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Journal of Physical Chemistry Letters

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https://www.readbyqxmd.com/read/30226782/ultrafast-pump-repump-probe-photochemical-hole-burning-as-a-probe-of-excited-state-reaction-pathway-branching
#1
Joshua A Snyder, Arthur E Bragg
We demonstrate pump-repump-probe (PRP) transient hole burning as a spectroscopic tool for differentiating reactive from non-reactive deactivation of excited photochemical reactants observed by transient absorption spectroscopy (TAS). This method utilizes a time-delayed, wavelength-tunable ultrafast pulse to alter the excited reactant population, with the impact of "repumping" quantified through depletions in photoproduct absorption. We apply this approach to characterize dynamics affecting the nonadiabatic photocyclization efficiency to form S0 dihydrotriphenylene (DHT) following 266-nm excitation of ortho-terphenyl (OTP)...
September 18, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30226383/classification-of-epigenetic-biomarkers-with-atomically-thin-nanopores
#2
Aditya Sarathy, Nagendra B Athreya, Lav R Varshney, Jean-Pierre Leburton
We use the electronic properties of 2D solid-state nanopore materials to propose a versatile and generally applicable biosensor technology by using a combination of molecular dynamics, nanoscale device simulations, and statistical signal processing algorithms. As a case study, we explore the classification of three epigenetic biomarkers, the methyl-CpG binding domain 1 (MBD-1), MeCP2, and γ-cyclodextrin, attached to double-stranded DNA to identify regions of hyper- or hypomethylations by utilizing a matched filter...
September 18, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30212632/tracking-ultrafast-bond-dissociation-dynamics-with-0-1-%C3%A3-resolution-by-femtosecond-extreme-ultraviolet-absorption-spectroscopy
#3
Zhengrong Wei, Li Tian, Jialin Li, Yunpeng Lu, Minghui Yang, Zhi-Heng Loh
Visualizing the real-time dissociation of chemical bonds represents a challenge in the study of ultrafast molecular dynamics due to the simultaneous need for sub-angström spatial- and femtosecond temporal resolution. Here, we follow the C-I dissociation dynamics of strong-field-ionized 2-iodopropane (2-C3 H7 I) with femtosecond XUV absorption spectroscopy. By probing the iodine 4 d core-level absorption, we resolve a continuous XUV spectral shift on the sub-100-fs timescale that accompanies the dissociation of the 2-C3 H7 I+ spin-orbit-excited 2 E1/2 state to yield atomic I in the 2 P3/2 state...
September 13, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30211556/effects-of-preferential-counterion-interactions-on-the-specificity-of-rna-folding
#4
Joon Ho Roh, Duncan Kilburn, Reza Behrouzi, Wokyung Sung, R M Briber, Sarah A Woodson
The real-time search for native RNA structure is essential for the operation of regulatory RNAs. We previously reported that a fraction of the Azoarcus ribozyme achieves a compact structure in less than a millisecond. To scrutinize the forces that drive initial folding steps, we used time-resolved SAXS to compare the folding dynamics of this ribozyme in thermodynamically isostable concentrations of different counterions. The results show that the size of the fast-folding population increases with the number of available counterions and correlates with the flexibility of initial RNA structures...
September 18, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30204448/direct-measurements-of-carrier-transport-in-polycrystalline-methylammonium-lead-iodide-perovskite-films-with-transient-grating-spectroscopy
#5
Dylan H Arias, David T Moore, Jao van de Lagemaat, Justin C Johnson
Hybrid organic-inorganic halide perovskites have been proposed in many optoelectronic applications, but critical to their increasing functionality and utility is understanding and controlling carrier transport. Here, we use light-induced transient grating spectroscopy to probe directly carrier transport in polycrystalline methylammonium lead iodide perovskite thin films using a weakly perturbative and noncontact method. The data reveal intrinsic diffusion characteristics of the charge carriers in the material and agree well with a simulated model of charge transport in which grain boundaries act as barriers to carrier movement...
September 18, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30081630/fast-and-accurate-molecular-property-prediction-learning-atomic-interactions-and-potentials-with-neural-networks
#6
Masashi Tsubaki, Teruyasu Mizoguchi
The discovery of molecules with specific properties is crucial to developing effective materials and useful drugs. Recently, to accelerate such discoveries with machine learning, deep neural networks (DNNs) have been applied to quantum chemistry calculations based on the density functional theory (DFT). While various DNNs for quantum chemistry have been proposed, these networks require various chemical descriptors as inputs and a large number of learning parameters to model atomic interactions. In this paper, we propose a new DNN-based molecular property prediction that (i) does not depend on descriptors, (ii) is more compact, and (iii) involves additional neural networks to model the interactions between all the atoms in a molecular structure...
September 18, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30222363/optical-fluid-pump-generation-of-directional-flow-via-micro-phase-segregation-homogenization
#7
Hiroki Sakuta, Shunsuke Seo, Shuto Kimura, Marcel Hoerning, Koichiro Sadakane, Takahiro Kenmotsu, Motomu Tanaka, Kenichi Yoshikawa
We report the successful generation of directional liquid-flow under stationary laser irradiation at a fixed position in a chamber. We adopt a homogeneous solution consisting of a mixture of water and triethylamine (TEA), with a composition near the critical point for phase segregation. When geometrical asymmetry is introduced around the laser focus in the chamber, continuous directional flow is generated, accompanied by the emergence of micro water-rich microdroplets at the laser focus. The emerg- ing microdroplets tend to escape toward the surrounding bulk solution, and then merge/annihilate into the homogeneous solution...
September 17, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30222361/atypical-defect-motions-in-brittle-layered-sodium-titanate-nanowires
#8
Arixin Bo, Kai Chen, Edmund Pickering, Haifei Zhan, John Bell, Aijun Du, Yongqiang Zhang, Xiaoguang Wang, Huaiyong Zhu, Zhiwei Shan, YuanTong Gu
In situ tensile tests show atypical defect motions in the brittle NTO nanowire (NW) within the elastic deformation range. After brittle fracture, elastic recovery of the NTO NW is followed by reversible motion of the defects in a time-dependent manner. In situ cyclic loading-unloading test shows that these mobile defects shift back and forth along the NW in accordance with the loading-unloading cycles and eventually restore their initial positions after the load is completely removed. The Exsistence of the defects within the NTO NWs and their motions do not lead to plastic deformation of the NW...
September 17, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30222358/two-channel-thermal-transport-in-ordered-disordered-superionic-ag-2-te-and-its-traditionally-contradictory-enhancement-by-nanotwin-boundary
#9
Biyao Wu, Yanguang Zhou, Ming Hu
A recent experiment [ J. Mater. Chem. A 2015 , 3 , 10303 ] has proved that superionic Ag2 Te can achieve a figure of merit as high as 1.39 due to its extremely low thermal conductivity. However, the traditional lattice vibration concept, i.e., phonons regarded as heat carriers, fails to explain the governing mechanism in such structures where anions vibrate around their equilibrium positions while cations flow like a liquid. As a result, the underlying physics for thermal transport properties in superionic Ag2 Te is still a mystery...
September 17, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30196700/two-step-to-one-step-nucleation-of-a-zeolite-through-a-metastable-gyroid-mesophase
#10
Abhinaw Kumar, Valeria Molinero
The importance of nonclassical nucleation pathways in the formation of complex crystals has become apparent in recent years. Nonclassical pathways were unraveled for, among others, the crystallization of proteins, colloids, and clathrates. In those cases, the formation of a metastable fluid with density close to the crystal decreases the crystallization barrier. Recent simulations indicate that mesophases can facilitate the nucleation of zeolites. Here, we use molecular simulations to investigate the role of a gyroid mesophase on the crystallization of a model zeolite from liquid...
September 17, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30193068/sizable-excitonic-effects-undermining-the-photocatalytic-efficiency-of-%C3%AE-cu-2-v-2-o-7
#11
Julia Wiktor, Igor Reshetnyak, Michal Strach, Mariateresa Scarongella, Raffaella Buonsanti, Alfredo Pasquarello
Copper vanadates have been proposed as promising photoanodes for water-splitting photoelectrochemical cells, but their performance has recently been shown to be severely limited. To understand this behavior, we study the electronic structure and the optical properties of β-Cu2 V2 O7 both experimentally and computationally. The measured absorption spectrum shows an absorption peak at 1.5 eV followed by the onset of an apparent continuum at 2.26 eV, as generally found for this class of materials. We perform calculations within the framework of the QS GW̃ method and the Bethe-Salpeter equation while including effects of magnetic ordering, nuclear quantum motion, and thermal vibrations...
September 17, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30212222/spectroscopy-of-molecular-ions-in-coulomb-crystals
#12
Aaron T Calvin, Kenneth R Brown
In this Perspective, we examine the use of laser-cooled atomic ions and sympathetically cooled molecular ions in Coulomb crystals for molecular spectroscopy. Coulomb crystals are well-isolated environments that provide localization and long storage times for sensitive measurements of weak signals and cold temperatures for precise spectroscopy. Coulomb crystals of molecular and atomic ions enable the detection of single photon molecular ion transitions at a range of wavelengths by a change in atomic ion fluorescence at visible wavelengths...
September 13, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30212219/surface-potential-of-a-planar-charged-lipid-water-interface-what-do-vibrating-plate-methods-second-harmonic-and-sum-frequency-measure
#13
Lisa Barbara Dreier, Christoph Bernhard, Grazia Gonella, Ellen H G Backus, Mischa Bonn
The interfacial electrical potential is an important parameter influencing, for instance, electrochemical reactions and biomolecular interactions at membranes. A deeper understanding of different methods that measure quantities related to the surface potential is thus of great scientific and technological relevance. We use lipid monolayers with varying charge density and thoroughly compare the results of surface potential measurements performed with the vibrating plate capacitor method and second harmonic generation spectroscopy...
September 13, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30212218/nano-structured-bi-grown-on-epitaxial-graphene-sic
#14
Tingwei Hu, Xin Hui, Xiaohe Zhang, Xiangtai Liu, Dayan Ma, Ran Wei, Kewei Xu, Fei Ma
Controllable growth of metal nano-structures on epitaxial graphene (EG) is particularly interesting and important for the applications in electric devices. In this paper, Bi nanostructures on EG/SiC are fabricated through thermal decomposition of SiC and subsequent low-flux evaporation of Bi. The orientation, atomic structure and thickness dependent electronic states of Bi are investigated by scanning tunneling microscopy/spectroscopy (STM/S). It is found that metallic Bi nano-flakes and nano-rods prefer to grow on SiC buffer layer (BL) region with higher diffusion barrier, but Bi nano-ribbons are formed on regularly ordered EG...
September 13, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30212213/charge-mobility-and-dynamics-in-spin-crossover-nanoparticles-studied-by-time-resolved-microwave-conductivity
#15
Julien Dugay, Wiel H Evers, Ramón Torres-Cavanillas, Mónica Giménez-Marqués, Eugenio Coronado, Herre S J van der Zant
We use the electrode-less time-resolved microwave conductivity (TRMC) technique to characterize spin-crossover (SCO) nanoparticles. We show that TRMC is a simple and accurate mean for simultaneously as-sessing the magnetic state of SCO compounds and charge transport information on the nanometre length scale. In the low-spin state from liquid nitrogen temperature up to 360 K the TRMC measurements present two well-defined regimes in the mobility and in the half-life times, in which the former transition tempera-ture TR occurs near 225 K...
September 13, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30212207/thermal-decoherence-and-disorder-effects-on-chiral-induced-spin-selectivity
#16
Elena Diaz, Francisco Dominguez-Adame, Rafael Gutierrez, Gianaurelio Cuniberti, Vladimiro Mujica
We use a nonlinear master equation formalism to account for thermal and disorder effects on spin-dependent electron transport in helical organic molecules coupled to two ideal leads. The inclusion of these two effects has important consequences in understanding the observed length and temperature dependence of spin polarization in the experiments, which cannot be accounted for in a purely coherent tunneling model. Our model considers a tight-binding helical Hamiltonian with disordered onsite energies to describe the resulting electronic states when low-frequency interacting modes break the electron coherence...
September 13, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30212206/precision-deer-distances-from-spin-label-ensemble-refinement
#17
Katrin Reichel, Lukas S Stelzl, Juergen Koefinger, Gerhard Hummer
Double electron-electron resonance (DEER) experiments probe nanometer-scale distances in spin-labeled proteins and nucleic acids. Rotamer libraries of the covalently attached spin labels help reduce position uncertainties. Here we show that rotamer reweighting is essential for precision distance measurements, making it possible to resolve Ångstrom-scale domain motions. We analyze extensive DEER measurements on the three N-terminal polypeptide-transport-associated (POTRA) domains of the outer membrane protein Omp85...
September 13, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30205006/near-infrared-spectroscopy-and-anharmonic-theory-of-protonated-water-clusters-higher-elevations-in-the-hydrogen-bonding-landscape
#18
D C McDonald, J P Wagner, A B McCoy, M A Duncan
Near-infrared spectroscopy measurements are presented for protonated water clusters, H+ (H2 O) n , in the size range of n = 1-8. Clusters are produced in a pulsed-discharge supersonic expansion, mass selected, and studied with infrared laser photodissociation spectroscopy in the regions of 3600-4550 and 4850-7350 cm-1 . Although there is some variation with cluster size, the main features of these spectra are a broad absorption near 5300 cm-1 , a sharp doublet near 7200 cm-1 , as well as a structured absorption near 4100 cm-1 for n ≥ 2...
September 13, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30203654/direct-link-between-structure-and-hydration-in-ammonium-and-aminium-bisulfate-clusters-implicated-in-atmospheric-new-particle-formation
#19
Yi Yang, Sarah E Waller, John J Kreinbihl, Christopher J Johnson
The acid-base chemistry of amines and sulfuric acid promotes growth in the early stages of atmospheric new particle formation, with more basic amines enhancing growth rates. Hydration of these particles has been proposed to depend on acidity or basicity but is difficult to quantify; therefore, the role of water in this process is not well understood. Using tandem mass spectrometry coupled to a temperature-controlled ion trap, we show that water uptake by aminium bisulfate clusters depends on the total number of free hydrogen bond donors in the cluster and is unaffected by the interchange of amines featuring the same number of substituents but differing gas-phase basicity...
September 13, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30200766/nonadiabatic-excited-state-dynamics-with-machine-learning
#20
Pavlo O Dral, Mario Barbatti, Walter Thiel
We show that machine learning (ML) can be used to accurately reproduce nonadiabatic excited-state dynamics with decoherence-corrected fewest switches surface hopping in a 1-D model system. We propose to use ML to significantly reduce the simulation time of realistic, high-dimensional systems with good reproduction of observables obtained from reference simulations. Our approach is based on creating approximate ML potentials for each adiabatic state using a small number of training points. We investigate the feasibility of this approach by using adiabatic spin-boson Hamiltonian models of various dimensions as reference methods...
September 13, 2018: Journal of Physical Chemistry Letters
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