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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Synthesis and characterization of 5,15-bis(hydroxymethyl)porphyrins – simple compounds distantly inspired by the chlorosomal bacteriochlorophylls

A self-assembly paradigm is provided in green photosynthetic bacteria by the chlorin macrocycle bacteriochlorophyll (BChl) c, which contains a 3-(1-hydroxyethyl) substituent, central magnesium ion, and 13-keto group. The assembled BChl c structure is a powerful light-harvesting apparatus that can support life even under extreme low-light conditions. Here, inspired by the work of Balaban, two far simpler porphyrins have been synthesized, 5,15-bis(hydroxymethyl)-10,20-diphenylporphinatozinc(II) (Ph/CH 2 OH) and 5,15-bis(hydroxymethyl)porphinatozinc(II) (H/CH 2 OH), and analogues wherein ethyl replaces hydroxymethyl (Ph/Et and H/Et). Examination of Ph/CH 2 OH and H/CH 2 OH by time-resolved spectroscopy showed an ∼2-fold enhancement in the singlet excited-state lifetime compared to meso-tetraphenylporphinatozinc(II) (ZnTPP). The single-crystal X-ray diffraction revealed distinct packing patterns. Porphyrin Ph/CH 2 OH exhibited double staircases wherein (1) each zinc is pentacoordinate (by apical coordination of one hydroxymethyl group of a porphyrin in the same staircase), (2) the second hydroxymethyl group is hydrogen-bonded to an apically coordinated hydroxymethyl oxygen atom in the adjacent staircase, (3) the porphyrins in a given staircase are coplanar but cofacially offset with each other, and (4) the adjacent staircases are oriented approximately 72° relative to each other. Porphyrin H/CH 2 OH assembled wherein (1) each zinc is hexacoordinate by ligation of hydroxymethyl moieties, (2) each hydroxymethyl –OH is hydrogen-bonded with an acetonitrile solvent molecule in the lattice, and (3) the planes of the four nearest neighbor porphyrins are essentially perpendicular to a given porphyrin. Study of the solid-state packing patterns of sparsely substituted porphyrins enables insights into how the structural design of tetrapyrroles can guide their aggregate self-assembly.

Tran, Vy-Phuong [North Carolina State University, ↗
DOE OSTI2015

The electron–phonon coupling of fundamental, overtone, and combination modes and its effects on the resonance Raman spectra

Highlights: • The Huang–Rhys factors and electron–phonon coupling constants are calculated. • The changes of overtone mode are larger than those of fundamental mode. • The variation pattern of electron–phonon coupling well interprets the changes of spectra. - Abstract: External field plays a very important role in the interaction between the π-electron transition and atomic vibration of polyenes. It has significant effects on both the Huang–Rhys factor and the electron–phonon coupling. In this paper, the visible absorption and resonance Raman spectra of all-trans-β-carotene are measured in the 345–295 K temperature range and it is found that the changes of the 0–1 and 0–2 vibration bands of the absorption spectra with the temperature lead to the different electron–phonon coupling of fundamental, overtone, and combination modes. The electron-phonon coupling constants of all the modes are calculated and analyzed under different temperatures. The variation law of the electron–phonon coupling with the temperature well interprets the changes of the resonance Raman spectra, such as the shift, intensity and line width of the overtone and combination modes, which are all greater than those of the fundamental modes.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Electron-Beam Induced Emergence of Mesoscopic Ordering in Layered MnPS 3

Ordered mesoscale structures in 2D materials induced by small misorientations have allowed for a wide variety of electronic, ferroelectric, and quantum phenomena to be explored. Until now, the only mechanism to induce this periodic ordering was via mechanical rotations between the layers, with the periodicity of the resulting moiré pattern being directly related to twist angle. Here we report a fundamentally distinct mechanism for emergence of mesoscopic periodic patterns in multilayer sulfur-containing metal phosphorus trichalcogenide, MnPS3, induced by the electron beam. The formation under the beam of periodic hexagonal patterns with several characteristic length scales, nucleation and transitions between the phases, and local dynamics are demonstrated. The associated mechanisms are attributed to the relative contraction of the layers caused by beam-induced sulfur vacancy formation with subsequent ordering and lattice parameter change. As a result, the plasmonic response of the system is locally altered, suggesting an element of control over plasmon resonances by electron beam patterning. To conclude, we pose that harnessing this phenomenon provides both insight into fundamental physics of quantum materials and enables device applications by enabling controlled periodic potentials on the atomic scale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Real-time tracking of protein unfolding with time-resolved x-ray solution scattering

The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Probing Light Atoms at Subnanometer Resolution: Realization of Scanning Transmission Electron Microscope Holography

Atomic resolution imaging of light elements in electron-transparent materials has long been a challenge. Biomolecular materials, for example, are rapidly altered by incident electrons. We demonstrate a scanning transmission electron microscopy (STEM) technique, called STEM holography, capable of efficient structural analysis of beam-sensitive nanomaterials. STEM holography measures the absolute phase and amplitude of electrons passed through a specimen via interference with a vacuum reference wave. We use an amplitude-dividing nanofabricated grating to prepare multiple beams focused at the sample. We configure the postspecimen microscope imaging system to overlap the beams, forming an interference pattern. We record and analyze the pattern at each 2D-raster-scan-position, reconstructing the complex object wave. As a demonstration, we image gold nanoparticles on an amorphous carbon substrate at 2.4 Å resolution. In conclusion STEM holography offers higher contrast of the carbon while maintaining gold atomic lattice resolution compared to high angle annular dark field STEM.

4D-STEM↗
DOE OSTI2017

Thermodynamic Stability of Molybdenum Oxycarbides Formed from Orthorhombic Mo 2 C in Oxygen-Rich Environments

Molybdenum carbide (Mo 2 C) nanoparticles and thin films are particularly suitable catalysts for catalytic fast pyrolysis (CFP) as they are effective for deoxygenation and can catalyze certain reactions that typically occur on noble metals. Oxygen deposited during deoxygenation reactions may alter the carbide structure, leading to the formation of oxycarbides, which can determine changes in catalytic activity or selectivity. Despite emerging spectroscopic evidence of bulk oxycarbides, so far there have been no reports of their precise atomic structure or their relative stability with respect to orthorhombic Mo 2 C. This knowledge is essential for assessing the catalytic properties of molybdenum (oxy)carbides for CFP. In this article, we use density functional theory (DFT) calculations to (a) describe the thermodynamic stability of surface and subsurface configurations of oxygen and carbon atoms for a commonly studied Mo-terminated surface of orthorhombic Mo 2 C and (b) determine atomic structures for oxycarbides with a Mo:C ratio of 2:1. The surface calculations suggest that oxygen atoms are not stable under the top Mo layer of the Mo 2 C(100) surface. Coupling DFT calculations with a polymorph sampling method, we determine (Mo 2 C) x O y oxycarbide structures for a wide range of oxygen compositions. Oxycarbides with lower oxygen content (y/x = 2) adopt layered structures reminiscent of the parent carbide phase, with flat Mo layers separated by layers of oxygen and carbon; for higher oxygen content, our results suggest the formation of amorphous phases, as the atomic layers lose their planarity with increasing oxygen content. We characterize the oxidation states of Mo in the oxycarbide structures determined computationally, and simulate their X-ray diffraction (XRD) patterns in order to facilitate comparisons with experiments. Our study may provide a platform for large-scale investigations of the catalytic properties of oxycarbides and their surfaces and for tailoring the catalytic properties for different desired reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid

The variety and complexity of DNA-based structures make them attractive candidates for nanotechnology, yet insufficient stability and mechanical rigidity, compared to polyamide-based molecules, limit their application. Here, we combine the advantages of polyamide materials and the structural patterns inspired by nucleic-acids to generate a mechanically rigid fluorenylmethyloxycarbonyl (Fmoc)-guanine peptide nucleic acid (PNA) conjugate with diverse morphology and photoluminescent properties. The assembly possesses a unique atomic structure, with each guanine head of one molecule hydrogen bonded to the Fmoc carbonyl tail of another molecule, generating a non-planar cyclic quartet arrangement. This structure exhibits an average stiffness of 69.6 ± 6.8 N m –1 and Young’s modulus of 17.8 ± 2.5 GPa, higher than any previously reported nucleic acid derived structure. This data suggests that the unique cation-free “basket” formed by the Fmoc-G-PNA conjugate can serve as an attractive component for the design of new materials based on PNA self-assembly for nanotechnology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Continuous wave room temperature operation of the 2 $μ$m GaSb-based photonic crystal surface emitting diode lasers

Continuous wave room temperature operation of 2 μm GaSb-based photonic-crystal surface-emitting diode lasers has been realized. The deep etched square mesa devices showed threshold current densities of 500 A/cm 2 at 20 °C. The epi-side down mounted lasers generated above 10 mW of output power in the continuous wave regime and tens of milliwatts in pulses from the 200 × 200 μm 2 aperture. Here, the breakthrough in the device performance parameters was achieved thanks to a highly homogeneous air-pocket retaining epitaxial regrowth process optimized for a specifically designed antimonide diode laser heterostructure. The nanofabrication method utilizing low temperature atomic hydrogen surface cleaning yielded low disorder square lattice of droplet-shaped voids covered by uniform p-cladding layer. The laser emission spectrum as well as near/far field patterns demonstrated peculiar features presumably linked to deformation of the void shape during regrowth and formation of the array of filaments.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Coexistence of vitreous and crystalline phases of H 2 O at ambient temperature

Formation of vitreous ice during rapid compression of water at room temperature is important for biology and the study of biological systems. Here, we show that Raman spectra of rapidly compressed water at greater than 1 GPa at room temperature exhibits the signature of high-density amorphous ice, whereas the X-ray diffraction (XRD) pattern is dominated by crystalline ice VI. To resolve this apparent contradiction, we used molecular dynamics simulations to calculate full vibrational spectra and diffraction patterns of mixtures of vitreous ice and ice VI, including embedded interfaces between the two phases. We show quantitatively that Raman spectra, which probe the local polarizability with respect to atomic displacements, are dominated by the vitreous phase, whereas a small amount of the crystalline component is readily apparent by XRD. The results of our combined experimental and theoretical studies have implications for detecting vitreous phases of water, survival of biological systems under extreme conditions, and biological imaging. The results provide additional insight into the stable and metastable phases of H 2 O as a function of pressure and temperature, as well as of other materials undergoing pressure-induced amorphization and other metastable transitions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Approaching Angstrom-Scale Resolution in Lithography Using Low-Molecular-Mass Resists (<500 Da)

Resists that enable high-throughput and high-resolution patterning are essential in driving the semiconductor technology forward. The ultimate patterning performance of a resist in lithography is limited because of the trade-off between resolution, line-width roughness, and sensitivity; improving one or two of these parameters typically leads to a loss in the third. As the patterned feature sizes approach angstrom scale, the trade-off between these three metrics becomes increasingly hard to resolve and calls for a fundamental rethinking of the resist chemistry. Low-molecular-mass monodispersed metal-containing resists of high atom economy can provide not only very high resolution but also very low line-width roughness without sacrificing sensitivity. Here we describe a modular metal-containing resist platform (molecular mass <500 Da) where a molecular resist consists of just two components: a metal and a radical initiator bonded to it. This simple system not only is amenable to high-resolution electron beam lithography (EBL) and extreme ultraviolet lithography (EUVL) but also unites them mechanistically, giving a consolidated perspective of molecular and chemical processes happening during exposure. Irradiation of the resist leads to the production of secondary electrons that generate radicals in the initiator bonded to metal. This brings about an intramolecular rearrangement and causes solubility switch in the exposed resist. We demonstrate record 1.9–2.0 nm isolated patterns and 7 nm half-pitch dense line-space features over a large area using EBL. With EUVL, 12 nm half-pitch line-space features are shown at a dose of 68 mJ/cm 2 . In both of these patterning techniques, the line-width roughness was found to be ≤2 nm, a record low value for any resist platform, also leading to a low-performance trade-off metric, Z factor, of 0.6 × 10 –8 mJ·nm 3 . With the ultimate resolution limited by instrumental factors, potential patterning at the level of a unit cell can be envisaged, making low-molecular-mass resists best poised for angstrom-scale lithography.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Effects of warming on bacterial growth rates in a peat soil under ambient and elevated CO 2

Boreal peatlands are important global carbon reservoirs that are particularly vulnerable to predicted climate changes such as increasing CO 2 and temperature. Since microbial activities regulate the balance of carbon sequestered into soil organic matter or remineralized to CO 2 , characterizing their response to these environmental factors is critical to predicting how peatland ecosystems will affect climate-carbon cycle feedbacks. Here we examined in-situ taxon-specific variation in microbial growth under long-term elevated CO 2 and across a gradient of warming treatments in a northern Minnesota peat bog using quantitative stable isotope probing with 18 O-water. Across temperatures, bacterial taxa were grouped according to the excess atom fraction 18 O (EAF) of their genomes, a proxy for DNA replication and hence, growth. Taxon-specific growth across CO 2 and temperature treatments clustered into relatively few response patterns. While a large portion of taxa showed little to no growth under ambient CO 2 , many of the same taxa grew rapidly under elevated CO 2 . We found support for phylogenetic conservation of response patterns among Acidobacteria and Proteobacteria, the two most abundant phyla in our data. Our results suggest certain taxa may be primed for new climate conditions and have a greater influence on carbon cycling with implications for future climate mitigation strategies.

16S amplicon sequencing, Carbon Dioxide (CO2), pea↗
DOE OSTI2025

Characterization of Two Positional Isomers of the Cs + Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions

Metal ion binding to amino acid residues is an important interaction motif that controls the tertiary structures of oligopeptides. Analyses of the vibrational band patterns displayed by the amino acid scaffolds are commonly used to characterize the local docking motifs. Here we carry out two-color, IR-IR photobleaching measurements to obtain isomer-selective vibrational spectra of the Cs + Gly ion-molecule complex isolated in a cryogenically cooled, radiofrequency ion trap. The distinct band patterns of two non-interconverting isomers are observed and traced to different bidentate binding motifs between Cs + and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid head group yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. Furthermore, the band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.

Infrared spectroscopy↗
DOE OSTI2024

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↗
DOE OSTI2022

Meso bromination and derivatization of synthetic bacteriochlorins

Here, the ability to prepare and tailor synthetic analogues of native bacteriochlorophylls enables diverse applications. A de novo route entails dimerization of a dihydrodipyrrin-acetal to afford the corresponding 5-methoxy and/or 5-unsubstituted bacteriochlorin, wherein each pyrroline ring contains a gem-dimethyl group to ensure stability toward adventitious dehydrogenation. The presence of a 5-methoxy group facilitates bromination at the distal meso-(15-)position. While bromination of 5-unsubstituted bacteriochlorins typically affords a mixture of brominated products, here the presence of two substitution patterns (2,12-dicarboethoxy, 2,12-diacetyl) has been found to facilitate selective meso-bromination in the absence of the methoxy substituent. The introduction of a single meso-bromine atom in a bacteriochlorin opens opportunities for Pd-mediated derivatization, which include (1) preparation of four ethynylphenyl building blocks (and two benchmark bacteriochlorins) with long-wavelength absorption bands tuned across 725–757 nm, for use in preparation of multichromophore arrays; (2) installation of a bioconjugatable group to free base bacteriochlorins or a copper bacteriochlorin, the latter for possible use in photoacoustic imaging; and (3) installation of an S-acetylthio group for surface attachment. Altogether, 25 new bacteriochlorins are described including 5 meso-bromobacteriochlorin intermediates and 12 target bacteriochlorins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Consequences of Lattice Mismatch for Phase Equilibrium in Heterostructured Solids

Lattice mismatch - the difference in natural bond length between two species comprising a solid is a common occurrence in modern materials. Spatial patterns in certain nanocrystal heterostructures, for instance, are thought to be a result of elastic forces arising from lattice mismatch. However, the role of lattice mismatch in mediating the arrangement of atoms in such materials is incompletely understood. Here we consider a simple microscopic model for lattice mismatch, in which the difference in natural lengths between bonded atoms produces interactions mediated by elastic strain. Computer simulations reveal that the model exhibits rich phase behavior, including structures with periodic order and unusual coexistence scenarios. To explain this phase behavior, we derive an effective pairwise interaction potential between atoms, revealing preferred spatial arrangements of atoms driven by spatial variations in the interaction potential. We then develop a mean field theory based on this effective interaction which qualitatively captures observed transition to phases with modulated order. Finally, we explain the observed scenarios of coexistence between using a graphical construction, based on the realization that the free energy cost of phase separation in elastic systems grows with system size. Here, these results clarify the equilibrium effects of lattice mismatch in macroscopic solids and suggest a role for lattice mismatch in creating spatially heterogeneous compositions in nanoscale materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Tuning 3-D Nanomaterial Architectures Using Atomic Layer Deposition to Direct Solution Synthesis

The ability to synthesize nanoarchitected materials with tunable geometries provides a means to control their functional properties, with applications in biological, environmental, and energy fields. To this end, various bottom-up and top-down synthesis processes have been developed. However, many of these processes require prepatterning or etching steps, making them challenging to scale-up to complex, nonplanar substrates. Furthermore, the ability to integrate nanomaterials into hierarchical arrays with precise control of feature spacing and orientation remains a challenge. One approach to overcome these patterning challenges is the use of surface modification layers to guide the resulting geometry of nanomaterial architectures grown from the substrate. A powerful strategy to accomplish this is what we will refer to as “surface-directed assembly,” where the resulting geometric parameters (feature size, shape, orientation) are predetermined by the initial surface layer. In particular, the use of Atomic Layer Deposition (ALD) to form a surface layer, followed by solution-based growth processes, has the ability to synthesize architected structures with tunable geometries on complex, nonplanar surfaces. Over the past decade, we have reported a series of studies where surface-directed assembly is used to synthesize ZnO nanowires (NWs) on top of a variety of substrates. In this case, a thin film of ZnO is deposited onto the substrate using ALD, which can guide the NW diameter, spacing, and angular orientation with respect to the substrate by controlling epitaxial relationships. Furthermore, we have shown that by depositing a submonolayer overcoat of a secondary material (e.g., amorphous TiO 2 ), nucleation sites are partially blocked, which can further tune the spacing between nanowires while minimizing changes to their other geometric properties. This approach can be used to generate multilevel hierarchical structures, such as hyperbranched NW arrays with tunable control of each level of hierarchy using ALD. Finally, we have demonstrated that the tunable control of geometric parameters can be scaled-up to curved, nonplanar substrates. This highlights the power of ALD to conformally and uniformly deposit the seed layers on complex substrates with subnanometer precision. To complement these seeded hydrothermal approaches, we expanded this strategy to include conversion chemistry of the initial ALD seed layers. For example, by replacing ZnO with Al 2 O 3 as the seed layer without changing the hydrothermal growth conditions, Al–Zn layered-double hydroxide nanosheets can be formed instead of nanowires. In another example of conversion chemistry, a solution anion-exchange process was used to incorporate sulfur into ALD metal oxide films. In both of these conversion processes, the properties of the initial ALD film enabled tuning of the resulting nanostructure geometry. In this Account, we describe the use of ALD to guide the growth of diverse nanomaterial systems, with tunable control over their geometry and composition. We further show how these approaches can be used to tune functional properties for a range of applications, including superomniphobic surfaces, antibiofouling coatings, and photocatalysis. In conclusion, we conclude with an outlook on how the combination of ALD and solution synthesis can enable future directions in scalable nanomanufacturing to overcome the limitations of traditional top-down and bottom-up approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Non-volatile polarization switch of magnetic domain wall velocity

Controlled propagation speed of individual magnetic domains in metal channels at the room temperature is obtained via the non-volatile field effect associated with the switchable polarization of P(VDF-TrFE) (polyvinylidene fluoride-trifluoroethylene) ferroelectric polymer. Polarization domains directly written using conducting atomic force microscope probe locally accelerate/decelerate the magnetic domains in the 0.6 nm thick Co film. The change of the magnetic domain wall velocity is consistent with the magnetic anisotropy energy modulation through the polarization upward/downward orientation. Excellent retention is observed. The demonstrated local non-destructive and reversible change of magnetic properties via rewritable patterning of ferroelectric domains could be attractive for exploring the ultimate limit of miniaturization in devices based on ferromagnetic/ferroelectric bilayers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗