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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Adsorption and Solvation Modulate Rhodamine B Diffusion in Ethanol/Water-Filled Anodic Alumina Nanopores

Confinement of solvents and solutes within nanoporous materials frequently leads to the emergence of unique mass transport behaviors that, once fully understood, may lead to improved chemical separations. Here, the diffusion of Rhodamine B (RhB) dye within 10 and 20 nm diameter anodic aluminum oxide (AAO) nanopores filled with binary ethanol/water mixtures is investigated. Mixture compositions spanning from pure ethanol to pure water are employed. The results of confocal fluorescence correlation spectroscopy studies reveal that RhB diffusion occurs by a two-component mechanism comprising composition-dependent fast and slow motions, characterized by diffusion coefficients D f and D s . The results are consistent with those of previous studies performed under more limited conditions [J. Phys. Chem. C, 2023, 127, 411-420]. The fast component scales with mixture viscosity and is assigned to hindered bulk-like diffusion in central pore regions. Slow diffusion likely involves adsorption of RhB to the pore surface and may be described by a desorption mediated mechanism. The occurrence of RhB adsorption to the AAO surface is verified at the single-molecule level by wide-field fluorescence imaging of membrane cross-sectional surfaces. Unique composition dependent trends in the autocorrelation amplitude and in D s that mimic bulk RhB solubility are revealed. D s is found to be smallest in pure ethanol and pure water and largest in intermediate mixtures. These results suggest that RhB surface adsorption is strongest in the pure liquids and weakest in mixtures of intermediate composition, where the dye is least soluble, and most soluble, respectively. As a result, molecular dynamics simulations reveal that a water layer appears on the pore surface under most conditions, while RhB is solvated primarily by ethanol. The composition dependence of RhB diffusion is concluded to reflect its solvation dependent interactions with the pore walls.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Glutamine-rich regions of the disordered CREB transactivation domain mediate dynamic intra- and intermolecular interactions

The cyclic AMP response element (CRE) binding protein (CREB) is a transcription factor that contains a 280-residue N-terminal transactivation domain and a basic leucine zipper that mediates interaction with DNA. The transactivation domain comprises three subdomains, the glutamine-rich domains Q1 and Q2 and the kinase inducible activation domain (KID). NMR chemical shifts show that the isolated subdomains are intrinsically disordered but have a propensity to populate local elements of secondary structure. The Q1 and Q2 domains exhibit a propensity for formation of short β-hairpin motifs that function as binding sites for glutamine-rich sequences. These motifs mediate intramolecular interactions between the CREB Q1 and Q2 domains as well as intermolecular interactions with the glutamine-rich Q1 domain of the TATA-box binding protein associated factor 4 (TAF4) subunit of transcription factor IID (TFIID). Using small-angle X-ray scattering, NMR, and single-molecule Förster resonance energy transfer, we show that the Q1, Q2, and KID regions remain dynamically disordered in a full-length CREB transactivation domain (CREB TAD ) construct. The CREB TAD polypeptide chain is largely extended although some compaction is evident in the KID and Q2 domains. Paramagnetic relaxation enhancement reveals transient long-range contacts both within and between the Q1 and Q2 domains while the intervening KID domain is largely devoid of intramolecular interactions. Phosphorylation results in expansion of the KID domain, presumably making it more accessible for binding the CBP/p300 transcriptional coactivators. In conclusion, our study reveals the complex nature of the interactions within the intrinsically disordered transactivation domain of CREB and provides molecular-level insights into dynamic and transient interactions mediated by the glutamine-rich domains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Potential-Dependent Adhesion Forces between dsDNA and Electroactive Surfaces

A promising approach to regulating the interactions between polyelectrolytes and materials is the use of electroactive surfaces that can change their charge state. However, common electroactive groups are too unstable to be practical for this purpose. Here we have performed a single molecule force spectroscopy study of the interactions between dsDNA and an 1,1'-biferrocenylene (BFD = bis(fulvalene)diiron)-terminated self-assembled monolayer surface that allows us to reversibly change the charge state. We found that the interaction force between DNA and the surface is correlated to the oxidation state of the BFD groups, which is conveniently controlled by the electrochemical potentials. We discovered that the electroactive SAM produces much stronger interaction forces than its nonelectroactive counterpart. A model based on the Grahame equation was able to quantitatively reproduce the experimentally observed relation between the applied potentials and adhesion forces. Our electroactive surface provides a model system for quantitative studies of the interactions between polyelectrolyte and charged surfaces in liquid. Furthermore, these insights may enable new opportunities for actively manipulating the binding, orientations, and conformations of polyelectrolytes for biosensing, nanomotors, and other applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Multi-level Force-dependent Allosteric Enhancement of αE-catenin Binding to F-actin by Vinculin

Classical cadherins are transmembrane proteins whose extracellular domains link neighboring cells, and whose intracellular domains connect to the actin cytoskeleton via β-catenin and α-catenin. The cadherin-catenin complex transmits forces that drive tissue morphogenesis and wound healing. In addition, tension-dependent changes in αE-catenin conformation enables it to recruit the actin-binding protein vinculin to cell-cell junctions, which contributes to junctional strengthening. How and whether multiple cadherin-complexes cooperate to reinforce cell-cell junctions in response to load remains poorly understood. Here, we used single-molecule optical trap measurements to examine how multiple cadherin-catenin complexes interact with F-actin under load, and how this interaction is influenced by the presence of vinculin. We show that force oriented toward the (-) end of the actin filament results in mean lifetimes 3-fold longer than when force was applied towards the barbed (+) end. We also measured force-dependent actin binding by a quaternary complex comprising the cadherin-catenin complex and the vinculin head region, which cannot itself bind actin. Binding lifetimes of this quaternary complex increased as additional complexes bound F-actin, but only when load was oriented toward the (-) end. In contrast, the cadherin-catenin complex alone did not show this form of cooperativity. Furthermore, these findings reveal multi-level, force-dependent regulation that enhances the strength of the association of multiple cadherin/catenin complexes with F-actin, conferring positive feedback that may strengthen the junction and polarize F-actin to facilitate the emergence of higher-order cytoskeletal organization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Zymogen and activated protein C have similar structural architecture

Activated protein C is a trypsin-like protease with anticoagulant and cytoprotective properties that is generated by thrombin from the zymogen precursor protein C in a reaction greatly accelerated by the cofactor thrombomodulin. The molecular details of this activation remain elusive due to the lack of structural information. We now fill this gap by providing information on the overall structural organization of these proteins using single molecule Förster resonance energy transfer and small angle X-ray scattering. Under physiological conditions, both zymogen and protease adopt a conformation with all domains vertically aligned along an axis 76 Å long and maximal particle size of 120 Å. This conformation is stabilized by binding of Ca 2+ to the Gla domain and is affected minimally by interaction with thrombin. Hence, the zymogen protein C likely interacts with the thrombin-thrombomodulin complex through a rigid body association that produces a protease with essentially the same structural architecture. This scenario stands in contrast to an analogous reaction in the coagulation cascade where conversion of the zymogen prothrombin to the protease meizothrombin by the prothrombinase complex is linked to a large conformational transition of the entire protein. The presence of rigid EGF domains in protein C as opposed to kringles in prothrombin likely accounts for the different conformational plasticity of the two zymogens. The new structural features reported here for protein C have general relevance to vitamin K-dependent clotting factors containing EGF domains, such as factors VII, IX, and X.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Magnetic exchange interactions in binuclear and tetranuclear iron(III) complexes described by spin‐flip DFT and Heisenberg effective Hamiltonians

Abstract Low‐energy spectra of single‐molecule magnets (SMMs) are often described by Heisenberg Hamiltonians. Within this formalism, exchange interactions between magnetic centers determine the ground‐state multiplicity and energy separation between the ground and excited states. In this contribution, we extract exchange coupling constants ( J ) for a set of iron (III) binuclear and tetranuclear complexes from all‐electron calculations using non‐collinear spin‐flip time‐dependent density functional theory (NC‐SF‐TDDFT). For 12 binuclear complexes with J ‐values ranging from −6 to −132 cm −1 , our benchmark calculations using the short‐range hybrid ω PBEh functional and 6‐31G(d,p) basis set agree well with the experimentally derived values (mean absolute error of 4.7 cm −1 ). For the tetranuclear SMMs, the computed J constants are within 6 cm −1 from the experimentally derived values. We explore the range of applicability of the Heisenberg model by analyzing bonding patterns in these Fe(III) complexes using natural orbitals (NO), their occupations, and the number of effectively unpaired electrons. The results illustrate the efficiency of the spin‐flip protocol for computing the exchange couplings and the utility of the NO analysis in assessing the validity of effective spin Hamiltonians.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Observation of microwave shielding of ultracold molecules

Harnessing the potential wide-ranging quantum science applications of molecules will require control of their interactions. Here, we used microwave radiation to directly engineer and tune the interaction potentials between ultracold calcium monofluoride (CaF) molecules. By merging two optical tweezers, each containing a single molecule, we probed collisions in three dimensions. The correct combination of microwave frequency and power created an effective repulsive shield, which suppressed the inelastic loss rate by a factor of six, in agreement with theoretical calculations. The demonstrated microwave shielding shows a general route to the creation of long-lived, dense samples of ultracold polar molecules and evaporative cooling.

Anderegg, Loïc↗
DOE OSTI2023

Molecules Functionalized with Cycling Centers for Quantum Information Science

The ability for a single molecule to produce enough laser-induced fluorescence to control and detect its quantum state is known as optical cycling. This property has been used to great effect in atoms, where the relatively small number of states promotes their ability to repeatedly fluoresce, for applications such as laser cooling, precision measurement, atomic clocks, and quantum information processing. The extension of this capability to molecular species, however, has been difficult, primarily due to their propensity to become vibrationally excited during illumination. This project brought together experts from atomic physics, physical chemistry, and computational quantum chemistry to develop means to create molecules capable of optical cycling. In particular, this program sought to produce an optical cycling center (OCC), a quantum functional group capable of chemical attachment to a wide variety of molecular hosts while retaining (and thereby furnishing to its host) the ability to optically cycle. Following our team’s theoretical identification of promising species, including alkaline-earth phenoxides, we then created these species and in many cases confirmed their optical cycle closure. We now not only know of the existence of a handful of large, molecular species that can be deployed for applications in quantum technologies and measurement, but have improved our knowledge of the molecular mechanisms leading to this discovery, which will enable generalization in the future. The extension of these ideas for informed chemical design of cycling molecules with bespoke properties is now being pursued by multiple groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Effect of Methyl Groups on Formation of Ordered or Layered Graphitic Materials from Aromatic Molecules

Abstract Developing functionally complex carbon materials from small aromatic molecules requires an understanding of how the chemistry and structure of its constituent molecules evolve and crosslink, to achieve a tailorable set of functional properties. Here, molecular dynamics (MD) simulations are used to isolate the effect of methyl groups on condensation reactions during the oxidative process and evaluate the impact on elastic modulus by considering three monodisperse pyrene‐based systems with increasing methyl group fraction. A parameter to quantify the reaction progression is designed by computing the number of new covalent bonds formed. Utilizing the previously developed MD framework, it is found that increasing methylation leads to an almost doubling of bond formation, a larger fraction of the new bonds oriented in the direction of tensile stress, and a higher basal plane alignment of the precursor molecules along the direction of tensile stress, resulting in enhanced tensile modulus. Additionally, via experiments, it is demonstrated that precursors with a higher fraction of methyl groups result in a higher alignment of molecules. Moreover, increased methylation results in the lower spread of single molecule alignment which may lead to smaller variations in tensile modulus and more consistent properties in carbon materials derived from methyl‐rich precursors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Slow spin relaxation in single endohedral fullerene molecules

Well-protected magnetization, tunable quantum states, and long spin-relaxation time are desired for the use of magnetic molecules in spintronics and quantum information technologies. In this work, endohedral fullerene molecules M@C 28 with different transition-metal cores were explored through systematic first-principles calculations and spin dynamics analyses. Many of them have bias-tunable structure, stable magnetization, and sizable magnetic anisotropy energy. Furthermore, some of them may have spin-relaxation time up to several milliseconds for their quantum spin states at high temperature (~10 K) after full consideration of spin-vibration couplings. In conclusion, our results suggest that these M@C 28 provide a rich pool of single-molecule magnets for diverse applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Targeting the Bet-Hedging Strategy with an Inhibitor of Bacterial Efflux Capacity Enhances Antibiotic Efficiency and Ameliorates Bacterial Persistence In Vitro

Persistence is a bet-hedging strategy in bacterial populations that increases antibiotic tolerance and leads to the establishment of latent infections. In this study, we demonstrated that a synthetic non-toxic taxane-based reversal agent (tRA), developed as an inhibitor of ABC transporter systems in mammalian cancer cells, enhanced antibiotic killing of persister populations from different pathogens, including Burkholderia, Pseudomonas, Francisella, and Yersinia. Acting as an inhibitor of bacterial efflux at 100 nM, tRA99020 enhanced antibiotic efficiency and suppressed the production of natural products of Burkholderia species polyketide synthase (PKS) function. We demonstrate that the metabolites produced by PKS in response to stress by different antibiotics act as inhibitors of mammalian histone deacetylase activity and stimulate cell death. Applying a single-molecule fluorescence in situ hybridization (smFISH) assay, we analyzed on a single-cell level the activation profiles of the persistence regulating pks gene in Burkholderia thailandensis treated with tRA99020 and antibiotics. We posit that a multi-pronged approach encompassing antibiotic therapies and inhibition of efflux systems and fatty acid catabolism will be required for efficient eradication of persistent bacterial populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Controlling the Fluctuating Tip-Enhanced Raman Spectra of Chloramben on Silver Nanocubes

Tip-enhanced Raman (TER) scattering from molecules residing at plasmonic junctions can be used to detect, identify, and image single molecules. This is most evident for flat molecules interrogated under extreme conditions of temperatures and pressure. It is also the case for (bio)molecular systems that feature preferred orientations/conformations under ambient laboratory conditions. More complex molecules that can adopt multiple conformations and/or that feature different protonation and/or charge states give rise to complex TER spectra. Here we illustrate how the latter can be controlled in the case of chloramben molecules coated onto plasmonic silver nanocubes. We show that characteristic molecular Raman spectra cannot be obtained when tunneling plasmons are operative, i.e., when the tip is in direct contact with the chemically functionalized plasmonic nanoparticles. We rationalize these observations and propose an approach to less invasive, and hence, more analytical TER spectral imaging.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Single nuclear spin detection and control in a van der Waals material

Optically active spin defects in solids are leading candidates for quantum sensing and quantum networking. Recently, single spin defects were discovered in hexagonal boron nitride (hBN), a layered van der Waals (vdW) material. Owing to its two-dimensional structure, hBN allows spin defects to be positioned closer to target samples than in three-dimensional crystals, making it ideal for atomic-scale quantum sensing, including nuclear magnetic resonance (NMR) of single molecules. However, the chemical structures of these defects remain unknown and detecting a single nuclear spin with a hBN spin defect has been elusive. Here we report the creation of single spin defects in hBN using 13 C ion implantation and the identification of three distinct defect types based on hyperfine interactions. We observed both S = 1/2 and S = 1 spin states within a single hBN spin defect. We demonstrated atomic-scale NMR and coherent control of individual nuclear spins in a vdW material, with a π-gate fidelity up to 99.75% at room temperature. By comparing experimental results with density functional theory (DFT) calculations, we propose chemical structures for these spin defects. Our work advances the understanding of single spin defects in hBN and provides a pathway to enhance quantum sensing using hBN spin defects with nuclear spins as quantum memories.

Quantum metrology↗
DOE OSTI2025

Bridging the gap between molecules and materials in quantum chemistry with localized active spaces

The number of materials that “bridge the gap” between single molecules and extended solids, such as metal-organic frameworks and organic semiconductors, has been increasing. Consequently, there is a growing need for modeling approaches that effectively integrate the real-space molecular perspective employed by computational chemists and the reciprocal-space dispersive perspective employed by computational physicists. Here, we propose the localized active space (LAS) approach as a promising method to successfully bridge this gap. The LAS approach extends the active space concept from multiconfigurational methods such as complete active space self-consistent field theory to multiple molecular fragments via a product-form wave function ansatz. Here, we apply this method to solid state phenomena by treating each unit cell as a fragment with different sets of local quantum numbers (e.g., charge and excitation number). State interaction between these LAS states (LASSI) thus provides a comprehensive basis for the study of charge and energy transfer, meeting and surpassing the capabilities of single-reference fragmentation approaches such as constrained density functional theory (cDFT). Most centrally, we show how combining this LASSI approach with multiconfigurational pair-density functional theory (MC-PDFT) provides an elegant and efficient method to compute band structures that capture multiconfigurational character. We apply the LASSI band structure approach to the computation of band gaps in stretched hydrogen chain, polyacetylene, and bulk nickel oxide (NiO), finding good or excellent quantitative agreement with reference values in all cases. Additionally, we use the LAS basis in one-dimensional model systems to demonstrate its ability to treat difficult solid-state phenomena such as exciton transfer and excitation at p-n junctions.

method development↗
DOE OSTI2022

Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. We design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Sub-10 nm upconversion nanocrystals for long-term single-particle tracking

Lanthanide-doped upconversion nanoparticles are attractive single-molecule imaging probes due to their high photostability and anti-Stokes luminescence. However, achieving both small particle size and strong brightness has remained a major challenge, as reducing size often leads to dimmer emission. Herein, we fabricate a sub-10 nm cascade actively protected upconversion nanoparticles, which shows a 33-fold enhanced upconversion efficiency at the single-particle level compared to larger ~19 nm conventional nanoparticles. Theoretical modeling and time-resolved measurements show that emission loss mainly comes from energy leakage of Er 3+ ions to surface defects. By introducing a NaYbF 4 layer as photon-harvesting and protective intermediate layer, we minimize this energy loss and significantly boost brightness. A monolayer of inert NaLuF 4 can effectively suppress the surface quenching to Yb 3+ . Using these ultra-small bright probes, we successfully tracked single epidermal growth factor receptor molecules on live cells for up to one hour, revealing dynamic switching between different diffusion modes.

Qiu, Xiaochen [Fudan Univ., Shanghai (China); Shen↗
DOE OSTI2024

Differentiating Three-Dimensional Molecular Structures Using Laser-Induced Coulomb Explosion Imaging

Coulomb explosion imaging (CEI) with x-ray free electron lasers has recently been shown to be a powerful method for obtaining detailed structural information of gas-phase planar ring molecules [R. Boll et al., X-ray multiphoton-induced Coulomb explosion images complex single molecules, Nat. Phys. 18, 423 (2022).]. In this Letter, we investigate the potential of CEI driven by a tabletop laser and extend this approach to differentiating three-dimensional structures. We study the static CEI patterns of planar and nonplanar organic molecules that resemble the structures of typical products formed in ring-opening reactions. Here, our results reveal that each molecule exhibits a well-localized and distinctive pattern in three-dimensional fragment-ion momentum space. We find that these patterns yield direct information about the molecular structures and can be qualitatively reproduced using a classical Coulomb explosion simulation. Our findings suggest that laser-induced CEI can serve as a robust method for differentiating molecular structures of organic ring and chain molecules. As such, it holds great promise as a method for following ultrafast structural changes, e.g., during ring-opening reactions, by tracking the motion of individual atoms in pump-probe experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗