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Coarse-Graining Conformational Dynamics with Multidimensional Generalized Langevin Equation: How, When, and Why
A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained (CG) conformational dynamics. Constrained by the fluctuation–dissipation theorem, the approach can build CG models in dynamical consistency (DC) with all-atom molecular dynamics. Here, we also propose practical criteria for AIGLE to enforce long-term DC. Case studies of a toy polymer, with 20 CG sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling CG conformational dynamics in practice.
Cryogenic Vibrationally Resolved Photoelectron Spectroscopy of OH–(H2O): Confirmation of Multidimensional Franck-Condon Simulation Results for the Transition State of the OH + H2O Reaction
We present a transition state spectroscopic study of the OH + H2O reaction using the experimental technique of cryogenic Negative Ion Photoelectron Spectroscopy (NIPES). The recorded NIPE spectrum at 193 nm exhibits multiple vibrational progressions that include excitations to the shared H atom antisymmetric stretching mode with an interval of 0.32 eV as well as other progressions, mainly involving the H bending and O…O symmetric stretching modes. The Vertical Detachment Energy (VDE) was measured at 3.53 eV, whereas an upper limit for the Adiabatic Detachment Energy (ADE) was estimated at 2.90 eV. These values are in excellent agreement with the theoretically computed values of 3.51 eV and 2.83 eV respectively, obtained at the CCSD(T)/aug-cc-pV5Z level of theory. The recorded NIPE spectrum is in very good agreement when compared to the one recently reported from four-dimensional Franck-Condon simulations, in which a similar spectral profile was predicted. Besides observing the ground state, a charge-transfer excited state in the form of [OH–(H2O)+] is identified with a relative energy of 1.39 eV, well matching the previous prediction of 1.36 eV. This work was supported by U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, and performed using EMSL, a national scientific user facility sponsored by DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory, which is operated by Battelle Memorial Institute for the DOE. The theoretical calculations were conducted on EMSL’s “Cascade” Supercomputer. This research also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
Probing surface hydrogen bonding and dynamics by natural abundance, multidimensional, 17 O DNP-NMR spectroscopy
Dynamic nuclear polarization (DNP)-enhanced solid-state nuclear magnetic resonance (SSNMR) spectroscopy is increasingly being used as a tool for the atomic-level characterization of surface sites. DNP surface-enhanced SSNMR spectroscopy of materials has, however, been limited to studying relatively receptive nuclei, and the particularly rare 17 O nuclide, which is of great interest for materials science, has not been utilized. We demonstrate that advanced 17 O SSNMR experiments can be performed on surface species at natural isotopic abundance using DNP. We use 17 O DNP surface-enhanced 2D SSNMR to measure 17 O{ 1 H} HETCOR spectra as well as dipolar oscillations on a series of thermally treated mesoporous silica nanoparticle samples having different pore diameters. These experiments allow for a nonintrusive and unambiguous characterization of hydrogen bonding and dynamics at the surface of the material; no other single experiment can give such details about the interactions at the surface. Lastly, our data show that, upon drying, strongly hydrogen-bonded surface silanols, whose motions are greatly restricted by the interaction when compared to lone silanols, are selectively dehydroxylated.
A Multidimensional Operando Study Showing the Importance of the Electrode Macrostructure in Lithium Sulfur Batteries
Lithium sulfur batteries are one of the most promising next-generation energy storage technologies, because of their impressive theoretical energy density, low materials cost, and relative safety. However, incomplete understanding of their underlying operation mechanisms has hindered their further development and commercialization. In this work, to gain a better understanding of the operation mechanisms in the lithium sulfur battery, three macroscopically different (woven and nonwoven) and microscopically similar (made from the same carbon fibers) free-standing carbon felts are used as the conductive matrices to show how the macrostructure influences the redox reactions and the electrochemical performance. Additionally, an operando radiography and simultaneous in situ electrochemical impedance spectroscopy study are performed to highlight the differences of the carbon hosts and how they compare electrochemically in a lithium sulfur battery. The electrochemical results show that the carbon host with a more open structure results in increased capacity as well as a higher diffusion coefficient. The operando radiography shows that the open structures are more conducive to efficient redox reactivity in forming solid sulfur species, mostly in the form of elongated needlelike structures identified as β-S8, near the end of charge, which is corroborated by the impedance data. The data also reveal a “breathing” mechanism, where the polysulfides are pushed to the edges during discharge and pulled back during charge. Furthermore, it is also revealed that the “breathing” process is a limiting factor in the high rate performance. Overall, this study shows that there is a close relationship between the macrostructure of the carbon matrix and the electrochemical performance of the sulfur cathode.
Pressure-Induced Multidimensional Assembly and Sintering of CuInS 2 Nanoparticles into Lamellar Nanosheets with Band Gap Narrowing
Two-dimensional (2D) nanomaterials have fascinating structural, electrical, and optical properties, especially strong excitonic effects due to decreased dielectric screening. However, constructing 2D ultrathin nanomaterials, with the exception of layered materials, remains a challenge. In this work, we successfully realize oriented attachment on guiding one-dimensional chalcopyrite CuInS 2 nanocrystal (NC) formation and 2D assembly into lamellar nanosheets by applying pressure-driven sintering of zero-dimensional CuInS2 nanoparticles (NPs). We discuss the atomic-level mechanism of such phenomena and illustrate a pressure-driven processing diagram that reveals the sintering process of NPs coordinated by pressure and structural transformation. Optical measurements exhibit that the band gap has a narrowing by 0.21 eV compared with the initial 2.03 eV upon decompression to ambient conditions. Our findings represent a significant step forward in gaining an in-depth understanding of the pressure-driven morphology engineering of nanomaterials and provide a promising strategy to prepare 2D NCs, thereby greatly increasing the choice of materials for various applications.
Mechanisms of Symmetry Breaking in a Multidimensional Flashing Particle Ratchet
Ratcheting is a mechanism that produces directional transport of particles by rectifying nondirectional energy using local asymmetries rather than a net bias in the direction of transport. In a flashing ratchet, an oscillating force (here, an AC field) is applied perpendicular to the direction of transport. In an effort to explore the properties of current experimentally realizable ratchet systems, and to design new ones, this paper describes classical simulations of a damped flashing ratchet that transports charged nanoparticles within a transport layer of finite, non-zero thickness. The thickness of the layer, and the decay of the applied field in the z -direction throughout that thickness, provide a mechanism of symmetry breaking in the system that allows the ratchet to produce directional transport using a temporally unbiased oscillation of the AC driving field, a sine wave. Sine waves are conveniently produced experimentally or harvested from natural sources but cannot produce transport in a 1D or pseudo-1D system. The sine wave drive produces transport velocities an order of magnitude higher than those produced by the common on/off drive, but lower than those produced by a temporally biased square wave drive (unequal durations of the positive and negative states). Finally, the dependence of the particle velocity on the thickness of the transport layer, and on the homogeneity of the oscillating field within the layer, is presented for all three driving schemes.
Identifying Toxicity Mechanisms Associated with Early Lanthanide Exposure through Multidimensional Genome-Wide Screening
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Tailoring Triuranium Octoxide into Multidimensional Uranyl Fluoride Micromaterials
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Signatures of Biologically Driven Hemicellulose Modification Quantified by Analytical Pyrolysis Coupled with Multidimensional Gas Chromatography Mass Spectrometry
Biomass storage operation is one major source of feedstock quality variability that impacts on downstream preprocessing, feeding, handling and conversion into biofuels, chemicals and products. In field Ccorn stover biomass bales undergoes degradation and cell wall components modification resulting from microbial biological heating occurring during storage. A molecular characterization of the modification was achieved to unveil and understand the changes of structural cell wall modification in corn stover samples by conducting low temperature (400°C) pyrolysis, comparing samples that were mildly biologicallyun heated to those that had been subjected to microbial severe biological heating (~60°C). Pyrolysis of the samples originating from biomass that had been heated during storage generated small oxygenates such as furfural, 5-methylfurfural and 2-(5H)-furanone with efficiencies that were as much as ten times greater than those measured for the mildly unheated samples. Most of the compounds having enhanced efficiencies were C5 oxygenates, suggesting that the pyrolysis products may be formed from hemicellulosic precursor polymers in the corn stover. The findings suggest that microbial heating may be disrupting the cell wall structure, fragmenting the hemicellulose or cellulose chains, generating more polymer termini that have higher efficiency for generating the oxygenates at lower temperatures. Pyrolysis variability with temperature may be a beneficial strategy for improved biomass cell wall characterization, and for guiding control strategies for enhanced control over product distributions , providing insights to understand and manage the feedstock variability as well as to inform harvest and storage best management practices.