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Journal of Chemical Physics

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https://www.readbyqxmd.com/read/30316292/percolation-probability-in-a-system-of-cylindrical-particles
#1
Anatoly Golovnev, Matthew E Suss
A broad variety of materials, ranging from composites and heat transfer nano-fluids to electrochemical energy storage electrodes, widely employ cylindrical particles of various aspect ratios, such as carbon nanotubes. These particles are generally excellent conductors of heat and electricity and when dispersed in a continuous medium influence dramatically the transport properties of the heterogeneous material by forming a percolating network. Numerous theories exist to predict key parameters such as particle concentration at the percolation threshold and transport properties at concentrations beyond the threshold...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316291/orbital-free-approximations-to-the-kinetic-energy-density-in-exchange-correlation-mgga-functionals-tests-on-solids
#2
Fabien Tran, Péter Kovács, Leila Kalantari, Georg K H Madsen, Peter Blaha
A recent study of Mejia-Rodriguez and Trickey [Phys. Rev. A 96 , 052512 (2017)] showed that the deorbitalization procedure (replacing the exact Kohn-Sham kinetic-energy density by an approximate orbital-free expression) applied to exchange-correlation functionals of the meta-generalized gradient approximation (MGGA) can lead to important changes in the results for molecular properties. For the present work, the deorbitalization of MGGA functionals is further investigated by considering various properties of solids...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316290/probing-the-structures-and-bonding-of-auropolyynes-au-c%C3%A2-c-n-au-n-1-3-using-high-resolution-photoelectron-imaging
#3
Iker León, Fernando Ruipérez, Jesus M Ugalde, Lai-Sheng Wang
We report an investigation of a series of auropolyynes, Au-(C≡C) n -Au- ( n = 1-3), using high-resolution photoelectron imaging and ab initio calculations. Vibrationally resolved photoelectron spectra are obtained, allowing the electron affinities of Au-(C≡C) n -Au to be accurately measured as 1.651(1), 1.715(1), and 1.873(1) eV for n = 1-3, respectively. Both the Au-C symmetric stretching and a bending vibrational frequency are observed for each neutral auropolyyne. Theoretical calculations find that the ground state of Au2 C2 - has a linear acetylenic Au-C≡C-Au- structure, whereas the asymmetric Au-Au-C≡C- structure is a low-lying isomer...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316289/perspective-crossing-the-widom-line-in-no-man-s-land-experiments-simulations-and-the-location-of-the-liquid-liquid-critical-point-in-supercooled-water
#4
Nicholas J Hestand, J L Skinner
The origin of liquid water's anomalous behavior continues to be a subject of interest and debate. One possible explanation is the liquid-liquid critical point hypothesis, which proposes that supercooled water separates into two distinct liquids at low temperatures and high pressures. According to this hypothesis, liquid water's anomalies can be traced back to the critical point associated with this phase separation. If such a critical point actually exists, it is located in a region of the phase diagram known as No Man's Land (NML), where it is difficult to characterize the liquid using conventional experimental techniques due to rapid crystallization...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316288/sub-doppler-slit-jet-infrared-spectroscopy-of-astrochemically-relevant-cations-the-nh-stretching-mode-in-nd-3-h
#5
Chih-Hsuan Chang, Preston G Scrape, David J Nesbitt
High-resolution rotationally resolved spectra of the N-H stretch vibrational mode ( ν 1 ) of jet-cooled ND3 H+ ions are collected and analyzed in a sub-Doppler slit-jet infrared spectrometer. The isotopomeric ammonium ions are generated by proton transfer from H3 + to ND3 in a discharge of an ND3 /H2 gas mixture, whereby the slit jet expansion cools the nascent ND3 H+ ions into lower rotational states. Rotational assignments are confirmed by four-line combination differences that agree to within the spectrometer precision (9 MHz)...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316287/photoionization-of-the-iodine-3d-4s-and-4p-orbitals-in-methyl-iodide
#6
Ruaridh Forbes, Alberto De Fanis, Cédric Bomme, Daniel Rolles, Stephen T Pratt, Ivan Powis, Nicholas A Besley, Marc Simon, Saikat Nandi, Aleksandar R Milosavljević, Christophe Nicolas, John D Bozek, Jonathan G Underwood, David M P Holland
Ionization of the I 3d, 4s, and 4p orbitals in methyl iodide (CH3 I) has been studied by using synchrotron radiation to measure the total ion yield and by recording photoelectron spectra with linearly polarized radiation in two polarization orientations. The complete photoelectron spectrum of CH3 I has been recorded at several photon energies, and bands due to the C 1s, I 3d, 4s, 4p, and 4d atomic-like orbitals, as well as the molecular orbitals, have been observed and assigned. In the vicinity of the I 3d5/2 and 3d3/2 ionization thresholds at 626...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316286/bethe-salpeter-correlation-energies-of-atoms-and-molecules
#7
Christof Holzer, Xin Gui, Michael E Harding, Georg Kresse, Trygve Helgaker, Wim Klopper
A variety of approaches are presented for the computation of atomic and molecular correlation energies based on the Bethe-Salpeter equation in the framework of the adiabatic-connection fluctuation-dissipation theorem. The performance of the approaches is assessed by computing the total energies of the atoms H-Ne and the atomization energies of the high-accuracy extrapolated ab initio thermochemistry set of small molecules as well as by determining the bond lengths and harmonic vibrational frequencies of the metal monoxides MO with M=Ca-Zn...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316285/two-dimensional-monte-carlo-simulations-of-coarse-grained-poly-3-hexylthiophene-p3ht-adsorbed-on-striped-substrates
#8
Nicolai Oberthür, Jonathan Gross, Wolfhard Janke
We investigate the structural phases of single poly(3-hexylthiophene) (P3HT) polymers that are adsorbed on a two-dimensional substrate with a striped pattern. We use a coarse-grained representation of the polymer and sophisticated Monte Carlo techniques such as a parallelized replica exchange scheme and local as well as non-local updates to the polymer's configuration. From peaks in the canonically derived observables, it is possible to obtain structural phase diagrams for varying substrate parameters. We find that the shape of the stripe pattern has a substantial effect on the obtained configurations of the polymer and can be tailored to promote either more stretched out or more compact configurations...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316284/microtubule-buckling-in-an-elastic-matrix-with-quenched-disorder
#9
Cheng-Tai Lee, Eugene M Terentjev
The intracellular elastic matrix has been recognized as an important factor to stabilize microtubules and increase their critical buckling force P c in vivo . This phenomenon was qualitatively explained by the Winkler model, which investigated the buckling of a filament embedded in a homogeneous elastic medium. However, the assumption of homogeneity of the matrix in Winkler's, and other advanced models, is unrealistic inside cells, where the local environment is highly variable along the filament. Considering this to be a quenched-disorder system, we use a Poisson distribution for confinements and apply the replica technique combined with the Gaussian variational method to study the buckling of a long filament...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316283/semiclassical-tunneling-splittings-for-arbitrary-vibrational-states-in-multidimensional-double-wells
#10
Kenneth G Kay
A semiclassical theory developed in a previous paper [K. G. Kay, Phys. Rev. A 96 , 042116 (2017)] is applied to calculate tunneling splittings for arbitrary vibrational states of model two-dimensional double-well systems. Cases in which the classical dynamics for the wells is chaotic, mixed, and regular are considered. A perturbative treatment, based on the condition of small tunneling amplitudes, is found to be sufficiently accurate for the cases studied and is applied for most of the calculations. Treatments that approximate certain imaginary-time trajectories in the classically forbidden region by linearization about a variety of judiciously selected reference trajectories yield good results for all systems treated...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316282/communication-nickel-hydroxide-as-an-exceptional-deviation-from-the-quantum-size-effect
#11
Michael Nagli, Maytal Caspary Toroker
The quantum size effect is a well-known fundamental scientific phenomenon. Due to quantum confinement, downscaling a system to small sizes should increase the bandgap of a solid state material. However, in this work, we present an exception: monolayers of nickel hydroxide have smaller bandgaps than their bulk analogues, due to the surface states appearing at energies within the bandgap region. Our findings are obtained by several state-of-the-art first principles calculations.
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316281/dynamic-correlation-for-non-orthogonal-reference-states-improved-perturbational-and-variational-methods
#12
Sven Kähler, Jeppe Olsen
The use of non-orthogonal orbitals allows the construction and use of more compact wave functions than offered by standard methods using orthogonal molecular orbitals; in particular, for molecules containing partly occupied atomic orbitals as present, for example, in transition metal complexes. With the purpose of developing efficient dynamic correlation methods, we discuss several new internal correlation methods employing a reference state containing non-orthogonal active orbitals. The non-orthogonal internally contracted perturbation theory approach is improved in several directions...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316280/an-efficient-first-principles-method-for-molecular-pump-probe-nexafs-spectra-application-to-thymine-and-azobenzene
#13
Christopher Ehlert, Markus Gühr, Peter Saalfrank
Pump-probe near edge X-ray absorption fine structure (PP-NEXAFS) spectra of molecules offer insight into valence-excited states, even if optically dark. In PP-NEXAFS spectroscopy, the molecule is "pumped" by UV or visible light enforcing a valence excitation, followed by an X-ray "probe" exciting core electrons into (now) partially empty valence orbitals. Calculations of PP-NEXAFS have so far been done by costly, correlated wavefunction methods which are not easily applicable to medium-sized or large molecules...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316279/ewald-sum-for-hydrodynamic-interactions-of-rigid-spherical-microswimmers
#14
Tapan Chandra Adhyapak, Sara Jabbari-Farouji
We derive the Ewald sum decomposition of the grand mobility tensor which captures the hydrodynamic interactions in an infinite suspension of rigid spherical microswimmers. The grand mobility tensor connects the motion of an individual swimmer to the active and passive forces and torques acting on all the swimmers, and it is calculated based on a minimal microswimmer model incorporating the swimmers' finite body size. Our results have direct applications to the Stokesian dynamics simulations of an infinite suspension of rigid-bodied microswimmers...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316278/vacuum-ultraviolet-excited-state-dynamics-of-the-smallest-ring-cyclopropane-i-a-reinterpretation-of-the-electronic-spectrum-and-the-effect-of-intensity-borrowing
#15
Simon P Neville, Albert Stolow, Michael S Schuurman
Cyclopropane, the smallest organic ring compound, exhibits complex spectroscopy and excited state dynamics. In Paper I, we reinterpret the vacuum ultraviolet (VUV) electronic absorption spectrum of cyclopropane via ab initio computation. The first two bands in the VUV spectrum are simulated using wavepacket propagations employing the multiconfigurational time-dependent Hartee method and a newly parameterized linear vibronic coupling Hamiltonian. The parameters of the model Hamiltonian are obtained directly from high level multireference configuration interaction calculations...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316277/self-diffusion-coefficient-of-the-square-well-fluid-from-molecular-dynamics-simulations-within-the-constant-force-approach
#16
Alexis Torres-Carbajal, Victor M Trejos, Luz Adriana Nicasio-Collazo
We present a systematic study of the self-diffusion coefficient for a fluid of particles interacting via the square-well pair potential by means of molecular dynamics simulations in the canonical ( N , V , T ) ensemble. The discrete nature of the interaction potential is modeled by the constant force approximation, and the self-diffusion coefficient is determined for several fluid densities at supercritical thermodynamic states. The dependence of the self-diffusion coefficient on the potential range λ is analyzed in the range of 1...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316276/statistical-efficiency-of-methods-for-computing-free-energy-of-hydration
#17
Ahmet Yildirim, Tsjerk A Wassenaar, David van der Spoel
The hydration free energy (HFE) is a critical property for predicting and understanding chemical and biological processes in aqueous solution. There are a number of computational methods to derive HFE, generally classified into the equilibrium or non-equilibrium methods, based on the type of calculations used. In the present study, we compute the hydration free energies of 34 small, neutral, organic molecules with experimental HFE between +2 and -16 kcal/mol. The one-sided non-equilibrium methods Jarzynski Forward (JF) and Backward (JB), the two-sided non-equilibrium methods Jarzynski mean based on the average of JF and JB, Crooks Gaussian Intersection (CGI), and the Bennett Acceptance Ratio (BAR) are compared to the estimates from the two-sided equilibrium method Multistate Bennett Acceptance Ratio (MBAR), which is considered as the reference method for HFE calculations, and experimental data from the literature...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316275/molecular-structure-of-the-substrate-induced-thin-film-phase-of-tetracene
#18
Linus Pithan, Dmitrii Nabok, Caterina Cocchi, Paul Beyer, Giuliano Duva, Joseph Simbrunner, Jonathan Rawle, Chris Nicklin, Peter Schäfer, Claudia Draxl, Frank Schreiber, Stefan Kowarik
We present a combined experimental and theoretical study to solve the unit-cell and molecular arrangement of the tetracene thin film (TF) phase. TF phases, also known as substrate induced phases (SIPs), are polymorphs that exist at interfaces and decisively impact the functionality of organic thin films, e.g., in a transistor channel, but also change the optical spectra due to the different molecular packing. As SIPs only exist in textured ultrathin films, their structure determination remains challenging compared to bulk materials...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316274/communication-nucleation-rates-of-supersaturated-aqueous-nacl-using-a-polarizable-force-field
#19
Hao Jiang, Pablo G Debenedetti, Athanassios Z Panagiotopoulos
In this work, we use molecular dynamics simulations with a polarizable force field, namely, the modified AH/BK3 model [J. Kolafa, J. Chem. Phys. 145 , 204509 (2016)], in combination with the forward flux sampling technique, to calculate the rates of homogeneous nucleation of NaCl from supersaturated aqueous solutions at 298 K and 1 bar. A non-polarizable model that reproduces the experimental equilibrium solubility {AH/TIP4P-2005 of Benavides et al. [J. Chem. Phys. 147 , 104501 (2017)]} is also used for comparison...
October 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/30316273/permutation-invariant-polynomial-neural-network-approach-to-fitting-potential-energy-surfaces-iv-coupled-diabatic-potential-energy-matrices
#20
Changjian Xie, Xiaolei Zhu, David R Yarkony, Hua Guo
A machine learning method is proposed for representing the elements of diabatic potential energy matrices (PEMs) with high fidelity. This is an extension of the so-called permutation invariant polynomial-neural network (PIP-NN) method for representing adiabatic potential energy surfaces. While for one-dimensional irreducible representations the diagonal elements of a diabatic PEM are invariant under exchange of identical nuclei in a molecular system, the off-diagonal elements require special symmetry consideration, particularly in the presence of a conical intersection...
October 14, 2018: Journal of Chemical Physics
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