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At least 739 records · Page 41

SERS-based ssDNA composition analysis with inhomogeneous peak broadening and reservoir computing

Surface-enhanced Raman spectroscopy employed in conjunction with post-processing machine learning methods is a promising technique for effective data analysis, allowing one to enhance the molecular and chemical composition analysis of information rich DNA molecules. In this work, we report on a room temperature inhomogeneous broadening as a function of the increased adenine concentration and employ this feature to develop one-dimensional and two dimensional chemical composition classification models of 200 long single stranded DNA sequences. Afterwards, we develop a reservoir computing chemical composition classification scheme of the same molecules and demonstrate enhanced performance that does not rely on manual feature identification.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Assigning Optical Absorption Transitions with Light-Induced Crystal Structures: Case Study of a Single-Crystal Nanooptomechanical Transducer

UV/vis absorption spectroscopy affords indirect structural information about the photochemistry and photophysics of molecules by inferring types of electronic transitions from spectral features. Direct structural information would become available, though, if light-induced crystal structures could be mapped against changes in optical absorption spectra as a photochemical process evolves. We present a series of light-induced crystal structures that track real-time changes in solid-state optical absorption spectra of a crystalline nanooptomechanical transducer, while the transduction process unfolds within its crystal lattice at 100 K. Results afford a combined structural and spectral mapping of its solid-state optical absorption, from which the operational mechanism of nanooptomechanical transduction is revealed. Metal-to-ligand and metal-centered charge-transfer bands are assigned to optical absorption peaks directly from their 3-D light-induced crystal structures. This approach could be used to characterize many solid-state optoelectronic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tuning the Dimensionality of Excitons in Colloidal Quantum Dot Molecules

Electrically coupled quantum dots (QDs) can support unique optoelectronic properties arising from the superposition of single-particle excited states. Experimental methods for integrating colloidal QDs within the same nano-object, however, have remained elusive to the rational design. Here, we demonstrate a chemical strategy that allows for the assembling of colloidal QDs into coupled composites, where proximal interactions give rise to unique optoelectronic behavior. The assembly method employing “adhesive” surfactants was used to fabricate both homogeneous (e.g., CdS–CdS, PbS–PbS, CdSe–CdSe) and heterogeneous (e.g., PbS–CdS, CdS–CdSe) nanoparticle assemblies, exhibiting quasi-one-dimensional exciton fine structure. In addition, tunable mixing of single-particle exciton states was achieved for dimer-like assemblies of CdSe/CdS core–shell nanocrystals. The nanoparticle assembly mechanism was explained within the viscoelastic interaction theory adapted for molten-surface colloids. Furthermore, we expect that the present work will provide the synthetic and theoretical foundation needed for building assemblies of many inorganic nanocrystals.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Interfacial dynamics and catalytic behavior of single Ni atom site

Single-atom catalysts (SACs) have garnered significant interest due to their ability to reduce metal particles to the atomic scale, enabling finely tunable local environments and enhanced catalytic properties in terms of reactivity and selectivity. Despite this potential, their application has largely been confined to small-molecule transformations as metal-catalyzed reaction. Here, in this study, we present a diverse single-atom nickel (Ni) catalyst established via a nanoporous carbon (NPC) supported practice. This catalyst represents a breakthrough by achieving the bond formation between carbon and nitrogen and interfacial dynamics in the SAC. The present first principle-based density functional simulations establish the reaction dynamics and catalytic behaviour of such SAC. This dynamic nature comprises an exclusive nitrogen intercalated site showing excellent base effects. This base quickly tunes the interfacial atmosphere, enabling dynamic movement of adatoms into the NPC species, significantly changing the reaction path in Ni SACs due to superior steric effects. The research demonstrates that SACs can extend the capabilities of catalytic systems to include a wider range of complex reactions, offering substantial promise for the development of new, efficient synthetic methods for creating value-added molecular products.

36 MATERIALS SCIENCE↗

High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules

Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae. The flavivirus genome contains a 5’ end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5’ guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small-molecule inhibitors to disrupt the promoter function. To facilitate identification of small molecule binding sites in flavivirus SLA, we determined high-resolution structures of bottom and top stems of ZIKV SLA, which contain a single U- or G-bulge, respectively. Both bulge nucleotides exhibit multiple orientations, from folded back on the adjacent nucleotide to flipped out of the helix, and are stabilized by stacking or base triple interactions. These structures suggest that even a single unpaired nucleotide can provide flexibility to RNA structures and its conformation is mainly determined by the stabilizing chemical environment. To facilitate discovery of small molecule inhibitors that interfere with the functions of ZIKV SLA, we screened and identified compounds that bind to the bottom and top stems of ZIKV SLA.

Biochemistry & Molecular Biology↗

Electroluminescence from Single-Walled Carbon Nanotubes with Quantum Defects

Individual single-walled carbon nanotubes with covalent sidewall defects have emerged as a class of photon sources whose photoluminescence spectra can be tailored by the carbon nanotube chirality and the attached functional group/molecule. Here we present electroluminescence spectroscopy data from single-tube devices based on (7, 5) carbon nanotubes, functionalized with dichlorobenzene molecules, and wired to graphene electrodes. We observe electrically generated, defect-induced emissions that are controllable by electrostatic gating and strongly red-shifted compared to emissions from pristine nanotubes. The defect-induced emissions are assigned to excitonic and trionic recombination processes by correlating electroluminescence excitation maps with electrical transport and photoluminescence data. At cryogenic conditions, additional gate-dependent emission lines appear, which are assigned to phonon-assisted hot-exciton electroluminescence from quasi-levels. Similar results were obtained with functionalized (6, 5) nanotubes. We also compare functionalized (7, 5) electroluminescence data with photoluminescence of pristine and functionalized (7, 5) nanotubes redox-doped using gold(III) chloride solution. This work shows that electroluminescence excitation is selective toward neutral defect-state configurations with the lowest transition energy, which in combination with gate-control over neutral versus charged defect-state emission leads to high spectral purity.

36 MATERIALS SCIENCE↗

Probing the subtle differences between promethium and curium

Curium and promethium share similar chemical and physical properties thereby complicating their separation. Co-located processing at Oak Ridge National Laboratory results in curium contamination of the fission product stream containing promethium. To gain insight into the difficulty of this separation, the fundamental properties of these elements are experimentally and computationally probed in a 2,2’:6’,2”-terpyridine crystal system. Analysis of the isostructural compounds via single crystal X-ray diffraction and quantum theory of atoms in molecules reveals that bonding between promethium and curium is quite similar in this particular structure type. The small differences in the analysis of these two elements in this isostructural series sheds light on the difficulty required to separate the elements from each other. More so, this study develops the fundamental chemistries of two rare elements in the solid state and experimentally portrays the often-omitted position of promethium within the lanthanide series.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Linking optical spectra to free charges in donor/acceptor heterojunctions: cross-correlation of transient microwave and optical spectroscopy

The primary photoexcited species in excitonic semiconductors is a bound electron–hole pair, or exciton. An important strategy for producing separated electrons and holes in photoexcited excitonic semiconductors is the use of donor/acceptor heterojunctions, but the degree to which the carriers can escape their mutual Coulomb attraction is still debated for many systems. Here, we employ a combined pump–probe ultrafast transient absorption (TA) spectroscopy and time-resolved microwave conductivity (TRMC) study on a suite of model excitonic heterojunctions consisting of mono-chiral semiconducting single-walled carbon nanotube (s-SWCNT) electron donors and small-molecule electron acceptors. Comparison of the charge-separated state dynamics between TA and TRMC photoconductance reveals a quantitative match over the 0.5 microsecond time scale. Charge separation yields derived from TA allow extraction of s-SWCNT hole mobilities of ca. 1.5 cm 2 V -1 s -1 (at 9 GHz) by TRMC. We find that the correlation between the techniques conclusively demonstrates that photoinduced charge carriers separated across these heterojunctions do not form bound charge transfer states, but instead form free/mobile charge carriers.

36 MATERIALS SCIENCE↗

Y-shaped tricatenar azobenzenes – functional liquid crystals with synclinic–anticlinic transitions and spontaneous helix formation

A series of achiral tricatenar rod-like molecules with a 3,5-disubstitution pattern at one end and a single alkyl chain at the other end of a rod-like azobenzene derived core is reported. Depending on temperature and alkyl chain length, these Y-shaped compounds self-assemble into different types of liquid crystalline (LC) phases, ranging from non-tilted and synclinic tilted hexatic, via non-tilted and anticlinic tilted smectic and bicontinuous cubic LC phases, to a spontaneous mirror symmetry broken isotropic liquid (Iso 1 [*]) or a related achiral liquid network phase (Iso 1 ). An additional tilted, but uniaxial smectic phase was observed at the transition between anticlinic and synclinic tilt correlation and was investigated by soft resonant X-ray scattering with respect to possible helix formation. This work provides a new concept for the design of technological interesting azobenzene based LC materials with anticlinic tilted smectic C phases (SmC a ) and with azobenzene units organized in the long range or short range helical network structures of bicontinuous cubic and chiral isotropic liquid phases, respectively. Core fluorination removes all lamellar phases, leaving only the cubic phase over wide temperature ranges, even at ambient temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single photon simultaneous K-shell ionization/excitation in C 6 H 6 : experiment and theory

Single photon simultaneous core ionization/core excitation (K -2 V) of the Benzene molecule has been observed experimentally, using synchrotron radiation, by electron coincidence spectroscopy with a magnetic bottle time-of-flight electron spectrometer and reveals a rich spectrum. DFT and Post–Hartree–Fock calculations provide detailed assignments of K -2 V states. The specific Auger decay of these states has also been determined experimentally with a new technique to improve the energy resolution.

Optics↗

Deformations, relaxation, and broken symmetries in liquids, solids, and glasses: A unified topological field theory

Here, we combine hydrodynamic and field theoretic methods to develop a general theory of phonons as Goldstone bosons in crystals, glasses, and liquids based on nonaffine displacements and the consequent Goldstone phase relaxation. We relate the conservation, or lack thereof, of specific higher-form currents with properties of the underlying deformation field—nonaffinity—which dictates how molecules move under an applied stress or deformation. In particular, the single-valuedness of the deformation field is associated with conservation of higher-form charges that count the number of topological defects. Our formalism predicts, from first principles, the presence of propagating shear waves above a critical wave vector in liquids, thus giving a formal derivation of the phenomenon in terms of fundamental symmetries. The same picture provides also a theoretical explanation of the corresponding “positive sound dispersion” phenomenon for longitudinal sound. Importantly, accordingly to our theory, the main collective relaxation timescale of a liquid or a glass (known as the α relaxation for the latter) is given by the phase relaxation time, which is not necessarily related to the Maxwell time. Finally, we build a nonequilibrium effective action using the in-in formalism defined on the Schwinger-Keldysh contour, that further supports the emerging picture. In summary, our work suggests that the fundamental difference between solids, fluids, and glasses has to be identified with the associated generalized higher-form global symmetries and their topological structure, and that the Burgers vector for the displacement fields serves as a suitable topological order parameter distinguishing the solid (ordered) phase and the amorphous ones (fluids, glasses).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells

The intracellular cholesterol transporter NPC1 functions in late endosomes and lysosomes to efflux unesterified cholesterol, and its deficiency causes Niemann–Pick disease Type C, an autosomal recessive lysosomal disorder characterized by progressive neurodegeneration and early death. Here, we use single-nucleus RNA-seq on the forebrain of Npc1 –/– mice at P16 to identify cell types and pathways affected early in pathogenesis. Our analysis uncovers significant transcriptional changes in the oligodendrocyte lineage during developmental myelination, accompanied by diminished maturation of myelinating oligodendrocytes. We identify upregulation of genes associated with neurogenesis and synapse formation in Npc1 –/– oligodendrocyte lineage cells, reflecting diminished gene silencing by H3K27me3. Npc1 –/ – oligodendrocyte progenitor cells reproduce impaired maturation in vitro, and this phenotype is rescued by treatment with GSK-J4, a small molecule inhibitor of H3K27 demethylases. Moreover, mobilizing stored cholesterol in Npc1 –/– mice by a single administration of 2-hydroxypropyl-β-cyclodextrin at P7 rescues myelination, epigenetic marks, and oligodendrocyte gene expression. Our findings highlight an important role for NPC1 in oligodendrocyte lineage maturation and epigenetic regulation, and identify potential targets for therapeutic intervention.

59 BASIC BIOLOGICAL SCIENCES↗

Single vs double atom catalyst for N 2 activation in nitrogen reduction reaction: A DFT perspective

Abstract Ammonia synthesis through electrochemical reduction of nitrogen molecules is a promising strategy to significantly reduce the energy consumption in traditional industrial process. Detailed mechanism study of multistep complex nitrogen reduction reaction is prerequisite for the design of highly efficient catalyst. Stable atomically dispersed catalyst with unique geometric and electronic structure is suitable for the mechanism clarification of such a complex reaction. In this study, d ‐block transition‐metal (TM) anchored C 2 N single layer catalyst is investigated by the density functional theory (DFT) calculation. Both single TM‐anchored single atom catalyst (SAC) and double TM‐anchored double atom catalyst (DAC) exhibit good thermodynamic stability in atomically dispersed catalyst. In the case of SACs, IVB metals (Ti, Zr, Hf) exhibit the highest reactivity and lowest overpotential. While in the case of DACs, Cr─Cr system leads to the NH 3 formation, but V─V system leads to the N 2 H 4 formation. The SACs show much lower overpotential and stronger activation of N 2 molecule than the DACs due to the different activation mechanisms: traditional σ ‐donation/ π ‐backdonation N 2 activation mechanism is found in SACs, while a new π ‐donation/π‐backdonation N 2 activation mechanism is found in the DACs. The present work demonstrates that the different catalytic effect for NRR between SAC and DAC and their corresponding electronic structure origin, which gives more insight into the single atom catalyst. image

Qian, Yumin↗

Strong Rashba-Dresselhaus Effect in Nonchiral 2D Ruddlesden-Popper Perovskites

Chirality transfer from organic chiral molecules to lead halides is theorized as the origin of the strong Rashba-Dresselhaus effect causing large circular dichroism (CD) and circularly polarized luminescence (CPL) in metal halide perovskites (MHPs). In this report a concrete empirical evidence is provided that such strong CD and CPL can occur even in nonchiral 2D Ruddlesden-Popper perovskites (RPPs) (BA) 2 (MA) n-1 Pb n I 3n+1 (where MA = CH 3 NH 3 and BA = CH 3 (CH 2 ) 3 NH 3 ). The CD and CPL responses occurring at the excitonic transition of the MHPs are strongest (≈100 mdeg and 4.8%, respectively) when a single lead halide octahedral [PbI 6 ] 4- layer is repeatedly stacked between two nonchiral molecules BA + (n = 1). However, they are rapidly quenched as n increases. It is hypothesized that strong Rashba-Dresselhaus splitting in the 2D RPPs originates the strong CD and CPL signatures. Density functional theory calculations reveal that the large interlayer distortions in the inorganic layers at the organic/inorganic interface give rise to the strong Rashba-Dresselhaus splitting. A Rashba-Dresselhaus field of ≈600 and ≈50 mT for n = 1 and 2, respectively, is estimated by magnetic circular dichroism spectroscopy. The studies may have significant impact on designing 2D RPPs with large Rashba-Dresselhaus effects at room temperature for spintronic applications.

circular dichroism↗

Pilgrim : A thermal rate constant calculator and a chemical kinetics simulator

Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC). For reaction processes with many elementary steps, the rate constant of each of these steps can be calculated by means of conventional transition state theory (TST) or by using VTST. In the current version, Pilgrim can evaluate thermal rates using the canonical version of reaction-path VTST, which requires the calculation of the minimum energy path (MEP) associated with each elementary step or transition structure. Multi-dimensional quantum effects can be incorporated through the small-curvature tunneling (SCT) approximation. These methodologies are available both for reactions involving a single structure of the reactants and the transition state and also for reactions involving flexible molecules with multiple conformations of the reactant and/or of the transition state. For systems with many conformers, the program can evaluate each of the elementary reaction rate constants by multipath canonical VTST or multi-structural VTST. Moreover, the reactant can be unimolecular or bimolecular. Torsional anharmonicity can be incorporated through either the MSTor or the Q2DTor programs. Dual-level calculations are also available in Pilgrim: automatic high-level single-point energies can be used to correct the energy of reactants, transition states, products, and MEP points using the interpolated single-point energies (ISPE) algorithm. When the rate constants of all the chemical processes of interest are known, by means of their calculation using Pilgrim or alternatively through analytical fits to the rate constants as functions of temperature, it is possible to simulate a multistep mechanism under specified laboratory conditions using KMC. Finally, this algorithm allows performing a kinetic simulation to monitor the evolution of each chemical species with time and obtain the product yields.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Electron emission from fluorene (C 13 H 10 ) upon 3.5 MeV/u Si 8+ ion impact: double differential distributions

In this work, we have studied the electron emission from one of the polycyclic aromatic hydrocarbon (PAH) molecules namely, fluorene (C13H10), upon 3.5 MeV/u Si8+ ion impact. The experimentally measured absolute double differential cross sections (DDCS) are compared with the continuum distorted wave-eikonal initial state (CDW-EIS) model and the first Born approximation including correct boundary conditions (CB1). The measurements are carried out in the ejected e⁻-energy range of 1 eV–400 eV and in the angular range of 20°–160°. We have obtained the single differential and the total cross sections (TCSs) of e⁻-emission as well. The CB1 calculation largely underestimates the data. The CDW-EIS model, which is applied for the PAH molecule for the first time, provides an overall better agreement with the double differential, single differential and TCS data. The DDCS data for fluorene has also been compared with that for CH4 molecule, at a few angles. The forward–backward angular asymmetry shows a relatively flatter distribution compared to the theoretical predictions. The contribution due to the giant plasmon resonance could not be clearly observed except a mild indication in the asymmetry parameter. The angular distribution of the carbon KLL Auger electron cross section shows certain variations. The study of the KLL hyper-satellite component indicates the double K-ionization cross section is about 8.6% of the single K-ionization one.

74 ATOMIC AND MOLECULAR PHYSICS↗

Single- and multi-photon-induced ultraviolet excitation and photodissociation of CH 3 I probed by coincident ion momentum imaging

The UV-induced photodissociation dynamics of iodomethane (CH 3 I) in its A-band are investigated by time-resolved coincident ion momentum imaging using strong-field ionization as a probe. The delay-dependent kinetic energy distribution of the photofragments resulting from double ionization of the molecule maps the cleavage of the carbon–iodine bond and shows how the existence of a potential well in the di-cationic potential energy surfaces shapes the observed distribution at small pump–probe delays. Furthermore, the competition between single- and multi-photon excitation and ionization of the molecule is studied as a function of the intensity of the UV-pump laser pulse. Two-photon excitation to Rydberg states is identified by tracking the transformation of the delay-dependent singly-charged iodomethane yield from a pure Gaussian distribution at low intensity to a Gaussian with an exponentially decaying tail at higher intensities. In conclusion, dissociative ionization induced by absorption of three UV photons is resolved as an additional delay-dependent feature in the kinetic energy of the fragment ions detected in coincidence.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dispersion-Engineered Deep Sub-Wavelength Plasmonic Metasurfaces for Broadband Seira Applications

Surface enhanced infrared absorption (SEIRA) spectroscopy is a powerful tool in which plasmonically enhanced electromagnetic fields provide high-sensitivity molecular detection. Most SEIRA platforms operate at a single resonant frequency, which must be tuned to match that of the target molecule, and commonly rely on time-consuming lithographic techniques. This study presents a high-throughput and cost-effective plasmonic metasurface for broadband, tunable, and strong infrared signal enhancement. The platform is built upon the principle of dispersion-engineered plasmonic Fabry–Pérot (FP) nanocavity arrays. It offers 1) tight squeezing of infrared (IR) photons into deep sub-wavelength nano-volumes and 2) spectrally tunable near-field enhancements of up to ≈10 6 , two to three orders of magnitude higher than most optical metasurface systems. By coupling multilayer nano-thin film deposition and nanoskiving fabrication techniques, the dispersive FP metasurfaces can be rapidly and reproducibly constructed in a scalable and lithography-free manner. Using IR spectroscopy, the selective and sensitive label-free detection of a molecular monolayer is achieved at a range of frequencies. An enhancement factor of nearly 10 5 is measured at the carbonyl (C = O) vibrational marker band of the molecule. The confluence of high field enhancement, broadband plasmonic response, and facile fabrication makes this metasurface a promising platform for SEIRA spectroscopy.

36 MATERIALS SCIENCE↗