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At least 73 records · Page 4

X‑ray Coherent Diffractive Imaging of Large Helium Nanodroplets Doped with Small Molecules

We report the first X-ray coherent diffractive imaging experiment on molecule-doped helium nanodroplets. It complements previous work, where we reported single-shot X-ray coherent diffractive imaging studies of Xe dopant clusters formed in 4He and 3He droplets. These noble gas clusters were used to visualize the impact of rotational excitation of the droplets on the spatial distribution of atomic dopants within the droplets, and to study the differences and connections between quantum and classical droplet rotational motion. Here, we expand our studies to the molecular dopants CF4, CHF3, CH3CN, and SF6, imaged with 1.5 keV photons. We find multiple Bragg spots in the diffraction patterns of molecule-doped droplets with radii of approximately 600 nm, which provide evidence that molecules form elongated clusters with preferential alignment along the angular momentum axis of the 4He droplets, in agreement with our previous results on the aggregation of Xe clusters on quantum vortices. Real-space reconstructions of molecular dopant cluster density profiles are obtained for droplets with smaller radii of approximately 300 nm. The diffuse images suggest the formation of low-density, potentially porous, molecular clusters upon aggregation at T = 0.4 K in 4He droplets. In the normal fluid 3He droplets, molecules aggregate into loose clusters on the droplets' equator, similar to previous observations for Xe atoms. Time-of-flight mass spectra reveal that the doped helium nanodroplet moieties fragment extensively into constituent atomic ions, producing only a small fraction of molecular fragment ions. The findings are discussed in the context of previously proposed schemes to use He droplets as potential tamper materials for ultrafast X-ray imaging experiments.

Feinberg, AlexandraJ↗

Observation of a single protein by ultrafast X-ray diffraction

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Imaging beyond the surface region: Probing hidden materials via atomic force microscopy

Probing material properties at surfaces down to the single-particle scale of atoms and molecules has been achieved, but high-resolution subsurface imaging remains a nanometrology challenge due to electromagnetic and acoustic dispersion and diffraction. The atomically sharp probe used in scanning probe microscopy (SPM) has broken these limits at surfaces. Subsurface imaging is possible under certain physical, chemical, electrical, and thermal gradients present in the material. Of all the SPM techniques, atomic force microscopy has entertained unique opportunities for nondestructive and label-free measurements. Here, we explore the physics of the subsurface imaging problem and the emerging solutions that offer exceptional potential for visualization. We discuss materials science, electronics, biology, polymer and composite sciences, and emerging quantum sensing and quantum bio-imaging applications. The perspectives and prospects of subsurface techniques are presented to stimulate further work toward enabling noninvasive high spatial and spectral resolution investigation of materials including meta- and quantum materials.

74 ATOMIC AND MOLECULAR PHYSICS↗

Emerging Electrochemical Techniques for Probing Site Behavior in Single-Atom Electrocatalysts

Single-atom catalysts (SACs) have aroused tremendous interest over the past decade, particularly in the community of energy and environment-related electrocatalysis. A rapidly growing number of recent publications have recognized it as a promising candidate with maximum atomic utilization, distinct activity, and selectivity in comparison to bulk catalysts and nanocatalysts. However, the complexity of localized coordination environments and the dispersion of isolated sites lead to significant difficulties when it comes to gaining insight into the intrinsic behavior of electrocatalytic reactions. Furthermore, the low metal loadings of most SACs make conventional ensemble measurements less likely to be accurate on the subnanoscale. Thus, it remains challenging to probe the activity and properties of individual atomic sites by available commercial instruments and analytical methods. In spite of this, continuing efforts have lately focused on the development of advanced measurement methodologies, which are very useful to the fundamental understanding of SACs. There have recently been a number of in situ/operando techniques applied to SACs, such as electron microscopy, spectroscopy, and other analysis methods, which support relevant functions to identify the active sites and reaction intermediates and to investigate the dynamic behavior of localized structures of the catalytic sites. This Account aims to present recent electrochemical probing techniques which can be used to identify single-atomic catalytic sites within solid supports. First, we describe the basic principles of molecular probe methods for the study and analysis of electrocatalytic site behavior. In particular, the in situ probing technique enabled by surface interrogation scanning electrochemical microscopy (SISECM) can measure the active site density and kinetic rate with high resolution. An alternative electrochemical probing technique is further demonstrated on the basis of single-entity electrochemistry, which allows the unique electrochemical imaging of the size and catalytic rate of single atoms, molecules, and clusters. Next, the merits and limitations of different electrochemical techniques are then discussed, along with perspectives for future prospects. Apart from this, we further showcase the powerful capability of emerging electrochemical probing techniques for determining significant effects and properties of SACs for various electrocatalytic reactions, including oxygen reduction and evolution, hydrogen evolution, and nitrate reduction. Overall, electrochemical techniques with atomic resolution have greatly increased opportunities for observing, measuring, and understanding the surface and interface chemistry during energy conversion. In the future, it is anticipated that the development of electrochemical probing techniques will be advanced with innovative perspectives on the behavior and features of SACs. We hope that this Account can contribute in several ways to promoting the fundamental knowledge and technical progress of emerging electrochemical measurements for studying SACs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A gain series method for accurate EMCCD calibration

Abstract Calibration of the gain and digital conversion factor of an EMCCD is necessary for accurate photon counting. We present a new method to quickly calibrate multiple gain settings of an EMCCD camera. Acquiring gain-series calibration data and analyzing the resulting images with the EMCCD noise model more accurately estimates the gain response of the camera. Furthermore, we develop a method to compare the results from different calibration approaches. Gain-series calibration outperforms all other methods in this self-consistency test.

36 MATERIALS SCIENCE↗

Counting mRNA copies in intact bacterial cells by fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH)

A method for measuring mRNA copies in intact bacterial cells by fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) is presented. Unlike conventional single molecule FISH, where the presence of a transcript is determined by fluorescence intensity, fliFISH relies on On-Off duty cycles of photo-switching dyes to set a predetermined threshold for distinguishing true signals from background noise. The method provides a quantitative approach for detecting and counting true mRNA copies and rejecting false signals with high accuracy.

Hu, Dehong↗

Autonomous Molecular Structure Imaging with High-Resolution Atomic Force Microscopy for Molecular Mixture Discovery

Due to its single-molecule sensitivity, high-resolution atomic force microscopy (HR-AFM) has proved to be a valuable and uniquely advantageous tool to study complex molecular mixtures, which hold promise for developing clean energy and achieving environmental sustainability. However, significant challenges remain to achieve the full potential of the sophisticated and time-consuming experiments. Automation combined with machine learning (ML) and artificial intelligence (AI) is key to overcoming these challenges. Here we present Auto-HR-AFM, an AI tool to automatically collect HR-AFM images of petroleum-based mixtures. In this study, we trained an instance segmentation model to teach Auto-HR-AFM how to recognize features in HR-AFM images. Auto-HR-AFM then uses that information to optimize the imaging by adjusting the probe-molecule distance for each molecule in the run. Auto-HR-AFM is the initial tool that will lead to fully automated scanning probe microscopy (SPM) experiments, from start to finish. This automation will allow SPM to become a mainstream characterization technique for complex mixtures, an otherwise unattainable target.

36 MATERIALS SCIENCE↗

Nanophotonics for Chemical Imaging and Spectroscopy

The manipulation of light and light-matter interactions on the nanoscale is enabled by the unique optical properties of plasmonic metal nanostructures and nanoparticles. Indeed, engineered hybrid molecular-plasmonic nanostructures have enabled single molecule detection and identification via surface-enhanced Raman scattering (SERS). Further, the same effect is at the core of visualizing single molecules with sub-nanometer spatial resolution via tip-enhanced Raman scattering (TERS). More generally, modern applications of plasmon-enhanced spectroscopy and microscopy fueled advances in fields as diverse as quantum and semiconductor materials, heterogeneous catalysis, and the health sciences, to name a few. All these exciting developments and many more are touched in this virtual special issue (VSI) on nanophotonics. From ultra-precise chemical imaging measurements performed in a scanning tunneling microscope chamber to single molecule spectroscopic measurements performed at solid-air and solid-liquid interfaces, this VSI includes contributions from active practitioners that are all striving to better-understand increasingly complex interfaces encountered in the biological, materials, and chemical sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single Molecule Spectroscopy Studies of Acid–Base Chemical Gradients Using Nile Red as a Probe of Local Surface Acidity

Single molecule spectroscopy studies of local acidity along bifunctional acid-base gradients are reported. Gradients are prepared by directional vapor phase diffusion and subsequent reaction of 3-aminopropyl-trimethoxysilane with a uniform silica film. Gradient formation is confirmed by spectroscopic ellipsometry and by static water contact angle measurements. X-ray photoelectron spectroscopy is used to characterize the nitrogen content and degree of nitrogen protonation along the gradient. Nile Red is employed as the probe dye in single molecule spectroscopy studies of these gradients. While Nile Red is well-known for its solvent sensitivity, it is used here, for the first time, to sense the acid/base properties of the film in two-color wide-field fluorescence imaging experiments. The data reveal broad bimodal distributions of Nile Red emission spectra that vary along the gradient direction. The single-molecule results are consistent with solution-phase ensemble acid/base studies of the dye. The former reveal a gradual transition from a surface dominated by basic aminosilane sites at the high-amine end of the gradient to one dominated by acidic silanol sites at the low-amine end. The sub-diffraction-limited spatial resolution afforded by superlocalization of the single molecules reveals spatial correlations in the acid/base properties of the gradient over ~ 200 nm distances. Furthermore, these studies provide data relevant to the use of aminosilane-modified silica in bifunctional, cooperative chemical catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hyperdimensional Imaging Contrast Using an Optical Fiber

Fluorescence properties of a molecule can be used to study the structural and functional nature of biological processes. Physical properties, including fluorescence lifetime, emission spectrum, emission polarization, and others, help researchers probe a molecule, produce desired effects, and infer causes and consequences. Correlative imaging techniques such as hyperdimensional imaging microscopy (HDIM) combine the physical properties and biochemical states of a fluorophore. Here we present a fiber-based imaging system that can generate hyper-dimensional contrast by combining multiple fluorescence properties into a single fluorescence lifetime decay curve. Fluorescence lifetime imaging microscopy (FLIM) with controlled excitation polarization and temporally dispersed emission can generate a spectrally coded, polarization-filtered lifetime distribution for a pixel. This HDIM scheme generates a better contrast between different molecules than that from individual techniques. This setup uses only a single detector and is simpler to implement, modular, cost-efficient, and adaptable to any existing FLIM microscope. We present higher contrast data from Arabidopsis thaliana epidermal cells based on intrinsic anthocyanin emission properties under multiphoton excitation. This work lays the foundation for an alternative hyperdimensional imaging system and demonstrates that contrast-based imaging is useful to study cellular heterogeneity in biological samples.

47 OTHER INSTRUMENTATION↗

Facile hermetic TEM grid preparation for molecular imaging of hydrated biological samples at room temperature

Abstract Although structures of vitrified supramolecular complexes have been determined at near-atomic resolution, elucidating in situ molecular structure in living cells remains a challenge. Here, we report a straightforward liquid cell technique, originally developed for real-time visualization of dynamics at a liquid-gas interface using transmission electron microscopy, to image wet biological samples. Due to the scattering effects from the liquid phase, the micrographs display an amplitude contrast comparable to that observed in negatively stained samples. We succeed in resolving subunits within the protein complex GroEL imaged in a buffer solution at room temperature. Additionally, we capture various stages of virus cell entry, a process for which only sparse structural data exists due to their transient nature. To scrutinize the morphological details further, we used individual particle electron tomography for 3D reconstruction of each virus. These findings showcase this approach potential as an efficient, cost-effective complement to other microscopy technique in addressing biological questions at the molecular level.

59 BASIC BIOLOGICAL SCIENCES↗

Space-Time Quantum Information from the Entangled States of Magnetic Molecule (STI Product)

This collaborative project combines synthesis, measurement, and theory by three faculty members at the Eddleman Quantum Institute of UC Irvine to effectively investigate the quantum properties of molecules in the space, time, and frequency domains. Through synthetic chemistry, molecules are tailored for their magnetic and coherent properties. By combining femtosecond (fs) terahertz (THz) light and a continuous wave (cw) THz laser with a low temperature scanning tunneling microscope (STM), quantum phenomena are probed with simultaneous femtosecond temporal and atomic-scale spatial resolution. In particular, the invention of the quantum superposition microscope (QSM) advances quantum sensing for enhanced spectroscopy and imaging capabilities. Coupling theory to the experimental efforts offers a deeper understanding and predictive power for the molecular systems. The phenomena of superposition, entanglement, and coherence is central to quantum information science and can be realized in qubit states. Many systems can be modeled by a double-well potential in which two levels are formed in the two lowest energy states interacting with the environment and external radiation. In focusing on molecules as two-level systems, the underlying expectation is that their tunable composition and structure allows an effective parameter space to optimize their use as qubits for quantum sensing and computing. The THz radiation induces the superposition between the two states, appearing as temporal oscillations that damp in amplitude. Enhanced spectroscopy and imaging in the time and frequency domains is achieved through the extreme sensitivity of the frequency and damping of coherence of two-level systems to its environment. A single hydrogen molecule trapped in the STM tunneling gap experiences a double-well potential and absorption of THz femtosecond pulses of light creates the superposition of its two levels, appearing as damped oscillations in the light induced direct current (DC). The oscillation frequency depends sensitively on the electric field distribution of the copper nitride (Cu 2 N) surface, through the Stark effect, and associated with the different charge distributions at the copper and nitrogen sites and in between. This QSM can resolve variation in the surface electric field with 0.02 nanometer resolution. In addition, the single hydrogen molecule entaes with nearby hydrogen molecules as seen in the avoided level crossings of energy (oscillation frequency) versus the voltage across the tunneling gap. Thus, the first application of the QSM senses and images the surface electric field at the atomic scale. Results from this project advance fundamental understanding of quantum phenomena, develop novel synthesis, measurement, and theory, provide the knowledge foundation for molecule-based qubits and sensing that enable the development of the QSM and emergent technologies. This project trained researchers in quantum information science, extended knowledge in classrooms, and outreached to the community.

47 OTHER INSTRUMENTATION↗

Beyond single crystals: Imaging rubrene polymorphism across crystalline batches through lattice phonon Raman microscopy

Polymorphism is an issue troubling numerous scientific fields. A phenomenon where molecules can arrange in different orientations in a crystal lattice, polymorphism in the field of organic photovoltaic materials can dramatically change electronic properties of these materials. Rubrene is a benchmark photovoltaic material showing high carrier mobility in only one of its three polymorphs. To use rubrene in devices, it is important to quantify the polymorph distribution arising from a particular crystal growth method. However, current methods for characterizing polymorphism are either destructive or inefficient for batch scale characterization. Lattice phonon Raman spectroscopy has the ability to distinguish between polymorphs based on low frequency intermolecular vibrations. Here, we present here the addition of microscopy to lattice phonon Raman spectroscopy, which allows us to not only characterize polymorphs efficiently and nondestructively through Raman spectroscopy but also concurrently gain information on the size and morphology of the polymorphs. We provide examples for how this technique can be used to perform large, batch scale polymorph characterization for crystals grown from solution and physical vapor transport.We end with a case study showing how Raman microscopy can be used to efficiently optimize a green crystal growth method, selecting for large orthorhombic crystals desired for rubrene electronic device applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aerosol and Surface Parameter Retrievals for a Multi-Angle, Multiband Spectrometer

This software retrieves the surface and atmosphere parameters of multi-angle, multiband spectra. The synthetic spectra are generated by applying the modified Rahman-Pinty-Verstraete Bidirectional Reflectance Distribution Function (BRDF) model, and a single-scattering dominated atmosphere model to surface reflectance data from Multiangle Imaging SpectroRadiometer (MISR). The aerosol physical model uses a single scattering approximation using Rayleigh scattering molecules, and Henyey-Greenstein aerosols. The surface and atmosphere parameters of the models are retrieved using the Lavenberg-Marquardt algorithm. The software can retrieve the surface and atmosphere parameters with two different scales. The surface parameters are retrieved pixel-by-pixel while the atmosphere parameters are retrieved for a group of pixels where the same atmosphere model parameters are applied. This two-scale approach allows one to select the natural scale of the atmosphere properties relative to surface properties. The software also takes advantage of an intelligent initial condition given by the solution of the neighbor pixels.

Broderick, Daniel↗

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (Φ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5's orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, Φ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Simultaneous measurements of velocity, temperature, and pressure using rapid CW wavelength-modulation laser-induced fluorescence of OH

In high speed flows, laser induced fluorescence (LIF) on Doppler shifted transitions is an attractive technique for velocity measurement. LIF velocimetry was applied to combined single-point measurements of velocity, temperature, and pressure and 2-D imaging of velocity and pressure. Prior to recent research using NO, LIF velocimetry in combustion related flows relied largely on the use of seed molecules. Simultaneous, single-point LIF measurements is reported of velocity, temperature, and pressure using the naturally occurring combustion species OH. This experiment is an extension of earlier research in which a modified ring dye laser was used to make time resolved temperature measurements behind reflected shock waves by using OH absorption an in postflame gases by using OH LIF. A pair of fused-silica rhombs mounted on a single galvanonmeter in an intracavity-doubled Spectra-Physics 380 ring laser permit the UV output to be swept continuously over a few wave numbers at an effective frequency of 3kHz.

Chang, A. Y.↗

Comprehensive single-shot biophysical cytometry using simultaneous quantitative phase imaging and Brillouin spectroscopy

Abstract Single-cell analysis, or cytometry, is a ubiquitous tool in the biomedical sciences. Whereas most cytometers use fluorescent probes to ascertain the presence or absence of targeted molecules, biophysical parameters such as the cell density, refractive index, and viscosity are difficult to obtain. In this work, we combine two complementary techniques—quantitative phase imaging and Brillouin spectroscopy—into a label-free image cytometry platform capable of measuring more than a dozen biophysical properties of individual cells simultaneously. Using a geometric simplification linked to freshly plated cells, we can acquire the cellular diameter, volume, refractive index, mass density, non-aqueous mass, fluid volume, dry volume, the fractional water content of cells, both by mass and by volume, the Brillouin shift, Brillouin linewidth, longitudinal modulus, longitudinal viscosity, the loss modulus, and the loss tangent, all from a single acquisition, and with no assumptions of underlying parameters. Our methods are validated across three cell populations, including a control population of CHO-K1 cells, cells exposed to tubulin-disrupting nocodazole, and cells under hypoosmotic shock. Our system will unlock new avenues of research in biophysics, cell biology, and medicine.

Steelman, Zachary A.↗

Imaging Valence Electron Rearrangement in a Chemical Reaction Using Hard X-Ray Scattering

We have observed the signatures of valence electron rearrangement in photoexcited ammonia using ultrafast hard x-ray scattering. Time-resolved x-ray scattering is a powerful tool for imaging structural dynamics in molecules because of the strong scattering from the core electrons localized near each nucleus. Such core-electron contributions generally dominate the differential scattering signal, masking any signatures of rearrangement in the chemically important valence electrons. Ammonia represents an exception to the typically high core-to-valence electron ratio. Here, we measured 9.8 keV x-ray scattering from gas-phase deuterated ammonia following photoexcitation via a 200 nm pump pulse to the 3s Rydberg state. We observed changes in the recorded scattering patterns due to the initial photoexcitation and subsequent deuterium dissociation. Ab initio calculations confirm that the observed signal is sensitive to the rearrangement of the single photoexcited valence electron as well as the interplay between adiabatic and nonadiabatic dissociation channels. The use of ultrafast hard x-ray scattering to image the structural rearrangement of single valence electrons constitutes an important advance in tracking valence electronic structure in photoexcited atoms and molecules.

Gabalski, Ian [SLAC National Accelerator Laborator↗