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Unimolecular fragmentation and radiative cooling of isolated PAH ions: A quantitative study.

Mark H Stockett, James N Bull, Jack T Buntine, Eduardo Carrascosa, MingChao Ji, Naoko Kono, Henning T Schmidt, Henning Zettergren,

Time-resolved spontaneous and laser-induced unimolecular fragmentation of perylene cations (C20H12 +) has been measured on timescales up to 2 s in a cryogenic electrostatic ion beam storage ring. We elaborate a quantitative model, which includes fragmentation in competition with radiative cooling via both vibrational and electronic (recurrent fluorescence) de-excitation. Excellent ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(15):154303]

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Kinetics and free energy of ligand dissociation using weighted ensemble milestoning.

Dhiman Ray, Trevor Gokey, David L Mobley, Ioan Andricioaei,

We consider the recently developed weighted ensemble milestoning (WEM) scheme [D. Ray and I. Andricioaei, J. Chem. Phys. 152, 234114 (2020)] and test its capability of simulating ligand-receptor dissociation dynamics. We performed WEM simulations on the following host-guest systems: Na+/Cl- ion pair and 4-hydroxy-2-butanone ligand with FK506 binding protein. As ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(15):154117]

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Enhanced intersystem crossing of boron dipyrromethene by TEMPO radical.

Zihao Xu, Yiming Huang, Yulei Cao, Tao Jin, Kristen A Miller, Alexey L Kaledin, Djamaladdin G Musaev, Tianquan Lian, Eilaf Egap,

Radical enhanced intersystem crossing (EISC) of organic chromophores is an important approach to generate a long-lived triplet state for various electronic and optoelectronic applications. However, structural factors and design rules to promote EISC are not entirely clear. In this work, we report a series of boron dipyrromethene (BODIPY) derivatives covalently ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(15):154201]

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Multiband enhanced second-harmonic generation via plasmon hybridization.

Shaoxin Shen, Weimin Yang, Jiejie Shan, Guoya Sun, Tien-Mo Shih, Yongliang Zhou, Zhilin Yang,

Boosting nonlinear frequency-conversion efficiencies in hybrid metal-dielectric nanostructures generally requires the enhancement of optical fields that interact constructively with nonlinear dielectrics. Inevitably for localized surface plasmons, spectra subject to this enhancement tend to span narrowly. As a result, because of the spectral mismatch of resonant modes at frequencies participating in ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(15):151102]

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Linear and nonlinear chiroptical response from individual 3D printed plasmonic and dielectric micro-helices.

Nicole R Famularo, Lei Kang, Zehua Li, Tian Zhao, Kenneth L Knappenberger, Christine D Keating, Douglas H Werner,

Sub-wavelength chiral resonators formed from artificial structures exhibit exceedingly large chiroptical responses compared to those observed in natural media. Owing to resonant excitation, chiral near fields can be significantly enhanced for these resonators, holding great promise for developing enantioselective photonic components such as biochemical sensors based on circular dichroism (CD) ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(15):154702]

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Influence of tungsten doping on nonradiative electron-hole recombination in monolayer MoSe2 with Se vacancies.

Yating Yang, Marina V Tokina, Wei-Hai Fang, Run Long, Oleg V Prezhdo,

Two-dimensional transition metal dichalcogenides (TMDs) are receiving significant attention due to their excellent electronic and optoelectronic properties. The material quality is greatly affected by defects that are inevitably generated during material synthesis. Focusing on chalcogenide vacancies, which constitute the most common defect, we use the state-of-the-art simulation methodology developed in ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(15):154701]

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Energy barriers and cooperative motion at the surface of freestanding glassy polystyrene films.

D Fujimoto, W A MacFarlane, J Rottler,

We investigate the near-surface relaxation of freestanding atactic polystyrene films with molecular dynamics simulations. As in previous coarse-grained simulations, relaxation times for backbone segments and phenyl rings are linked to their bulk relaxation times via a power-law coupling relation. Variation of the coupling exponent with distance from the surface is ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(15):154901]

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Ab initio structure and thermodynamics of the RPBE-D3 water/vapor interface by neural-network molecular dynamics.

Oliver Wohlfahrt, Christoph Dellago, Marcello Sega,

Aided by a neural network representation of the density functional theory potential energy landscape of water in the Revised Perdew-Burke-Ernzerhof approximation corrected for dispersion, we calculate several structural and thermodynamic properties of its liquid/vapor interface. The neural network speed allows us to bridge the size and time scale gaps required ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(14):144710]

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Plasma modification of vanadium oxynitride surfaces: Characterization by in situ XPS experiments and DFT calculations.

A Osonkie, V Lee, P Chukwunenye, T Cundari, J Kelber,

Plasma modification of transition metal nitride/oxynitride (MOxNy) surfaces for enhanced surface properties is highly desirable, given the scalability of such methods and limitations of thermal treatments. In situ x-ray excited photoelectron spectroscopy demonstrates that the O2 plasma oxidation of VOxNy films generates non-lattice N1s surface features with binding energies near ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(14):144709]

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Formation and stability of small polarons at the lithium-terminated Li4Ti5O12 (LTO) (111) surface.

Matthias Kick, Christoph Scheurer, Harald Oberhofer,

Zero strain insertion, high cycling stability, and a stable charge/discharge plateau are promising properties rendering Lithium Titanium Oxide (LTO) a possible candidate for an anode material in solid state Li ion batteries. However, the use of pristine LTO in batteries is rather limited due to its electronically insulating nature. In ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(14):144701]

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Targeted free energy estimation via learned mappings.

Peter Wirnsberger, Andrew J Ballard, George Papamakarios, Stuart Abercrombie, Sébastien Racanière, Alexander Pritzel, Danilo Jimenez Rezende, Charles Blundell,

Free energy perturbation (FEP) was proposed by Zwanzig [J. Chem. Phys. 22, 1420 (1954)] more than six decades ago as a method to estimate free energy differences and has since inspired a huge body of related methods that use it as an integral building block. Being an importance sampling based ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(14):144112]

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N4Mg6M (M = Li, Na, K) superalkalis for CO2 activation.

Celina Sikorska, Nicola Gaston,

Superatoms have exciting properties, including diverse functionalization, redox activity, and magnetic ordering, so the resulting cluster-assembled solids hold the promise of high tunability, atomic precision, and robust architectures. By utilizing adamantane-like clusters as building blocks, a new class of superatoms N4Mg6M (M = Li, Na, K) is proposed here. The ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(14):144301]

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Sensitivity and dimensionality of atomic environment representations used for machine learning interatomic potentials.

Berk Onat, Christoph Ortner, James R Kermode,

Faithfully representing chemical environments is essential for describing materials and molecules with machine learning approaches. Here, we present a systematic classification of these representations and then investigate (i) the sensitivity to perturbations and (ii) the effective dimensionality of a variety of atomic environment representations and over a range of material ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(14):144106]

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Analytical canonical partition function of a quasi-one-dimensional system of hard disks.

V M Pergamenshchik,

The exact canonical partition function of a hard disk system in a narrow quasi-one-dimensional pore of given length and width is derived analytically in the thermodynamic limit. As a result, the many body problem is reduced to solving the single transcendental equation. The pressures along and across the pore, distributions ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(14):144111]

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The role of thermal history on spontaneous polarization and phase transitions of amorphous solid water films studied by contact potential difference measurements.

Roey Sagi, Michelle Akerman, Sujith Ramakrishnan, Micha Asscher,

Monitoring thermal processes occurring in molecular films on surfaces can provide insights into physical events such as morphology changes and phase transitions. Here, we demonstrate that temperature-programmed contact potential difference (TP-∆CPD) measurements employed by a Kelvin probe under ultrahigh vacuum conditions and their temperature derivative can track films' restructure and ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(14):144702]

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Active learning for robust, high-complexity reactive atomistic simulations.

Rebecca K Lindsey, Laurence E Fried, Nir Goldman, Sorin Bastea,

Machine learned reactive force fields based on polynomial expansions have been shown to be highly effective for describing simulations involving reactive materials. Nevertheless, the highly flexible nature of these models can give rise to a large number of candidate parameters for complicated systems. In these cases, reliable parameterization requires a ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(13):134117]

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Stable glassy configurations of the Kob-Andersen model using swap Monte Carlo.

Anshul D S Parmar, Benjamin Guiselin, Ludovic Berthier,

The swap Monte Carlo algorithm allows the preparation of highly stable glassy configurations for a number of glass-formers but is inefficient for some models, such as the much studied binary Kob-Andersen (KA) mixture. We have recently developed generalizations to the KA model where swap can be very effective. Here, we ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(13):134505]

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First principles calculations of the vibrational properties of single and dimer F-type centers in corundum crystals.

Alexander Platonenko, Denis Gryaznov, Anatoly I Popov, Roberto Dovesi, Eugene A Kotomin,

The present paper investigates the F-type centers in α-Al2O3 through their electronic and vibrational properties from first principle calculations using a periodic supercell approach, a hybrid functional, and all-electron Gaussian basis sets as implemented in the CRYSTAL17 code. Single F-type and dimer F2-type centers related to oxygen vacancies in various ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(13):134107]

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An efficient and accurate model for water with an improved non-bonded potential.

Mohamad Mohebifar, Christopher N Rowley,

A molecular mechanical model for liquid water is developed that uses a physically motivated potential to represent Pauli repulsion and dispersion instead of the standard Lennard-Jones potential. The model has three atomic sites and a virtual site located on the ∠HOH bisector (i.e., a TIP4P-type model). Pauli-repulsive interactions are represented ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(13):134105]

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Tunneling splittings of vibrationally excited states using general instanton paths.

Mihael Eraković, Marko T Cvitaš,

A multidimensional semiclassical method for calculating tunneling splittings in vibrationally excited states of molecules using Cartesian coordinates is developed. It is an extension of the theory by Mil'nikov and Nakamura [J. Chem. Phys. 122, 124311 (2005)] to asymmetric paths that are necessary for calculating tunneling splitting patterns in multi-well systems, ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(13):134106]

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Vibronic coupling density analysis and quantum dynamics simulation for singlet fission in pentacene and its halogenated derivatives.

Takanori Nagami, Takayoshi Tonami, Kenji Okada, Wataru Yoshida, Hajime Miyamoto, Masayoshi Nakano,

We theoretically investigate microscopic origins of vibronic coupling (VC) contributing to singlet fission (SF) dynamics in pentacene and its halogenated derivatives. The features of VCs related to diabatic exciton states and interstate electronic couplings (Holstein and Peierls couplings, respectively) are interpreted by the VC density (VCD) analysis, which allows one ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(13):134302]

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Extending nudged elastic band method to reaction pathways involving multiple spin states.

Liming Zhao, K-Jiro Watanabe, Naoki Nakatani, Akira Nakayama, Xin Xu, Jun-Ya Hasegawa,

There are diverse reactions including spin-state crossing, especially the reactions catalyzed by transition metal compounds. To figure out the mechanisms of such reactions, the discussion of minimum energy intersystem crossing (MEISC) points cannot be avoided. These points may be the bottleneck of the reaction or inversely accelerate the reactions by ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(13):134114]

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Analytic energy gradients for the self-consistent direct random phase approximation.

Adrian Thierbach, Andreas Görling,

Analytic energy gradients with respect to nuclear coordinates are derived and implemented for the self-consistent direct random phase approximation (sc-dRPA) method. In contrast to the more common non-self-consistent dRPA methods, the sc-dRPA method does not require a choice for the approach to generate the Kohn-Sham orbitals and eigenvalues serving as ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(13):134113]

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Secondary structure specified polarizabilities of residues for an evaluation of circular dichroism spectra of proteins.

Carmen Giovana Granados-Ramírez, Mauricio D Carbajal-Tinoco,

We present a model of circular dichroism for proteins that is based on the classical electromagnetic theory for optical activity. The two additional constituents of the model are as follows: an appropriate characterization of the secondary structure of the protein residues and the assignment of an effective polarizability to each ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(15):155101]

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Molecular determinants of Ebola nucleocapsid stability from molecular dynamics simulations.

Chaoyi Xu, Nidhi Katyal, Tanya Nesterova, Juan R Perilla,

Ebola virus (EBOV) is a human pathogen with the ability to cause hemorrhagic fever and bleeding diathesis in hosts. The life cycle of EBOV depends on its nucleocapsid. The Ebola nucleocapsid consists of a helical assembly of nucleoproteins (NPs) encapsidating single-stranded viral RNA (ssRNA). Knowledge of the molecular determinants of ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(15):155102]

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