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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/28734314/theoretical-study-of-resonance-formation-in-microhydrated-molecules-i-pyridine-h2o-n-n-1-2-3-5
#2
Agnieszka Sieradzka, Jimena D Gorfinkiel
We present R-matrix calculations for electron scattering from microhydrated pyridine. We studied the pyridine-H2O cluster at static-exchange (SE), SE + polarization, and close-coupling levels, and pyridine-(H2O)n n = 2, 3, and 5 at SE level only in order to investigate the effect of hydrogen bonding on the resonances of pyridine. We analyse the results in terms of direct and indirect effects. We observe that the total (direct plus indirect) effect of microhydration leads to the stabilization of all resonances studied, both shape and core-excited...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734313/singlet-fission-in-chiral-carbon-nanotubes-density-functional-theory-based-computation
#3
Andrei Kryjevski, Deyan Mihaylov, Brendan Gifford, Dmitri Kilin
Singlet fission (SF) process, where a singlet exciton decays into a pair of spin one exciton states which are in the total spin singlet state, is one of the possible channels for multiple exciton generation (MEG). In chiral single-wall carbon nanotubes (SWCNTs), efficient SF is present within the solar spectrum energy range which is shown by the many-body perturbation theory calculations based on the density functional theory simulations. We calculate SF exciton-to-biexciton decay rates R1→2 and biexciton-to-exciton rates R2→1 in the (6,2), (6,5), (10,5) SWCNTs, and in the (6,2) SWCNT functionalized with Cl atoms...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734312/diffusion-quantum-monte-carlo-calculations-of-srfeo3-and-lafeo3
#4
Juan A Santana, Jaron T Krogel, Paul R C Kent, Fernando A Reboredo
The equations of state, formation energy, and migration energy barrier of the oxygen vacancy in SrFeO3 and LaFeO3 were calculated with the diffusion quantum Monte Carlo (DMC) method. Calculations were also performed with various Density Functional Theory (DFT) approximations for comparison. DMC reproduces the measured cohesive energies of these materials with errors below 0.23(5) eV and the structural properties within 1% of the experimental values. The DMC formation energies of the oxygen vacancy in SrFeO3 and LaFeO3 under oxygen-rich conditions are 1...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734311/a-monte-carlo-simulation-of-ionic-conductivity-and-viscosity-of-highly-concentrated-electrolytes-based-on-a-pseudo-lattice-model
#5
Hiroyuki Ozaki, Kentaro Kuratani, Hikaru Sano, Tetsu Kiyobayashi
Simulating three transport phenomena-ionic conductivity, viscosity, and self-diffusion coefficient-in a common Monte-Carlo framework, we discuss their relationship to the intermolecular interactions of electrolyte solutions at high concentrations (C/mol l(-1) ∼ 1). The simulation is predicated on a pseudolattice model of the solution. The ions and solvents (collectively termed "molecules") are considered dimensionless points occupying the lattice sites. The molecular transport is realized by a repetition of swapping two adjacent molecules by the stochastic Gibbs sampling process based on simple intermolecular interactions...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734310/stability-limits-for-the-supercooled-liquid-and-superheated-crystal-of-lennard-jones-particles
#6
Ernesto S Loscar, Daniel A Martin, Tomás S Grigera
We have studied the limits of stability in the first order liquid-solid phase transition in a Lennard-Jones system by means of the short-time relaxation method and using the bond-orientational order parameter Q6. These limits are compared with the melting line. We have paid special attention to the supercooled liquid, comparing our results with the point where the free energy cost of forming a nucleating droplet goes to zero. We also indirectly estimate the dimension associated to the critical nucleus at the spinodal, expected to be fractal according to mean field theories of nucleation...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734309/universal-two-dimensional-characteristics-in-perovskite-type-oxyhydrides-atio2h-a-li-na-k-rb-cs
#7
Nobuya Sato, Ryosuke Akashi, Shinji Tsuneyuki
A series of unsynthesized perovskite-type oxyhydrides ATiO2H (A = Li, Na, K, Rb, Cs) are investigated by the density functional calculations. These oxyhydrides are stable in the sense of the formation energies for some possible synthesis reactions. They are crystallized into quite similar crystal structures with the long c-axis, and the corner-sharing TiO4H2 octahedra of the ideal perovskite-type structure are deformed into the 5-fold coordinated titanium atoms with the OH plane and the apical oxygen atoms...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734308/molecular-simulation-of-caloric-properties-of-fluids-modelled-by-force-fields-with-intramolecular-contributions-application-to-heat-capacities
#8
William R Smith, Jan Jirsák, Ivo Nezbeda, Weikai Qi
The calculation of caloric properties such as heat capacity, Joule-Thomson coefficients, and the speed of sound by classical force-field-based molecular simulation methodology has received scant attention in the literature, particularly for systems composed of complex molecules whose force fields (FFs) are characterized by a combination of intramolecular and intermolecular terms. The calculation of a thermodynamic property for a system whose molecules are described by such a FF involves the calculation of the residual property prior to its addition to the corresponding ideal-gas property, the latter of which is separately calculated, either using thermochemical compilations or nowadays accurate quantum mechanical calculations...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734307/a-confinement-induced-spectroscopic-study-of-noble-gas-atoms-using-equation-of-motion-architecture-encapsulation-within-fullerene-s-voids
#9
Supriya K Chaudhuri, Rajat K Chaudhuri, Prasanta K Mukherjee, Sudip Chattopadhyay
A relativistic study of spectroscopic properties of the endohedral fullerenes Ng@C60(q) (where Ng = He, Ne and q=0,±1,±2 are the charges) associated with the C60 molecule has been done using the equation of motion coupled cluster (EOM-CC) methodology. Specific properties estimated are the transition energies, dipole oscillator strengths, and transition probabilities for the low-lying excitations 1s(2)((1)S0) → 1snp ((1)P1) (n = 2, 3, 4) for He@C60(q) and 1s(2)2s(2)2p(6) ((1)S0) → 1s(2)2s(2)2p(5)ns∕nd ((1)P1) (n = 3, 4) for Ne@C60(q), which have been compared with those for the isolated atom to depict the confinement effect of the host molecule on the encapsulated atom...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734306/theoretical-study-of-resonance-formation-in-microhydrated-molecules-ii-thymine-h2o-n-n-1-2-3-5
#10
Agnieszka Sieradzka, Jimena D Gorfinkiel
We have investigated the effect of microsolvation on the low-lying pure shape π(*) resonances of thymine. Static-exchange R-matrix calculations for elastic electron scattering from microhydated thymine, i.e., Thy-(H2O)n with n = 1,2,3,5 are discussed. We look at the additive effect of water molecules hydrogen-bonding to thymine. The results for Thy-(H2O)5 show that both π(*) resonances appear at lower energy in the cluster than in isolated thymine, but that the energy shift is different for each resonance...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734305/exploring-the-free-energy-gain-of-phase-separation-via-markov-state-modeling
#11
Myra Biedermann, Andreas Heuer
The gain of free energy upon unmixing is determined via application of Markov state modeling (MSM), using an Ising model with a fixed number of up- and down-spins. MSM yields reasonable estimates of the free energies. However, a closer look reveals significant differences that point to residual non-Markovian effects. These non-Markovian effects are rather unexpected since the typical criteria to study the quality of Markovianity indicate complete Markovian behavior. We identify the sparse connectivity between different Markov states as a likely reason for the observed bias...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734304/temperature-dependence-of-the-translocation-time-of-polymer-through-repulsive-nanopores
#12
Meng-Bo Luo, Dessalegne A Tsehay, Li-Zhen Sun
The forced translocation of a polymer chain through repulsive nanopores was studied by using Langevin dynamics simulations. The polymer is in the compact globule state at low temperature and in the random coil state at high temperature. Simulation results show that the mean translocation time 〈τ〉 is highly dependent on the temperature T and the minimal 〈τ〉 is located near the coil-globule transition temperature. Moreover, the scaling behaviors 〈τ〉 ∼ N(α) and 〈τ〉 ∼ F(-δ) are studied, with N the polymer length and F the driving force inside the nanopore...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734303/behavior-of-a-supercooled-chalcogenide-liquid-in-the-non-newtonian-regime-under-steady-vs-oscillatory-shear
#13
S Sen, W Zhu, B G Aitken
The steady and oscillatory shear rate dependence of viscosity of a supercooled chalcogenide liquid of composition As10Se90 is measured at Newtonian viscosities ranging between 10(3) and 10(7) Pa s using capillary and parallel plate rheometry. The liquid displays strong violation of the Cox-Merz rule in the non-Newtonian regime where the viscosity under steady shear is nearly an order of magnitude lower than that under oscillatory shear. This behavior is argued to be related to the emergence of unusually large (6-8 nm) cooperatively rearranging regions with long relaxation times in the liquid that result from significant structural rearrangements under steady shear...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734302/analytical-derivatives-of-the-individual-state-energies-in-ensemble-density-functional-theory-method-i-general-formalism
#14
Michael Filatov, Fang Liu, Todd J Martínez
The state-averaged (SA) spin restricted ensemble referenced Kohn-Sham (REKS) method and its state interaction (SI) extension, SI-SA-REKS, enable one to describe correctly the shape of the ground and excited potential energy surfaces of molecules undergoing bond breaking/bond formation reactions including features such as conical intersections crucial for theoretical modeling of non-adiabatic reactions. Until recently, application of the SA-REKS and SI-SA-REKS methods to modeling the dynamics of such reactions was obstructed due to the lack of the analytical energy derivatives...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734301/communication-influence-of-external-static-and-alternating-electric-fields-on-water-from-long-time-non-equilibrium-ab-initio-molecular-dynamics
#15
Zdenek Futera, Niall J English
The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734300/potential-energy-surfaces-of-quintet-and-singlet-o4
#16
Yuliya Paukku, Ke R Yang, Zoltan Varga, Guoliang Song, Jason D Bender, Donald G Truhlar
We present global ground-state potential energy surfaces for the quintet and singlet spin states of the O4 system that are suitable for treating high-energy vibrational-rotational energy transfer and collision-induced dissociation in electronically adiabatic, spin-conserving O2-O2 collisions. The surfaces are based on MS-CASPT2/maug-cc-pVTZ electronic structure calculations with scaled external correlation. The active space has 16 electrons in 12 orbitals. The calculations cover nine kinds of geometrical arrangements corresponding to dissociative diatom-diatom collisions of O2, geometries corresponding to O3-O, geometries identified by running trajectories, and geometries along linear synchronous transit paths...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734299/state-of-the-art-ab-initio-potential-energy-curve-for-the-xenon-atom-pair-and-related-spectroscopic-and-thermophysical-properties
#17
Robert Hellmann, Benjamin Jäger, Eckard Bich
A new ab initio interatomic potential energy curve for two ground-state xenon atoms is presented. It is based on supermolecular calculations at the coupled-cluster level with single, double, and perturbative triple excitations [CCSD(T)] employing basis sets up to sextuple-zeta quality, which were developed as part of this work. In addition, corrections were determined for higher coupled-cluster levels up to CCSDTQ as well as for scalar and spin-orbit relativistic effects at the CCSD(T) level. A physically motivated analytical function was fitted to the calculated interaction energies and used to compute the vibrational spectrum of the dimer, the second virial coefficient, and the dilute gas transport properties...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734298/excited-state-absorption-spectra-of-dissolved-and-aggregated-distyrylbenzene-a-td-dft-state-and-vibronic-analysis
#18
Eliezer Fernando Oliveira, Junqing Shi, Francisco Carlos Lavarda, Larry Lüer, Begoña Milián-Medina, Johannes Gierschner
A time-dependent density functional theory study is performed to reveal the excited state absorption (ESA) features of distyrylbenzene (DSB), a prototype π-conjugated organic oligomer. Starting with a didactic insight to ESA based on simple molecular orbital and configuration considerations, the performance of various density functional theory functionals is tested to reveal the full vibronic ESA features of DSB at short and long probe delay times.
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734297/nonequilibrium-phase-coexistence-and-criticality-near-the-second-explosion-limit-of-hydrogen-combustion
#19
Lucas B Newcomb, Mohammad Alaghemandi, Jason R Green
While hydrogen is a promising source of clean energy, the safety and optimization of hydrogen technologies rely on controlling ignition through explosion limits: pressure-temperature boundaries separating explosive behavior from comparatively slow burning. Here, we show that the emergent nonequilibrium chemistry of combustible mixtures can exhibit the quantitative features of a phase transition. With stochastic simulations of the chemical kinetics for a model mechanism of hydrogen combustion, we show that the boundaries marking explosive domains of kinetic behavior are nonequilibrium critical points...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734296/spherical-harmonics-analysis-of-surface-density-fluctuations-of-spherical-ionic-sds-and-nonionic-c12e8-micelles-a-molecular-dynamics-study
#20
Noriyuki Yoshii, Yuki Nimura, Kazushi Fujimoto, Susumu Okazaki
The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C12E8) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor...
July 21, 2017: Journal of Chemical Physics
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