Nanometer Distances Research Articles

Direct optical measurement of intramolecular distances with angstrom precision.

Optical investigations of nanometer distances between proteins, their subunits, or other biomolecules have been the exclusive prerogative of Förster resonance energy transfer (FRET) microscopy for decades. In this work, we show that MINFLUX fluorescence nanoscopy measures intramolecular distances down to 1 nanometer-and in planar projections down to 1 angstrom-directly, linearly, and with angstrom precision. Our method was validated by quantifying well-characterized 1- to 10-nanometer distances in polypeptides and proteins. Moreover, we visualized the orientations of immunoglobulin subunits, applied the method in human cells, and revealed specific configurations of a histidine kinase PAS domain dimer. Our results open the door for examining proximities and interactions by direct position measurements at the intramacromolecular scale.

DC Electric Fields Promote Biodegradation of Waterborne Naphthalene in Biofilter Systems.

Biofiltration is a simple and low-cost method for the cleanup of contaminated water. However, the reduced availability of dissolved chemicals to surface-attached degrader bacteria may limit its efficient use at certain hydraulic loadings. When a direct current (DC) electric field is applied to an immersed packed bed, it invokes electrokinetic processes, such as electroosmotic water flow (EOF). EOF is a surface-charge-induced plug-flow-shaped movement of pore fluids. It acts at a nanometer distance above surfaces and allows the change of microscale pressure-driven flow profiles and, hence, the availability of dissolved contaminants to microbial degraders. In laboratory percolation columns, we assessed the effects of a weak DC electric field (E = 0.5 V·cm-1) on the biodegradation of waterborne naphthalene (NAH) by surface-attached Pseudomonas fluorescens LP6a. To vary NAH bioavailability, we used different NAH concentrations (C0 = 2.7, 5.1, or 7.8 × 10-5 mol·L-1) and Darcy velocities typical for biofiltration ( = 0.2-1.2 × 10-4 m·s-1). In DC-free controls, we observed higher specific degradation rates (qc) at higher NAH concentrations. The qc depended on , suggesting bioavailability restrictions depending on the hydraulic residence times. DC fields consistently increased qc and resulted in linearly increasing benefits up to 55% with rising hydraulic loadings relative to controls. We explain these biodegradation benefits by EOF-altered microscale flow profiles allowing for better NAH provision to bacteria attached to the collectors even though the EOF was calculated to be 100-800 times smaller than bulk water flow. Our data suggest that electrokinetic approaches may give rise to future technical applications that allow regulating biodegradation, for example, in response to fluctuating hydraulic loadings.

Diffractionless transmission of optical beams through a four-level atomic system affected by a plasmonic nanostructure

A nondiffracting propagation of an optical beam through a four-level double-V-type quantum system near a plasmonic nanostructure is investigated. We study the linear absorption and dispersion properties of the quantum system as it interacts with two laser fields. We discuss the effect of the control beam with a Laguerre-Gaussian (LG) profile on the focusing of the probe beam in the presence of a plasmonic nanostructure. An appropriately selected control beam excites one transition of the atomic system and generates a spatially varying refraction index modulation for a weak probe beam that couples to the other transition. We demonstrate that placing a plasmonic nanostructure at a nanometer distance from the atomic system and using a control field with the spatial structure leads to the diffraction-less propagation of the probe beam through the atomic system. Also, it is shown that the optical properties and probe beam focusing can be controlled by adjusting the distance of the plasmonic nanostructure from the atomic system. The proposed all-optical waveguide with high contrast and transmission can be used to implement applications such as image transfer through the medium and image processing.

Functionalizing Surfaces by Physical Vapor Deposition To Measure the Degree of Nanoscale Contact Using FRET.

Adhesion between solid materials is caused by intermolecular forces that only take place if the adhering surfaces are at nanoscale contact (NSC) (i.e., 0.1-0.4 nm. To study adhesion, NSC can be evaluated with Förster Resonance Energy Transfer (FRET). FRET uses the interaction of compatible fluorescence molecules to measure the nanometer distance between bonded surfaces. For this, each surface is labeled with one fluorescence dye, named the Donor or Acceptor. If these molecules are in NSC, a nonradiative Donor-Acceptor energy transfer will occur and can be detected using FRET spectroscopy. Here, for the first time, we introduce an innovative concept of a FRET-based NSC measurement employing dye-nanolayer films prepared by a physical vapor deposition (PVD). The dye nanolayers were prepared by PVD from the vaporization of the Donor and Acceptor molecules separately. The selected molecules, 7-Amino-4-methyl-cumarin (C120) and 5(6)-Carboxy-2',7'-dichlor-fluorescein (CDCF), present high quantum yields (QY, QYD = 0.91 and QYA = 0.64) and a low FRET distance range of 0.6-2.2 nm, adequate for the study of NSC. The produced dye-nanolayer films exhibit a uniform dye distribution (verified by atomic force microscopy) and suitable fluorescence intensities. To validate the NSC measurements, FRET spectroscopy experiments were performed with bonded dye-nanolayer films prepared under different loads (from 1.5 to 140 bar), thus creating different degrees of NSC. The results show an increase in FRET intensity (R 2 = 0.95) with the respective adhesion energy between the films, which is directly related to the degree of NSC. Hence, this work establishes FRET as an experimental technique for the measurement of NSC, and its relation to surface adhesion. Additionally, thanks to the FRET dye-nanolayer approach, the method can be employed on arbitrary surfaces. Essentially, any sufficiently transparent substrate can be functionalized with FRET compatible dyes to evaluate NSC, which represents a breakthrough in contact mechanics investigations of soft and hard solid materials.

Molecular dynamics simulation and experimental study of the material machinability characteristics and crack propagation mechanisms for fused silica double nanoscratches

Fused silica is a high-purity, hard and brittle, difficult-to-machine amorphous material that is widely used in the aerospace, optical instruments, semiconductors, microelectronics and other important fields. However, the influence of adjacent scratches on material deformation and subsurface damage during ultraprecision machining by abrasive particles is not well understood. This study aims to investigate the influence of micron-spaced double scratches on the deformation and damage for fused silica through molecular dynamics simulations and double nanoscratch experiments. An amorphous model of fused silica is created using a two-step simulated annealing method with three-directional periodic boundary conditions. Variable loaded double scratches with different nanometer distances are simulated on the surface of the model, and variable loaded double scratch experiments with varying micron-sized distances between scratches are conducted for fused silica wafers. The simulation and experimental results reveal that the deformation of fused silica during nanoscale double scratching involves both elastic and plastic deformation, and the surface and subsurface damage primarily consists of radial, lateral, Hertzian, and median cracks. The distance between the double scratches affects the load variation, surface and subsurface crack propagation, extent of material damage and removal rate, and surface roughness. Examination of the material subsurfaces using the FIB-TEM sample preparation and testing technique shows that the distance between the double scratches also influences the subsurface damage to the material.

The innate interfacial elastic strain field of a transformable B2 precipitate embedded in an amorphous matrix

When a transformable B2 precipitate is embedded in an amorphous matrix, it is often experimentally observed that the crystalline-amorphous interface not only serves as an initiation site for the martensitic transformation due to local stress concentrations, but also as an inhibitor to stabilize the transformation, the latter being attributed to the “confinement effect” exerted by the amorphous matrix, according to the Eshelby solution. These two seemingly incongruous factors are examined in this study using molecular dynamics simulations from an atomic interaction perspective. An innate strain gradient in the vicinity of the crystalline-amorphous interface is identified. The actual interface, the compressive/dilatative transition, and the interfacial maximum strain are investigated to differentiate from the conventional “interface” located within a distance of a few nanometers. Our innate interfacial elastic strain field model is applicable for the design of materials with a higher degree of martensitic transformation and controllable stress concentration, even in cryogenic environments.

Charge Stability and Charge-State-Based Spin Readout of Shallow Nitrogen-Vacancy Centers in Diamond.

Spin-based applications of the negatively charged nitrogen-vacancy (NV) center in diamonds require an efficient spin readout. One approach is the spin-to-charge conversion (SCC), relying on mapping the spin states onto the neutral (NV0) and negative (NV-) charge states followed by a subsequent charge readout. With high charge-state stability, SCC enables extended measurement times, increasing precision and minimizing noise in the readout compared to the commonly used fluorescence detection. Nanoscale sensing applications, however, require shallow NV centers within a few nanometers distance from the surface where surface related effects might degrade the NV charge state. In this article, we investigate the charge state initialization and stability of single NV centers implanted ≈5 nm below the surface of a flat diamond plate. We demonstrate the SCC protocol on four shallow NV centers suitable for nanoscale sensing, obtaining a reduced readout noise of 5-6 times the spin-projection noise limit. We investigate the general applicability of the SCC for shallow NV centers and observe a correlation between the NV charge-state stability and readout noise. Coating the diamond with glycerol improves both the charge initialization and stability. Our results reveal the influence of the surface-related charge environment on the NV charge properties and motivate further investigations to functionalize the diamond surface with glycerol or other materials for charge-state stabilization and efficient spin-state readout of shallow NV centers suitable for nanoscale sensing.

Single-Molecule FRET X.

Fluorescence resonance energy transfer (FRET) is a photophysical phenomenon that has been repurposed as a biophysical tool to measure nanometer distances. With FRET by DNA eXchange, or FRET X, many points of interest (POIs) in a single object can be probed, overcoming a major limitation of conventional single-molecule FRET. In FRET X, short fluorescently labeled DNA imager strands specifically and transiently bind their complementary docking strands on a target molecule, such that at most a single FRET pair is formed at each point in time and multiple POIs on a single molecule can be readily probed. Here, we describe the sample preparation, image acquisition, and data analysis for structural analysis of DNA nanostructures with FRET X.

Long-distance transport of hot carriers due to acoustic phonon bottleneck in PbSe with room-temperature sensitive mid-infrared sensing

In the optoelectronic conversion process of semiconductors, the photo-excited carriers with energy higher than energy band edge, i.e., hot carriers, have always fast (picoseconds scale) dissipated within 100 nanometers distance through lattice scattering. Specifically, the hot carriers relaxation accounts for more than 60% energy loss in narrow bandgap semiconductor. Herein, we observe an ultralong transport of hot carriers (558 nm) by local light excitation in single-crystalline thermoelectric semiconductor PbSe via the time-resolved reflectivity dynamics. The ultraweak phonon emission of PbSe results in a long-distance thermalized carriers transport due to acoustic phonon bottleneck. Furthermore, the hot carriers effect gives rise to a self-driven (zero bias), fast (900 ns), and sensitive (D* = 1.1 × 1010 cm Hz1/2 W−1 at 3.3 μm) mid-infrared detection and imaging at room temperature. Our discovery provides an insight into optoelectronic conversion mechanism of narrow bandgap thermoelectric semiconductors with intriguing optoelectronic applications.

Consequences of metal-acid site proximity for alkane isomerization and β-scission mediated by bifunctional catalytic cascades

Bifunctional isomerization and β-scission of alkanes involve kinetic cascades mediated by alkenes that form at a (de)hydrogenation function that resides within diffusion distances from the acid function at which alkenes react. Such distances matter for reactivity and selectivity, especially within voids of molecular dimensions, because of gradients in reactant and product concentrations within acid domains. Dispersing Pt nanoparticles within zeolite crystals places the two functions within nanometer distances, instead of the larger distances prevalent when the Pt function resides outside zeolite crystals. Such intimacy leads to higher n-heptane conversion turnover rates (per H+) and shifts selectivities towards primary isoalkanes, most evidently on medium-pore zeolites (MFI), because confinement effects lead to slower diffusion and higher intrinsic H+ reactivity than in larger-pore zeolites, and for shorter Pt-H+ distances, which define the dimensions of the acid domain. Intracrystalline Pt nanoparticles do not affect the number or intrinsic properties of the metal or acid functions or introduce reaction channels mediated by more reactive (but less abundant) diene intermediates, as demonstrated here by reactive probes of metal (CO oxidation) and acid (CH3OH dehydration) functions, infrared spectra of OH groups and chemisorbed CO, kinetic effects of H2 pressures, and transition state energies from density functional theory. Metal-acid distances influence the requisite kinetic cascades instead through the formation and scavenging of reactants and intermediates along the isomerization-scission sequence in the presence of significant gradients in their concentrations. Reaction-transport treatments show that such gradients weaken with increasing intracrystalline densities of Pt nanoparticles (and consequent smaller acid domains), thus circumventing isoalkene equilibration and local thermodynamic bottlenecks through hydrogenation of the primary isoalkene products. Such scavenging inhibits the formation of dimethylpentenes, which act as required precursors to β-scission products, leading to higher selectivities to isoalkanes as Pt-H+ distances decrease. These data and reaction-transport formalisms resolve persistent controversies about the chemical or diffusional origins of rate and selectivity consequences of the location of a metal function. They demonstrate the essential, but often neglected, need to determine the precise location of the metal function and to develop reaction-transport treatments to describe rates and selectivity in bifunctional metal-acid catalysis.

Inside Back Cover: Measurement of Nanometer Distances in Solution via 13C NMR Spectroscopy—Shrinking of Macrocycles with Increasing Temperature (Angew. Chem. Int. Ed. 25/2023)

The determination of nanometer-scale distances in solution is an enormous challenge. In their Research Article (e202301465) Gebhard Haberhauer and co-workers demonstrate that distances in macrocycles can be measured using a molecular spring and 13C-NMR spectroscopy. The sensitivity of the method even allows the determination of thermoelasticity at the molecular level: One studied system expands at low temperatures and shrinks at high temperatures.

Quenched Excitons in WSe2/α-RuCl3 Heterostructures Revealed by Multimessenger Nanoscopy.

We investigate heterostructures composed of monolayer WSe2 stacked on α-RuCl3 using a combination of Terahertz (THz) and infrared (IR) nanospectroscopy and imaging, scanning tunneling spectroscopy (STS), and photoluminescence (PL). Our observations reveal itinerant carriers in the heterostructure prompted by charge transfer across the WSe2/α-RuCl3 interface. Local STS measurements show the Fermi level is shifted to the valence band edge of WSe2 which is consistent with p-type doping and verified by density functional theory (DFT) calculations. We observe prominent resonances in near-IR nano-optical and PL spectra, which are associated with the A-exciton of WSe2. We identify a concomitant, near total, quenching of the A-exciton resonance in the WSe2/α-RuCl3 heterostructure. Our nano-optical measurements show that the charge-transfer doping vanishes while excitonic resonances exhibit near-total recovery in "nanobubbles", where WSe2 and α-RuCl3 are separated by nanometer distances. Our broadband nanoinfrared inquiry elucidates local electrodynamics of excitons and an electron-hole plasma in the WSe2/α-RuCl3 system.

Measurement of Nanometer Distances in Solution via 13 C NMR Spectroscopy-Shrinking of Macrocycles with Increasing Temperature.

For a molecular system, size and shape are of elementary importance for its function and properties. Therefore, the determination of distances within a molecule is essential. However, the commonly used methods are only suitable for distances smaller than 4 Å or larger than 15 Å. Here, we show that by incorporating a molecular spring, we can measure distances in macrocycles in the range of 10 Å using 13 C NMR spectroscopy. The accuracy of the method also allows to determine the temperature dependence of the distances. In one case, we find a contraction of the length by almost 10 % upon heating. This shrinking due to heating can be considered as inverse thermoelasticity at the molecular level and is a previously completely overlooked phenomenon that can be used in the future as a tool to change the length and, thus, the function of a system.

Tailoring the dielectric screening in WS2–graphene heterostructures

The environment contributes to the screening of Coulomb interactions in two-dimensional semiconductors. This can potentially be exploited to tailor material properties as well as for sensing applications. Here, we investigate the tuning of the band gap and the exciton binding energy in the two-dimensional semiconductor WS2 via the external dielectric screening. Embedding WS2 in van der Waals heterostructures with graphene and hBN spacers of thicknesses between one and 16 atomic layers, we experimentally determine both energies as a function of the WS2-to-graphene interlayer distance and the charge carrier density in graphene. We find that the modification to the band gap as well as the exciton binding energy are well described by a one-over-distance dependence, with a significant effect remaining at several nanometers distance, at which the two layers are electrically well isolated. This observation is explained by a screening arising from an image charge induced by the graphene layer. Furthermore, we find that the effectiveness of graphene in screening Coulomb interactions in nearby WS2 depends on its doping level and can therefore be controlled via the electric field effect. We determine that, at room temperature, it is modified by approximately 20% for charge carrier densities of 2 × 1012 cm−2.

Classical nucleation of vapor between hydrophobic plates.

In this work, an extended classical nucleation theory (CNT), including line tension, is used to disentangle classical and non-classical effects in the nucleation of vapor from a liquid confined between two hydrophobic plates at a nanometer distance. The proposed approach allowed us to gauge, from the available simulation work, the importance of elusive nanoscale effects, such as line tension and non-classical modifications of the nucleation mechanism. Surprisingly, the purely macroscopic theory is found to be in quantitative accord with the microscopic data, even for plate distances as small as 2nm, whereas in extreme confinement (<1.5 nm), the CNT approximations proved to be unsatisfactory. These results suggest how classical nucleation theory still offers a computationally inexpensive and predictive tool useful in all domains where nanoconfined evaporation occurs-including nanotechnology, surface science, and biology.

Dynamics of Target DNA Binding and Cleavage by Staphylococcus aureus Cas9 as Revealed by High-Speed Atomic Force Microscopy.

Programmable DNA binding and cleavage by CRISPR-Cas9 has revolutionized the life sciences. However, the off-target cleavage observed in DNA sequences with some homology to the target still represents a major limitation for a more widespread use of Cas9 in biology and medicine. For this reason, complete understanding of the dynamics of DNA binding, interrogation and cleavage by Cas9 is crucial to improve the efficiency of genome editing. Here, we use high-speed atomic force microscopy (HS-AFM) to investigate Staphylococcus aureus Cas9 (SaCas9) and its dynamics of DNA binding and cleavage. Upon binding to single-guide RNA (sgRNA), SaCas9 forms a close bilobed structure that transiently and flexibly adopts also an open configuration. The SaCas9-mediated DNA cleavage is characterized by release of cleaved DNA and immediate dissociation, confirming that SaCas9 operates as a multiple turnover endonuclease. According to present knowledge, the process of searching for target DNA is mainly governed by three-dimensional diffusion. Independent HS-AFM experiments show a potential long-range attractive interaction between SaCas9-sgRNA and its target DNA. The interaction precedes the formation of the stable ternary complex and is observed exclusively in the vicinity of the protospacer-adjacent motif (PAM), up to distances of several nanometers. The direct visualization of the process by sequential topographic images suggests that SaCas9-sgRNA binds to the target sequence first, while the following binding of the PAM is accompanied by local DNA bending and formation of the stable complex. Collectively, our HS-AFM data reveal a potential and unexpected behavior of SaCas9 during the search for DNA targets.

Deciphering the Properties of Nanoconfined Aqueous Solutions by Vibrational Sum Frequency Generation Spectroscopy.

When confined between walls at nanometer distances, water exhibits surprisingly different properties with reference to bare interfacial water. Based on computer simulations, we demonstrate how vibrational sum frequency generation (VSFG) spectroscopy can be used-even with very mild symmetry breaking-to discriminate multilayer water in wide slit pores from both bilayer and monolayer water confined within molecularly narrow pores. Applying the technique, the VSFG lineshapes of monolayer, bilayer, and multilayer water are found to differ in characteristic ways, which is explained by their distinct density stratifications giving rise to different H-bonding patterns in the respective solvation layers.

Orientational dynamics in supercooled glycerol computed from MD simulations: self and cross contributions.

The orientational dynamics of supercooled glycerol is probed using molecular dynamics simulations for temperatures ranging from 323 K to 253 K, through correlation functions of first and second ranks of Legendre polynomials, pertaining respectively to dielectric spectroscopy (DS) and depolarized dynamic light scattering (DDLS). The self, cross, and total correlation functions are compared with relevant experimental data. The computations reveal the low sensitivity of DDLS to cross-correlations, in agreement with what is found in experimental work, and strengthen the idea of directly comparing DS and DDLS data to evaluate the effect of cross-correlations in polar liquids. The analysis of the net static cross-correlations and their spatial decomposition shows that, although cross-correlations extend over nanometric distances, their net magnitude originates, in the case of glycerol, from the first shell of neighbouring molecules. Accessing the angular dependence of the static correlation allows us to get a microscopic understanding of why the rank-1 correlation function is more sensitive to cross-correlation than its rank-2 counterpart.

Colour-coded nanoscale calibration and optical quantification of axial fluorophore position

Total internal reflection fluorescence (TIRF) has come of age, but a reliable and easy-to-use tool for calibrating evanescent-wave penetration depths is missing. We provide a test-sample for TIRF and other axial super-resolution microscopies for emitter axial calibration. Our originality is that nanometer(nm) distances along the microscope’s optical axis are color-encoded in the form of a multi-layered multi-colored transparent sandwich. Emitter layers are excited by the same laser but they emit in different colors. Layers are deposited in a controlled manner onto a glass substrate and protected with a non-fluorescent polymer. Decoding the penetration depth of the exciting evanescent field, by spectrally unmixing of multi-colored samples is presented as well. Our slide can serve as a test sample for quantifying TIRF, but also as an axial ruler for nm-axial distance measurements in single-molecule localization microscopies, supercritical-angle fluorescence, and related super-resolution.

Dynamic viscosity of hydrocarbons and ionic liquids at high-temperature

In this work, dynamic viscosities of hydrocarbons and ionic liquids are studied. At high temperatures in these materials, a decrease in the value of dynamic viscosity was observed. Intermolecular interactions in the objects of study have been studied. It has been established that the intermolecular interaction in hydrocarbons is determined by the Born potential ([Formula: see text]. In this case, the temperature dependence of the dynamic viscosity of hydrocarbons is described by the law [Formula: see text]. It has been established that the dynamic viscosity of hydrocarbons in liquid form has a non-activating character. This occurs directly due to momentum transfer by phonons between adjacent layers located at a distance of nanometers.