A Chalcogen-Bonding Cascade Switch for Planarizable Push-Pull Probes

Synthesis, X-ray characterization and DFT analysis of dicyanidoaurate telluronium salts: on the importance of charge assisted chalcogen bonds

In this manuscript we report the synthesis and X-ray characterization of two cyanidoaurate telluronium salts, namely (3-fluorophenyl)(methyl)(phenyl)telluronium dicyanidoaurate [(3-F-Ph)(Me)(Ph)Te][Au(CN)2] (1) and methyldiphenyltelluronium dicyanidoaurate [(Me)(Ph)2Te][Au(CN)2] (2). In the solid state, the tellurium atom establishes three concurrent and directional chalcogen bonds (ChBs) with the adjacent anions, in both compounds. These charge-assisted ChBs (CAChBs) have been analyzed using DFT calculations and several computational tools. The MEP surface analysis discloses the existence of three σ-holes at the Te-atoms capable of establishing strong CAChBs with the counter-ions. In addition, significant charge transfer from the lone pair orbital at the N-atom of the anion to the antibonding σ*(Te-C) orbital of the cation is observed in some cases.

Fluorogenic In Situ Thioacetalization: Expanding the Chemical Space of Fluorescent Probes, Including Unorthodox, Bifurcated, and Mechanosensitive Chalcogen Bonds

Progress with fluorescent flippers, small-molecule probes to image membrane tension in living systems, has been limited by the effort needed to synthesize the twisted push-pull mechanophore. Here, we move to a higher oxidation level to introduce a new design paradigm that allows the screening of flipper probes rapidly, at best in situ. Late-stage clicking of thioacetals and acetals allows simultaneous attachment of targeting units and interfacers and exploration of the critical chalcogen-bonding donor at the same time. Initial studies focus on plasma membrane targeting and develop the chemical space of acetals and thioacetals, from acyclic amino acids to cyclic 1,3-heterocycles covering dioxanes as well as dithiolanes, dithianes, and dithiepanes, derived also from classics in biology like cysteine, lipoic acid, asparagusic acid, DTT, and epidithiodiketopiperazines. From the functional point of view, the sensitivity of membrane tension imaging in living cells could be doubled, with lifetime differences in FLIM images increasing from 0.55 to 1.11 ns. From a theoretical point of view, the complexity of mechanically coupled chalcogen bonding is explored, revealing, among others, intriguing bifurcated chalcogen bonds.

Substituent Effects in Tetrel Bonds Involving Aromatic Silane Derivatives: An ab initio Study

In this manuscript substituent effects in several silicon tetrel bonding (TtB) complexes were investigated at the RI-MP2/def2-TZVP level of theory. Particularly, we have analysed how the interaction energy is influenced by the electronic nature of the substituent in both donor and acceptor moieties. To achieve that, several tetrafluorophenyl silane derivatives have been substituted at the meta and para positions by several electron donating and electron withdrawing groups (EDG and EWG, respectively), such as -NH₂, -OCH₃, -CH₃, -H, -CF₃ and -CN substituents. As electron donor molecules, we have used a series of hydrogen cyanide derivatives using the same EDGs and EWGs. We have obtained the Hammett's plots for different combinations of donors and acceptors and in all cases we have obtained good regression plots (interaction energies vs. Hammet's σ parameter). In addition, we have used the electrostatic potential (ESP) surface analysis as well as the Bader's theory of atoms in molecules (AIM) and noncovalent interaction plot (NCI plot) techniques to further characterize the TtBs studied herein. Finally, a Cambridge Structural Database (CSD) inspection was carried out, retrieving several structures where halogenated aromatic silanes participate in tetrel bonding interactions, being an additional stabilization force of their supramolecular architectures.

Dynamic Covalent Michael Acceptors to Penetrate Cells: Thiol-Mediated Uptake with Tetrel-Centered Exchange Cascades, Assisted by Halogen-Bonding Switches

Chalcogen-centered cascade exchange chemistry is increasingly understood to account for thiol-mediated uptake, that is, the ability of reversibly thiol-reactive agents to penetrate cells. Here, reversible Michael acceptors are shown to enable and inhibit thiol-mediated uptake, including the cytosolic delivery of proteins. Dynamic cyano-cinnamate dimers rival the best chalcogen-centered inhibitors. Patterns generated in inhibition heatmaps reveal contributions from halogen-bonding switches that occur independent from the thyroid transporter MCT8. The uniqueness of these patterns supports that the entry of tetrel-centered exchangers into cells differs from chalcogen-centered systems. These results expand the chemical space of thiol-mediated uptake and support the existence of a universal exchange network to bring matter into cells, abiding to be decoded for drug delivery and drug discovery in the broadest sense.

Dithieno[3,2-b:2',3'-d]thiophene (DTT): an emerging heterocyclic building block for future organic electronic materials & functional supramolecular chemistry

Heterocyclic compounds being potent biochemical materials are ubiquitous molecules in our life. Amongst, the five membered aromatic ring systems, thiophene has emerged as a remarkable entity in organic electronics owing to its (i) high resonance energy, (ii) more electrophilic reactivity than benzene, (iii) high π-electron density, (iv) planar structure and, (v) presence of vacant d-orbital in addition to the presence of loosely bind lone-pairs of electrons on sulfur atoms. In recent past, thiophene-fused molecule namely, dithienothiophene (DTT) has attracted a tremendous attention of the researchers worldwide due to their potential applicability in organic electronics such as in solar cells, electrochromic devices (ECDs), organic field effect transistors (OFETs), organic limiting diodes (OLEDs), fluorescent probes, redox switching and so forth because of their (i) higher charge mobility, (ii) extended π-conjugation, and (iii) better tuning of band gaps, etc. In this particular review article, we envisioned to report the recent advancements made on the DTT-based architectures not only because of the potential applicability of this valuable scaffold in organic electronic but also to motivate the young researchers worldwide to look for the challenging opportunities related to this privileged building block in both material sciences and functional supramolecular chemistry.

Importance of Cu and Ag regium-π bonds in supramolecular chemistry and biology: a combined crystallographic and ab initio study

Identifying and characterizing new binding events between electron donor and acceptor counterparts represents a crucial step to complete the molecular recognition and aggregation picture, which is key to chemistry and biology. In this study we interrogated both the PDB (Protein Data Bank) and CSD (Cambridge Structural Database) for the presence of Cu and Ag regium-π (Rg-π) bonds (an attractive noncovalent force between elements from group 11 and π-systems). Concretely, we found evidence of the plausible biological role of the interaction in protein-DNA systems, bacterial Ag extrusion processes and Heme group redox functionality. Furthermore, we also highlighted the implications of Rg-π bonds in the crystal packing of two host-guest systems, where this interaction is key for the binding and recognition of small organic molecules as well as for the encapsulation of organometallic complexes. Theoretical models were used to analyse the strength of the interaction (RI-MP2/def2-TZVP level of theory) together with QTAIM (Quantum Theory of Atoms in Molecules), NBO (Natural Bonding Orbital) and NCIplot (Non Covalent Interactions plot) analyses, which further assisted in the characterization of the regium-π interactions described herein. We expect the results from this study will be useful to attract the attention of chemical biologists as well as to expand the potential of the interaction to the supramolecular chemistry and crystal engineering communities.

Crystallographic and Theoretical Study of Osme Bonds in Nitrido-Osmium(VI) Complexes

Osme bonds have been recently defined as the attractive interaction between an element of group 8 acting as an electrophile and any atom or group of atoms acting as a nucleophile. To date, the known examples of osme bonds in X-ray structures involve mostly the highly reactive OsO4 and amines and amine oxides. In this work, evidence supporting the existence of osme bonds in osmium(VI) derivatives is reported. In particular, nitrido-osmium(VI) complexes that present square-pyramidal geometries are well disposed to participate in osme bonds opposite to the Os≡N bond. By using a combination of experimental and theoretical results, the existence and importance of this new class of σ-hole interactions is demonstrated in the solid state of several nitrido-osmium(VI) derivatives.

Noncovalent Interactions Involving Group 6 in Biological Systems: The Case of Molybdopterin and Tungstopterin Cofactors

In this study we propose to coin the term Wolfium bond (WfB) to refer to a net attractive force (noncovalent interaction) between any element of group 6 and electron donor atoms (neutral molecules or anions) and to differentiate it from a coordination bond (metal‐ligand interaction). We provide evidence of the existence of this interaction by inspecting the X‐ray crystal structure of proteins containing Molybdopterin and Tungstopterin cofactors from the Protein Data Bank (PDB). The plausible biological role of the interaction as well as its physical nature (antibonding Wf‐Ligand orbital involved) are also analyzed by means of ab initio calculations (RI‐MP2/def2‐TZVP level of theory), Atoms in Molecules (AIM), Natural Bond Orbital (NBO) and Noncovalent Interactions plot (NCIplot) analyses.

Cyclic Thiosulfonates for Thiol-Mediated Uptake: Cascade Exchangers, Transporters, Inhibitors

Thiol-mediated uptake is emerging as a powerful method to penetrate cells. Cyclic oligochalcogenides (COCs) have been identified as privileged scaffolds to enable and inhibit thiol-mediated uptake because they can act as dynamic covalent cascade exchangers, i.e., every exchange produces a new, covalently tethered exchanger. In this study, our focus is on the essentially unexplored COCs of higher oxidation levels. Quantitative characterization of the underlying dynamic covalent exchange cascades reveals that the initial ring opening of cyclic thiosulfonates (CTOs) proceeds at a high speed even at a low pH. The released sulfinates exchange with disulfides in aprotic but much less in protic environments. Hydrophobic domains were thus introduced to direct CTOs into hydrophobic pockets to enhance their reactivity. Equipped with such directing groups, fluorescently labeled CTOs entered the cytosol of living cells more efficiently than the popular asparagusic acid. Added as competitive agents, CTOs inhibit the uptake of various COC transporters and SARS-CoV-2 lentivectors. Orthogonal trends found with different transporters support the existence of multiple cellular partners to account for the diverse expressions of thiol-mediated uptake. Dominant self-inhibition and high activity of dimers imply selective and synergistic exchange in hydrophobic pockets as distinguishing characteristics of thiol-mediated uptake with CTOs. The best CTO dimers with hydrophobic directing groups inhibit the cellular entry of SARS-CoV-2 lentivectors with an IC₅₀ significantly lower than the previous best CTO, below the 10 μM threshold and better than ebselen. Taken together, these results identify CTOs as an intriguing motif for use in cytosolic delivery, as inhibitors of lentivector entry, and for the evolution of dynamic covalent networks in the broadest sense, with reactivity-based selectivity of cascade exchange emerging as a distinguishing characteristic that deserves further attention.

HydroFlipper membrane tension probes: imaging membrane hydration and mechanical compression simultaneously in living cells

HydroFlippers are introduced as the first fluorescent membrane tension probes that report simultaneously on membrane compression and hydration. The probe design is centered around a sensing cycle that couples the mechanical planarization of twisted push–pull fluorophores with the dynamic covalent hydration of their exocyclic acceptor. In FLIM images of living cells, tension-induced deplanarization is reported as a decrease in fluorescence lifetime of the dehydrated mechanophore. Membrane hydration is reported as the ratio of the photon counts associated to the hydrated and dehydrated mechanophores in reconvoluted lifetime frequency histograms. Trends for tension-induced decompression and hydration of cellular membranes of interest (MOIs) covering plasma membrane, lysosomes, mitochondria, ER, and Golgi are found not to be the same. Tension-induced changes in mechanical compression are rather independent of the nature of the MOI, while the responsiveness to changes in hydration are highly dependent on the intrinsic order of the MOI. These results confirm the mechanical planarization of push–pull probes in the ground state as most robust mechanism to routinely image membrane tension in living cells, while the availability of simultaneous information on membrane hydration will open new perspectives in mechanobiology.

HydroFlippers respond to membrane compression and hydration in the same fluorescence lifetime imaging microscopy histogram: the responses do not correlate.

Flipper Probes for the Community

This article describes four fluorescent membrane tension probes that have been designed, synthesized, evaluated, commercialized and applied to current biology challenges in the context of the NCCR Chemical Biology. Their names are Flipper-TR^®, ER Flipper-TR^®, Lyso Flipper-TR^®, and Mito Flipper-TR^®. They are available from Spirochrome.

Frustrated Lewis Pairs Based on Carbon⋅⋅⋅Carbon+ Tetrel Bonds: A DFT Study

The ability of Triangulenium (TA⁺ ) compounds to form Frustrated Lewis Pairs (FLPs) with N-HeteroCycle Carbenes (NHCs) is analysed in this manuscript at the PBE0-D3/def2-TZVP level of theory. We have used six TA⁺ -based moieties, three presenting similar bridging groups (O (trioxo), -CH₂ (triaryl) and -NH (triaza)) and another three mixing, O, -CH₂ and NH moieties. In addition, several aryl-substituted NHCs have been used as electron donor moieties to undergo carbon⋅⋅⋅carbon⁺ tetrel bonds with the TA⁺ derivatives. More precisely, -Me,-iPr, -tBu and -Ph groups were used. Finally, we have used Bader's quantum theory of "atoms in molecules" (QTAIM) and Natural Bonding Analysis (NBO) to characterize the carbon⋅⋅⋅carbon⁺ tetrel bonds described herein. We expect the results gathered herein will be useful for further exploitation of carbon⋅⋅⋅carbon⁺ bonds in the formation of FLPs as well as to expand the current knowledge of tetrel bonds to the fields of synthetic chemistry and catalysis.

Design of Azobenzene beyond Simple On-Off Behavior

Azobenzenes are without a doubt the most widely used light-induced switching units, and there is a plethora of application examples ranging from supramolecular chemistry to material science and biological chemistry. Here, we present a smart azobenzene, in which the photoswitching capability of the azobenzene moiety can be reversibly switched on and off using a second unit (redox switch). This second switching unit is based on the variation of the strength of a chalcogen bond between the azo group and a Te-Ph unit in ortho position to the azo group. This allows the selective switching of only one azobenzene unit in the presence of other azobenzene switches. The entire double-switch is a very simple, small system that can also be easily synthesized. As a result, this double-switch can be used as a smarter replacement for the established azobenzene system in the future. For example, in contrast to the latter this double-switch could be employed to store state information analogous to a flip-flop in digital electronic systems.

Computational Evaluation of Me2 TCCP as Lewis Acid

Supramolecular adducts between dimethyl-2,2,3,3-tetracyanocyclopropane (Me2 TCCP) with 21 small (polar) molecules and 10 anions were computed with DFT (B3LYP-D3/def2-TZVP). Their optimized geometries were used to obtain interaction energies, and perform energy decomposition and 'atoms-in-molecules' analyses. A set of 38 other adducts were also evaluated for comparison purposes. Selected examples were further scrutinized by inspection of the molecular electrostatic potential maps, Noncovalent Interaction index plots, the Laplacian, the orbital interactions, and by estimating the Gibbs free energy of complexation in hexane solution. These calculations divulge the thermodynamic feasibility of Me2 TCCP adducts and show that complexation is typically driven by dispersion with less polarized partners, but by orbital interactions when more polarized or anionic guests are deployed. Most Me2 TCCP adducts are more stable than simple hydrogen bonding with water, but less stable than traditional Lewis adducts involving Me3 B, or a strong halogen bond such as with Br2 . Several bonding analyses showed that the locus of interaction is found near the electron poor sp3 -hydridized (NC)2 C-C(CN)2 carbon atoms. An empty hybrid σ*/π* orbital on Me2 TCCP was identified that can be held responsible for the stability of the most stable adducts due to donor-acceptor interactions.

Selenium chalcogen bonds are involved in protein-carbohydrate recognition: a combined PDB and theoretical study

In this manuscript the ability of selenium carbohydrates to undergo chalcogen bonding (ChB) interactions with protein residues has been studied at the RI-MP2/def2-TZVP level of theory. An inspection of the Protein Data Bank (PDB) revealed SeA (A = O, C and S) intermolecular contacts involving Se-pyranose ligands and ASP, TYR, SER and MET residues. Theoretical models were built to analyse the strength and directionality of the interaction together with "Atoms in Molecules" (AIM), Natural Bonding Orbital (NBO) and Non Covalent Interactions plot (NCIplot) analyses, which further assisted in the characterization of the ChBs described herein. We expect that the results from this study will be useful to expand the current knowledge regarding biological ChBs as well as to increase the visibility of the interaction among the carbohydrate chemistry community.

The primary dipole of flipper probes

Despite their growing popularity in biology to image membrane tension, central design principles of flipper probes have never been validated. Here we report that upon deletion of their primary dipole, from electron-poor and electron-rich dithienothiophenes, absorptions blue-shift, lifetimes shorten dramatically, and mechanosensitivity in cells vanishes not partially, but completely.

Genetically Encoded Supramolecular Targeting of Fluorescent Membrane Tension Probes within Live Cells: Precisely Localized Controlled Release by External Chemical Stimulation

To image membrane tension in selected membranes of interest (MOI) inside living systems, the field of mechanobiology requires increasingly elaborated small-molecule chemical tools. We have recently introduced HaloFlipper, i.e., a mechanosensitive flipper probe that can localize in the MOI using HaloTag technology to report local membrane tension changes using fluorescence lifetime imaging microscopy. However, the linker tethering the probe to HaloTag hampers the lateral diffusion of the probe in all the lipid domains of the MOI. For a more global membrane tension measurement in any MOI, we present here a supramolecular chemistry strategy for selective localization and controlled release of flipper into the MOI, using a genetically encoded supramolecular tag. SupraFlippers, functionalized with a desthiobiotin ligand, can selectively accumulate in the organelle having expressed streptavidin. The addition of biotin as a biocompatible external stimulus with a higher affinity for Sav triggers the release of the probe, which spontaneously partitions into the MOI. Freed in the lumen of endoplasmic reticulum (ER), SupraFlippers report the membrane orders along the secretory pathway from the ER over the Golgi apparatus to the plasma membrane. Kinetics of the process are governed by both the probe release and the transport through lipid domains. The concentration of biotin can control the former, while the expression level of a transmembrane protein (Sec12) involved in the stimulation of the vesicular transport from ER to Golgi influences the latter. Finally, the generation of a cell-penetrating and fully functional Sav-flipper complex using cyclic oligochalcogenide (COC) transporters allows us to combine the SupraFlipper strategy and HaloTag technology.

DFT and IsoStar Analyses to Assess the Utility of σ- and π-Hole Interactions for Crystal Engineering

The interpretation of 36 charge neutral 'contact pairs' from the IsoStar database was supported by DFT calculations of model molecules 1-12, and bimolecular adducts thereof. The 'central groups' are σ-hole donors (H2 O and aromatic C-I), π-hole donors (R-C(O)Me, R-NO2 and R-C6 F5 ) and for comparison R-C6 H5 (R=any group or atom). The 'contact groups' are hydrogen bond donors X-H (X=N, O, S, or R2 C, or R3 C) and lone-pair containing fragments (R3 C-F, R-C≡N and R2 C=O). Nearly all the IsoStar distributions follow expectations based on the electrostatic potential of the 'central-' and 'contact group'. Interaction energies (ΔEBSSE ) are dominated by electrostatics (particularly between two polarized molecules) or dispersion (especially in case of large contact area). Orbital interactions never dominate, but could be significant (∼30 %) and of the n/π→σ*/π* kind. The largest degree of directionality in the IsoStar plots was typically observed for adducts more stable than ΔEBSSE ≈-4 kcal⋅mol-1 , which can be seen as a benchmark-value for the utility of an interaction in crystal engineering. This benchmark could be met with all the σ- and π-hole donors studied.

Chalcogen bonding interactions in chelating, chiral bis(selenocyanates)

Both anti (racemic mixture) and syn (meso) forms of a chiral, chelating chalcogen bond (ChB) donor interact with halides through short Se⋯X⁻ directional interactions.

Chemistry Evolves, Terms Evolve, but Phenomena Do Not Evolve: From Chalcogen-Chalcogen Interactions to Chalcogen Bonding

Chalcogen bonding is important in numerous aspects of chemistry, both in the solid state and in solution. Surveying the literature, it becomes clear that during its rebranding from chalcogen-chalcogen interactions, some parts of the community have somewhat neglected to recall its discovery and the initial studies referring to it in its previous guise. In this Viewpoint, we trace the path of research into this phenomenon, from its discovery, through its renaming, and to some of the varied and interesting chemistry it has led to so far, ranging from crystal engineering through supramolecular assembly to modern catalysis.

Naphthalenediimides with Cyclic Oligochalcogenides in Their Core

Naphthalenediimides (NDIs) are privileged scaffolds par excellence, of use in functional systems from catalysts to ion channels, photosystems, sensors, ordered matter in all forms, tubes, knots, stacks, sheets, vesicles, and colored over the full visible range. Despite this extensively explored chemical space, there is still room to discover core-substituted NDIs with fundamentally new properties: NDIs with cyclic trisulfides (i.e., trisulfanes) in their core absorb at 668 nm, emit at 801 nm, and contract into disulfides (i.e., dithietes) upon irradiation at <475 nm. Intramolecular 1,5-chalcogen bonds account for record redshifts with trisulfides, ring-tension mediated chalcogen-bond-mediated cleavage for blueshifts to 492 nm upon ring contraction. Cyclic oligochalcogenides (COCs) in the NDI core open faster than strained dithiolanes as in asparagusic acid and are much better retained on thiol exchange affinity columns. This makes COC-NDIs attractive not only within the existing multifunctionality, particularly artificial photosystems, but also for thiol-mediated cellular uptake.

HaloFlippers: A General Tool for the Fluorescence Imaging of Precisely Localized Membrane Tension Changes in Living Cells

Tools to image membrane tension in response to mechanical stimuli are badly needed in mechanobiology. We have recently introduced mechanosensitive flipper probes to report quantitatively global membrane tension changes in fluorescence lifetime imaging microscopy (FLIM) images of living cells. However, to address specific questions on physical forces in biology, the probes need to be localized precisely in the membrane of interest (MOI). Herein we present a general strategy to image the tension of the MOI by tagging our newly introduced HaloFlippers to self-labeling HaloTags fused to proteins in this membrane. The critical challenge in the construction of operational HaloFlippers is the tether linking the flipper and the HaloTag: It must be neither too taut nor too loose, be hydrophilic but lipophilic enough to passively diffuse across membranes to reach the HaloTags, and allow partitioning of flippers into the MOI after the reaction. HaloFlippers with the best tether show localized and selective fluorescence after reacting with HaloTags that are close enough to the MOI but remain nonemissive if the MOI cannot be reached. Their fluorescence lifetime in FLIM images varies depending on the nature of the MOI and responds to myriocin-mediated sphingomyelin depletion as well as to osmotic stress. The response to changes in such precisely localized membrane tension follows the validated principles, thus confirming intact mechanosensitivity. Examples covered include HaloTags in the Golgi apparatus, peroxisomes, endolysosomes, and the ER, all thus becoming accessible to the selective fluorescence imaging of membrane tension.

Engineering Crystals Using sp3 -C Centred Tetrel Bonding Interactions

1,1,2,2-Tetracyanocyclopropane derivatives 1 and 2 were designed and synthesized to probe the utility of sp3 -C centred tetrel bonding interactions in crystal engineering. The crystal packing of 1 and 2 and their 1,4-dioxane cocrystals is dominated by sp3 -C(CN)2 ⋅⋅⋅O interactions, has significant C⋅⋅⋅O van der Waals overlap (≤0.266 Å) and DFT calculations indicate interaction energies of up to -11.0 kcal mol-1 . A cocrystal of 2 with 1,4-thioxane reveals that the cyclopropane synthon prefers interacting with O over S. Computational analyses revealed that the electropositive C2 (CN)4 pocket in 1 and 2 can be seen as a strongly directional 'tetrel-bond donor', similar to halogen bond or hydrogen bond donors. This disclosure is expected to have implications for the utility of such 'tetrel bond donors' in molecular disciplines such as crystal engineering, supramolecular chemistry, molecular recognition and medicinal chemistry.

Noble Gas Bonding Interactions Involving Xenon Oxides and Fluorides

Noble gas (or aerogen) bond (NgB) can be outlined as the attractive interaction between an electron-rich atom or group of atoms and any element of Group-18 acting as an electron acceptor. The IUPAC already recommended systematic nomenclature for the interactions of groups 17 and 16 (halogen and chalcogen bonds, respectively). Investigations dealing with noncovalent interactions involving main group elements (acting as Lewis acids) have rapidly grown in recent years. They are becoming acting players in essential fields such as crystal engineering, supramolecular chemistry, and catalysis. For obvious reasons, the works devoted to the study of noncovalent Ng-bonding interactions are significantly less abundant than halogen, chalcogen, pnictogen, and tetrel bonding. Nevertheless, in this short review, relevant theoretical and experimental investigations on noncovalent interactions involving Xenon are emphasized. Several theoretical works have described the physical nature of NgB and their interplay with other noncovalent interactions, which are discussed herein. Moreover, exploring the Cambridge Structural Database (CSD) and Inorganic Crystal Structure Database (ICSD), it is demonstrated that NgB interactions are crucial in governing the X-ray packing of xenon derivatives. Concretely, special attention is given to xenon fluorides and xenon oxides, since they exhibit a strong tendency to establish NgBs.

Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements

The term spodium (Sp) bond is proposed to refer to a net attractive interaction between any element of Group 12 and electron-rich atoms (Lewis bases or anions). These noncovalent interactions are markedly different from coordination bonds (antibonding Sp-ligand orbital involved). Evidence is provided for the existence of this interaction by calculations at the RI-MP2/aug-cc-pVTZ level of theory, atoms-in-molecules, and natural bond orbital analyses and by examining solid-state structures in the Cambridge Structure Database.

Fluorescent Membrane Tension Probes for Super-Resolution Microscopy: Combining Mechanosensitive Cascade Switching with Dynamic-Covalent Ketone Chemistry

We report the design, synthesis, and evaluation of fluorescent flipper probes for single-molecule super-resolution imaging of membrane tension in living cells. Reversible switching from bright-state ketones to dark-state hydrates, hemiacetals, and hemithioacetals is demonstrated for twisted and planarized mechanophores in solution and membranes. Broadband femtosecond fluorescence up-conversion spectroscopy evinces ultrafast chalcogen-bonding cascade switching in the excited state in solution. According to fluorescence lifetime imaging microscopy, the new flippers image membrane tension in live cells with record red shifts and photostability. Single-molecule localization microscopy with the new tension probes resolves membranes well below the diffraction limit.

Twisting and tilting of a mechanosensitive molecular probe detects order in membranes

Lateral forces in biological membranes affect a variety of dynamic cellular processes. Recent synthetic efforts have introduced fluorescent "flippers" as environment-sensitive planarizable push-pull probes that can detect lipid packing and membrane tension, and respond to lipid-induced mechanical forces by a shift in their spectroscopic properties. Herein, we investigate the molecular origin of the mechanosensitivity of the best known flipper, Flipper-TR, by an extended set of molecular dynamics (MD) simulations in membranes of increasing complexity and under different physicochemical conditions, revealing unprecedented details of the sensing process. Simulations enabled by accurate refinement of Flipper-TR force field using quantum mechanical calculations allowed us to unambiguously correlate the planarization of the two fluorescent flippers to spectroscopic response. In particular, Flipper-TR conformation exhibits bimodal distribution in disordered membranes and a unimodal distribution in highly ordered membranes. Such dramatic change was associated with a shift in Flipper-TR excitation spectra, as supported both by our simulated and experimentally-measured spectra. Flipper-TR sensitivity to phase-transition is confirmed by a temperature-jump protocol that alters the lipid phase of an ordered membrane, triggering an instantaneous mechanical twisting of the probe. Simulations show that the probe is also sensitive to surface tension, since even in a naturally disordered membrane, the unimodal distribution of coplanar flippers can be achieved if a sufficiently negative surface tension is applied to the membrane. MD simulations in ternary mixtures containing raft-like nanodomains show that the probe can discriminate lipid domains in phase-separated complex bilayers. A histogram-based approach, called DOB-phase classification, is introduced that can differentiate regions of disordered and ordered lipid phases by comparing dihedral distributions of Flipper-TR. Moreover, a new sensing mechanism involving the orientation of Flipper-TR is elucidated, corroborating experimental evidence that the probe tilt angle is strongly dependent on lipid ordering. The obtained atomic-resolution description of Flipper-TR mechanosensitivity is key to the interpretation of experimental data and to the design of novel mechanosensors with improved spectroscopic properties.

Radicalradical chalcogen bonds: CSD analysis and DFT calculations

This manuscript reports a combination of crystallographic analysis (Cambridge Structural Database) and theoretical DFT calculations in chalcogen bonding interactions involving radicals in both the Ch bond (ChB) donor and acceptor. As a radical ChB acceptor (nucleophile) we have used benzodithiazolyl radical (BDTA) and as Ch bond donors (electrophile) we have used dithiadiazolyl and diselenadiazolyl radicals of the general formula p-X-C6F4-CNChChN (Ch = S, and Se). We have evaluated how the para substituent (X) affects the interaction energy, spin density and charge/spin transfer from the electron rich BDTA radical to the electron poor dichalcogenadiazolyl ring. The ability of the latter rings to form ChBs in the solid state has been examined by a comprehensive search in the CSD; several cases are used to exemplify the preferred geometric features of the complexes and they are compared with the theory. The molecular surface electrostatic potentials calculated for these ChB donors allow for a very precise rationalization of the self-assembly motifs most frequently adopted in the crystalline state and of their relative robustness.

Methyl Scanning for Mechanochemical Chalcogen-Bonding Cascade Switches

Chalcogen-bonding cascade switching was introduced recently to produce the chemistry tools needed to image physical forces in biological systems. In the original flipper probe, one methyl group appeared to possibly interfere with the cascade switch. In this report, this questionable methyl group is replaced by a hydrogen. The deletion of this methyl group in planarizable push-pull probes was not trivial because it required the synthesis of dithienothiophenes with four different substituents on the four available carbons. The mechanosensitivity of the resulting demethylated flipper probe was nearly identical to that of the original. Thus methyl groups in the switching region are irrelevant for function, whereas those in the twisting region are essential. This result supports the chalcogen-bonding cascade switching concept and, most importantly, removes significant synthetic demands from future probe development.