The hit-and-return system enables efficient time-resolved serial synchrotron crystallography.

We present a 'hit-and-return' (HARE) method for time-resolved serial synchrotron crystallography with time resolution from milliseconds to seconds or longer. Timing delays are set mechanically, using the regular pattern in fixed-target crystallography chips and a translation stage system. Optical pump-probe experiments to capture intermediate structures of fluoroacetate dehalogenase binding to its ligand demonstrated that data can be collected at short (30 ms), medium (752 ms) and long (2,052 ms) intervals.

Unraveling a Ligand-Induced Twist of a Homodimeric Enzyme by Pulsed Electron-Electron Double Resonance.

Mechanistic insights into protein-ligand interactions can yield chemical tools for modulating protein function and enable their use for therapeutic purposes. For the homodimeric enzyme tRNA-guanine transglycosylase (TGT), a putative virulence target of shigellosis, ligand binding has been shown by crystallography to transform the functional dimer geometry into an incompetent twisted one. However, crystallographic observation of both end states does neither verify the ligand-induced transformation of one dimer into the other in solution nor does it shed light on the underlying transformation mechanism. We addressed these questions in an approach that combines site-directed spin labeling (SDSL) with distance measurements based on pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy. We observed an equilibrium between the functional and twisted dimer that depends on the type of ligand, with a pyranose-substituted ligand being the most potent one in shifting the equilibrium toward the twisted dimer. Our experiments suggest a dissociation-association mechanism for the formation of the twisted dimer upon ligand binding.

Molecular Recognition and Cocrystallization of Methylated and Halogenated Fragments of Danicalipin A by Enantiopure Alleno-Acetylenic Cage Receptors.

Enantiopure (P)4- and (M)4-configured alleno-acetylenic cage (AAC) receptors offer a highly defined interior for the complexation and structure elucidation of small molecule fragments of the stereochemically complex chlorosulfolipid danicalipin A. Solution (NMR), solid state (X-ray), and theoretical investigations of the formed host-guest complexes provide insight into the conformational preferences of 14 achiral and chiral derivatives of the danicalipin A chlorohydrin core in a confined, mostly hydrophobic environment, extending previously reported studies in polar solvents. The conserved binding mode of the guests permits deciphering the effect of functional group replacements on Gibbs binding energies ΔG. A strong contribution of conformational energies toward the binding affinities is revealed, which explains why the denser packing of larger apolar domains of the guests does not necessarily lead to higher association. Enantioselective binding of chiral guests, with energetic differences ΔΔG293 K up to 0.7 kcal mol-1 between diastereoisomeric complexes, is explained by hydrogen- and halogen-bonding, as well as dispersion interactions. Calorimetric studies (ITC) show that the stronger binding of one enantiomer is accompanied by an increased gain in enthalpy ΔH but at the cost of a larger entropic penalty TΔS stemming from tighter binding.

Stimuli-Responsive Resorcin[4]arene Cavitands: Toward Visible-Light-Activated Molecular Grippers.

Resorcin[4]arene cavitands, equipped with diverse quinone (Q) and [Ru(bpy)2 dppz]2+ (bpy=2,2'-bipyridine, dppz=dipyrido[3,2-a:2',3'-c]phenazine) photosensitizing walls in different configurations, were synthesized. Upon visible-light irradiation at 420 nm, electron transfer from the [Ru(bpy)2 dppz]2+ to the Q generates the semiquinone (SQ) radical anion, triggering a large conformational switching from a flat kite to a vase with a cavity for the encapsulation of small guests, such as cyclohexane and heteroalicyclic derivatives, in CD3 CN. Depending on the molecular design, the SQ radical anion can live for several minutes (≈10 min) and the vase can be generated in a secondary process without need for addition of a sacrificial electron donor to accumulate the SQ state. Switching can also be triggered by other stimuli, such as changes in solvent, host-guest complexation, and chemical and electrochemical processes. This comprehensive investigation benefits the development of stimuli-responsive nanodevices, such as light-activated molecular grippers.

The Quest for Molecular Grippers: Photo-Electric Control of Molecular Gripping Machinery.

The quest for nanoscale molecular machines has inspired the search for their close relatives, molecular grippers. This path was paved by the development of resorcin[4]arene cavitands and their quinone-based redox-active congeners. In this Concept article, the efforts to design and establish the control of quinone-functionalized resorcin[4]arenes by electronic and electromagnetic stimuli is described. This was achieved by relying on paramagnetic semiquinone radical anions formed electrochemically or by photoredox catalysis. The gripper-like motion of such species could not be studied by conventional NMR spectroscopy. Instead, an entirely different approach had to be developed that included various electroanalytical and spectroelectrochemical methods, including UV/Vis/NIR spectroelectrochemistry, pulsed EPR and Davies 1 H ENDOR spectroscopy, transient absorption spectroscopy, and time-resolved luminescence measurements, besides density functional theory calculations and X-ray crystallography. The conceptual breakthroughs are reviewed as well as the current state and future perspectives of photoredox-switchable molecular grippers.

Helicene Monomers and Dimers: Chiral Chromophores Featuring Strong Circularly Polarized Luminescence.

The synthesis and chiroptical properties of a series of enantiomerically pure, C2 -symmetrical carbo[6]helicene dimers are reported. Two helicene cores are connected through a buta-1,3-diyne-1,4-diyl linker or a heteroaromatic bridge and bear arylethynyl substituents at their 15-positions. This ensures the possibility of extended electronic communication throughout the whole molecule. The new chromophores exhibit intense ECD spectra with strong bands in the UV/Vis region well above 400 nm. The anisotropy factor gabs (defined as Δϵ/ϵ) reaches values up to 0.047, which are unusually large for single organic molecules. They also display blue fluorescence, with good quantum yields (Φf ∼0.25). The emitted light is circularly polarized to an outstanding extent: in some cases, the luminescence dissymmetry factor glum =2(IL -IR )/(IL +IR ) attains values of |0.025|. To the best of our knowledge, such values are among the highest ever reported for non-aggregated organic fluorophores.

Chalcogen Bonding "2S-2N Squares" versus Competing Interactions: Exploring the Recognition Properties of Sulfur.

Chalcogen bonding (CB) is the focus of increased attention for its applications in medicinal chemistry, materials science, and crystal engineering. However, the origin of sulfur's recognition properties remains controversial, and experimental evidence for supporting theories is still emerging. Here, a comprehensive evaluation of sulfur CB interactions is presented by investigating 2,1,3-benzothiadiazole X-ray crystallographic structures gathered from the Cambridge Structure Database (CSD), Protein Data Bank (PDB), and own laboratory findings. Through the systematic analysis of substituent effects on a subset library of over thirty benzothiadiazole derivatives, the competing interactions have been categorized into four main classes, namely 2S-2N CB square, halogen bonding (XB), S⋅⋅⋅S, and hydrogen-bonding (HB). A geometric model is employed to characterize the 2S-2N CB square motifs and discuss the role of electrostatic, dipole, and orbital contributions toward the interaction.

Targeting a Large Active Site: Structure-Based Design of Nanomolar Inhibitors of Trypanosoma brucei Trypanothione Reductase.

Trypanothione reductase (TR) plays a key role in the unique redox metabolism of trypanosomatids, the causative agents of human African trypanosomiasis (HAT), Chagas' disease, and leishmaniases. Introduction of a new, lean propargylic vector to a known class of TR inhibitors resulted in the strongest reported competitive inhibitor of Trypanosoma (T.) brucei TR, with an inhibition constant Ki of 73 nm, which is fully selective against human glutathione reductase (hGR). The best ligands exhibited in vitro IC50 values (half-maximal inhibitory concentration) against the HAT pathogen, T. brucei rhodesiense, in the mid-nanomolar range, reaching down to 50 nm. X-Ray co-crystal structures confirmed the binding mode of the ligands and revealed the presence of a HEPES buffer molecule in the large active site. Extension of the propargylic vector, guided by structure-based design, to replace the HEPES buffer molecule should give inhibitors with low nanomolar Ki and IC50 values for in vivo studies.

Molecular Recognition with Resorcin[4]arene Cavitands: Switching, Halogen-Bonded Capsules, and Enantioselective Complexation.

The development of synthetic host-guest chemistry to investigate and quantify weak, non-covalent interactions has been key to unraveling the complexity of molecular recognition in chemical and biological systems. Macrocycles have shown great utility in the design of receptors, enabling the development of highly preorganized structures. Among macrocycles, resorcin[4]arene-based cavitands have become privileged scaffolds due to their synthetic tunability, which allows access to structures with precisely defined geometries, as well as receptors that display conformational switching between two distinct states with a large difference in guest-binding properties. Here, we highlight three case studies demonstrating redox- and photoredox-controlled switching of molecular recognition properties, the formation of guest-binding supramolecular capsules based solely on halogen-bonding interactions, and enantioselective encapsulation of chiral, substituted cyclohexanes by enantiopure cage compounds as a result of perfect shape complementarity, dispersion interactions, and halogen bonding. The high geometrical and conformational control that can be achieved with resorcin[4]arene-derived host systems will continue to be a powerful resource in future molecular recognition studies.

Selective Extraction of C70 by a Tetragonal Prismatic Porphyrin Cage.

Along with the advent of supramolecular chemistry, research on fullerene receptors based on noncovalent bonding interactions has attracted a lot of attention. Here, we present the design and synthesis of a cationic molecular cage: a cyclophane composed of two tetraphenylporphyrins, bridged face-to-face by four viologen units in a rhomboid prismatic manner. The large cavity inside the cage, as well as the favorable donor-acceptor interactions between the porphyrin panels and the fullerene guests, enables the cage to be an excellent fullerene receptor. The 1:1 host-guest complexes formed between the cage and both C60 and C70 were characterized in solution by HRMS and NMR, UV-vis and fluorescence spectroscopies, and confirmed in the solid state by single-crystal X-ray diffraction analyses. The results from solution studies reveal that the cage has a much stronger binding for C70 than for C60, resulting in a selective extraction of C70 from a C60-enriched fullerene mixture (C60/C70 = 10/1), demonstrating the potential of the cage as an attractive receptor for fullerene separation.

Charge-Transfer Salts of 6,6-Dicyanopentafulvenes: From Topology to Charge Separation in Solution.

6,6-Dicyanopentafulvene derivatives and metallocenes with redox potentials appropriate for forming their radical anions form highly persistent donor-acceptor salts. The charge-transfer salts of 2,3,4,5-tetraphenyl-6,6-dicyanofulvene with cobaltocene (1⋅Cp2 Co) and 2,3,4,5-tetrakis(triisopropylsilyl)-6,6-dicyanofulvene with decamethylferrocene (2⋅Fc*) have been prepared. The X-ray structures of the two salts, formed as black plates, were obtained and are discussed herein. Compared with neutral dicyanopentafulvenes, the chromophores in the metallocene salts show substantial changes in bond lengths and torsional angles in the solid state. EPR, NMR, and optical spectroscopy, as well as superconducting quantum interference device (SQUID) measurements, reveal that charge-separation in the crystalline states and in frozen and fluid solutions depends on subtle differences of redox potentials, geometry, and on ion pairing. Whereas 1⋅Cp2 Co reveals paramagnetic character in the crystalline state and in solution, compound 2⋅Fc* shows a delicate balance between para- and diamagnetism, depending on the temperature and solvent characteristics.

Photoredox-Switchable Resorcin[4]arene Cavitands: Radical Control of Molecular Gripping Machinery via Hydrogen Bonding.

Semiquinones (SQ) are generated in photosynthetic organisms upon photoinduced electron transfer to quinones (Q). They are stabilized by hydrogen bonding (HB) with the neighboring residues, which alters the properties of the reaction center. We designed, synthesized, and investigated resorcin[4]arene cavitands inspired by this function of SQ in natural photosynthesis. Cavitands were equipped with alternating quinone and quinoxaline walls bearing hydrogen bond donor groups (HBD). Different HBD were analyzed that mimic natural amino acids, such as imidazole and indole, along with their analogues, pyrrole and pyrazole. Pyrroles were identified as the most promising candidates that enabled the cavitands to remain open in the Q state until strengthening of HB upon reduction to the paramagnetic SQ radical anion provided stabilization of the closed form. The SQ state was generated electrochemically and photochemically, whereas properties were studied by UV/Vis spectroelectrochemistry, transient absorption, and EPR spectroscopy. This study demonstrates a photoredox-controlled conformational switch towards a new generation of molecular grippers.

A Four-Step Synthesis of Substituted 5,11-Dicyano-6,12-diaryltetracenes with Enhanced Stability and High Fluorescence Emission.

A four-step synthesis of substituted 5,11-dicyano-6,12-diaryltetracenes was developed, starting from readily available para-substituted benzophenones. The key step of this straightforward route is the complex cascade reaction between tetraaryl[3]cumulenes and tetracyanoethene (TCNE) resulting in 5,5,11,11-tetracyano-5,11-dihydrotetracenes. The mechanism of this transformation was reinvestigated by means of theoretical calculations. The target tetracenes were obtained by a newly developed decyanation/aromatization reaction catalyzed by CuI or CuII complexes in solution, conditions compatible with a broad range of functional groups. A computational mechanistic study sheds light on this transformation. Structures of all tetracene derivatives were confirmed by X-ray crystallography. The presented dicyanotetracene derivatives exhibit outstanding optoelectronic properties and enhanced photostability, significantly surpassing the reference rubrene (5,6,11,12-tetraphenyltetracene).

Unconventional Synthesis of a CuI Rotaxane with a Superacceptor Stopper: Ultrafast Excited-State Dynamics and Near-Infrared Luminescence.

A CuI bis-phenanthroline rotaxane was prepared by using the [2+2] cycloaddition-retroelectrocyclization (CA-RE) reaction to graft a bulky dicyanoquinodimethane (DCNQ) stopper. The electronic properties were investigated with electrochemical and photophysical techniques, in parallel with three reference compounds, namely, the DCNQ derivative alone, the DCNQ-based phenanthroline ligand, and an analogue CuI complex lacking the DCNQ moiety. In all the systems containing the DCNQ unit, the lowest electronic excited states are centered thereon, with the singlet level (S1 ) located at about 1.0 eV, as suggested by TDDFT calculations. Accordingly, in the DCNQ-equipped rotaxane, the typical metal-to-ligand charge-transfer luminescence of the CuI center is totally quenched. Ultrafast transient absorption and emission studies show that, in the rotaxane, the final sink of photoinduced processes is the lowest singlet state of the DCNQ moiety (S1 ), which exhibits strong charge-transfer character and a lifetime of 0.4 ps. Its deactivation leads to population of another excited state with a lifetime of 1.3 ps, which can be the related triplet state (T1 ) or a vibrationally hot level (hot-S0 ). Notably, S1 also shows stimulated fluorescence in the near-infrared (NIR) region between 1100 and 1500 nm, corroborating the TDDFT prediction. This unusual finding opens up the study of ultrashort-lived NIR luminescence in organic donor-acceptor systems.

Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase.

The intestinal disease shigellosis caused by Shigella bacteria affects over 120 million people annually. There is an urgent demand for new drugs as resistance against common antibiotics emerges. Bacterial tRNA-guanine transglycosylase (TGT) is a druggable target and controls the pathogenicity of Shigella flexneri. We report the synthesis of sugar-functionalized lin-benzoguanines addressing the ribose-33 pocket of TGT from Zymomonas mobilis. Ligand binding was analyzed by isothermal titration calorimetry and X-ray crystallography. Pocket occupancy was optimized by variation of size and protective groups of the sugars. The participation of a polycyclic water-cluster in the recognition of the sugar moiety was revealed. Acetonide-protected ribo- and psicofuranosyl derivatives are highly potent, benefiting from structural rigidity, good solubility, and metabolic stability. We conclude that sugar acetonides have a significant but not yet broadly recognized value in drug development.

The [2+2] Cycloaddition-Retroelectrocyclization (CA-RE) Click Reaction: Facile Access to Molecular and Polymeric Push-Pull Chromophores.

The [2+2] cycloaddition-retroelectrocyclization (CA-RE) reaction between electron-rich alkynes and electron-deficient alkenes is an efficient procedure to create nonplanar donor-acceptor (D-A) chromophores in both molecular and polymeric platforms. They feature attractive properties including intramolecular charge-transfer (ICT) bands, nonlinear optical properties, and redox activities for use in next-generation electronic and optoelectronic devices. This Review summarizes the development of the CA-RE reaction, starting from the initial reports with organometallic compounds to the extension to purely organic systems. The structural requirements for rapid, high-yielding transformations with true click chemistry character are illustrated by examples that include the broad alkyne and alkene substitution modes. The CA-RE click reaction has been successfully applied to polymer synthesis, with the resulting polymeric push-pull chromophores finding many interesting applications.

Supramolecular Capsules: Strong versus Weak Chalcogen Bonding.

Resorcin[4]arene cavitands containing either 2,1,3-benzotelluradiazole or 2,1,3-benzothiadiazole motifs were dimerized to supramolecular capsules by chalcogen bonding. Their respective behavior varied depending on the interaction strength of the chalcogen bonds with Te forming strong interactions and S weak interactions. The tremendous strength of multiple 2Te-2N square interactions led to formation of a chalcogen-bonded dimeric capsule in all solvents, as shown by X-ray crystal structures with 16 short Te⋅⋅⋅N distances (≤2.9 Å) and confirmed by native electrospray ionization mass spectrometry (ESI-MS). With the S cavitand, solvent-dependent crystallization resulted in different arrangements: either a shifted 2S-2N square-bonded capsule or an interlocked 1D polymer with an infinite π-π stacking array. The association constant to form the dimeric capsule in [D8 ]THF at 283 K, solely based on weak 2S-2N square interactions, was determined as Ka =786 m-1 .

Hydrogen-Bonded Networks: Molecular Recognition of Cyclic Alcohols in Enantiopure Alleno-Acetylenic Cage Receptors.

Enantiopure (P)4 - and (M)4 -alleno-acetylenic cage (AAC) receptors form circular fourfold hydrogen-bonding networks in their closed cage conformation. Theoretical studies reveal a preferential clockwise (cw) orientation of the H-bonding array for (P)4 -configured and counterclockwise (ccw) for (M)4 -configured receptors (ΔEcw-ccw =-2.6 to -3.1 kcal mol-1 ). Solution and solid-state studies show how the H-bonding network of the receptor is expanded upon encapsulation of alcohol-containing guests. Topologies reminiscent of those found in isolated water clusters are observed: circular fourfold & docking, pentagonal, linear fivefold, and hexagonal boat-shaped. Expansion of the H-bonding network together with optimal space occupancy yields very high ligand affinities (ΔG293 K =-9.0 kcal mol-1 for endo-tropine). The H-bonding network in the complexes also contributes substantially to the enantioselective complexation of chiral diols, such as (R,R)- and (S,S)-trans-cyclohexane-1,2-diol.

Swapping Interface Contacts in the Homodimeric tRNA-Guanine Transglycosylase: An Option for Functional Regulation.

The enzyme tRNA-guanine transglycosylase, a target to fight Shigellosis, recognizes tRNA only as a homodimer and performs full nucleobase exchange at the wobble position. Active-site inhibitors block the enzyme function by competitively replacing tRNA. In solution, the wild-type homodimer dissociates only marginally, whereas mutated variants show substantial monomerization in solution. Surprisingly, one inhibitor transforms the protein into a twisted state, whereby one monomer unit rotates by approximately 130°. In this altered geometry, the enzyme is no longer capable of binding and processing tRNA. Three sugar-type inhibitors have been designed and synthesized, which bind to the protein in either the functionally competent or twisted inactive state. They crystallize with the enzyme side-by-side under identical conditions from the same crystallization well. Possibly, the twisted inactive form corresponds to a resting state of the enzyme, important for its functional regulation.

Dispersion and Halogen-Bonding Interactions: Binding of the Axial Conformers of Monohalo- and (±)-trans-1,2-Dihalocyclohexanes in Enantiopure Alleno-Acetylenic Cages.

Enantiopure alleno-acetylenic cage (AAC) receptors with a resorcin[4]arene scaffold, from which four homochiral alleno-acetylenes converge to shape a cavity closed by a four-fold OH-hydrogen-bonding array, form a highly ordered porous network in the solid state. They enable the complexation and co-crystallization of otherwise non-crystalline small molecules. This paper analyzes the axial conformers of monohalo- and (±)-trans-1,2-dihalocyclohexanes, bound in the interior cavity of the AACs, on the atomic level in the solid state and in solution, accompanied by accurate calculations. The dihedral angles ϑa,a (X-C(1)-C(2)-X/H) of the axial/diaxial conformers deviate substantially from 180°, down to 144°, accompanied by strong flattening of the ring dihedral angles. Structure optimization of the isolated guest molecules demonstrates that the non-covalent interactions with the host hardly affect the dihedral angles, validating that the host is an ideal means to study the elusive axial/diaxial conformers. X-ray co-crystal structures of AACs further allowed for a detailed investigation, both experimentally and theoretically, on the interplay between space occupancy, guest conformation, and chiral recognition based purely on dispersion forces and weak C-X···π (X = Cl, Br, I) and C-X···||| (acetylene) contacts (X = Cl, Br). The theoretical analysis of the non-covalent interactions between host and guest confirmed the high shape complementarity with fully enveloping dispersive interactions between the binding partners, rationalizing the high degree of enantioselectivity in the previously communicated complexation of (±)-trans-1,2-dimethylcyclohexane. This study also showed that (±)-trans-1,2-dihalocyclohexanes (X = Cl, Br) engage in significant halogen bonding (XB) interactions C-X···||| with the hosts. Slow host-guest exchange on the NMR time scale enabled the characterization of the encapsulated guests in solution, demonstrating that the complexes have identical geometries to those seen in the solid state, with the guests bound in axial/diaxial conformations.