The Journal of Chemical Physics
Editors' Choice for 2009

The Editors at The Journal of Chemical Physics facilitate publication of the most innovative and influential articles in the field of Chemical Physics each year. In the following collection, the Editors have selected a few of the many notable JCP articles published in 2009 that present ground-breaking research. This collection represents only a small fraction of the critical research published in JCP in 2009 and is representative of the broad cross-section of topics that the journal covers. These seminal articles are freely available online at until the end of August 2010. Download the entire list (PDF).


Theoretical Methods and Algorithms
Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry
Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation
Surfaces, Interfaces, and Materials
Polymers and Complex Systems
Biological Molecules, Biopolymers, and Biological Systems




Theory of competitive adsorption-nucleation in polypeptide-mediated biomineralization
M. Muthukumar

This work deals with the mechanism of biomineralization: the nucleation and growth of mineral structures through interaction with biomolecules. In addressing how specific biopolymers direct selection of mineral morphologies and their growth kinetics, the authors present a new model based on a competition between adsorption of polymers onto selective interfaces and nucleation growth of minerals.

J. Chem. Phys. 130, 161101 (2009)


The work-Hamiltonian connection and the usefulness of the Jarzynski equality for free energy calculations
Eric N. Zimanyi and Robert J. Silbey

The authors discuss the relationship between two possible definitions of free energy and show how some recent disagreements regarding the applicability of the Jarzynski equality are the result of different authors using different definitions of free energy.

J. Chem. Phys. 130, 171102 (2009)


On the phase diagram of water with density functional theory potentials: The melting temperature of ice Ih with the Perdew-Burke-Ernzerhof and Becke-Lee-Yang-Parr functionals
Soohaeng Yoo, Xiao Cheng Zeng, and Sotiris S. Xantheas

The authors used Born-Oppenheimer molecular dynamics simulation and two commonly-used density functionals to investigate the properties of water. They found that ambient condition simulations at ρ = 1 g/cm3 will describe a supercooled state that is overstructured when compared to liquid water.

J. Chem. Phys. 130, 221102 (2009)

Approaching the Hartree-Fock limit by perturbative methods
Jia Deng, Andrew T. B. Gilbert, and Peter M. W. Gill

Described are perturbative methods for improving finite-basis Hartree-Fock calculations toward the complete-basis limit. The best method appears to offer quadratic error reduction and preliminary numerical applications that demonstrate remarkably accurate Hartree-Fock energies can be obtained.

J. Chem. Phys. 130, 231101 (2009)

Local explicitly correlated coupled-cluster methods: Efficient removal of the basis set incompleteness and domain errors
Thomas B. Adler and Hans-Joachim Werner

Proposed is an explicitly correlated local LCCSD-F12 method in which the basis set incompleteness error as well as the error caused by truncating the virtual orbital space to pair-specific local domains are strongly reduced.

J. Chem. Phys. 130, 241101 (2009)


Production of O2 Herzberg states in the deep UV photodissociation of ozone
R. Schinke, G. C. McBane, L. Shen, P. C. Singh, and A. G. Suits

There are strong indications that the O(3P)+O2 products with very low kinetic energy release formed in the deep UV (226 nm) photodissociation of ozone reflect excitation of the Herzberg states of O2—contradicting the earlier assignment to very high vibrational states.

J. Chem. Phys. 131, 011101 (2009)


Diversity of kinetic pathways in amyloid fibril formation
Giovanni Bellesia and Joan-Emma Shea

The kinetics of peptide oligomerization was investigated using Langevin Dynamics simulations and a coarse-grained peptide model. The simulations show a rich diversity of aggregation pathways, modulated by the β-sheet propensity (flexibility) of the peptide.

J. Chem. Phys. 131, 111102 (2009)


Al13H: Hydrogen atom site selectivity and the shell model
A. Grubisic, X. Li, S. T. Stokes, K. Vetter, G. F. Ganteför, K. H. Bowen, P. Jena, B. Kiran, R. Burgert, and H. Schnöckel

A combination of anion photoelectron spectroscopy and density functional theory calculations are used to explore the influence of the shell model on H atom site selectivity in Al13H.

J. Chem. Phys. 131, 121103 (2009)

Combined temperature-programmed reaction and in situ x-ray scattering studies of size-selected silver clusters under realistic reaction conditions in the epoxidation of propene
Stefan Vajda, Sungsik Lee, Kristian Sell, Ingo Barke, Armin Kleibert, Viola von Oeynhausen, Karl-Heinz Meiwes-Broer, Arantxa Fraile Rodríguez, Jeffrey W. Elam, Michael M. Pellin, Byeongdu Lee, Sönke Seifert, and Randall E. Winans

The catalytic activity and dynamical shape changes in size-selected nanoclusters are studied under realistic reaction conditions by using a combination of temperature-programmed reaction with in situ grazing-incidence small angle x-ray scattering.

J. Chem. Phys. 131, 121104 (2009)


Direct visualization of the H-Xe bond in xenon hydrides: Xenon isotopic shift in the IR spectra
Vladimir I. Feldman, Alexey V. Kobzarenko, Irina A. Baranova, Alexander V. Danchenko, Fedor F. Sukhov, Ehud Tsivion, and R. Benny Gerber

Direct experimental evidence of isotopic shifts and complementary quantum calculations are presented for the H-Xe bond in HXeY type compounds.

J. Chem. Phys. 131, 151101 (2009)


Observation of buried water molecules in phospholipid membranes by surface sum-frequency generation spectroscopy
Maria Sovago, Erik Vartiainen, and Mischa Bonn

The structure and orientation of water molecules at the water-lipid interface is investigated using vibrational sum-frequency generation in conjunction with a maximum entropy phase retrieval method.

J. Chem. Phys. 131, 161107 (2009)

Universal nonexponential relaxation: Complex dynamics in simple liquids
David A. Turton and Klaas Wynne

Using optical Kerr-effect spectroscopy it is shown that for argon, krypton, and xenon, both the librational and diffusional contributions to the spectrum are surprisingly complex. The measured behavior is shown to be similar to that observed for water, suggesting certain fundamental or universal properties of liquids.

J. Chem. Phys. 131, 201101 (2009)

Charge transfer by electronic excitation: Direct measurement by high resolution spectroscopy in the gas phase
A. J. Fleisher, P. J. Morgan, and D. W. Pratt

The amount of charge transferred when a single ammonia complex of the photoacid β-naphthol (2HNA) is excited by light is reported. The measurement was made by comparing the permanent electric dipole moments of cis-2HNA in its ground (S0) and excited (S1) states, determined by Stark-effect studies of its fully resolved S1←S0 electronic spectrum.

J. Chem. Phys. 131, 211101 (2009)


Theoretical Methods and Algorithms


Phase-space surface hopping: Nonadiabatic dynamics in a superadiabatic basis
Neil Shenvi

The author constructs a phase-space surface hopping algorithm for use in systems that exhibit strong nonadiabatic coupling. For a simple model problem, phase-space surface hopping is shown to be more accurate than position-space surface hopping, especially when the nonadiabatic coupling is strong.

J. Chem. Phys. 130, 124117 (2009)


Simulated x-ray scattering of protein solutions using explicit-solvent models
Sanghyun Park, Jaydeep P. Bardhan, Benoît Roux, and Lee Makowski

A novel formulation based on the atomistic description of water is presented in which scattering patterns are calculated from atomic coordinates of protein and water. Without any empirical adjustments, this method produces scattering patterns of unprecedented accuracy in the length scale between 5 and 100 Å.

J. Chem. Phys. 130, 134114 (2009)


On the relation between time-dependent and variational density functional theory approaches for the determination of excitation energies and transition moments
Tom Ziegler, Michael Seth, Mykhaylo Krykunov, Jochen Autschbach, and Fan Wang

The authors show that it is possible to derive the basic eigenvalue equation of adiabatic time-dependent density functional theory within the Tamm-Dancoff approximation from a variational principle.

J. Chem. Phys. 130, 154102 (2009)


Approximated electron repulsion integrals: Cholesky decomposition versus resolution of the identity methods
Florian Weigend, Marco Kattannek, and Reinhart Ahlrichs

The authors compare two procedures to gain efficiency by approximating two-electron integrals in molecular electronic structure calculations.  "Resolution of the identity" methods are superior in speed, whereas Cholesky decomposition methods have certain advantages for extended basis sets.

J. Chem. Phys. 130, 164106 (2009)


Second-order Møller-Plesset perturbation theory applied to extended systems. I. Within the projector-augmented-wave formalism using a plane wave basis set
Martijn Marsman, Andreas Grüneis, Joachim Paier, and Georg Kresse

The authors present an implementation of the canonical formulation of second-order Møller-Plesset perturbation theory within the projector-augmented-wave method under periodic boundary conditions using a plane wave basis set.

J. Chem. Phys. 130, 184103 (2009)


Time propagation of the Kadanoff–Baym equations for inhomogeneous systems
Adrian Stan, Nils Erik Dahlen, and Robert van Leeuwen

The authors present a time-propagation scheme for the Kadanoff-Baym equations for general inhomogeneous systems.  These equations describe the time evolution of the nonequilibrium Green function for interacting many-body systems in the presence of time-dependent external fields.

J. Chem. Phys. 130, 224101 (2009)


Transition state-finding strategies for use with the growing string method
Anthony Goodrow, Alexis T. Bell, and Martin Head-Gordon

The authors develop three transition state-finding search algorithms to complement the speedup of the modified-growing string method: (1) a hybrid strategy, (2) an energy-weighted strategy, and (3) a substring strategy.

J. Chem. Phys. 130, 244108 (2009)


Probing hot spots on protein-protein interfaces with all-atom free-energy simulation
Irene Meliciani, Konstantin Klenin, Timo Strunk, Katja Schmitz, and Wolfgang Wenzel

Computational alanine screening has been developed for the prediction of hot spots based on existing structural information.

J. Chem. Phys. 131, 034114 (2009)

Explicitly correlated combined coupled-cluster and perturbation methods
Toru Shiozaki, Edward F. Valeev, and So Hirata

Coupled-cluster methods have been extended to include the basis functions that explicitly depend on interelectronic distances in the wave function expansions with the aim of dramatically accelerating the basis-set convergence of correlation energies.

J. Chem. Phys. 131, 044118 (2009)

thumbnail Fermion Monte Carlo without fixed nodes: A game of life, death, and annihilation in Slater determinant space
George H. Booth, Alex J. W. Thom, and Ali Alavi

The authors have developed a new quantum Monte Carlo method for the simulation of correlated many-electron systems in full configuration-interaction spaces.

J. Chem. Phys. 131, 054106 (2009)


A simple model for the treatment of imaginary frequencies in chemical reaction rates and molecular liquids
Jian Liu and William H. Miller

A simple model for treating local imaginary frequencies that are important in the study of quantum effects in chemical reactions and various dynamical processes in molecular liquids is presented.

J. Chem. Phys. 131, 074113 (2009)


Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions
Uwe Winter and Tihamér Geyer

The authors show that an analytic integration of the equations of damped motion with hydrodynamic interactions between the particles leads to a fast multiparticle propagation scheme, which captures short-time and short-range solvent effects.

J. Chem. Phys. 131, 104102 (2009)

thumbnail Extended ensemble approach for deriving transferable coarse-grained potentials
J. W. Mullinax and W. G. Noid

An extended ensemble framework for calculating transferable coarse-grained potentials that accurately reproduce the structure of atomistic models for multiple systems is presented.

J. Chem. Phys. 131, 104110 (2009)

Benchmarking density-functional-theory calculations of rotational g tensors and magnetizabilities using accurate coupled-cluster calculations
Ola B. Lutnæs, Andrew M. Teale, Trygve Helgaker, David J. Tozer, Kenneth Ruud, and Jürgen Gauss

An accurate set of benchmark rotational g tensors and magnetizabilities are calculated using coupled-cluster singles-doubles theory and coupled-cluster single-doubles-perturbative-triples theory, in a variety of basis sets consisting of (rotational) London atomic orbitals.

J. Chem. Phys. 131, 144104 (2009)

Ring-polymer molecular dynamics rate-theory in the deep-tunneling regime: Connection with semiclassical instanton theory
Jeremy O. Richardson and Stuart C. Althorpe

The ring-polymer molecular dymanics method is demonstrated to be equivalent to an automated and approximate implemenation of the "Im F" version of semiclassical instanton theory when used to calculate reaction rates in the deep-tunneling regime.

J. Chem. Phys. 131, 214106 (2009)


Density functional method including weak interactions: Dispersion coefficients based on the local response approximation
Takeshi Sato and Hiromi Nakai

The authors propose a new method to calculate the atom-atom dispersion coefficients in a molecule for use in density functional theory with dispersion correction. This local response dispersion method is able to calculate the dispersion energy from the ground-state electron density.

J. Chem. Phys. 131, 224104 (2009)

Critical points bifurcation analysis of high- bending dynamics in acetylene
Vivian Tyng and Michael E. Kellman

The bending dynamics of acetylene with pure vibrational angular momentum excitation and nonzero quantum number s are analyzed through the method of critical points analysis to find new anharmonic modes born in bifurcations of the low energy normal modes.

J. Chem. Phys. 131, 244111 (2009)


Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry


Accurate ab initio potential energy surface, dynamics, and thermochemistry of the F+CH4 to HF+CH3 reaction
Gábor Czakó, Benjamin C. Shepler, Bastiaan J. Braams, and Joel M. Bowman

The reaction dynamics of the gas-phase reaction between a fluorine atom and a methane molecule are studied, and an accurate 12-dimensional potential energy surface (PES) is developed based on 19,384 ab initio energy points. Quasiclassical trajectory calculations of the reaction using the new PES are reported.

J. Chem. Phys. 130, 084301 (2009)


The parent anion of the RGD tripeptide: Photoelectron spectroscopy and quantum chemistry calculations
Xiang Li, Haopeng Wang, Kit H. Bowen, G. Grégoire, F. Lecomte, Jean-Pierre Schermann, and Charles Desfrançois

The gas-phase conformation of the intact (parent) unprotected RGD-peptide anion is investigated using a combination of anion photoelectron spectroscopy and quantum chemistry calculations of its low-energy stable structures.

J. Chem. Phys. 130, 214301 (2009)

Probing the stiffness of the simplest double hydrogen bond: The symmetric hydrogen bond modes of jet-cooled formic acid dimer
Z. Xue and M. A. Suhm

Raman active fundamentals, overtones, and combination bands involving out-of-plane bending and stretching vibrations of the hydrogen bonds in jet-cooled formic acid dimer are reported.  Preliminary experimental evidence for the most elusive fundamental vibration, symmetric OH torsion, is presented.

J. Chem. Phys. 131, 054301 (2009)


An ab initio study of the (H2O)20H+ and (H2O)21H+ water clusters
Tomasz Kuś, Victor F. Lotrich, Ajith Perera, and Rodney J. Bartlett

The study of the minimum Born–Oppenheimer structures of the protonated water clusters, (H2O)nH+ for n=20 and 21. The results confirm that the lowest energy structure of the magic number n=21 clusters corresponds to a more stable form than that of the 20-mer clusters.

J. Chem. Phys. 131, 104313 (2009)

Vibration-rotation pattern in acetylene. II. Introduction of Coriolis coupling in the global model and analysis of emission spectra of hot acetylene around 3 µm
Badr Amyay, Séverine Robert, Michel Herman, André Fayt, Balakrishna Raghavendra, Audrey Moudens, Jonathan Thiévin, Bertrand Rowe, and Robert Georges

A global model, updated as compared to previous work, allows all lines in the database to be simultaneously fitted, successfully. The updates are discussed taking into account, in particular, the systematic inclusion of Coriolis interaction.

J. Chem. Phys. 131, 114301 (2009)


Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation


Purely absorptive three-dimensional infrared spectroscopy
Sean Garrett-Roe and Peter Hamm

Three-dimensional fifth-order vibrational infared spectroscopy is described. The measured spectra agree very well with simulations of the data based on the cumulant expansion.

J. Chem. Phys. 130, 164510 (2009)


Linking microscopic guest properties to macroscopic observables in clathrate hydrates: Guest-host hydrogen bonding
Saman Alavi, Robin Susilo, and John A. Ripmeester

The authors use molecular dynamics simulations to compare the properties of clathrate hydrates with cyclopentane, tetrahydrofuran (THF), 1,3-dioxolane, tetrahydropyran (THP), and p-dioxane as guests.  Significant differences are observed between structural parameters and rotational dynamics for the different guests and related to the formation of guest-host hydrogen bonds in some (THF and THP) and the absence of similar hydrogen bonds in the clathrate hydrates of the other guests.

J. Chem. Phys. 130, 174501 (2009)


Local structure of reaction intermediates probed by time-resolved x-ray absorption near edge structure spectroscopy
G. Smolentsev, G. Guilera, M. Tromp, S. Pascarelli, and A. V. Soldatov

The proposed method combines principal component analysis of the series of experimental spectra, multidimensional interpolation of theoretical XANES as a function of structural parameters, and ab initio XANES calculations.

J. Chem. Phys. 130, 174508 (2009)


Relaxation effects in low density amorphous ice: Two distinct structural states observed by neutron diffraction
K. Winkel, D. T. Bowron, T. Loerting, E. Mayer, and J. L. Finney

The structure of low density amorphous ice, produced from high density amorphous ice by isobaric warming and very high density amorphous ice by isothermal decompression, are investigated via neutron diffraction with H/D isotopic substitution.

J. Chem. Phys. 130, 204502 (2009)


Growing correlation length in supercooled water
Emily B. Moore and Valeria Molinero

The evolution of the structure of water from the stable liquid to its glass, the low-density amorphous ice, at the critical cooling rate for vitrification is studied by molecular dynamics. A continuous transition to a tetrahedrally ordered low-density liquid is observed at 50 K below the temperature of maximum density and 25 K above a temperature of minimum density.  The liquid-liquid transition temperature coincides with the maximum rate of change in the local structure.

J. Chem. Phys. 130, 244505 (2009)


Ultrafast H2 and D2 rotational Raman responses in near critical CO2: An experimental and theoretical study of anisotropic solvation dynamics
J. Peng, T. C. Castonguay, D. F. Coker, and L. D. Ziegler

The optical heterodyne detected anisotropic rotational Raman responses of H2 and D2 in a near critical CO2 solution are reported.

J. Chem. Phys. 131, 054501 (2009)


Isotope effects in the vibrational lifetime of hydrogen on germanium(100): Theory and experiment
Sung Sakong, Peter Kratzer, Xu Han, Thorsten Balgar, and Eckart Hasselbrink

Combining first-principles calculations and sum frequency generation spectroscopy, the authors elucidate the microscopic details in the relaxation of the stretching vibration of hydrogen adsorbed on Ge(100).

J. Chem. Phys. 131, 124502 (2009)

Dissociative adsorption of hydrogen fluoride onto amorphous solid water
Patrick Ayotte, Zohreh Rafiei, François Porzio, and Patrick Marchand

Hydrogen fluoride is shown to be extensively ionically dissociated upon its adsorption onto and its dissolution within amorphous solid water films at 50 K. The results suggest a re-examination of dielectric and transport properties of HF-doped ice, including atmospheric processes involving this important halogen reservoir species.

J. Chem. Phys. 131, 124517 (2009)


Three-dimensional electronic spectroscopy of excitons in GaAs quantum wells
Daniel B. Turner, Katherine W. Stone, Kenan Gundogdu, and Keith A. Nelson

The phase stability of four fully phase-coherent fields that are controlled using a spatiotemporal femtosecond pulse shaper is exploited to create 3D Fourier transform electronic spectral solids through a four-wave-mixing process in GaAs quantum wells.

J. Chem. Phys. 131, 144510 (2009)

Water structure, dynamics, and vibrational spectroscopy in sodium bromide solutions
Y.-S. Lin, B. M. Auer, and J. L. Skinner

A theoretical study of steady-state and ultrafast vibrational spectroscopy, in the OD-stretch region, of dilute HOD in aqueous solutions of sodium bromide is presented where new spectroscopic maps are developed to undertake the study.

J. Chem. Phys. 131, 144511 (2009)


Energy transport via coordination bonds
Valeriy M. Kasyanenko, Zhiwei Lin, Grigory I. Rubtsov, James P. Donahue, and Igor V. Rubtsov

The energy transport across coordination bonds in tetraethylammonium bis(maleonitriledithiolate) iron(III)nitrosyl complex is investigated using dual-frequency RA 2DIR spectroscopy. A simple modeling of the energy transport is presented.

J. Chem. Phys. 131, 154508 (2009)

The role of intramolecular barriers on the glass transition of polymers: Computer simulations versus mode coupling theory
Marco Bernabei, Angel J. Moreno, and Juan Colmenero

By systematically tuning the strength of the barriers, the authors investigate their role on the glass transition. Dynamic observables are analyzed within the framework of the mode coupling theory.

J. Chem. Phys. 131, 204502 (2009)


Surfaces, Interfaces, and Materials


Vibrational mode specific bond dissociation in a single molecule
J. R. Hahn and W. Ho

Tunneling electrons from a scanning tunneling microscope were used to image and dissociate single O2-water-O complexes adsorbed on a Ag(110) surface at 13 K. The dissociation rate increases by ~100 times when the electron energy is equivalent to that of an O–H stretch.

J. Chem. Phys. 131, 044706 (2009)

A first-principles study of bulk oxide formation on Pd(100)
Nicola Seriani, Judith Harl, Florian Mittendorfer, and Georg Kresse

The results give a framework for the interpretation of experiments of Pd oxide growth, showing the most stable orientation of the oxide film. A simple model employing density functional theory energies predicts a Stranski-Krastanov growth mode for the oxide film.

J. Chem. Phys. 131, 054701 (2009)


Casimir chemistry
D. P. Sheehan

At the nanoscale, the Casimir effect can be used to mechanically tune critical aspects of chemical reactions by varying the spacing and composition of reaction vessel boundaries.

J. Chem. Phys. 131, 104706 (2009)


Polymers and Complex Systems

Time-resolved specular and off-specular neutron reflectivity measurements on deuterated polystyrene and poly(vinyl methyl ether) blend thin films during dewetting process
Hiroki Ogawa, Toshiji Kanaya, Koji Nishida, Go Matsuba, Jaroslaw P. Majewski, and Erik Watkins

Off-specular reflectivity was analyzed, for the first time, to evaluate kinetics of structure formation in the film plane during the dewetting process, showing that the droplets formation in micrometer scale occurred in the late stage of dewetting.

J. Chem. Phys. 131, 104907 (2009)


Biological Molecules, Biopolymers, and Biological Systems

Effect of trehalose on amyloid β(29–40)-membrane interaction
Allam S. Reddy, Aslin Izmitli, and J. J. de Pablo

The authors show that the insertion of amyloid β peptide into a membrane is more favorable when the peptide is folded into an α-helix than in a random coil conformation, suggesting that trehalose promotes the insertion of α-helical amyloid β into biological membranes.

J. Chem. Phys. 131, 085101 (2009)

Protein dynamics from single-molecule fluorescence intensity correlation functions
Irina V. Gopich, Daniel Nettels, Benjamin Schuler, and Attila Szabo

The authors propose and implement a simple procedure to analyze fluorescence intensity correlation functions measured in the presence of resonance energy transfer.

J. Chem. Phys. 131, 095102 (2009)

The transition state transit time of WW domain folding is controlled by energy landscape roughness
Feng Liu, Marcelo Nakaema, and Martin Gruebele

The duration τm of the molecular phase measured provides the best current estimate for the transit time from folded to unfolded state of a single protein molecule. The authors confirm this by directly comparing relaxation and single molecule signals computed by using Langevin trajectory models.

J. Chem. Phys. 131, 195101 (2009)

Free energies of stable and metastable pores in lipid membranes under tension
Wouter K. den Otter

The free energy profile of pore formation in a lipid membrane has been calculated by molecular dynamics simulations with a coarse-grained lipid model. Details are provided of the simulation approach, which combines the potential of mean constraint force method with a reaction coordinate based on the local lipid density.

J. Chem. Phys. 131, 205101 (2009)

Computer simulation of water-mediated forces between gel-phase phospholipid bilayers
Alexander Pertsin, Ivan Fedyanin, and Michael Grunze

Water-mediated forces between gel-phase phospholipid bilayers were calculated as a function of interbilayer separation using the grand canonical Monte Carlo technique and all-atom CHARMM force field.

J. Chem. Phys. 131, 215102 (2009)

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