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Journal of Chemical Physics

Benoit Mignolet, Basile F E Curchod
We propose a pump-dump control scheme using sub-10 fs pulses to enhance the photochemical formation of the three-membered C-S-O ring oxathiirane from the parent H2 CSO sulfine molecule. The ultrashort nature of the pulses is essential to promptly alter the photoinduced dynamics, e.g., while a bond is elongating, which is key to selectively form the oxathiirane by radiative dumping. We carried out an in silico pump-dump experiment with excited-state dynamics simulations that include the interaction with electric field of the pump and dump pulses...
March 14, 2019: Journal of Chemical Physics
A Jabri, D Fontanari, A Roucou, C Bray, F Hindle, G Dhont, G Mouret, R Bocquet, A Cuisset
Because methoxyphenols (MP) are emitted in significant quantities during biomass fires and contribute to the secondary organic aerosols formation which impacts the climate, their gas phase monitoring in the atmosphere is crucial and requires accurate rovibrational cross sections determined with a good knowledge of their ground state (GS) and vibrationally excited state (ES) molecular parameters. Therefore, the rotational spectra of the two isomers, 2-MP (guaïacol) and 4-MP (mequinol), have been measured in absorption and in emission at room temperature using a frequency multiplication chain and a mm-wave Fourier transform chirped-pulse spectrometer, respectively...
March 14, 2019: Journal of Chemical Physics
Thomas la Cour Jansen, Shinji Saito, Jonggu Jeon, Minhaeng Cho
Two-dimensional (2D) vibrational spectroscopy has emerged as one of the most important experimental techniques useful to study the molecular structure and dynamics in condensed phases. Theory and computation have also played essential and integral roles in its development through the nonlinear optical response theory and computational methods such as molecular dynamics (MD) simulations and electronic structure calculations. In this article, we present the fundamental theory of coherent 2D vibrational spectroscopy and describe computational approaches to simulate the 2D vibrational spectra...
March 14, 2019: Journal of Chemical Physics
Weijian Li, Xiaoliang Zuo, Xiaoyan Zhou, Hangjun Lu
Using molecular dynamics simulations, we have investigated the hydrophobic interactions and influence of nitrogen molecules on the critical distance of dewetting between the nanoscale hydrophobic plates. We show that dewetting transition is very sensitive to the distribution of nitrogen molecules. The nitrogen molecules prefer to aggregate in the vicinity of the two hydrophobic plates and exclude water molecules. Furthermore, our simulation results indicate that the effective range of hydrophobic attraction between the two nanoscale plates is enhanced by the aggregated nitrogen molecules...
March 14, 2019: Journal of Chemical Physics
S Peter Bierwirth, Gabriel Honorio, Catalin Gainaru, Roland Böhmer
Monohydroxy alcohols (MAs) with methyl and hydroxyl side groups attached to the same carbon atom in the alkyl backbone can display very weak structural and supramolecular dielectric relaxation processes when probed in the regime of small electrical fields. This can render their separation and assignment difficult in the pure liquids. When mixing with bromoalkanes, a faint Debye-like process can be resolved dielectrically for 4-methyl-4-heptanol. To achieve a separation of structural and supramolecular processes in pure 4-methyl-4-heptanol and 3-methyl-3-heptanol, mechanical experiments are carried out in the linear-response regime as well as using medium-angle oscillatory shear amplitudes...
March 14, 2019: Journal of Chemical Physics
Yifan Dong, Hyojung Cha, Jiangbin Zhang, Ernest Pastor, Pabitra Shakya Tuladhar, Iain McCulloch, James R Durrant, Artem A Bakulin
Recent progress in organic photovoltaics (OPVs) has been enabled by optimization of the energetic driving force for charge separation, and thus maximization of open-circuit voltage, using non-fullerene acceptor (NFA) materials. In spite of this, the carrier dynamics and relative energies of the key states controlling the photophysics of these systems are still under debate. Herein, we report an in-depth ultrafast spectroscopic study of a representative OPV system based on a polymer donor PffBT4T-2OD and a small-molecule NFA EH-IDTBR...
March 14, 2019: Journal of Chemical Physics
Igor Gayday, Alexander Teplukhin, Dmitri Babikov
Accurate calculations of vibrational states in singly and doubly substituted ozone molecules are carried out, up to dissociation threshold. Analysis of these spectra reveals noticeable deviations from the statistical factor of 2 for the ratio between the number of states in asymmetric and symmetric ozone molecules. It is found that, for the lower energy parts of spectra, the ratio is less than 2 in the singly substituted ozone molecules, but it is more than 2 in the doubly substituted ozone molecules. However, the upper parts of spectra, just below dissociation thresholds, exhibit a different behavior...
March 14, 2019: Journal of Chemical Physics
James Lincoff, Sukanya Sasmal, Teresa Head-Gordon
Molecular dynamics simulations of intrinsically disordered proteins (IDPs) can provide high resolution structural ensembles if the force field is accurate enough and if the simulation sufficiently samples the conformational space of the IDP with the correct weighting of sub-populations. Here, we investigate the combined force field-sampling problem by testing a standard force field as well as newer fixed charge force fields, the latter specifically motivated for better description of unfolded states and IDPs, and comparing them with a standard temperature replica exchange (TREx) protocol and a non-equilibrium Temperature Cool Walking (TCW) sampling algorithm...
March 14, 2019: Journal of Chemical Physics
Xiong-Xiong Xue, Li-Ming Tang, Keqiu Chen, Lixin Zhang, En-Ge Wang, Yexin Feng
The development of bifunctional catalysts for oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) is highly desirable for fuel cells and rechargeable metal-air batteries. Till now, it is still challenging to achieve both efficient activities on a single commercial noble-metal catalyst. Recently, N, P co-doped graphene has shown good bifunctional evidence. However, the atomic-scale understanding of the bifunctional mechanism is still lacking. Here, we show that the N and P atoms prefer to bond with each other, forming embedded N-P clusters in graphene...
March 14, 2019: Journal of Chemical Physics
Michael J Wilhelm, Mohammad Sharifian Gh, Hai-Lung Dai
We present an experimental study, using the surface sensitive technique, second harmonic light scattering (SHS), to examine the influence of structure on the propensity of a molecule to passively diffuse across a phospholipid membrane. Specifically, we monitor the relative tendency of the structurally similar amphiphilic cationic dyes, malachite green (MG) and crystal violet (CV), to transport across membranes in living cells (E. coli) and biomimetic liposomes. Despite having nearly identical molecular structures, molecular weights, cationic charges, and functional groups, MG is of lower overall symmetry and consequently has a symmetry allowed permanent dipole moment, which CV does not...
March 14, 2019: Journal of Chemical Physics
Sergio Pérez-Conesa, Francisco Torrico, José M Martínez, Rafael R Pappalardo, Enrique Sánchez Marcos
A set of new ab initio force fields for aqueous [AnO2 ]2+/+ (An = Np(vi,v), Pu(vi), Am(vi)) has been developed using the Hydrated Ion (HI) model methodology previously used for [UO2 ]2+ . Except for the non-electrostatic contribution of the HI-bulk water interaction, the interaction potentials are individually parameterized. Translational diffusion coefficients, hydration enthalpies, and vibrational normal mode frequencies were calculated from the MD simulations. Physico-chemical properties satisfactorily agree with experiments validating the robustness of the force field strategy...
March 14, 2019: Journal of Chemical Physics
Kira Rundel, Yufeng Liang, Adam Welford, David Prendergast, Christopher R McNeill
The near edge X-ray absorption fine structure (NEXAFS) spectra of naphthalene diimide molecules with increasing degrees of thionation show distinct and systematic changes in the C 1s → π* manifold. However, interpretation of such spectra is difficult using experimental data alone, due to the limitation in experimental NEXAFS resolution. In this work, we have calculated the NEXAFS spectra of naphthalene diimide molecules with increasing degrees of thionation using the density functional theory-based eXcited electron and Core Hole approach...
March 14, 2019: Journal of Chemical Physics
Marco Bacci, Amedeo Caflisch, Andreas Vitalis
Classical atomistic simulations of biomolecules play an increasingly important role in molecular life science. The structure of current computing architectures favors methods that run multiple trajectories at once without requiring extensive communication between them. Many advanced sampling strategies in the field fit this mold. These approaches often rely on an adaptive logic and create ensembles of comparatively short trajectories whose starting points are not distributed according to the correct Boltzmann weights...
March 14, 2019: Journal of Chemical Physics
Carlos Cabezas, Jean-Claude Guillemin, Yasuki Endo
Four conformers of the n-propyl-substituted Criegee intermediate, CH3 CH2 CH2 CHOO, also named n-butyraldehyde oxide, have been observed by Fourier transform microwave spectroscopy. The transient species was produced using a pulsed electric discharge of a gas mixture of 1,1-diiodobutane/O2 diluted in Ar or Ne. The observation of only syn species is in contrast to the results of other previous studies of alkyl-substituted Criegee intermediates, in particular, those for the structural isomers, isobutyraldehyde oxide ((CH3 )2 CHCHOO), and methyl-ethyl-ketone oxide (C2 H5 C(CH3 )OO), for which syn and anti species have been observed coexisting in the gas phase...
March 14, 2019: Journal of Chemical Physics
Lenzi J Williams, Patrick J Herbert, Marcus A Tofanelli, Christopher J Ackerson, Kenneth L Knappenberger
Electronic spin-state dynamics were studied for a series of Au25 (SC8 H9 )18 q and Au24 Pd(SC8 H9 )18 monolayer-protected clusters (MPCs) prepared in a series of oxidation states, q, including q = -1, 0, +1. These clusters were chosen for study because Au25 (SC8 H9 )18 -1 is a closed-shell superatomic cluster, but Au25 (SC8 H9 )18 0 is an open-shell (7-electron) system; Au25 (SC8 H9 )18 +1 and PdAu24 (SC8 H9 )18 0 are isoelectronic (6-electron) closed-shell systems. Carrier dynamics for electronic fine structure spin states were isolated using femtosecond time-resolved circularly polarized transient-absorption spectroscopy (fs-CPTA)...
March 14, 2019: Journal of Chemical Physics
Stephen J Cotton, William H Miller
In the previous work of Cotton and Miller [J. Chem. Phys. 145, 144108 (2016)], an improved symmetrical quasi-classical (SQC) windowing model for the molecular dynamics treatment of electronically non-adiabatic processes was developed in order to extend the original SQC approach to the regime of weak-coupling between the electronic states. The improved SQC model-based on triangular-shaped window functions-handled the weak-coupling limit as intended and, as a bonus, was shown to be universally superior to the original square/histogram SQC windowing model over all coupling regimes, but only for treating systems of two electronic states, as no higher-dimensional generalization was evident...
March 14, 2019: Journal of Chemical Physics
J Süß, J Wehner, J Dostál, T Brixner, V Engel
We present a theoretical study on exciton-exciton annihilation (EEA) in a molecular dimer. This process is monitored using a fifth-order coherent two-dimensional (2D) spectroscopy as was recently proposed by Dostál et al. [Nat. Commun. 9, 2466 (2018)]. Using an electronic three-level system for each monomer, we analyze the different paths which contribute to the 2D spectrum. The spectrum is determined by two entangled relaxation processes, namely, the EEA and the direct relaxation of higher lying excited states...
March 14, 2019: Journal of Chemical Physics
Raymond Jin, Lutz Maibaum
Complementary deoxyribonucleic acid (DNA) strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We adopt a multi-step computational approach. First, we perform a large number of Brownian dynamics simulations of the hybridization process using the coarse-grained oxDNA2 model. Second, we use these simulations to construct a Markov state model of DNA dynamics that uses a state decomposition based on the inter-strand hydrogen bonding pattern...
March 14, 2019: Journal of Chemical Physics
Manish J Thapa, Wei Fang, Jeremy O Richardson
We propose a new quantum transition-state theory for calculating Fermi's golden-rule rates in complex multidimensional systems. This method is able to account for the nuclear quantum effects of delocalization, zero-point energy, and tunneling in an electron-transfer reaction. It is related to instanton theory but can be computed by path-integral sampling and is thus applicable to treat molecular reactions in solution. A constraint functional based on energy conservation is introduced which ensures that the dominant paths contributing to the reaction rate are sampled...
March 14, 2019: Journal of Chemical Physics
Yamil J Colón, Ashley Z Guo, Lucas W Antony, Kyle Q Hoffmann, Juan J de Pablo
Metal-organic frameworks (MOFs) represent an important class of materials. Careful selection of building blocks allows for tailoring of the properties of the resulting framework. The self-assembly process, however, is not understood, and without detailed knowledge of the underlying molecular mechanism, it is difficult to anticipate whether a particular design can be realized, or whether the material adopts a metastable, kinetically arrested state. We present a detailed examination of early-stage self-assembly pathways of the MOF-5...
March 14, 2019: Journal of Chemical Physics
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