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Journal of Chemical Physics

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https://www.readbyqxmd.com/read/29166124/some-connections-between-importance-sampling-and-enhanced-sampling-methods-in-molecular-dynamics
#1
H C Lie, J Quer
In molecular dynamics, enhanced sampling methods enable the collection of better statistics of rare events from a reference or target distribution. We show that a large class of these methods is based on the idea of importance sampling from mathematical statistics. We illustrate this connection by comparing the Hartmann-Schütte method for rare event simulation (J. Stat. Mech. Theor. Exp. 2012, P11004) and the Valsson-Parrinello method of variationally enhanced sampling [Phys. Rev. Lett. 113, 090601 (2014)]...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166123/tunneling-of-coupled-methyl-quantum-rotors-in-4-methylpyridine-single-rotor-potential-versus-coupling-interaction
#2
Somayeh Khazaei, Daniel Sebastiani
We study the influence of rotational coupling between a pair of methyl rotators on the tunneling spectrum in condensed phase. Two interacting adjacent methyl groups are simulated within a coupled-pair model composed of static rotational potential created by the chemical environment and the interaction potential between two methyl groups. We solve the two-dimensional time-independent Schrödinger equation analytically by expanding the wave functions on the basis set of two independent free-rotor functions. We investigate three scenarios which differ with respect to the relative strength of single-rotor and coupling potential...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166122/bulk-and-interfacial-structures-of-reline-deep-eutectic-solvent-a-molecular-dynamics-study
#3
Supreet Kaur, Shobha Sharma, Hemant K Kashyap
We apply all-atom molecular dynamics simulations to describe the bulk morphology and interfacial structure of reline, a deep eutectic solvent comprising choline chloride and urea in 1:2 molar ratio, near neutral and charged graphene electrodes. For the bulk phase structural investigation, we analyze the simulated real-space radial distribution functions, X-ray/neutron scattering structure functions, and their partial components. Our study shows that both hydrogen-bonding and long-range correlations between different constituents of reline play a crucial role to lay out the bulk structure of reline...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166121/photoinduced-transformations-of-indole-and-3-formylindole-monomers-isolated-in-low-temperature-matrices
#4
Igor Reva, Leszek Lapinski, A J Lopes Jesus, Maciej J Nowak
Photochemical transformations were studied for monomers of indole and 3-formylindole isolated in low-temperature noble-gas matrices. Upon UV (λ > 270 nm) irradiation of indole trapped in argon and neon matrices, the initial 1H-form of the compound converted into the 3H-tautomer. Alongside this photoinduced hydrogen-atom transfer, an indolyl radical was also generated by photodetachment of the hydrogen atom from the N1-H bond. Excitation of 3-formylindole isolated in an argon matrix with UV (λ > 335 nm) light led to interconversion between the two conformers of the 1H-tautomer, differing from each other in the orientation of the formyl group (cis or trans)...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166120/mechanical-response-of-transient-telechelic-networks-with-many-part-stickers
#5
Michelle K Sing, Jorge Ramírez, Bradley D Olsen
A central question in soft matter is understanding how several individual, weak bonds act together to produce collective interactions. Here, gel-forming telechelic polymers with multiple stickers at each chain end are studied through Brownian dynamics simulations to understand how collective interaction of the bonds affects mechanical response of the gels. These polymers are modeled as finitely extensible dumbbells using an explicit tau-leap algorithm and the binding energy of these associations was kept constant regardless of the number of stickers...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166119/two-phase-thermodynamic-model-for-computing-entropies-of-liquids-reanalyzed
#6
Tao Sun, Jiawei Xian, Huai Zhang, Zhigang Zhang, Yigang Zhang
The two-phase thermodynamic (2PT) model [S.-T. Lin et al., J. Chem. Phys. 119, 11792-11805 (2003)] provides a promising paradigm to efficiently determine the ionic entropies of liquids from molecular dynamics. In this model, the vibrational density of states (VDoS) of a liquid is decomposed into a diffusive gas-like component and a vibrational solid-like component. By treating the diffusive component as hard sphere (HS) gas and the vibrational component as harmonic oscillators, the ionic entropy of the liquid is determined...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166118/photofragmentation-of-gas-phase-acetic-acid-and-acetamide-clusters-in-the-vacuum-ultraviolet-region
#7
Marta Berholts, Hanna Myllynen, Kuno Kooser, Eero Itälä, Sari Granroth, Helena Levola, Joakim Laksman, Shabnam Oghbaiee, Bart Oostenrijk, Ergo Nõmmiste, Edwin Kukk
Photofragmentation of gas-phase acetamide and acetic acid clusters produced by a supersonic expansion source has been studied using time-of-flight mass spectrometry and the partial ion yield (PIY) technique combined with tunable vacuum-ultraviolet synchrotron radiation. Appearance energies of the clusters and their fragments were experimentally determined from the PIY measurements. The effect of clusterization conditions on the formation and fragmentation of acetic acid clusters was investigated. Ab initio quantum mechanical calculations were performed on both samples' dimers to find their neutral and ionized geometries as well as proton transfer energy barriers leading to the optimal geometries...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166117/adsorption-and-conformations-of-lysozyme-and-%C3%AE-lactalbumin-at-a-water-octane-interface
#8
David L Cheung
As proteins contain both hydrophobic and hydrophilic amino acids, they will readily adsorb onto interfaces between water and hydrophobic fluids such as oil. This adsorption normally causes changes in the protein structure, which can result in loss of protein function and irreversible adsorption, leading to the formation of protein interfacial films. While this can be advantageous in some applications (e.g., food technology), in most cases it limits our ability to exploit protein functionality at interfaces...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166116/theoretical-study-of-photodetachment-spectroscopy-of-hydrogenated-boron-cluster-anion-h2b7-and-its-deuterated-isotopomer
#9
Rudraditya Sarkar, S Mahapatra
Photodetachment spectroscopy of H2B7(-) and its deuterated isotopomer probing the energetically low-lying electronic states of the respective neutral cluster is theoretically investigated in this paper. The theoretical methodology is based on detailed quantum chemistry calculations of electronic state energies, construction of a vibronic coupling model in the diabatic electronic basis, and nuclear dynamics calculations from first principles using time-dependent and time-independent quantum mechanical methods...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166115/resonant-electron-attachment-to-mixed-hydrogen-oxygen-and-deuterium-oxygen-clusters
#10
Michael Renzler, Lorenz Kranabetter, Erik Barwa, Lukas Grubwieser, Paul Scheier, Andrew M Ellis
Low energy electron attachment to mixed (H2)x/(O2)y clusters and their deuterated analogs has been investigated for the first time. These experiments were carried out using liquid helium nanodroplets to form the clusters, and the effect of the added electron was then monitored via mass spectrometry. There are some important differences between electron attachment to the pure clusters and to the mixed clusters. A particularly notable feature is the formation of HO2(-) and H2O(-) ions from an electron-induced chemical reaction between the two dopants...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166114/communication-recovering-the-flat-plane-condition-in-electronic-structure-theory-at-semi-local-dft-cost
#11
Akash Bajaj, Jon Paul Janet, Heather J Kulik
The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addition and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local density functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166113/statistical-mechanics-of-transport-processes-in-active-fluids-equations-of-hydrodynamics
#12
Katherine Klymko, Dibyendu Mandal, Kranthi K Mandadapu
The equations of hydrodynamics including mass, linear momentum, angular momentum, and energy are derived by coarse-graining the microscopic equations of motion for systems consisting of rotary dumbbells driven by internal torques. In deriving the balance of linear momentum, we find that the symmetry of the stress tensor is broken due to the presence of non-zero torques on individual particles. The broken symmetry of the stress tensor induces internal spin in the fluid and leads us to consider the balance of internal angular momentum in addition to the usual moment of momentum...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166112/charge-transfer-excited-states-seeking-a-balanced-and-efficient-wave-function-ansatz-in-variational-monte-carlo
#13
N S Blunt, Eric Neuscamman
We present a simple and efficient wave function ansatz for the treatment of excited charge-transfer states in real-space quantum Monte Carlo methods. Using the recently introduced variation-after-response method [E. Neuscamman, J. Chem. Phys. 145, 081103 (2016)], this ansatz allows a crucial orbital optimization step to be performed beyond a configuration interaction singles expansion, while only requiring calculation of two Slater determinant objects. We demonstrate this ansatz for the illustrative example of the stretched LiF molecule, for a range of excited states of formaldehyde, and finally for the more challenging ethylene-tetrafluoroethylene molecule...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166111/effective-interactions-between-inclusions-in-an-active-bath
#14
Mahdi Zaeifi Yamchi, Ali Naji
We study effective two- and three-body interactions between non-active colloidal inclusions in an active bath of chiral or non-chiral particles, using Brownian dynamics simulations within a standard, two-dimensional model of disk-shaped inclusions and active particles. In a non-chiral active bath, we first corroborate previous findings on effective two-body repulsion mediated between the inclusions by elucidating the detailed non-monotonic features of the two-body force profiles, including a primary maximum and a secondary hump at larger separations that was not previously reported...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166110/total-cross-sections-for-electron-scattering-by-1-propanol-at-impact-energies-in-the-range-40-500-ev
#15
D G M da Silva, M Gomes, S Ghosh, I F L Silva, W A D Pires, D B Jones, F Blanco, G Garcia, S J Buckman, M J Brunger, M C A Lopes
Absolute total cross section (TCS) measurements for electron scattering from 1-propanol molecules are reported for impact energies from 40 to 500 eV. These measurements were obtained using a new apparatus developed at Juiz de Fora Federal University-Brazil, which is based on the measurement of the attenuation of a collimated electron beam through a gas cell containing the molecules to be studied at a given pressure. Besides these experimental measurements, we have also calculated TCS using the Independent-Atom Model with Screening Corrected Additivity Rule and Interference (IAM-SCAR+I) approach with the level of agreement between them being typically found to be very good...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166109/temperature-and-chain-length-dependence-of-ultrafast-vibrational-dynamics-of-thiocyanate-in-alkylimidazolium-ionic-liquids-a-random-walk-on-a-rugged-energy-landscape
#16
Thomas Brinzer, Sean Garrett-Roe
Ultrafast two-dimensional infrared spectroscopy of a thiocyanate vibrational probe (SCN(-)) was used to investigate local dynamics in alkylimidazolium bis-[trifluoromethylsulfonyl]imide ionic liquids ([Imn,1][Tf2N], n = 2, 4, 6) at temperatures from 5 to 80 °C. The rate of frequency fluctuations reported by SCN(-) increases with increasing temperature and decreasing alkyl chain length. Temperature-dependent correlation times scale proportionally to temperature-dependent bulk viscosities of each ionic liquid studied...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166108/a-simple-molecular-orbital-treatment-of-current-distributions-in-quantum-transport-through-molecular-junctions
#17
Sin-Mu Jhan, Bih-Yaw Jin
A simple molecular orbital treatment of local current distributions inside single molecular junctions is developed in this paper. Using the first-order perturbation theory and nonequilibrium Green's function techniques in the framework of Hückel theory, we show that the leading contributions to local current distributions are directly proportional to the off-diagonal elements of transition density matrices. Under the orbital approximation, the major contributions to local currents come from a few dominant molecular orbital pairs which are mixed by the interactions between the molecule and electrodes...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166107/simulations-of-water-nano-confined-between-corrugated-planes
#18
Jon Zubeltzu, Emilio Artacho
Water confined to nanoscale widths in two dimensions between ideal planar walls has been the subject of ample study, aiming at understanding the intrinsic response of water to confinement, avoiding the consideration of the chemistry of actual confining materials. In this work, we study the response of such nanoconfined water to the imposition of a periodicity in the confinement by means of computer simulations, both using empirical potentials and from first-principles. For that we propose a periodic confining potential emulating the atomistic oscillation of the confining walls, which allows varying the lattice parameter and amplitude of the oscillation...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166106/nodeless-vibrational-amplitudes-and-quantum-nonadiabatic-dynamics-in-the-nested-funnel-for-a-pseudo-jahn-teller-molecule-or-homodimer
#19
William K Peters, Vivek Tiwari, David M Jonas
The nonadiabatic states and dynamics are investigated for a linear vibronic coupling Hamiltonian with a static electronic splitting and weak off-diagonal Jahn-Teller coupling through a single vibration with a vibrational-electronic resonance. With a transformation of the electronic basis, this Hamiltonian is also applicable to the anti-correlated vibration in a symmetric homodimer with marginally strong constant off-diagonal coupling, where the non-adiabatic states and dynamics model electronic excitation energy transfer or self-exchange electron transfer...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166105/electrode-reactions-in-slowly-relaxing-media
#20
Dmitry V Matyushov, Marshall D Newton
Standard models of reaction kinetics in condensed materials rely on the Boltzmann-Gibbs distribution for the population of reactants at the top of the free energy barrier separating them from the products. While energy dissipation and quantum effects at the barrier top can potentially affect the transmission coefficient entering the rate pre-exponential factor, much stronger dynamical effects on the reaction barrier are caused by the breakdown of ergodicity for populating the reaction barrier (violation of the Boltzmann-Gibbs statistics)...
November 21, 2017: Journal of Chemical Physics
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