significantly shorter time (∼0...
July 27, 2017: Nano Letters
Miguel A Caro, Olga Lopez-Acevedo, Tomi Laurila
We present a complete methodology to consistently estimate redox potentials strictly from first-principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model, and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr(2+/3+), V(2+/3+), Ru(NH3)6(2+/3+), Sn(2+/4+), Cu(1+/2+), FcMeOH(0/1+), and Fe(2+/3+) (in aqueous solution) and Fc(0/1+) (in acetonitrile)...
July 27, 2017: Journal of Chemical Theory and Computation
Emiliana Fabbri, Maarten Nachtegaal, Tobias Binninger, Xi Cheng, Bae-Jung Kim, Julien Durst, Francesco Bozza, Thomas Graule, Robin Schäublin, Luke Wiles, Morgan Pertoso, Nemanja Danilovic, Katherine E Ayers, Thomas J Schmidt
The growing need to store increasing amounts of renewable energy has recently triggered substantial R&D efforts towards efficient and stable water electrolysis technologies. The oxygen evolution reaction (OER) occurring at the electrolyser anode is central to the development of a clean, reliable and emission-free hydrogen economy. The development of robust and highly active anode materials for OER is therefore a great challenge and has been the main focus of research. Among potential candidates, perovskites have emerged as promising OER electrocatalysts...
July 17, 2017: Nature Materials
Jason R Dwyer, Maher Harb
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing...
January 1, 2017: Applied Spectroscopy
Daniele De Martino
In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions...
June 2017: Physical Review. E
Suman G Das, Madan Rao, Garud Iyengar
The living cell uses a variety of molecular receptors to read and process chemical signals that vary in space and time. We model the dynamics of such molecular level measurements as Markov processes in steady state, with a coupling between the receptor and the signal. We prove exactly that, when the signal dynamics is not perturbed by the receptors, the free energy consumed by the measurement process is lower bounded by a quantity proportional to the mutual information. Our result is completely independent of the receptor architecture and dependent on signal properties alone, and therefore holds as a general principle for molecular information processing...
June 2017: Physical Review. E
Zeyu Jiang, Zhirong Liu, Yuanchang Li, Wenhui Duan
Using first-principles   GW Bethe-Salpeter equation calculations and the k·p theory, we unambiguously show that for two-dimensional (2D) semiconductors, there exists a robust linear scaling law between the quasiparticle band gap (E_{g}) and the exciton binding energy (E_{b}), namely, E_{b}≈E_{g}/4, regardless of their lattice configuration, bonding characteristic, as well as the topological property. Such a parameter-free universality is never observed in their three-dimensional counterparts. By deriving a simple expression for the 2D polarizability merely with respect to E_{g}, and adopting the screened hydrogen model for E_{b}, the linear scaling law can be deduced analytically...
June 30, 2017: Physical Review Letters
Amir Omidvarnia, Mangor Pedersen, Richard E Rosch, Karl J Friston, Graeme D Jackson
In this opinion paper, we describe a combined view of functional and effective brain connectivity along with the free-energy principle for investigating persistent disruptions in brain networks of patients with focal epilepsy. These changes are likely reflected in effective connectivity along the cortical hierarchy and construct the basis of increased local functional connectivity in focal epilepsy. We propose a testable framework based on dynamic causal modelling and functional connectivity analysis with the capacity of explaining commonly observed connectivity changes during interictal periods...
2017: NeuroImage: Clinical
Heike B Thomas, Matthias Hennemann, Patrick Kibies, Franziska Hoffgaard, Stefan Güssregen, Gerhard Hessler, Stefan M Kast, Timothy Clark
A neglect of diatomic differential overlap (NDDO) Hamiltonian has been parametrized as an electronic component of a polarizable force field. Coulomb and exchange potentials derived directly from the NDDO Hamiltonian in principle can be used with classical potentials, thus forming the basis for a new generation of efficiently applicable multipolar polarizable force fields. The new hpCADD Hamiltonian uses force-field-like atom types and reproduces the electrostatic properties (dipole moment, molecular electrostatic potential) and Koopmans' theorem ionization potentials closely, as demonstrated for a large training set and an independent test set of small molecules...
August 2, 2017: Journal of Chemical Information and Modeling
Shijie Sheng, Michael Miller, Jianzhong Wu
Solvation plays an important role in diverse chemical processes ranging from reaction kinetics to molecular recognition, solubility, and phase separations. Despite a long-history of theoretical exploration, quantitative prediction of solvation remains a theoretical challenge without relying on the macroscopic properties of the solvent as an input. Here we present a molecular density functional theory that provides a self-consistent description of the solvation structure and thermodynamic properties of small organic molecules in liquid water at different temperatures...
July 11, 2017: Journal of Physical Chemistry. B
Eric Cockayne
We use first-principles density functional theory total energy and linear response phonon calculations to compute the Helmholtz and Gibbs free energy as a function of temperature, pressure, and cell volume in the flexible metal-organic framework material MIL-53(Cr) within the quasiharmonic approximation. GGA and metaGGA calculations were performed, each including empirical van der Waals (vdW) forces under the D2, D3, or D3(BJ) parameterizations. At all temperatures up to 500 K and pressures from -30 MPa to 30 MPa, two minima in the free energy versus volume are found, corresponding to the narrow pore (np) and large pore (lp) structures...
March 2017: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
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