@article{8971, abstract = {The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.}, author = {Fäßler, Florian and Dimchev, Georgi A and Hodirnau, Victor-Valentin and Wan, William and Schur, Florian KM}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction}}, doi = {10.1038/s41467-020-20286-x}, volume = {11}, year = {2020}, } @article{13361, abstract = {In nature, light is harvested by photoactive proteins to drive a range of biological processes, including photosynthesis, phototaxis, vision, and ultimately life. Bacteriorhodopsin, for example, is a protein embedded within archaeal cell membranes that binds the chromophore retinal within its hydrophobic pocket. Exposure to light triggers regioselective photoisomerization of the confined retinal, which in turn initiates a cascade of conformational changes within the protein, triggering proton flux against the concentration gradient, providing the microorganisms with the energy to live. We are inspired by these functions in nature to harness light energy using synthetic photoswitches under confinement. Like retinal, synthetic photoswitches require some degree of conformational flexibility to isomerize. In nature, the conformational change associated with retinal isomerization is accommodated by the structural flexibility of the opsin host, yet it results in steric communication between the chromophore and the protein. Similarly, we strive to design systems wherein isomerization of confined photoswitches results in steric communication between a photoswitch and its confining environment. To achieve this aim, a balance must be struck between molecular crowding and conformational freedom under confinement: too much crowding prevents switching, whereas too much freedom resembles switching of isolated molecules in solution, preventing communication. In this Account, we discuss five classes of synthetic light-switchable compounds—diarylethenes, anthracenes, azobenzenes, spiropyrans, and donor–acceptor Stenhouse adducts—comparing their behaviors under confinement and in solution. The environments employed to confine these photoswitches are diverse, ranging from planar surfaces to nanosized cavities within coordination cages, nanoporous frameworks, and nanoparticle aggregates. The trends that emerge are primarily dependent on the nature of the photoswitch and not on the material used for confinement. In general, we find that photoswitches requiring less conformational freedom for switching are, as expected, more straightforward to isomerize reversibly under confinement. Because these compounds undergo only small structural changes upon isomerization, however, switching does not propagate into communication with their environment. Conversely, photoswitches that require more conformational freedom are more challenging to switch under confinement but also can influence system-wide behavior. Although we are primarily interested in the effects of geometric constraints on photoswitching under confinement, additional effects inevitably emerge when a compound is removed from solution and placed within a new, more crowded environment. For instance, we have found that compounds that convert to zwitterionic isomers upon light irradiation often experience stabilization of these forms under confinement. This effect results from the mutual stabilization of zwitterions that are brought into close proximity on surfaces or within cavities. Furthermore, photoswitches can experience preorganization under confinement, influencing the selectivity and efficiency of their photoreactions. Because intermolecular interactions arising from confinement cannot be considered independently from the effects of geometric constraints, we describe all confinement effects concurrently throughout this Account.}, author = {Grommet, Angela B. and Lee, Lucia M. and Klajn, Rafal}, issn = {1520-4898}, journal = {Accounts of Chemical Research}, keywords = {General Medicine, General Chemistry}, number = {11}, pages = {2600--2610}, publisher = {American Chemical Society}, title = {{Molecular photoswitching in confined spaces}}, doi = {10.1021/acs.accounts.0c00434}, volume = {53}, year = {2020}, } @article{13362, abstract = {Aggregation of organic molecules can drastically affect their physicochemical properties. For instance, the optical properties of BODIPY dyes are inherently related to the degree of aggregation and the mutual orientation of BODIPY units within these aggregates. Whereas the noncovalent aggregation of various BODIPY dyes has been studied in diverse media, the ill-defined nature of these aggregates has made it difficult to elucidate the structure–property relationships. Here, we studied the encapsulation of three structurally simple BODIPY derivatives within the hydrophobic cavity of a water-soluble, flexible PdII6L4 coordination cage. The cavity size allowed for the selective encapsulation of two dye molecules, irrespective of the substitution pattern on the BODIPY core. Working with a model, a pentamethyl-substituted derivative, we found that the mutual orientation of two BODIPY units in the cage’s cavity was remarkably similar to that in the crystalline state of the free dye, allowing us to isolate and characterize the smallest possible noncovalent H-type BODIPY aggregate, namely, an H-dimer. Interestingly, a CF3-substituted BODIPY, known for forming J-type aggregates, was also encapsulated as an H-dimer. Taking advantage of the dynamic nature of encapsulation, we developed a system in which reversible switching between H- and J-aggregates can be induced for multiple cycles simply by addition and subsequent destruction of the cage. We expect that the ability to rapidly and reversibly manipulate the optical properties of supramolecular inclusion complexes in aqueous media will open up avenues for developing detection systems that operate within biological environments.}, author = {Gemen, Julius and Ahrens, Johannes and Shimon, Linda J. W. and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {41}, pages = {17721--17729}, publisher = {American Chemical Society}, title = {{Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage}}, doi = {10.1021/jacs.0c08589}, volume = {142}, year = {2020}, } @article{13363, abstract = {Temporal activation of biological processes by visible light and subsequent return to an inactive state in the absence of light is an essential characteristic of photoreceptor cells. Inspired by these phenomena, light-responsive materials are very attractive due to the high spatiotemporal control of light irradiation, with light being able to precisely orchestrate processes repeatedly over many cycles. Herein, it is reported that light-driven proton transfer triggered by a merocyanine-based photoacid can be used to modulate the permeability of pH-responsive polymersomes through cyclic, temporally controlled protonation and deprotonation of the polymersome membrane. The membranes can undergo repeated light-driven swelling–contraction cycles without losing functional effectiveness. When applied to enzyme loaded-nanoreactors, this membrane responsiveness is used for the reversible control of enzymatic reactions. This combination of the merocyanine-based photoacid and pH-switchable nanoreactors results in rapidly responding and versatile supramolecular systems successfully used to switch enzymatic reactions ON and OFF on demand.}, author = {Moreno, Silvia and Sharan, Priyanka and Engelke, Johanna and Gumz, Hannes and Boye, Susanne and Oertel, Ulrich and Wang, Peng and Banerjee, Susanta and Klajn, Rafal and Voit, Brigitte and Lederer, Albena and Appelhans, Dietmar}, issn = {1613-6829}, journal = {Small}, keywords = {Biomaterials, Biotechnology, General Materials Science, General Chemistry}, number = {37}, publisher = {Wiley}, title = {{Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors}}, doi = {10.1002/smll.202002135}, volume = {16}, year = {2020}, } @article{13364, abstract = {Photochromic molecules undergo reversible isomerization upon irradiation with light at different wavelengths, a process that can alter their physical and chemical properties. For instance, dihydropyrene (DHP) is a deep-colored compound that isomerizes to light-brown cyclophanediene (CPD) upon irradiation with visible light. CPD can then isomerize back to DHP upon irradiation with UV light or thermally in the dark. Conversion between DHP and CPD is thought to proceed via a biradical intermediate; bimolecular events involving this unstable intermediate thus result in rapid decomposition and poor cycling performance. Here, we show that the reversible isomerization of DHP can be stabilized upon confinement within a PdII6L4 coordination cage. By protecting this reactive intermediate using the cage, each isomerization reaction proceeds to higher yield, which significantly decreases the fatigue experienced by the system upon repeated photocycling. Although molecular confinement is known to help stabilize reactive species, this effect is not typically employed to protect reactive intermediates and thus improve reaction yields. We envisage that performing reactions under confinement will not only improve the cyclic performance of photochromic molecules, but may also increase the amount of product obtainable from traditionally low-yielding organic reactions.}, author = {Canton, Martina and Grommet, Angela B. and Pesce, Luca and Gemen, Julius and Li, Shiming and Diskin-Posner, Yael and Credi, Alberto and Pavan, Giovanni M. and Andréasson, Joakim and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {34}, pages = {14557--14565}, publisher = {American Chemical Society}, title = {{Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage}}, doi = {10.1021/jacs.0c06146}, volume = {142}, year = {2020}, } @article{13365, abstract = {Photoswitchable molecules are employed for many applications, from the development of active materials to the design of stimuli-responsive molecular systems and light-powered molecular machines. To fully exploit their potential, we must learn ways to control the mechanism and kinetics of their photoinduced isomerization. One possible strategy involves confinement of photoresponsive switches such as azobenzenes or spiropyrans within crowded molecular environments, which may allow control over their light-induced conversion. However, the molecular factors that influence and control the switching process under realistic conditions and within dynamic molecular regimes often remain difficult to ascertain. As a case study, here we have employed molecular models to probe the isomerization of azobenzene guests within a Pd(II)-based coordination cage host in water. Atomistic molecular dynamics and metadynamics simulations allow us to characterize the flexibility of the cage in the solvent, the (rare) guest encapsulation and release events, and the relative probability/kinetics of light-induced isomerization of azobenzene analogues in these host–guest systems. In this way, we can reconstruct the mechanism of azobenzene switching inside the cage cavity and explore key molecular factors that may control this event. We obtain a molecular-level insight on the effects of crowding and host–guest interactions on azobenzene isomerization. The detailed picture elucidated by this study may enable the rational design of photoswitchable systems whose reactivity can be controlled via host–guest interactions.}, author = {Pesce, Luca and Perego, Claudio and Grommet, Angela B. and Klajn, Rafal and Pavan, Giovanni M.}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {21}, pages = {9792--9802}, publisher = {American Chemical Society}, title = {{Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage}}, doi = {10.1021/jacs.0c03444}, volume = {142}, year = {2020}, } @article{9054, abstract = {The fundamental and practical importance of particle stabilization has motivated various characterization methods for studying polymer brushes on particle surfaces. In this work, we show how one can perform sensitive measurements of neutral polymer coating on colloidal particles using a commercial zetameter and salt solutions. By systematically varying the Debye length, we study the mobility of the polymer-coated particles in an applied electric field and show that the electrophoretic mobility of polymer-coated particles normalized by the mobility of non-coated particles is entirely controlled by the polymer brush and independent of the native surface charge, here controlled with pH, or the surface–ion interaction. Our result is rationalized with a simple hydrodynamic model, allowing for the estimation of characteristics of the polymer coating: the brush length L, and the Brinkman length ξ, determined by its resistance to flows. We demonstrate that the Debye layer provides a convenient and faithful probe to the characterization of polymer coatings on particles. Because the method simply relies on a conventional zetameter, it is widely accessible and offers a practical tool to rapidly probe neutral polymer brushes, an asset in the development and utilization of polymer-coated colloidal particles.}, author = {Youssef, Mena and Morin, Alexandre and Aubret, Antoine and Sacanna, Stefano and Palacci, Jérémie A}, issn = {1744-6848}, journal = {Soft Matter}, keywords = {General Chemistry, Condensed Matter Physics}, number = {17}, pages = {4274--4282}, publisher = {Royal Society of Chemistry }, title = {{Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt}}, doi = {10.1039/c9sm01850f}, volume = {16}, year = {2020}, } @article{9067, abstract = {Gadolinium silicide (Gd5Si4) nanoparticles are an interesting class of materials due to their high magnetization, low Curie temperature, low toxicity in biological environments and their multifunctional properties. We report the magnetic and magnetothermal properties of gadolinium silicide (Gd5Si4) nanoparticles prepared by surfactant-assisted ball milling of arc melted bulk ingots of the compound. Using different milling times and speeds, a wide range of crystallite sizes (13–43 nm) could be produced and a reduction in Curie temperature (TC) from 340 K to 317 K was achieved, making these nanoparticles suitable for self-controlled magnetic hyperthermia applications. The magnetothermal effect was measured in applied AC magnetic fields of amplitude 164–239 Oe and frequencies 163–519 kHz. All particles showed magnetic heating with a strong dependence of the specific absorption rate (SAR) on the average crystallite size. The highest SAR of 3.7 W g−1 was measured for 43 nm sized nanoparticles of Gd5Si4. The high SAR and low TC, (within the therapeutic range for magnetothermal therapy) makes the Gd5Si4 behave like self-regulating heat switches that would be suitable for self-controlled magnetic hyperthermia applications after biocompatibility and cytotoxicity tests.}, author = {Nauman, Muhammad and Alnasir, Muhammad Hisham and Hamayun, Muhammad Asif and Wang, YiXu and Shatruk, Michael and Manzoor, Sadia}, issn = {2046-2069}, journal = {RSC Advances}, keywords = {General Chemistry, General Chemical Engineering}, number = {47}, pages = {28383--28389}, publisher = {Royal Society of Chemistry}, title = {{Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles}}, doi = {10.1039/d0ra05394e}, volume = {10}, year = {2020}, } @article{10341, abstract = {Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes.}, author = {Debets, V. E. and Janssen, L. M. C. and Šarić, Anđela}, issn = {1744-683X}, journal = {Soft Matter}, keywords = {condensed matter physics, general chemistry}, number = {47}, pages = {10628--10639}, publisher = {Royal Society of Chemistry}, title = {{Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes}}, doi = {10.1039/d0sm00712a}, volume = {16}, year = {2020}, } @article{10350, abstract = {The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation.}, author = {Dear, Alexander J. and Meisl, Georg and Šarić, Anđela and Michaels, Thomas C. T. and Kjaergaard, Magnus and Linse, Sara and Knowles, Tuomas P. J.}, issn = {2041-6539}, journal = {Chemical Science}, keywords = {general chemistry}, number = {24}, pages = {6236--6247}, publisher = {Royal Society of Chemistry}, title = {{Identification of on- and off-pathway oligomers in amyloid fibril formation}}, doi = {10.1039/c9sc06501f}, volume = {11}, year = {2020}, } @article{10351, abstract = {Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we found that most Aβ42 oligomers dissociate into their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar structures. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to those of aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases.}, author = {Michaels, Thomas C. T. and Šarić, Anđela and Curk, Samo and Bernfur, Katja and Arosio, Paolo and Meisl, Georg and Dear, Alexander J. and Cohen, Samuel I. A. and Dobson, Christopher M. and Vendruscolo, Michele and Linse, Sara and Knowles, Tuomas P. J.}, issn = {1755-4349}, journal = {Nature Chemistry}, keywords = {general chemical engineering, general chemistry}, number = {5}, pages = {445--451}, publisher = {Springer Nature}, title = {{Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide}}, doi = {10.1038/s41557-020-0452-1}, volume = {12}, year = {2020}, } @article{8405, abstract = {Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available.}, author = {Gauto, Diego F. and Estrozi, Leandro F. and Schwieters, Charles D. and Effantin, Gregory and Macek, Pavel and Sounier, Remy and Sivertsen, Astrid C. and Schmidt, Elena and Kerfah, Rime and Mas, Guillaume and Colletier, Jacques-Philippe and Güntert, Peter and Favier, Adrien and Schoehn, Guy and Schanda, Paul and Boisbouvier, Jerome}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex}}, doi = {10.1038/s41467-019-10490-9}, volume = {10}, year = {2019}, } @article{8408, abstract = {Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artefact-free dynamics measurements, and allows probing motions effectively without molecular-weight limitations. The application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (ps-ms). We quantitatively probe ring flip motions, and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.}, author = {Gauto, Diego F. and Macek, Pavel and Barducci, Alessandro and Fraga, Hugo and Hessel, Audrey and Terauchi, Tsutomu and Gajan, David and Miyanoiri, Yohei and Boisbouvier, Jerome and Lichtenecker, Roman and Kainosho, Masatsune and Schanda, Paul}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {28}, pages = {11183--11195}, publisher = {American Chemical Society}, title = {{Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR}}, doi = {10.1021/jacs.9b04219}, volume = {141}, year = {2019}, } @article{8413, abstract = {NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains.}, author = {Rovó, Petra and Smith, Colin A. and Gauto, Diego and de Groot, Bert L. and Schanda, Paul and Linser, Rasmus}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {2}, pages = {858--869}, publisher = {American Chemical Society}, title = {{Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques}}, doi = {10.1021/jacs.8b09258}, volume = {141}, year = {2019}, } @article{13370, abstract = {Efficient isomerization of photochromic molecules often requires conformational freedom and is typically not available under solvent-free conditions. Here, we report a general methodology allowing for reversible switching of such molecules on the surfaces of solid materials. Our method is based on dispersing photochromic compounds within polysilsesquioxane nanowire networks (PNNs), which can be fabricated as transparent, highly porous, micrometer-thick layers on various substrates. We found that azobenzene switching within the PNNs proceeded unusually fast compared with the same molecules in liquid solvents. Efficient isomerization of another photochromic system, spiropyran, from a colorless to a colored form was used to create reversible images in PNN-coated glass. The coloration reaction could be induced with sunlight and is of interest for developing “smart” windows.}, author = {Chu, Zonglin and Klajn, Rafal}, issn = {1530-6992}, journal = {Nano Letters}, keywords = {Mechanical Engineering, Condensed Matter Physics, General Materials Science, General Chemistry, Bioengineering}, number = {10}, pages = {7106--7111}, publisher = {American Chemical Society}, title = {{Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules}}, doi = {10.1021/acs.nanolett.9b02642}, volume = {19}, year = {2019}, } @article{13371, abstract = {Diamondoid nanoporous crystals represent a synthetically challenging class of materials that typically have been obtained from tetrahedral building blocks. In this issue of Chem, Stoddart and coworkers demonstrate that it is possible to generate diamondoid frameworks from a hexacationic building block lacking a tetrahedral symmetry. These results highlight the great potential of self-assembly for rapidly transforming small molecules into structurally complex functional materials.}, author = {Białek, Michał J. and Klajn, Rafal}, issn = {2451-9294}, journal = {Chem}, keywords = {Materials Chemistry, Biochemistry (medical), General Chemical Engineering, Environmental Chemistry, Biochemistry, General Chemistry}, number = {9}, pages = {2283--2285}, publisher = {Elsevier}, title = {{Diamond grows up}}, doi = {10.1016/j.chempr.2019.08.012}, volume = {5}, year = {2019}, } @article{13372, abstract = {The capacity to respond or adapt to environmental changes is an intrinsic property of living systems that comprise highly-connected subcomponents communicating through chemical networks. The development of responsive synthetic systems is a relatively new research area that covers different disciplines, among which nanochemistry brings conceptually new demonstrations. Especially attractive are ligand-protected gold nanoparticles, which have been extensively used over the last decade as building blocks in constructing superlattices or dynamic aggregates, under the effect of an applied stimulus. To reflect the importance of surface chemistry and nanoparticle core composition in the dynamic self-assembly of nanoparticles, we provide here an overview of various available stimuli, as tools for synthetic chemists to exploit. Along with this task, the review starts with the use of chemical stimuli such as solvent, pH, gases, metal ions or biomolecules. It then focuses on physical stimuli: temperature, magnetic and electric fields, as well as light. To reflect on the increasing complexity of current architectures, we discuss systems that are responsive to more than one stimulus, to finally encourage further research by proposing future challenges.}, author = {Grzelczak, Marek and Liz-Marzán, Luis M. and Klajn, Rafal}, issn = {1460-4744}, journal = {Chemical Society Reviews}, keywords = {General Chemistry}, number = {5}, pages = {1342--1361}, publisher = {Royal Society of Chemistry}, title = {{Stimuli-responsive self-assembly of nanoparticles}}, doi = {10.1039/c8cs00787j}, volume = {48}, year = {2019}, } @article{13373, abstract = {The reversible photoisomerization of azobenzene has been utilized to construct a plethora of systems in which optical, electronic, catalytic, and other properties can be controlled by light. However, owing to azobenzene’s hydrophobic nature, most of these examples have been realized only in organic solvents, and systems operating in water are relatively scarce. Here, we show that by coadsorbing the inherently hydrophobic azobenzenes with water-solubilizing ligands on the same nanoparticulate platforms, it is possible to render them essentially water-soluble. To this end, we developed a modified nanoparticle functionalization procedure allowing us to precisely fine-tune the amount of azobenzene on the functionalized nanoparticles. Molecular dynamics simulations helped us to identify two distinct supramolecular architectures (depending on the length of the background ligand) on these nanoparticles, which can explain their excellent aqueous solubilities. Azobenzenes adsorbed on these water-soluble nanoparticles exhibit highly reversible photoisomerization upon exposure to UV and visible light. Importantly, the mixed-monolayer approach allowed us to systematically investigate how the background ligand affects the switching properties of azobenzene. We found that the nature of the background ligand has a profound effect on the kinetics of azobenzene switching. For example, a hydroxy-terminated background ligand is capable of accelerating the back-isomerization reaction by more than 6000-fold. These results pave the way toward the development of novel light-responsive nanomaterials operating in aqueous media and, in the long run, in biological environments.}, author = {Chu, Zonglin and Han, Yanxiao and Bian, Tong and De, Soumen and Král, Petr and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {5}, pages = {1949--1960}, publisher = {American Chemical Society}, title = {{Supramolecular control of azobenzene switching on nanoparticles}}, doi = {10.1021/jacs.8b09638}, volume = {141}, year = {2019}, } @article{9060, abstract = {Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium.}, author = {Ramananarivo, Sophie and Ducrot, Etienne and Palacci, Jérémie A}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, number = {1}, publisher = {Springer Nature}, title = {{Activity-controlled annealing of colloidal monolayers}}, doi = {10.1038/s41467-019-11362-y}, volume = {10}, year = {2019}, } @article{10622, abstract = {We demonstrate a method for manipulating small ensembles of vortices in multiply connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux through the superconducting structure. By scanning the tip over the surface of the device and by utilizing the dynamical coupling between the vortices and the cantilever, a high-resolution spatial map of the different vortex configurations is obtained. Moving the tip to a particular location in the map stabilizes a distinct multivortex configuration. Thus, the scanning of the tip over a particular trajectory in space permits nontrivial operations to be performed, such as braiding of individual vortices within a larger vortex ensemble—a key capability required by many proposals for topological quantum computing.}, author = {Polshyn, Hryhoriy and Naibert, Tyler and Budakian, Raffi}, issn = {1530-6992}, journal = {Nano Letters}, keywords = {mechanical engineering, condensed matter physics, general materials science, general chemistry, bioengineering}, number = {8}, pages = {5476--5482}, publisher = {American Chemical Society}, title = {{Manipulating multivortex states in superconducting structures}}, doi = {10.1021/acs.nanolett.9b01983}, volume = {19}, year = {2019}, }