Quantitative measurement of cation-mediated adhesion of DNA to anionic surfaces
Single molecule force spectroscopy quantifies divalent-cation-mediated attraction of double-stranded DNA to an anionic self-assembled monolayer.
Hao, Xian↗
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Cumulene Wires Display Increasing Conductance with Increasing Length
One-dimensional sp-hybridized carbon wires, including cumulenes and polyynes, can be regarded as finite versions of carbynes. They are likely to be good candidates for molecular-scale conducting wires as they are predicted to have a high-conductance. In this study, we first characterize the single-molecule conductance of a series of cumulenes and polyynes with a backbone ranging in length from 4 to 8 carbon atoms, including [7]cumulene, the longest cumulenic carbon wire studied to date for molecular electronics. We observe different length dependence of conductance when comparing these two forms of carbon wires. Polyynes exhibit conductance decays with increasing molecular length, while cumulenes show a conductance increase with increasing molecular length. Their distinct conducting behaviors are attributed to their different bond length alternation, which is supported by theoretical calculations. Furthermore, this study confirms the long-standing theoretical predictions on sp-hybridized carbon wires and demonstrates that cumulenes can form highly conducting molecular wires.
36 MATERIALS SCIENCE↗
Viewing Optical Processes at the Nanoscale: Combining Scanning Tunneling Microscopy and Optical Spectroscopy
The combination of optical spectroscopy and scanning tunneling microscopy techniques has the potential to yield the unambiguous single-molecule level insight required to fully understand the complex structure–property relationship of emerging material systems. In this Perspective, we highlight the recent progress of single-molecule absorption detected by scanning tunneling microscopy (SMA-STM) to investigate light–matter interactions of supported (nano)particles, quantum dots, and molecular and thin films at the nanoscale. We further show how the SMA-STM technique has been recently extended to expand the classes of materials that can be investigated as well as recent design modifications that enable both time-resolved imaging and tomography. Finally, we hypothesize how these modifications can be further leveraged to advance our current knowledge of light–matter interactions and how the resulting nanoscale insight can be implemented for future material applications.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Simulating molecular polaritons in the collective regime using few-molecule models
The study of molecular polaritons beyond simple quantum emitter ensemble models (e.g., Tavis–Cummings) is challenging due to the large dimensionality of these systems and the complex interplay of molecular electronic and nuclear degrees of freedom. This complexity constrains existing models to either coarse-grain the rich physics and chemistry of the molecular degrees of freedom or artificially limit the description to a small number of molecules. In this work, we exploit permutational symmetries to drastically reduce the computational cost of ab initio quantum dynamics simulations for large N . Furthermore, we discover an emergent hierarchy of timescales present in these systems, that justifies the use of an effective single molecule to approximately capture the dynamics of the entire ensemble, an approximation that becomes exact as N → ∞. We also systematically derive finite N corrections to the dynamics and show that addition of k extra effective molecules is enough to account for phenomena whose rates scale as 𝒪( N − k ). Based on this result, we discuss how to seamlessly modify existing single-molecule strong coupling models to describe the dynamics of the corresponding ensemble. We call this approach collective dynamics using truncated equations (CUT-E), benchmark it against well-known results of polariton relaxation rates, and apply it to describe a universal cavity-assisted energy funneling mechanism between different molecular species. Beyond being a computationally efficient tool, this formalism provides an intuitive picture for understanding the role of bright and dark states in chemical reactivity, necessary to generate robust strategies for polariton chemistry.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Sequence-defined Pareto frontier of a copolymer structure
The correlations between the sequence of monomers in a macromolecule and its three-dimensional (3D) structure is a grand challenge in polymer science. The properties and functions of macromolecules depend on their 3D shape that has appeared to be dictated by their monomer sequence. However, the progress towards understanding the sequence–structure-property correlations and their utilization in materials engineering are slow because it is almost impossible to characterize an astronomically large number of possible sequences of a copolymer using traditional experimental and simulation methods. To address this problem, here, we combine evolutionary computing and coarse-grained molecular dynamics (CGMD) simulation and study the sequence-structure correlations of a model AB-type copolymer in a solution and assess the impact of sequence on the packing density in its bulk phase. The CGMD-based evolutionary algorithm (EA) screens the sequence space of a single chain copolymer efficiently and identifies a wide range of single-molecule structures including extremal radii of gyration. The data are utilized to estimate the Pareto front of the structure-space of a binary copolymer as a function of its composition. The monomer packings in single-molecule solution phase and multimolecular bulk phase are found to be identical. Finally, this work highlights the opportunities of sequence-specific control of macromolecular structure for designing target materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Three-Dimensional Patterning of Nanoparticles by Molecular Stamping
Directing the formation of nanoscale architectures from nanoparticles is one of the key challenges in designing nanomaterials with prescribed functions. Atomic systems, given their ability to form molecules and crystals via directional chemical bonds, provide an inspiration for establishing approaches where nanoparticles with designed anisotropic binding modalities can be assembled into nanoscale architectures. However, fabricating such nanoparticles has been challenging due to their small dimensions and limited ways for site-specific control of their surface. To this end, we present a Molecular Stamping (MOST) approach to pattern DNA-coated nanoparticles with molecules at the predefined positions on a nanoparticle surface. This patterning is realized by use of a rigid and coordinative DNA frame as a molecular stamping apparatus (MOST App). The MOST App transfers multiple types of molecular “inks”, DNA sequences, onto nanoparticle surface and fixes these molecular inks into place to form a designed pattern. After a nanoparticle release from MOST App, it possesses single-molecule patches that can provide anisotropic bonds with distinctive affinities. We further use these stamped nanoparticles to assemble prescribed clusters, whose structure is determined by the locations of patches. Using electron microscopy and tomographic methods, we investigate the efficiency of cluster formation and the resulting spatial arrangements of nanoparticles. The presented approach provides a single-molecule and spatiallydetermined control over nanoparticle functionalization for creating nanoparticles with designed placement of different molecules and for realizing a rational fabrication of nanomaterial architectures.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products
Nucleosome DNA unwrapping and its disassembly into hexasomes and tetrasomes is necessary for genomic access and plays an important role in transcription regulation. Previous single-molecule mechanical nucleosome unwrapping revealed a low- and a high-force transitions, and force-FRET pulling experiments showed that DNA unwrapping is asymmetric, occurring always first from one side before the other. However, the assignment of DNA segments involved in these transitions remains controversial. Here, using high-resolution optical tweezers with simultaneous single-molecule FRET detection, we show that the low-force transition corresponds to the undoing of the outer wrap of one side of the nucleosome (∼27 bp), a process that can occur either cooperatively or noncooperatively, whereas the high-force transition corresponds to the simultaneous unwrapping of ∼76 bp from both sides. This process may give rise stochastically to the disassembly of nucleosomes into hexasomes and tetrasomes whose unwrapping/rewrapping trajectories we establish. In contrast, nucleosome rewrapping does not exhibit asymmetry. To rationalize all previous nucleosome unwrapping experiments, it is necessary to invoke that mechanical unwrapping involves two nucleosome reorientations: one that contributes to the change in extension at the low-force transition and another that coincides but does not contribute to the high-force transition.
59 BASIC BIOLOGICAL SCIENCES↗
Thermobifida fusca Cel6B moves bidirectionally while processively degrading cellulose
Abstract Background Cellulose, an abundant biopolymer, has great potential to be utilized as a renewable fuel feedstock through its enzymatic degradation into soluble sugars followed by sugar fermentation into liquid biofuels. However, crystalline cellulose is highly resistant to hydrolysis, thus industrial-scale production of cellulosic biofuels has been cost-prohibitive to date. Mechanistic studies of enzymes that break down cellulose, called cellulases, are necessary to improve and adapt such biocatalysts for implementation in biofuel production processes. Thermobifida fusca Cel6B ( Tf Cel6B) is a promising candidate for industrial use due to its thermostability and insensitivity to pH changes. However, mechanistic studies probing Tf Cel6B hydrolytic activity have been limited to ensemble-scale measurements. Results We utilized optical tweezers to perform single-molecule, nanometer-scale measurements of enzyme displacement during cellulose hydrolysis by Tf Cel6B. Records featured forward motility on the order of 0.17 nm s −1 interrupted by backward motions and long pauses. Processive run lengths were on the order of 5 nm in both forward and backward directions. Motility records also showed rapid bidirectional displacements greater than 5 nm. Single-enzyme velocity and bulk ensemble activity were assayed on multiple crystalline cellulose allomorphs revealing that the degree of crystallinity and hydrogen bonding have disparate effects on the single-molecule level compared to the bulk scale. Additionally, we isolated and monitored the catalytic domain of Tf Cel6B and observed a reduction in velocity compared to the full-length enzyme that includes the carbohydrate-binding module. Applied force has little impact on enzyme velocity yet it readily facilitates dissociation from cellulose. Preliminary measurements at elevated temperatures indicated enzyme velocity strongly increases with temperature. Conclusions The unexpected motility patterns of Tf Cel6B are likely due to previously unknown mechanisms of processive cellulase motility implicating irregularities in cellulose substrate ultrastructure. While Tf Cel6B is processive, it has low motility at room temperature. Factors that most dramatically impact enzyme velocity are temperature and the presence of its native carbohydrate-binding module and linker. In contrast, substrate ultrastructure and applied force did not greatly impact velocity. These findings motivate further study of Tf Cel6B for its engineering and potential implementation in industrial processes.
Johnson, Madeline M. (ORCID:000000029518293X)↗
Genarris 2.0: A Random Structure Generator for Molecular Crystals
Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.
Crystal structure prediction↗
Transient local secondary structure in the intrinsically disordered C‐term of the Albino3 insertase
Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light‐harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma‐exposed C‐terminus (Alb3‐Cterm) that is responsible for binding the LHC‐loaded transit complex before LHC membrane insertion. Alb3‐Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single‐molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site‐directed mutagenesis, trypsin digestion assays, and all‐atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3‐Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter‐residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3‐Cterm for the LHC‐loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3‐Oxa1‐YidC family of insertases.
Okoto, Patience S.↗
Substituent Effects on Exchange Coupling and Magnetic Relaxation in 2,2'-Bipyrimidine Radical-Bridged Dilanthanide Complexes
Systematic analysis of related compounds is crucial to the design of single-molecule magnets with improved properties, yet such studies on multinuclear lanthanide complexes with strong magnetic coupling remain rare. In this work, we present the synthesis and magnetic characterization of the series of radical-bridged dilanthanide complex salts [(Cp* 2 Ln) 2 (μ-5,5'-R 2 bpym)](BPh 4 ) (Ln = Gd, Dy; R = NMe 2 (1), OEt (2), Me (3), F (4); bpym = 2,2'-bipyrimidine). Modification of the substituent on the bridging 5,5'-R 2 bpym radical anion allows the magnetic exchange coupling constant, J Gd-rad , for the gadolinium compounds in this series to be tuned over a range from -2.7 cm -1 (1) to -11.1 cm -1 (4), with electron-withdrawing or -donating substituents increasing or decreasing the strength of exchange coupling, respectively. Modulation of the exchange coupling interaction has a significant impact on the magnetic relaxation dynamics of the single-molecule magnets 1-Dy through 4-Dy, where stronger J Gd-rad for the corresponding Gd 3+ compounds is associated with larger thermal barriers to magnetic relaxation ( U eff ), open magnetic hysteresis at higher temperatures, and slower magnetic relaxation rates for through-barrier processes. Further, we derive an empirical linear correlation between the experimental U eff values for 1-Dy through 4-Dy and the magnitude of J Gd-rad for the corresponding gadolinium derivatives that provides insight into the electronic structure of these complexes. This simple model applies to other organic radical-bridged dysprosium complexes in the literature, and it establishes clear design criteria for increasing magnetic operating temperatures in radical-bridged molecules.
36 MATERIALS SCIENCE↗
Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds
We report a quasi-one-dimensional organic semiconductor, hepta(p-phenylene vinylene) (HPV), was incorporated into a DNA tensegrity triangle motif using a covalent strategy. 3D arrays were self-assembled from an HPV-DNA pseudo-rhombohedron edge by rational design and characterized by X-ray diffraction. Templated by the DNA motif, HPV molecules exist as single-molecule fluorescence emitters at the concentration of 8 mM within the crystal lattice. The anisotropic fluorescence emission from HPV-DNA crystals indicates HPV molecules are well aligned in the macroscopic 3D DNA lattices. Sophisticated nanodevices and functional materials constructed from DNA can be developed from this strategy by addressing functional components with molecular accuracy.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Spectroscopic Studies of the Magnetic Excitation and Spin;#8208;Phonon Couplings in a Single;#8208;Molecule Magnet
Abstract not provided
Stavretis, Shelby E.↗
Planar 2D wireframe DNA origami
Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility and curvature in solution; however, that may limit its suitability as a 2D structural template. In contrast, 2D wireframe DNA origami rendered with six-helix bundle edges offers local control over duplex orientations with enhanced in-plane rigidity. Here, we investigate the 3D structure of these assemblies using cryo–electron microscopy (cryo-EM). 3D reconstructions reveal a high degree of planarity and homogeneity in solution for polygonal objects with and without internal mesh, enabling 10-Å resolution for a triangle. Coarse-grained simulations were in agreement with cryo-EM data, offering molecular structural insight into this class of 2D DNA origami. Our results suggest that these assemblies may be valuable for 2D material applications and geometries that require high structural fidelity together with local control over duplex orientations, rather than parallel duplex assembly.
59 BASIC BIOLOGICAL SCIENCES↗
Phycobilisome core architecture influences photoprotective quenching by the Orange Carotenoid Protein
Photosynthetic organisms rely on sophisticated photoprotective mechanisms to prevent oxidative damage under high or fluctuating solar illumination. Cyanobacteria, which have evolved a unique, water-soluble light-harvesting complex—the phycobilisome—achieve photoprotection through a photoactivatable quencher called the Orange Carotenoid Protein (OCP). Phycobilisomes are highly symmetric and modular, formed by hierarchical assembly of conserved subunits into diverse geometries ranging from simple bundles to elaborate fan- or bouquet-like macromolecular architectures. Although OCP is known to provide photoprotection across species of cyanobacteria with different phycobilisome structures, it is not known whether or how these structural variations relate to changes in the photoprotective function of OCP. For example, OCP was recently discovered to bind as a dimer at two specific instances of an abundant structural motif on the tricylindrical phycobilisome of Synechocystis sp. PCC 6803, yet these sites are sterically inaccessible on a more common pentacylindrical phycobilisome ( Anabaena sp. PCC 7120). To understand how structural modularity and binding specificity contribute to conservation of OCP binding sites and function across different phycobilisome architectures, here we compare experimentally measured photophysical states accessible to these prototypical tricylindrical and pentacylindrical phycobilisomes, with and without OCP, at the single-molecule level. Together with Monte Carlo simulations of exciton transfer in OCP-quenched phycobilisomes, our results suggest that OCP binds at distinct and specific sites in each type of phycobilisome, yet provides nearly identical quenching strength to both phycobilisomes. Our findings highlight the utility of modular phycobilisome structures in balancing robust conservation of photoprotective function with adaptability of site-specific binding across species.
59 BASIC BIOLOGICAL SCIENCES↗
Ligand-induced transmembrane conformational coupling in monomeric $\mathrm{EGFR}$
Single pass cell surface receptors regulate cellular processes by transmitting ligand-encoded signals across the plasma membrane via changes to their extracellular and intracellular conformations. This transmembrane signaling is generally initiated by ligand binding to the receptors in their monomeric form. While subsequent receptor-receptor interactions are established as key aspects of transmembrane signaling, the contribution of monomeric receptors has been challenging to isolate due to the complexity and ligand-dependence of these interactions. By combining membrane nanodiscs produced with cell-free expression, single-molecule Förster Resonance Energy Transfer measurements, and molecular dynamics simulations, we report that ligand binding induces intracellular conformational changes within monomeric, full-length epidermal growth factor receptor (EGFR). Our observations establish the existence of extracellular/intracellular conformational coupling within a single receptor molecule. We implicate a series of electrostatic interactions in the conformational coupling and find the coupling is inhibited by targeted therapeutics and mutations that also inhibit phosphorylation in cells. Collectively, these results introduce a facile mechanism to link the extracellular and intracellular regions through the single transmembrane helix of monomeric EGFR, and raise the possibility that intramolecular transmembrane conformational changes upon ligand binding are common to single-pass membrane proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Tunable phononic quantum interference induced by two-dimensional metals
Harnessing quantum interference among bosons provides opportunities due to their longer coherence time than fermions. Fano resonance, an example of quantum interference between discrete and continuous states, is marked by an asymmetric lineshape. While photon-based Fano resonance has enabled high-sensitivity molecule sensing, phonon-based Fano resonance remains underexplored because of ineffective interference between discrete phonons and electronic continuum. In this work, we report phonon-based Fano resonance in a graphene/2D Ag/SiC heterostructure, arising from frequency and lifetime matching between discrete and continuous phonons of SiC. The observed Fano asymmetry is tunable over two orders of magnitude, surpassing previously reported phonon-based systems. The 2D Ag layer restructures the interfacial SiC and facilitates resonant scattering to enhance Fano asymmetry, which is unattainable in conventional Ag. We further demonstrated that this Fano resonance allows ultrasensitive molecule detection at the single-molecule level. Our work highlights phonon-based Fano resonance, opening avenues for engineering quantum interference with phonons.
Science & Technology - Other Topics↗
Solution-phase sample-averaged single-particle spectroscopy of quantum emitters with femtosecond resolution
Here, the development of many optical quantum technologies depends on the availability of solid-state single quantum emitters with near-perfect optical coherence. However, a standing issue that limits systematic improvement is the significant sample heterogeneity and lack of mechanistic understanding of microscopic energy flow at the single emitter level and ultrafast timescales. Here we develop solution-phase single-particle pump-probe spectroscopy with photon correlation detection that captures sample-averaged dynamics in single molecules and/or defect states with unprecedented clarity at femtosecond resolution. We apply this technique to single quantum emitters in two-dimensional hexagonal boron nitride, which suffers from significant heterogeneity and low quantum efficiency. From millisecond to nanosecond timescales, the translation diffusion, metastable-state-related bunching shoulders, rotational dynamics, and antibunching features are disentangled by their distinct photon-correlation timescales, which collectively quantify the normalized two-photon emission quantum yield. Leveraging its femtosecond resolution, spectral selectivity and ultralow noise (two orders of magnitude improvement over solid-state methods), we visualize electron-phonon coupling in the time domain at the single defect level, and discover the acceleration of polaronic formation driven by multi-electron excitation. Corroborated with results from a theoretical polaron model, we show how this translates to sample-averaged photon fidelity characterization of cascaded emission efficiency and optical decoherence time. Our work provides a framework for ultrafast spectroscopy in single emitters, molecules, or defects prone to photoluminescence intermittency and heterogeneity, opening new avenues of extreme-scale characterization and synthetic improvements for quantum information applications.
36 MATERIALS SCIENCE↗