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The interplay of molecules gives rise to collective phenomena absent in a single molecule. Many examples of collective phenomena have been reported as their knowledge is essential for understanding the behavior of matter. Here, we consider molecules sufficiently separated from each other to not form chemical bonds. If these molecules are excited, e.g., by a weak laser, can they concertedly relax by emitting a single high-energy photon possessing the total energy of all the relaxing molecules? We show that this concerted emission process is indeed possible. We estimate its probability and analyze its dependence on molecular properties, intermolecular distances, and relative orientations of the molecules. A numerical example on two pyridine molecules is given. The concerted emission found is a fundamental process expected to be operative in gas phase and clusters. Its true relevance lies in its intimate relationship to concerted emission of virtual photons and thus to collective energy transfer ionizing neighboring systems. The estimated rates and examples discussed of this collective intermolecular Coulombic decay shed much light on recent puzzling experiments. [ABSTRACT FROM AUTHOR]

Double phosphorescence components from a single organic molecule is rarely reported before because most organic molecules must follow Kasha's rule and merely emit phosphorescence from T1 state. We discover a unique phenomenon of conformation‐controlled expression of double phosphorescence components. The green phosphorescence component and the red phosphorescence component are assigned to the dinaphthylamine moiety and the pyrene unit of N,N‐di(naphthalen‐2‐yl)pyren‐1‐amine (NaPy), respectively. NaPy shows time‐dependent and excitation‐dependent afterglow color change in copolymerized MMA film at room temperature due to simultaneous expression of the double phosphorescence components. However, in PMMA film and copolymerized MA film, NaPy just expresses the red phosphorescence component, suggesting that matrix rigidity greatly affects expression of the double phosphorescence components via altering conformation of NaPy. In low‐rigidity matrix, the NaPy conformation is dyanmic due to free rotation and triplet excitons relax to T1 state via inner conversion or vibration relaxation, leading to the sole expression of the red phosphorescence component. In high‐rigidity matrix, the highly twisted conformation of NaPy is stabilized due to limitation of rotation and triplet excitons at T1 state and T2 state return to S0 state separately, resulting in simultaneous expression of the double phosphorescence components. Thus, NaPy follows Kasha's rule in low‐rigidity matrix but disobeys Kasha's rule in high‐rigidity matrix. In high‐rigidity matrix, the dinaphthylamine moiety and the pyrene unit can function relatively independently, resulting in time‐dependent and excitation‐dependent wide‐range afterglow color change. [ABSTRACT FROM AUTHOR]

Stable open‐shell luminescent radicals have recently attracted much attention due to their unique luminescence properties. However, a radical molecule with both Kasha and anti‐Kasha doublet emission properties has not been reported. Herein, we have successfully synthesized a stable chlorine‐substituted Chichibabin's hydrocarbon, TTM‐TTM, along with its mono‐radical counterpart, TTM‐HTTM. The emission of TTM‐TTM follows Kasha's rule in the near infrared region. However, TTM‐HTTM shows dual channel doublet emissions of Kasha and anti‐Kasha. Remarkably, these two types of emission compete dynamically in both solution and condensed states. Our findings provide valuable insights into the rational design and discovery of stable radicals that possess distinctive luminescent properties, thus broadening the horizons of luminescent materials research. [ABSTRACT FROM AUTHOR]

A regular method has been proposed to quantitatively describe the fluorescence of molecules randomly moving in a nanowell. Correlation functions of the fluorescence of single molecules depending on the geometry of the nanowell and the penetration depth of an exciting field into it have been determined. The obtained results can be used to quantitatively analyze the properties of molecules and to extract information on the parameters of the nanowell. [ABSTRACT FROM AUTHOR]

Gaseous signaling molecules (GSMs) including nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S) have presented excellent therapeutic efficacy such as anti‐inflammatory, anti‐microbial and anti‐cancer effects and multiple biomedical applications in recent years. As the three most vital signaling molecules in human physiology, these three GSMs show so intertwined and orchestrated interactions that the synergy of multiple gases may demonstrate a more complex therapeutic potential than single gas delivery. Consequently, researchers have been devoted to developing codelivery systems of GSMs by synthesizing a single molecule as a dual donor to maximize the gaseous therapeutic efficacy. In this minireview, we summarize the recent developments of molecules or materials enabling codelivery of GSMs for biomedical applications. It appears that compared with the abundant cases of codelivery of NO and H2S, research on codelivery of CO and the other two GSMs separately remains to be explored. [ABSTRACT FROM AUTHOR]

The dynamic characteristics of single DNA molecules translocating within micro/nano-channels are fundamental for a wide range of applications such as stretching, separating, mapping, and even sequencing of DNA molecules. In this study, a type of tapered microchannel chip with uniform height for all configurations was fabricated, with the major tapered structure having a length of 13 μm and a width that tapers from 5 μm to 20 μm. The dynamic characteristics such as the trajectories and velocities of λ-DNA molecules translocating from different positions driven by an external DC electric field force were systematically investigated by single-molecule fluorescence imaging technology. Some dynamic characteristics of DNA molecules translocation were found. Considering simply the effects of electrophoretic force and electro-osmotic force on the DNA molecules, the dynamic characteristics of DNA molecules are well understood. For example, the velocity of the DNA molecule is inversely proportional to the diameter of the tapered channel and the turning phenomena of the trajectory of the DNA molecules translocating through microchannels. This study is helpful and proposes new ideas for the design and development of microfluidic chips for the quantitative manipulation of DNA molecules. [ABSTRACT FROM AUTHOR]

This work aims to develop a method for analyzing the dynamic flow of single DNA molecules through nanochannels in fluidic chip which work passively. For this purpose, a two‐laser system was used, which is coupled into a fluorescence microscope and can detect labeled DNA molecules using a single photon counter for signal read‐out in real‐time. The two laser spots are focused at different points of the nanochannel, and can be used to obtain the speed and molecular extension of the DNA. For example, a velocity of 1.82 μm/ms and a spatial extension of 0.9 μm were determined for pUC18/19 DNA (2686 bp) in a nanochannel with a width and depth of 200 nm × 100 nm and a length of 10 μm. © 2024 Institute of Electrical Engineer of Japan and Wiley Periodicals LLC. [ABSTRACT FROM AUTHOR]

The utilization of single molecule electronic devices represents a significant avenue toward advancing next-generation circuits. Recent investigations have notably augmented our understanding of the optoelectronic characteristics exhibited by diverse single molecule materials. This comprehensive review underscores the latest progressions in probing photo-induced electron transport behaviors within molecular junctions. Encompassing both single molecule and self-assembled monolayer configurations, this review primarily concentrates on unraveling the fundamental mechanisms and guiding principles underlying photo-switchable devices within single molecule junctions. Furthermore, it presents an outlook on the obstacles faced and future prospects within this dynamically evolving domain. [ABSTRACT FROM AUTHOR]

Anisotropic colloidal particles have attracted great attention over the past few decades because of their significant properties that differ from isotropic particles. Molecular self‐assembly provides the possibility to design and construct anisotropic colloidal particles from the single‐molecule level, and molecular assemblies can both inherit the properties of molecules in single states and integrate the functions of molecules in collective states, which has attracted great interest to researchers. Even in recent years, the self‐assembly strategy of anisotropic colloidal particles has been greatly developed. This review article briefly summarizes the research progress of molecules from small molecules, block copolymers and homopolymers to anisotropic particles, including their self‐assembly strategies and applications. Finally, we discuss the remaining challenges of this topic and we expect that by manipulating the design of diverse molecules/polymers, anisotropic colloidal particles can evolve into a new era. [ABSTRACT FROM AUTHOR]

The article discusses the field of academic foreign compound metabolism, specifically focusing on the identification and characterization of drug metabolites. In the past, it was acceptable to identify metabolites down to a certain percentage of the given dose, but regulatory authorities now require the identification of metabolites representing 10% or more of the dosed product. Modern technology allows for the detection of metabolites at extremely low levels. The article also explores the significance of the absolute number of drug metabolite molecules and the challenges in detecting minor metabolites. It concludes by discussing the future directions of xenobiochemistry, including the study of polymorphic variation, genetic and epigenetic associations, and the importance of the microbiome. [Extracted from the article]

Photoblinking and photobleaching are commonly encountered problems for single-photon sources. Numerous methods have been devised to suppress these two impediments; however, either the preparation procedures or the operating conditions are relatively harsh, making them difficult to apply to practical applications. Here, we reported giant suppression of both photoblinking and photobleaching of a single fluorescent molecule, terrylene, via the utilization of hexagonal boron nitride (h-BN) flakes as substrates. Experimentally, a much-prolonged survival time of terrylene has been determined, which can have a photostable emission over 2 h at room temperature under ambient atmospheres. Compared with single molecules on a SiO2/Si substrate or glass coverslip, a more than 100-fold increase in the total number of photons collected from each terrylene on h-BN flakes has been demonstrated. We also proved that the photostability of terrylene molecules can be well maintained for more than 6 months even under ambient conditions without any further protection. Our results demonstrate that the utilization of h-BN flakes to suppress photoblinking and photobleaching of fluorescent molecules has promising applications in the production of high-quality single-photon sources at room temperature. [ABSTRACT FROM AUTHOR]

An investigation of electro‐optical and nonlinear optical properties of pure and halogenated (−Cl, −Br) hexahexyloxytriphenylene (HAT6) molecule is presented employing a density functional theory (DFT) approach. The effect of halogenation on HAT6 molecule is studied by introducing single and double halogens (Cl, Br) in its molecular geometry. The geometries are optimized progressively to achieve stability using B3LYP method with 6‐311 basis sets. The physical properties encompassing electro‐optical, thermodynamic, and electronic properties of single molecule of HAT6 are computed using DFT method. The introduction of halogens to discotic HAT6 molecule to an augmentation in molecular polarizability, rendering halogenated HAT6 a suitable candidate for nonlinear optical devices due to its π–π conjugation and improved optical parameters. The UV‐Vis spectra indicate the predominant absorptions and changes in absorption depend on the halogenations of the HAT6 molecule. Also, the halogenation effect leads to a significant reduction in the energy bandgap directly associated with electron‐electron correlation, facilitating straightforward tuning. [ABSTRACT FROM AUTHOR]

Research on the production of hydrogen from water by catalytic decomposition using metal clusters is of great significance in addressing the global energy crisis. Due to the quantum size effect, tunability, and ultra-high surface area, metal clusters exhibit many unique properties, including catalytic performance and optical properties. In this work, the lowest energy structure of Be 13 cluster and intermediate states, as well as the hydrogen production mechanism of Be 13 cluster and intermediate states + single water molecule were studied by DFT calculations at the PBE0-D3/DEF2TZVP level. The results show that both Be 13 cluster and intermediate states release energy during water molecules adsorption and both Be 13 cluster and its intermediate state + single water molecule reactions are exothermic. The electronic structures of the original and adsorbed structures were analyzed by ESP method, and their DOS plots were drawn. We investigated the chemical bonding and interactions of the initial structure, reactants and products using IRI analysis. Our results help to provide a basis for developing a more effective method for generating hydrogen from water molecules. [Display omitted] • The lowest energy structures of Be 13 cluster and intermediate states. • The dissociation of water on the Be 13 cluster to produce H 2 is an exothermic process. • The cluster are chemically adsorbed with H 2 O and H 2. • The adsorption energy of clusters adsorbed water molecules decreases with the increase of the number. [ABSTRACT FROM AUTHOR]

Intermolecular interactions of drug molecules can lead to aggregation, which has a significant impact on their application. This problem might escape the attention when studying their solubility as small aggregates might behave almost as single molecules. We studied the aggregation behaviour of doxorubicin (DOX) molecules through density functional (DFT) methods and molecular dynamics (MD) simulations in water, dimethylformamide (DMF), ethanol (EtOH), and dimethyl sulfoxide (DMSO). We described the degree of aggregation by MD-calculated radial distribution function, combined radial/angular distribution functions, autocorrelation functions, and the number of hydrogen bonds of individual DOX and solvent atoms. MD-calculated diffusion coefficients for DOX decrease along the series water > DMF > EtOH > DMSO (0.101 × 10−9, 0.047 × 10−9, 0.025 × 10−9, and 0.007 × 10−9 m2 s−1, respectively) consistent with increasing aggregation found in the MD simulations. These aggregates have different characters, depending on the DOX⋯solvent interactions, and include hydrogen bonding and π-stacking. Even though the solvation energy of a single DOX molecule in DMSO (−24.8 kcal mol−1) is higher than in other solvents, the formation of larger aggregates in this solvent prevents proper solvation. Further, the orientation of doxorubicin molecules at octanol/water and dipalmitoylphosphatidylcholine (DPPC)/water interfaces was studied with two different orientations from the bivariate maps. In the case of the DPPC/water interface, the anthracycline part points toward the aqueous phase, while this part is oriented almost parallel to the octanol/water interface in DMSO. [ABSTRACT FROM AUTHOR]

Exploiting the optimum wavelength of reactivity for efficient photochemical reactions has been well‐established based on the development of photochemical action plots. We herein demonstrate the power of such action plots by a remarkable example of the wavelength‐resolved photochemistry of two triazolinedione (TAD) substrates, i.e. aliphatic and aromatic substituted, that exhibit near identical absorption spectra yet possess vastly disparate photoreactivity. We present our findings in carefully recorded action plots, from which reaction selectivity is identified. The profound difference in photoreactivity is exploited by designing a 'hybrid' bisfunctional TAD molecule, enabling the formation of a dual‐gated reaction manifold that demonstrates the exceptional and site‐selective (photo)chemical behavior of both TAD substrates within a single small molecule. [ABSTRACT FROM AUTHOR]

Continuum modeling using the Lennard-Jones potential has been shown to provide a good estimation for the interaction energy between regular-shaped homogeneous molecules comprising the same type of atoms. However, this method may not be accurate for heterogeneous molecules, which are made up of more than one chemical element. The traditional method to deal with this involves approximating the molecule via multiple surfaces in a piecemeal fashion. While this approach works well for small sized molecules, calculations become intensive for large sized molecules as a large number of sums from multiple surface interactions are involved. To address this issue, we propose a new model that approximates a heterogeneous molecule with a single surface or volume, where attractive and repulsive constants (A and B) in the Lennard-Jones potential are replaced by functions A(r) and B(r), which depend on the parameterization of the surface r. We comment that this technique is suitable for regular-shaped nanostructures where their heterogeneity can be modeled by surface (or volume) parameterization. Validation of the new approach is carried out via two problems, namely, carbon nanotube--methane and carbon nanotube--coronene interactions. For coronene and methane, which are assumed to be radially symmetric, we propose A(r) and B(r) to be sigmoidal functions for which the interaction strength decreases from the inner region of the carbon atoms toward the outer region of the hydrogen atoms. Our results for both cases show that using the sigmoidal profiles for A(r) and B(r) gives rise to interaction energies that are in better agreement with those obtained from molecular dynamics studies compared to results using constant A and B. The new approach provides a significant improvement to the current continuum modeling using the Lennard-Jones potential. [ABSTRACT FROM AUTHOR]

Background: Ablynx NV, a subsidiary of Sanofi, has a long-standing focus on the development of Nanobody® molecules as biopharmaceuticals (Nanobody® is a registered trademark of Ablynx NV). Nanobody molecules are single variable domains, and they have been met with great success part due to their favorable expression properties in several microbial systems. Nevertheless, the search for the host of the future is an ongoing and challenging process. Komagataella phaffi (Pichia pastoris) is one of the most suitable organisms to produce Nanobody molecules. In addition, genetic engineering of Pichia is easy and an effective approach to improve titers. Results: Here we report that P. pastoris engineered to co-express genes encoding four auxiliary proteins (HAC1, KAR2, PDI and RPP0), leads to a marked improvement in the expression of Nanobody molecules using the AOX1 methanol induction system. Titer improvement is mainly attributed to HAC1, and its beneficial effect was also observed in a methanol-free expression system. Conclusion: Our findings are based on over a thousand fed-batch fermentations and offer a valuable guide to produce Nanobody molecules in P. pastoris. The presented differences in expressability between types of Nanobody molecules will be helpful for researchers to select both the type of Nanobody molecule and Pichia strain and may stimulate further the development of a more ecological methanol-free expression platform. [ABSTRACT FROM AUTHOR]

In the present study, we use high-level coupled-cluster-based methods to obtain benchmark geometries and lattice energy for small sodium chloride clusters up to (NaCl)15. Reliable geometries can be obtained with the CCSD(T)-F12b method in conjunction with a small double-ζ basis set, while accurate energies can be obtained with relatively economical methods (e.g. DLPNO-CCSD(T1)-F12) by adjusting for systematic bias against higher-level methods (e.g. W2). For the calculation of larger clusters, we find PBE0-D3BJ and GFN1-XTB to be suitable for geometry optimisation, while B97M-V and GFN1-XTB provide an adequate means for energy calculations once they are calibrated against high-level references. For much larger systems, a Born–Landé-type model can be used to obtain fairly good lattice energies. The results show the progression from a single NaCl molecule to bulk salt, with full convergence expected for cluster sizes in the range of 5–10 nm. The protocol for obtaining highly accurate lattice energies and calculating large clusters may be used to examine the energetics of ionic clusters more generally. [ABSTRACT FROM AUTHOR]

We have investigated the structure and spectra (NMR, UV/visible) of several Yariv reagents and models for these species, using both density functional theory (DFT) and approximate coupled‐cluster methods (ADC(2)). We have also studied the formation of dimers and model trimers as a first step to understand the aggregation of these species in aqueous solution. One question that our calculations help resolve is the origin of two strong bands in the visible region of the spectrum: these are confirmed as resulting from enol‐keto tautomerism, and are not a result of aggregation, which was a hypothesis that had been advanced previously. The UV/visible spectrum of the Yariv reagents can be explained entirely in terms of tautomerism within a single molecule – no dimers or clusters are involved. [ABSTRACT FROM AUTHOR]

Depending on the IO approaches the configuration of HONO, two different H-extraction pathways (IO + cis-HONO and IO + trans-HONO) were located at the CCSD(T)//ωB97X-D level. With the introduction of single water molecule, nine pathways were investigated for the IO + HONO reaction. The computed results manifested that the barriers of Pathway W11, Pathway W12, Pathway W21A, Pathway W21B, Pathway W22B, and Pathway W23 are reduced by 0.39, 3.05, 8.14, 12.63, 13.13, and 10.02 kcal/mol, respectively. The rate coefficients of the reaction of IO + cis-HONO and IO + trans-HONO at 298.15 K in the existence of water are 5.98 × 10−13 and 4.93 × 10−11 cm−3 molecule−1 s−1, which are lower than the corresponding reactions in the absence of water (1.14 × 10−14 and 1.39 × 10−19 cm−3 molecule−1 s−1). To further comprehend the influence of H2O on the IO + HONO reaction, the effective rate coefficients were computed through taking account on the water concentration. The effective rate coefficients of the IO + trans-HONO reaction are much larger than the IO + trans-HONO reaction in the absence of water, 'as water molecule could cause the inhibition of the IO + cis-HONO reaction. In contrast to the IO + HONO reaction with water-free, the feasible reaction is the IO + trans-HONO instead of the IO + cis-HONO reaction. The current investigation proved that water possesses positive influence on the IO + trans-HONO reaction, which could devote to the degradation of HONO. [ABSTRACT FROM AUTHOR]

Topoisomerase IIα (Topo IIα) and the centromere-specific histone H3 variant CENH3 are key proteins involved in chromatin condensation and centromere determination, respectively. Consequently, they are required for proper chromosome segregation during cell divisions. We combined two super-resolution techniques, structured illumination microscopy (SIM) to co-localize Topo IIα and CENH3, and photoactivated localization microscopy (PALM) to determine their molecule numbers in barley metaphase chromosomes. We detected a dispersed Topo IIα distribution along chromosome arms but an accumulation at centromeres, telomeres, and nucleolus-organizing regions. With a precision of 10-50 nm, we counted ~ 20,000-40,000 Topo IIα molecules per chromosome, 28% of them within the (peri)centromere. With similar precision, we identified ~13,500 CENH3 molecules per centromere where Topo IIα proteins and CENH3-containing chromatin intermingle. In short, we demonstrate PALM as a useful method to count and localize single molecules with high precision within chromosomes. The ultrastructural distribution and the detected amount of Topo IIα and CENH3 are instrumental for a better understanding of their functions during chromatin condensation and centromere determination. [ABSTRACT FROM AUTHOR]

We develop a supersensitive "turn-on format" fluorescence sandwich immunoassay for detecting small single molecules. Gold nanoplate-based biotin antibodies and streptavidin–fluorophores were used instead of streptavidin–horseradish peroxidase reacting with a biotin tracer in a microplate-based competitive enzyme-linked immunosorbent assay (ELISA). Our platform showed a low detection limit of 5 zeptomolar (5 × 10–21 M), 5.4 × 1010 times higher detection sensitivity than the conventional tune-off format ELISA. [ABSTRACT FROM AUTHOR]

Second near‐infrared (NIR‐II, 1000–1700 nm) window fluorescence imaging‐guided photothermal therapy probes are promising for precise cancer phototheranostics. However, most of the currently reported probes do not demonstrate high NIR‐II fluorescent brightness (molar absorption coefficient (ε) × quantum yield (QY)) and photothermal performance (ε × photothermal conversion efficiency (PCE)) in a single molecule. Herein, a versatile strategy to solve this challenge is reported by fabricating a large π‐conjugated molecule (BNDI‐Me) with a rigid molecular skeleton and flexible side groups. The proposed BNDI‐Me nanoprobe boosts the ε and simultaneously optimizes its QY and PCE. Therefore, high NIR‐II fluorescent brightness (ε × QY = 2296 m−1 cm−1) and strong photothermal performance (ε × PCE = 82 000) are successfully incorporated in a single small molecule, and, to the best of knowledge, either of these two parameters is better than the best currently available fluorescent or photothermal probes. Thus, superior NIR‐II imaging effect in vivo and high photothermal tumor inhibition rate (81.2%) at low systemic injection doses are obtained. The work provides further insights into the relationship of photophysical mechanisms and structures, and presents promising molecular design guidelines for the integration of more efficient multiple theranostic functions in a single molecule. [ABSTRACT FROM AUTHOR]

Temperature (T) dependent conductance G = G (T) data measured in molecular junctions are routinely taken as evidence for a two-step hopping mechanism. The present paper emphasizes that this is not necessarily the case. A curve of ln G versus 1 / T decreasing almost linearly (Arrhenius-like regime) and eventually switching to a nearly horizontal plateau (Sommerfeld regime), or possessing a slope gradually decreasing with increasing 1 / T is fully compatible with a single-step tunneling mechanism. The results for the dependence of G on T presented include both analytical exact and accurate approximate formulas and numerical simulations. These theoretical results are general, also in the sense that they are not limited, e.g., to the (single molecule electromigrated (SET) or large area EGaIn) fabrication platforms, which are chosen for exemplification merely in view of the available experimental data needed for analysis. To be specific, we examine in detail transport measurements for molecular junctions based on ferrocene (Fc). As a particularly important finding, we show how the present analytic formulas for G = G (T) can be utilized to compute the ratio f = A eff / A n between the effective and nominal areas of large area Fc-based junctions with an EGaIn top electrode. Our estimate of f ≈ 0.6 × 10 − 4 is comparable with previously reported values based on completely different methods for related large area molecular junctions. [ABSTRACT FROM AUTHOR]

Antioxidant activity studies usually focus on a single type of molecule and do not consider possible collaborations among different molecules. The purpose of this work was to obtain multicomponent extracts exerting protection against oxidation from apricot seeds and to study the individual role of these components in the whole protection. Pressurized liquid extraction was employed to obtain extracts, and a response surface methodology enabled exploration of the effect of extraction conditions on the composition and prevalence of the antioxidant mechanism. Extractions carried out at 170 °C, in up to 7% ethanol, and for up to 25 min guaranteed multifunctional protection against oxidation by the collaboration of different molecules. While phenolic compounds were the main contributors to radical-scavenging capacity (R2 = 90% for ABTS and 88% for DPPH), proteins and phenolic compounds showed similar roles in the whole reducing power (proteins (R2 = 86%) and TPC (R2 = 90%)), and other compounds inhibited the formation of hydroxyl radicals and, especially, the peroxidation of lipids. The presence of peptides modified the antioxidant protection of extracts. UHPLC-Q-Orbitrap-MS/MS confirmed the presence of phenolic compounds and other antioxidant molecules. The presence of different kinds of molecules led to a multifunctional and collaborative protection against oxidation that could not be exerted by individual molecules. [ABSTRACT FROM AUTHOR]

Quantum-dot cellular automata (QCA) is a nanoscale, transistor-less device technology. A single molecule may provide an elementary QCA device known as a cell. Molecular redox centers function as quantum dots, and the configuration of mobile charge on the dots encodes device states useful for classical computing. Molecular QCA may support ultra-high device densities and THz-scale switching speeds at room temperature. An applied electric field may be used to clock molecular QCA, providing power gain to boost weakened signals, as well as quasi-adiabatic device operation for minimal power dissipation in QCA devices and circuits. A zwitterionic, Y-shaped, three-dot molecule may function as a field-clocked QCA cell. We focus on the design of a counterion built into the center of the cell. Ab initio computations demonstrate that choice of counterion determines the number of mobile charges for encoding the device state on the three quantum dots. We use B 5 H 5 2 âˆ' or B 4 CH 5 âˆ' as the central counterionic linker for two different Y-shaped, three-dot QCA molecules. While both molecules support the desired device states, the number of trapped charges in the counterion determines the number of mobile holes on the molecular quantum dots. This, in turn, determines whether the device state is encoded by a hole or an electron. This choice of encoding determines how the molecular QCA cell responds to a clocking field. The two counterions studied here lead to two QCA molecules with opposite responses to the clock, similar to the complementary responses of PMOS and NMOS transistors to gated voltage control. [ABSTRACT FROM AUTHOR]

The discovery of chirality-induced spin selectivity (CISS), resulting from an interaction between the electron spin and handedness of chiral molecules, has sparked interest in surface-adsorbed chiral molecules due to potential applications in spintronics, enantioseparation, and enantioselective chemical or biological processes. We study the deposition of chiral heptahelicene by sublimation under ultra-high vacuum onto bare Cu(111), Co bilayer nanoislands on Cu(111), and Fe bilayers on W(110) by low-temperature spin-polarized scanning tunneling microscopy/spectroscopy (STM/STS). In all cases, the molecules remain intact and adsorb with the proximal phenanthrene group aligned parallel to the surface. Three degenerate in-plane orientations on Cu(111) and Co(111), reflecting substrate symmetry, and only two on Fe(110), i.e., fewer than symmetry permits, indicate a specific adsorption site for each substrate. Heptahelicene physisorbs on Cu(111) but chemisorbs on Co(111) and Fe(110) bilayers, which nevertheless remain for the sub-monolayer coverage ferromagnetic and magnetized out-of-plane. We are able to determine the handedness of individual molecules chemisorbed on Fe(110) and Co(111), as previously reported for less reactive Cu(111). The demonstrated deposition control and STM/STS imaging capabilities for heptahelicene on Co/Cu(111) and Fe/W(110) substrate systems lay the foundation for studying CISS in ultra-high vacuum and on the microscopic level of single molecules in controlled atomic configurations. [ABSTRACT FROM AUTHOR]

Molecules capable of emitting a large number of photons (also known as fortunate molecules) are crucial for achieving a resolution close to single molecule limit (the actual size of a single molecule). We propose a long-exposure single molecule localization microscopy (leSMLM) technique that enables detection of fortunate molecules, which is based on the fact that detecting a relatively small subset of molecules with large photon emission increases its localization precision (∼ r 0 / N ). Fortunate molecules have the ability to emit a large burst of photons over a prolonged time (> average blinking lifetime). So, a long exposure time allows the time window necessary to detect these elite molecules. The technique involves the detection of fortunate molecules to generate enough statistics for a quality reconstruction of the target protein distribution in a cellular system. Studies show a significant PArticle Resolution Shift (PAR-shift) of about 6 and 11 nm toward single-molecule-limit (far from diffraction-limit) for an exposure time window of 60 and 90 ms, respectively. In addition, a significant decrease in the fraction of fortunate molecules (single molecules with small localization precision) is observed. Specifically, 8.33% and 3.43% molecules are found to emit in 30–60 ms and >60 ms, respectively, when compared to single molecule localization microscopy (SMLM). The long exposure has enabled better visualization of the Dendra2HA molecular cluster, resolving sub-clusters within a large cluster. Thus, the proposed technique leSMLM facilitates a better study of cluster formation in fixed samples. Overall, leSMLM technique offers a spatial resolution improvement of ~ 10 nm compared to traditional SMLM at the cost of marginally poor temporal resolution. [ABSTRACT FROM AUTHOR]

The interaction of a high intensity x-ray pulse with matter causes ionization of the constituent atoms through various atomic processes, and the system eventually goes through a complex structural dynamics. Understanding this whole process is important from the perspective of structure determination of molecules using single particle imaging. XMDYN, which is a classical molecular dynamics-Monte Carlo based hybrid approach, has been successful in simulating the dynamical evolution of various systems under intense irradiation over the past years. The present study aims for extending the XMDYN toolkit to treat chemical bonds using the reactive force field. In order to study its impact, a highly intense x-ray pulse was made to interact with the simplest amino acid, glycine. Different model variants were used to highlight the consequences of charge rearrangement and chemical bonds on the time evolution. The charge-rearrangement-enhanced x-ray ionization of molecules effect is also discussed to address the capability of a classical MD based approach, i.e., XMDYN, to capture such a molecular phenomenon. [ABSTRACT FROM AUTHOR]

An asymmetric bis-phenol-β-diketone (H4L) has been designed as a ligand programmed to promote the assembly of a molecular arrangement composed of three magnetically exchanged [NiCu] pairs, each exhibiting an S = 1/2 spin. The latter are shown by EPR and magnetometry to be good qubit realizations and non-equivalent within the molecule in the solid state, as required for conditional quantum gates. [ABSTRACT FROM AUTHOR]

Functional molecules and their assemblies have attracted considerable attention arising from not only diverse structures with novel properties but also potential applications in molecular devices. The novel properties, which determine their applications, are strongly related to their structures. In recent years, benefiting from the development of atomically precise control technique of the structures, a lot of new materials constructing from molecules with novel properties emerged. Their novel properties enable them to be potentially applied in molecular spintronics, high‐density data storage, selective reaction and quantum topological devices, and so on. The present review focuses on new progress in predicting and controlling the structures and properties of functional molecules and their assemblies on metal surfaces by combining first‐principle calculations with scanning tunneling microscopy experiments. We aim at understanding the key factors which affect the physical and chemical properties of the metal–organic systems, especially from a theoretical perspective. This article is categorized under:Structure and Mechanism > Molecular StructuresElectronic Structure Theory > Density Functional Theory [ABSTRACT FROM AUTHOR]

Herein, single‐molecule conductance studies of TBT1‐TBT6 which entails 1,4‐dithienylbenzene as the backbone and SMe groups as the anchoring units, with the scanning tunneling microscope break junction (STM‐BJ) technique, are reported. The molecular conductance of TBT1 with intramolecular O•••S noncovalent interactions is enhanced by about one order of magnitude in comparison to their analogue TBT2 (which contains alkyl instead of alkoxy chains). By replacing the methoxy groups in TBT1 with extending alkoxy chains in TBT3, TBT4, and TBT5, the molecular backbones become twisted and as a consequence the single‐molecule conductance decreases gradually, showing that the intramolecular O•••S noncovalent interaction is influenced by the structural features of alkoxy chains. More importantly, the single‐molecule conductance of TBT3, TBT4, and TBT5 can be boosted by increasing the electric field applied to the molecular junctions. Remarkably, the conductance of TBT3, TBT4, and TBT5 can be reversibly modulated due to the conformational changes between twisted and planar ones by varying the electric field. These results demonstrate that molecules with intramolecular O•••S noncovalent interactions have the potential for in situ control of the electrical properties of molecular‐scale devices. [ABSTRACT FROM AUTHOR]

The title compound, baeocystin or 4-phosphoryloxy-N-methyltryptamine {systematic name: 3-[2-(methylazaniumyl)ethyl]-¹H-indol-4-yl hydrogen phosphate}, C11H15N2O4P, has a single zwitterionic molecule in the asymmetric unit. The molecule has an intramolecular N--H...O hydrogen bond between the ammonium cation and the hydrophosphate anion. In the crystal, the molecules are linked by N--H...O and O--H...O hydrogen bonds into a threedimensional network. [ABSTRACT FROM AUTHOR]

We report the effects of an electric field E on the spin orientations of nickelocene (Nc) deposited on the Cu surfaces by means of first-principles calculations. We employ the Hubbard-U corrected van der Waals density functional to take into account the strong correlation effects of the localized 3d electrons and the non-covalent binding involved in the molecule-surface coupling. We show that the deposited Nc molecule can switch between in-plane (in small E-field) and perpendicular magnetization (in large E-field). We find that the significant charge transfer between the molecule and the metallic surface plays a dominant role in the spin reorientation transition. From an electronic structure perspective, the shift in the Fermi level enhances the coupling between the occupied and unoccupied Ni-3d states of different spin states, which tends to facilitate the perpendicular magnetic anisotropy. These findings shed some light on the electrical control of the magnetic anisotropies of single-molecule magnets on metal surfaces. [ABSTRACT FROM AUTHOR]

The use of a highly localized plasmonic field has enabled us to achieve sub-nanometer resolution of Raman images for single molecules. The inhomogeneous spatial distribution of plasmonic field has become an important factor that controls the interaction between the light and the molecule. We present here a gauge invariant interaction Hamiltonian (GIIH) to take into account the non-uniformity of the electromagnetic field distribution in the non-relativistic regime. The theory has been implemented for both resonant and nonresonant Raman processes within the sum-over-state framework. It removes the gauge origin dependence in the phenomenologically modified interaction Hamiltonian (PMIH) employed in previous studies. Our calculations show that, in most resonant cases, the Raman images from GIIH are similar to those from PMIH when the origin is set to the nuclear charge center of the molecule. In the case of nonresonant Raman images, distinct differences can be found from two different approaches, while GIIH calculations provide more details and phase information of the images. Furthermore, the results from GIIH calculations are more stable with respect to the computational parameters. Our results not only help to correctly simulate the resonant and nonresonant Raman images of single molecules but also lay the foundation for developing gauge invariant theory for other linear and nonlinear optical processes under the excitation of non-uniform electromagnetic field. [ABSTRACT FROM AUTHOR]

MDGA molecules can bind neuroligins and interfere with trans-synaptic interactions to neurexins, thereby impairing synapse development. However, the subcellular localization and dynamics of MDGAs, or their specific action mode in neurons remain unclear. Here, surface immu-nostaining of endogenous MDGAs and single molecule tracking of recombinant MDGAs in dissociated hippocampal neurons reveal that MDGAs are homogeneously distributed and exhibit fast membrane diffusion, with a small reduction in mobility across neuronal maturation. Knocking-down/ out MDGAs using shRNAs and CRISPR/Cas9 strategies increases the density of excitatory synapses, the membrane confinement of neuroligin-1, and the phosphotyrosine level of neuroligins associated with excitatory post-synaptic differentiation. Finally, MDGA silencing reduces the mobility of AMPA receptors, increases the frequency of miniature EPSCs (but not IPSCs), and selectively enhances evoked AMPA-receptor-mediated EPSCs in CA1 pyramidal neurons. Overall, our results support a mechanism by which interactions between MDGAs and neuroligin-1 delays the assembly of functional excitatory synapses containing AMPA receptors. [ABSTRACT FROM AUTHOR]

To date, traditional pre-transplant risk factors have failed to provide accurate risk stratification in transplantation. As a result, the practice of precision medicine remains elusive, resulting in a one-size-fits-all therapeutic approach for most patients. However, recent advancements in the understanding of HLA molecules at the molecular level have revitalized interest in HLA mismatch assessment. This review discusses HLA molecular mismatch as a potential prognostic and predictive biomarker available at the time of transplantation and answers some of the common questions and critiques of this approach. We highlight the retrospective data that supports single molecule risk categorization and explore the next steps required to evaluate its potential in clinical practice. [ABSTRACT FROM AUTHOR]

Single molecule localization microscopy (SMLM) has the potential to resolve structural details of biological samples at the nanometer length scale. Compared to room temperature experiments, SMLM performed under cryogenic temperature achieves higher photon yields and, hence, higher localization precision. However, to fully exploit the resolution it is crucial to account for the anisotropic emission characteristics of fluorescence dipole emitters with fixed orientation. In case of slight residual defocus, localization estimates may well be biased by tens of nanometers. We show here that astigmatic imaging in combination with information about the dipole orientation allows to extract the position of the dipole emitters without localization bias and down to a precision of 1 nm, thereby reaching the corresponding Cramér Rao bound. The approach is showcased with simulated data for various dipole orientations, and parameter settings realistic for real life experiments. [ABSTRACT FROM AUTHOR]

[Display omitted] • FRET-based intramolecular kinetic fingerprinting (iSiMREPS) is described. • Intramolecular assembly of sensor generates rapid kinetic fingerprints of single molecules. • Kinetic fingerprinting is accelerated using denaturant formamide. • A pair of invader strands aids removal of non-target-bound fluorescent probes and reduces background counts. • Rapid, highly sensitive and ultraspecific detection of diverse nucleic acid biomarkers is enabled. Cell-free nucleic acids (cfNAs) such as short non-coding microRNA (miRNA) and circulating tumor DNA (ctDNA) that reside in bodily fluids have emerged as potential cancer biomarkers. Methods for the rapid, highly specific, and sensitive monitoring of cfNAs in biofluids have, therefore, become increasingly attractive as clinical diagnosis tools. As a next generation technology, we provide a practical guide for an amplification-free, single molecule Förster resonance energy transfer (smFRET)-based kinetic fingerprinting approach termed intramolecular single molecule recognition through equilibrium Poisson sampling, or iSiMREPS, for the rapid detection and counting of miRNA and mutant ctDNA with virtually unlimited specificity and single molecule sensitivity. iSiMREPS utilizes a pair of fluorescent detection probes, wherein one probe immobilizes the target molecules on the surface, and the other probe transiently and reversibly binds to the target to generate characteristic time-resolved fingerprints as smFRET signal that are detected in a total internal reflection fluorescence microscope. Analysis of these kinetic fingerprints enables near-perfect discrimination between specific binding to target molecules and nonspecific background binding. By accelerating kinetic fingerprinting using the denaturant formamide and reducing background signals by removing target-less probes from the surface via toehold-mediated strand displacement, iSiMREPS has been demonstrated to count miR-141 and EGFR exon 19 deletion ctDNA molecules with a limit of detection (LOD) of ~1 and 3 fM, respectively, as well as mutant allele fractions as low as 0.0001%, during a standard acquisition time of only ~10 s per field of view. In this review, we provide a detailed roadmap for implementing iSiMREPS more broadly in research and clinical diagnostics, combining rapid analysis, high specificity, and high sensitivity. [ABSTRACT FROM AUTHOR]

Dynamin-like proteins are membrane-associated GTPases, conserved in bacteria and in eukaryotes, that can mediate nucleotide-driven membrane deformation or membrane fusion reactions. Bacillus subtilis' DynA has been shown to play an important role in protecting cells against chemicals that induce membrane leakage, and to form an increased number of membrane-associated structures after induction of membrane stress. We have studied the dynamics of DynA at a single molecule level in real time, to investigate how assembly of stress-induced structures is accompanied by changes in molecule dynamics. We show that DynA molecule displacements are best described by the existence of three distinct populations, a static mode, a low-mobility, and a fast-mobile state. Thus, DynA is most likely freely diffusive within the cytosol, moves along the cell membrane with a low mobility, and arrests at division sites or at stress-induced lesions at the membrane. In response to stress-inducing membrane leakage, but not to general stress, DynA molecules become slightly more static, but largely retain their mobility, suggesting that only few molecules are involved in the repair of membrane lesions, while most molecules remain in a dynamic mode scanning for lesions. Our data suggest that even moderate changes in single molecule dynamics can lead to visible changes in protein localization patterns. [ABSTRACT FROM AUTHOR]

Even 100 years after its introduction by Louis de Broglie, the wave-nature of matter is often regarded as a mind-boggling phenomenon. To give an intuitive introduction to this field, we here discuss the diffraction of massive molecules through a single, a double, and a triple slit, as well as a nanomechanical grating. While the experiments are in good agreement with undergraduate textbook predictions, we also observe pronounced differences resulting from the molecules' mass and internal complexity. The molecules' polarizability causes an attractive van der Waals interaction with the slit walls, which can be modified by rotating the nanomechanical mask with respect to the molecular beam. The text is meant to introduce students and teachers to the concepts of molecule diffraction, supported by problems and solutions that can be discussed in class. [ABSTRACT FROM AUTHOR]

Suitable metal nanostructures may induce surface-enhanced Raman scattering (SERS) enhancement factors (EFs) large-enough to reach single-molecule sensitivity. However, the gap hot-spot EF probability density function (PDF) has the character of a long-tail distribution, which dramatically mines the reproducibility of SERS experiments. Herein, we carry out electrodynamic calculations based on a 3D finite element method of two plasmonic nanostructures, combined with Monte Carlo simulations of the EF statistics under different external conditions. We compare the PDF produced by a homodimer of nanoparticles with that provided by a self-similar trimer. We show that the PDF is sensitive to the spatial distribution of near-field enhancement specifically supported by the nanostructure geometry. Breaking the symmetry of the plasmonic system is responsible for inducing particular modulations of the PDF tail resembling a multiple Poisson distribution. We also study the influence that molecular diffusion towards the hottest hot-spot, or selective hot-spot targeting, might have on the EF PDF. Our results quantitatively assess the possibility of designing the response of a SERS substrate so as to contain the intrinsic EF PDF variance and significantly improving, in principle, the reproducibility of SERS experiments. [ABSTRACT FROM AUTHOR]

In this study, the ligand exchange mechanism at a biomimetic ZnII centre, embedded in a pocket mimicking the possible constrains induced by a proteic structure, is explored. The residence time of different guest ligands (dimethylformamide, acetonitrile and ethanol) inside the cavity of a calix[6]arene‐based tris(imidazole) tetrahedral zinc complex was probed using 1D EXchange SpectroscopY NMR experiments. A strong dependence of residence time on water content was observed with no exchange occurring under anhydrous conditions, even in the presence of a large excess of guest ligand. These results advocate for an associative exchange mechanism involving the transient exo‐coordination of a water molecule, giving rise to 5‐coordinate ZnII intermediates, and inversion of the pyramid at the ZnII centre. Theoretical modelling by DFT confirmed that the associative mechanism is at stake. These results are particularly relevant in the context of the understanding of kinetic stability/lability in Zn proteins and highlight the key role that a single water molecule can play in catalysing ligand exchange and controlling the lability of ZnII in proteins. [ABSTRACT FROM AUTHOR]

The creation of molecular components for use as electronic devices has made enormous progress. In order to advance the field further toward realistic electronic concepts, methods for the controlled modification of the conducting properties of the molecules contacted by metallic electrodes need to be further developed. Here a comprehensive study of charge transport in a class of molecules that allows modifications by introducing metal centers into organic structures is presented. Single molecules are electrically contacted and characterized in order to understand the role of the metal centers in the conductance mechanism through the molecular junctions. It is shown that the presence of single metal ions modifies the energy levels and the coupling of the molecules to the electrical contacts, and that these modifications lead to systematic variations in the statistical behavior of transport properties of the molecular junctions. A rigorous statistical analysis of thousands of junctions is performed to reveal this correlation. The understanding of the role of the metal ion in the resulting conductance properties is an essential step toward the development of molecular electronic circuits. [ABSTRACT FROM AUTHOR]

The RNA pseudoknot that stimulates programmed ribosomal frameshifting in SARS-CoV-2 is a possible drug target. To understand how it responds to mechanical tension applied by ribosomes, thought to play a key role during frameshifting, we probe its structural dynamics using optical tweezers. We find that it forms multiple structures: two pseudoknotted conformers with different stability and barriers, and alternative stem-loop structures. The pseudoknotted conformers have distinct topologies, one threading the 5′ end through a 3-helix junction to create a knot-like fold, the other with unthreaded 5′ end, consistent with structures observed via cryo-EM and simulations. Refolding of the pseudoknotted conformers starts with stem 1, followed by stem 3 and lastly stem 2; Mg2+ ions are not required, but increase pseudoknot mechanical rigidity and favor formation of the knot-like conformer. These results resolve the SARS-CoV-2 frameshift signal folding mechanism and highlight its conformational heterogeneity, with important implications for structure-based drug-discovery efforts. The RNA pseudoknot of SARS-CoV-2 promotes -1 programmed ribosomal frameshifting. Here the authors use single molecule force spectroscopy to study the folding of this pseudoknot, showing that it forms at least two different pseudoknot conformers with distinct fold topologies. [ABSTRACT FROM AUTHOR]

Detailed understanding of the electronic energy transfer dynamics in conjugated polymer molecules and their conformation dependence is central for improving the photophysical properties as well as the performance of devices based on conjugated polymers. In this work, we demonstrate simultaneous measurement of the absorption and emission sites in single conjugated polymer poly[2,7-(9,9-dioctyluorene)-alt-4,7-bis(thiophen-2-yl)benzo-2,1,3-thiadiazole] (PFO-DBT) molecules based on polarization-resolved confocal fluorescence microscopy with excitation of phase-modulated ultrashort pulse pairs. The evolution of absorbing chromophores can be derived by modulating the relative phase between ultrashort pulse pairs and extracting modulation information in phase-dependent fluorescence. Meanwhile, the emitting chromophore can be measured by polarization-resolved emission. Simultaneous absorption and emission measurements give new insights into the evolution of energy transfer pathways in individual conjugated polymer molecules. The results suggest that the conformation of single conjugated polymer chains can be influenced by solvents. Single PFO-DBT conjugated molecules spin-cast from toluene solution have relatively fixed absorption and emission dipole moments. In contrast, single conjugated polymer molecules prepared with chloroform show multichromophore behavior that is responsible for distribution of absorption and emission in a single chain. The proposed scheme paves the way for further understanding of conformation dependent photophysical properties and the possible role of quantum effects in the energy transfer pathway in both natural and artificial light harvesting systems in the nanoscale. [ABSTRACT FROM AUTHOR]

Top‐down fabricated nanoantenna architectures of both metallic and dielectric materials show powerful functionalities for Raman and fluorescence enhancement with relevance to single molecule sensing while inducing directionality of chromophore emission with implications for single photon sources. We synthesize the smallest bow‐tie nanoantenna by selective tip‐to‐tip fusion of two tetrahedral colloidal quantum dots (CQDs) forming a dimer. While the tetrahedral monomers emit non‐polarized light, the bow‐tie architecture manifests nanoantenna functionality of enhanced emission polarization along the bow‐tie axis, as predicted theoretically and revealed by single‐particle spectroscopy. Theory also predicts the formation of an electric‐field hotspot at the bow‐tie epicenter. This is utilized for selective light‐induced photocatalytic metal growth at that location, unlike growth on the free tips in dark conditions, thus demonstrating bow‐tie dimer functionality as a photochemical reaction center. [ABSTRACT FROM AUTHOR]

Structures of peptide-loaded major histocompatibility complex class I (pMHC-I) and class II (pMHC-II) complexes are similar. However, whereas pMHC-II complexes include similar-sized IIα and IIβ chains, pMHC-I complexes include a heavy chain (HC) and a single domain molecule β2-microglobulin (β2-m). Recently, we elucidated several pMHC-I and pMHC-II structures of primitive vertebrate species. In the present study, a comprehensive comparison of pMHC-I and pMHC-II structures helps to understand pMHC structural evolution and supports the earlier proposed—though debated—direction of MHC evolution from class II-type to class I. Extant pMHC-II structures share major functional characteristics with a deduced MHC-II-type homodimer ancestor. Evolutionary establishment of pMHC-I presumably involved important new functions such as (i) increased peptide selectivity by binding the peptides in a closed groove (ii), structural amplification of peptide ligand sequence differences by binding in a non-relaxed fashion, and (iii) increased peptide selectivity by syngeneic heterotrimer complex formation between peptide, HC, and β2-m. These new functions were associated with structures that since their establishment in early pMHC-I have been very well conserved, including a shifted and reorganized P1 pocket (aka A pocket), and insertion of a β2-m hydrophobic knob into the peptide binding domain β-sheet floor. A comparison between divergent species indicates better sequence conservation of peptide binding domains among MHC-I than among MHC-II, agreeing with more demanding interactions within pMHC-I complexes. In lungfishes, genes encoding fusions of all MHC-IIα and MHC-IIβ extracellular domains were identified, and although these lungfish genes presumably derived from classical MHC-II, they provide an alternative mechanistic hypothesis for how evolution from class II-type to class I may have occurred. [ABSTRACT FROM AUTHOR]

Single molecules in solid state matrices have been proposed as sources of single photon Fock states back 20 years ago. Their success in quantum optics and in many other research fields stems from the simple recipes used in the preparation of samples, with hundreds of nominally identical and isolated molecules. Main challenges as of today for their application in photonic quantum technologies are the optimization of light extraction and the on-demand emission of indistinguishable photons. We here present Hong–Ou–Mandel (HOM) experiments with photons emitted by a single molecule of dibenzoterrylene in an anthracene nanocrystal at 3 K, under continuous wave and also pulsed excitation. A detailed theoretical model is applied, which relies on independent measurements for most experimental parameters, hence allowing for an analysis of the different contributions to the two-photon interference visibility, from residual dephasing to spectral filtering. A HOM interference visibility of more than 75% is reported, which, according to the model, is limited by the residual dephasing present at the operating temperature. [ABSTRACT FROM AUTHOR]

We have studied the localization and dynamics of bacterial Ffh, part of the SRP complex, its receptor FtsY, and of ribosomes in the Gamma-proteobacterium Shewanella putrefaciens. Using structured illumination microscopy, we show that ribosomes show a pronounced accumulation at the cell poles, whereas SRP and FtsY are distributed at distinct sites along the cell membrane, but they are not accumulated at the poles. Single molecule dynamics can be explained by assuming that all three proteins/complexes move as three distinguishable mobility fractions: a low mobility/static fraction may be engaged in translation, medium-fast diffusing fractions may be transition states, and high mobility populations likely represent freely diffusing molecules/complexes. Diffusion constants suggest that SRP and FtsY move together with slow-mobile ribosomes. Inhibition of transcription leads to loss of static molecules and reduction of medium-mobile fractions, in favor of freely diffusing subunits, while inhibition of translation appears to stall the medium mobile fractions. Depletion of FtsY leads to aggregation of Ffh, but not to loss of the medium mobile fraction, indicating that Ffh/SRP can bind to ribosomes independently from FtsY. Heat maps visualizing the three distinct diffusive populations show that while static molecules are mostly clustered at the cell membrane, diffusive molecules are localized throughout the cytosol. The medium fast populations show an intermediate pattern of preferential localization, suggesting that SRP/FtsY/ribosome transition states may form within the cytosol to finally find a translocon. [ABSTRACT FROM AUTHOR]