Aromaticity and π-bond covalency: prominent intermolecular covalent bonding interaction of a Kekulé hydrocarbon with very significant singlet biradical character

An anthracene-linked bisphenalenyl Kekulé molecule with very significant singlet biradical character has shown a prominent covalent bonding interaction between molecules in a molecular aggregate. High aromatic stabilization energy in the anthracene linker is responsible for the significant singlet biradical character.     

Guanidiniocarbonylpyrrole–Aryl Derivatives: Structure Tuning for Spectrophotometric Recognition of Specific DNA and RNA Sequences and for Antiproliferative Activity

We present a systematic study of different guanidiniocarbonylpyrrole‐aryl derivatives designed to interact with DNA or RNA both through intercalation of an aromatic moiety into the base stack of the nucleotide and through groove binding of a guanidiniocarbonylpyrrole cation. We varied 1) the size of the aromatic ring (benzene, naphthalene, pyrene and acridine), 2) the length and flexibility of the linker connecting the two binding groups, and 3) the total number of positive charges present at different pH values. The compounds and their interactions with DNA and RNA were studied by UV/Vis, fluorescence and CD spectroscopy. Antiproliferative activities against human tumour cell lines were also determined. Our studies show that efficient interaction with, for example, DNA requires a significantly large aromatic ring (pyrene) connected through a flexible linker to the pyrrole moiety. However, a positive charge, as in 12 , is also needed. Compound 12 allows for base‐pair‐selective recognition of ds‐DNA at physiological pH values. The antiproliferative activities of these compounds correlate with their binding affinities towards DNA, suggesting that their biological effects are most probably due to DNA binding.     

Light‐Switchable Janus [2]Rotaxanes Based on α‐Cyclodextrin Derivatives Bearing Two Recognition Sites Linked with Oligo(ethylene glycol)

Two Janus [2]rotaxanes, 5a and 5b , with α‐cyclodextrin (α‐CD) derivatives substituted on the 6‐position with two recognition sites (azobenzene and heptamethylene (C7)) that were linked with linkers of different lengths (oligo(ethylene glycol) with a degree of polymerization equal to 2 or approximately 21) were synthesized and characterized. 2D ROESY NMR spectroscopy and circular dichroism (cd) spectra demonstrated that the recognition site of the α‐CD moiety was switched by photoisomerization of the azobenzene moiety in 5a and 5b . The different size changes of 5a and 5b in hydrodynamic radius (R_H) owing to the different length of linker between two recognition sites were observed by pulse‐field‐gradient spin‐echo NMR spectroscopy. The kinetic results indicated that the different length of linker had no or a weak effect for the photoisomerization process of 5a and 5b .     

Reaction of a Programmable Glycan Presentation of Glycodendrimersomes and Cells with Engineered Human Lectins To Show the Sugar Functionality of the Cell Surface

Chemical and biological tools are harnessed to investigate the impact of spatial factors for functional pairing of human lectins with counterreceptors. The homodimeric adhesion/growth‐regulatory galectin‐1 and a set of covalently linked homo‐oligomers from di‐ to tetramers serve as proof‐of‐principle test cases. Glycodendrimersomes provide a versatile and sensitive diagnostic platform to reveal thresholds for ligand density and protein concentration in aggregation assays (trans ‐activity), irrespective of linker length between lectin domains. Monitoring the affinity of cell binding and ensuing tumor growth inhibition reveal the linker length to be a bidirectional switch for cis ‐activity. The discovery that two aspects of lectin functionality (trans ‐ versus cis ‐activity) respond non‐uniformly to a structural change underscores the power of combining synthetic and biological tools to advance understanding of the sugar functionality of the cell surface.     

The First Zero‐Length Mass Spectrometry‐Cleavable Cross‐Linker for Protein Structure Analysis

Combining the properties of a zero‐length cross‐linker with cleavability by tandem mass spectrometry (MS/MS) poses great advantages for protein structure analysis using the cross‐linking/MS approach. These include a reliable, automated data analysis and the possibility to obtain short‐distance information of protein 3D‐structures. We introduce 1,1′‐carbonyldiimidazole (CDI) as an easy‐to‐use and commercially available, low‐cost reagent that ideally fulfils these features. CDI bridges primary amines and hydroxy groups in proteins with the lowest possible spacer length of one carbonyl unit (ca. 2.6 Å). The cross‐linking reaction can be conducted under physiological conditions in the pH range between 7.2 and 8. Urea and carbamate cross‐linked products are cleaved upon collisional activation during MS/MS experiments generating characteristic product ions, greatly improving the unambiguous identification of cross‐links. Our innovative analytical concept is exemplified and applied for bovine serum albumin (BSA), wild‐type tumor suppressor p53, an intrinsically disordered protein, and retinal guanylyl cyclase activating protein‐2 (GCAP‐2).     

Thermolyzable polymer networks and star polymers containing a novel,compact, degradable acylal‐based dimethacrylate cross‐linker: Synthesis,characterization, and thermolysis

A compact, cleavable acylal dimethacrylate cross‐linker, 1,1‐ethylenediol dimethacrylate (EDDMA), was synthesized from the anhydrous iron(III) chloride‐catalyzed reaction between methacrylic anhydride and acetaldehyde. The ability of EDDMA to act as cross‐linker was demonstrated by using it for the preparation of one neat cross‐linker network, four star polymers of methyl methacrylate (MMA), and four randomly cross‐linked MMA polymer networks using group transfer polymerization (GTP). For comparison, the corresponding polymer structures based on the commercially available ethylene glycol dimethacrylate (EGDMA) cross‐linker (isomer of EDDMA) were also prepared via GTP. The number of arms of the EDDMA‐based star polymers was lower than that of the corresponding EGDMA polymers, whereas the degrees of swelling in tetrahydrofuran of the EDDMA‐based MMA networks were higher than those of their EGDMA‐based counterparts. Although none of the EDDMA‐containing polymers could be cleanly hydrolyzed under basic or acidic conditions, they could be thermolyzed at 200 °C within 1 day giving lower molecular weight products. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5811–5823, 2007     

Voltammetric Determination of Surface‐Confined Biomolecules with N‐(2‐Ethyl‐ferrocene)maleimide

A thiol‐specific electroactive cross‐linker, N‐(2‐ethyl‐ferrocene)maleimide (Fc‐Mi), has been used to tag surface‐confined peptides containing cysteine residues or oligodeoxynucleotides (ODNs) whose 3′ ends have been modified with thiol groups. The peptides studied herein include both the oxidized and reduced forms of glutathione and a hexapeptide. Cyclic voltammograms (CVs) of the Fc‐Mi groups attached to the surfaces were used to quantify the total number of cysteine residues that are tagged and/or can undergo facile electron transfer reactions with the underlying electrodes. A quartz crystal microbalance was used in conjunction with CV to estimate the total number of cysteine groups labeled by Fc‐Mi per peptide molecule. By comparing to mass spectrometric studies, it is confirmed that not all of the Fc‐Mi linked to the cysteine groups can participate in the electron transfer reactions. The methodology is further extended to the determination of ODN samples in a sandwich assay wherein the thiol linker on the 3′ end can be tagged with Fc‐Mi. The analytical performance was evaluated through determinations of a complementary ODN target and targets with varying numbers of mismatching bases. ODN samples as low as 10 fmol can be detected. Such a low detection level is remarkable considering that no signal amplification scheme is involved in the current method. The approach is shown to be sequence‐ and/or structure‐specific and does not require sophisticated instrumentation and complex experimental procedure.     

Mechanical Behavior of Polymer Gels for RDCs and RCSAs Collection: NMR Imaging Study of Buckling Phenomena

Anisotropic NMR parameters, such as residual dipolar couplings (RDCs), residual chemical shift anisotropies (RCSAs) and residual quadrupolar couplings (RQCs or Δν_Q), appear in solution‐state NMR when the molecules under study are subjected to a degree of order. The tunable alignment by reversible compression/relaxation of gels (PMMA and p‐HEMA) is an easy, user‐friendly, and very affordable method to measure them. When using this method, a fraction of isotropic NMR signals is observed in the NMR spectra, even at a maximum degree of compression. To explain the origin of these isotropic signals we decided to investigate their physical location inside the NMR tube using deuterium 1D imaging and MRI micro‐imaging experiments. It was observed that after a certain degree of compression the gels start to buckle and they generate pockets of isotropic solvent, which are never eliminated. The amount of buckling depends on the amount of cross‐linker and the length of the gel.     

Precise Control of Intramolecular Charge‐Transport: The Interplay of Distance and Conformational Effects

A new series of donor–bridge–acceptor (D–B–A) compounds consisting of π‐conjugated oligofluorene (oFL) bridges between a ferrocene (Fc) electron‐donor and a fullerene (C₆₀) electron‐acceptor have been synthesized. In addition to varying the length of the bridge (i.e., mono‐ and bi‐fluorene derivatives), four different ways of linking ferrocene to the bridge have been examined. The Fc moiety is linked to oFL: 1) directly without any spacer, 2) by an ethynyl linkage, 3) by a vinylene linkage, and 4) by a p‐phenylene unit. The electronic interactions between the electroactive species have been characterized by cyclic voltammetry, absorption, fluorescence, and transient absorption spectroscopy in combination with quantum chemical calculations. The calculations reveal exceptionally close energy‐matching between the Fc and the oFL units, which results in strong electronic‐coupling. Hence, intramolecular charge‐transfer may easily occur upon exciting either the oFLs or Fcs. Photoexcitation of Fc–oFL–C₆₀ conjugates results in transient radical‐ion‐pair states. The mode of linkage of the Fc and FL bridge has a profound effect on the photophysical properties. Whereas intramolecular charge‐separation is found to occur rather independently of the distance, the linker between Fc and oFL acts (at least in oFL) as a bottleneck and significantly impacts the intramolecular charge‐separation rates, resulting in beta values between β_CS 0.08 and 0.19 Å^?1. In contrast, charge recombination depends strongly on the electron‐donor–acceptor distance, but not at all on the linker. A value of β_CR (0.35±0.01 Å^?1) was found for all the systems studied. Oligofluorenes prove, therefore, to be excellent bridges for probing how small structural variations affect charge transport in D–B–A systems.     

Ferrocene‐Donor and 4,5‐Dicyanoimidazole‐Acceptor Moieties in Charge‐Transfer Chromophores with π Linkers Tailored for Second‐Order Nonlinear Optics

A series of new nonlinear optical chromophores ( 1 – 15 ) that were comprised of ferrocene‐donor and 4,5‐dicyanoimidazole‐acceptor moieties and various π linkers of different length were synthesized. Support for the presence of significant D ? A interactions in these NLO‐phores was obtained from the evaluation of the quinoid character of the 1,4‐phenylene moieties and their electronic absorption spectra, which featured intense high‐energy (HE) bands that were accompanied by less‐intense low‐energy (LE) bands. The redox behavior of these compounds was investigated by cyclic voltammetry (CV) and by rotating‐disc voltammetry (RDV); their electrochemical gaps decreased steadily from 2.64 to 2.09 V. In addition to the experimentally obtained data, DFT calculations of their absorption spectra, HOMO/LUMO levels, and second‐order polarizabilities (β) (?2ω,ω,ω) were performed. A structure–property relationship study that was performed by systematically altering the π linker revealed that the intramolecular charge‐transfer and nonlinear optical properties of these inorganic–organic hybrid D? π? A systems ( 1 – 15 ) were primarily affected by: 1) The presence of olefinic/acetylenic subunits; 2) the length of the π linker; and 3) the spatial arrangement (planarity) of the π linker.     

Synthesis of vitamin D(3) and calcitriol dimers as potential chemical inducers of vitamin D receptor dimerization

The design and synthesis of vitamin D(3) dimers 2 and 3 and 1 alpha, 25-dihydroxyvitamin D(3) (calcitriol) dimers 4 and 5 are described. The dimers were designed with a view to doubly binding the vitamin D receptor (VDR) and inducing the receptor homodimerization. In the dimers the units are linked through the C-11 position in ring C by an alkyl side chain of six or 10 carbon atoms, far from the hydroxy groups responsible for the VDR binding. The linker is formed by olefin metathesis of an olefinic side chain at the C-11 position introduced by stereoselective cuprate addition. The synthesis, which is both short and convergent, uses the Wittig-Horner approach to construct the vitamin D triene system and allows the preparation of dimers with a linker of modulated length with the purpose of optimizing the vitamin D(3)-VDR interaction.     

Cluster Linker Approach: Preparation of a Luminescent Porous Framework with NbO Topology by Linking Silver Ions with Gold(I) Clusters

A cluster‐based luminescent porous metal–organic framework has been constructed through a “cluster linker” approach. The luminescent gold(I) cluster, prefunctionalized with pyrazinyl groups, was used as a cluster linker, similar to an organic linker, to connect silver ions in order to form a 3D framework. 1D channels with 1.1 nm diameter were observed in the framework. The cluster with its intrinsic luminescence was incorporated into a porous framework to give a luminescent bifunctional NbO net. This MOF shows solvatochromic behavior, and the interactions between solvent molecules and silver ions inside the channels account for the changes in absorption and emission spectra.     

How the Substitution Faraway from NHCs Affects the Structural Features and Catalytic Activity of Dicarbene Dipalladium Complexes

A series of [PdPyCl₂]₂(di‐NHC) complexes were prepared (di‐NHC are two 1‐(2,6‐dimethylphenyl)imidazolidene molecules bridged by an aliphatic –(CH₂)_n– linker (n = 3, 4, 5, 6, and 10)). All complexes were fully characterized by NMR spectroscopy and elemental analyses. The crystal structures of four complexes (n = 3, 4, 5 and 6) were determined by X‐ray diffraction. The influence of the distant methyl group on the structural features and catalytic activity with increasing of length of linker was investigated by comparing the results of these 2,6‐dimethylphenyl palladium complexes with those of their known mesityl analogues. X‐ray studies show the distant methyl substitution has big impact on the structure feature of the complexes with the shorter linker between two NHC (ethylene and propylene), but has a little or no effect on that of the complexes with longer linker (butylene and hexylene). Catalytic results of the arylation of styrene show that the remote substitute has big effect on the regioselectivity of the product in all complexes with shorter and longer linkers, but has a limited effect on the yield.     

Designed Synthesis of a 1D Polymer in Twist‐Stacked Topology via Single‐Crystal‐to‐Single‐Crystal Polymerization

To synthesize a fully organic 1D polymer in a novel twist‐stacked topology, we designed a peptide monomer HC≡CCH₂‐NH‐Ile‐Leu‐N₃, which crystallizes with its molecules H‐bonded along a six‐fold screw axis. These H‐bonded columns pack parallelly such that molecules arrange head‐to‐tail, forming linear non‐covalent chains in planes perpendicular to the screw axis. The chains arrange parallelly to form molecular layers which twist‐stack along the screw axis. Crystals of this monomer, on heating, undergo single‐crystal‐to‐single‐crystal (SCSC) topochemical azide–alkyne cycloaddition (TAAC) polymerization to yield an exclusively 1,4‐triazole‐linked polymer in a twist‐stacked layered topology. This topologically defined polymer shows better mechanical strength and thermal stability than its unordered form, as evidenced by nanoindentation studies and thermogravimetric analysis, respectively. This work illustrates the scope of topochemical polymerizations for synthesizing polymers in pre‐decided topologies.     

Saturation of hydrogen sorption in Zn benzenedicarboxylate and Zn naphthalenedicarboxylate

We report excess hydrogen saturation values from high-pressure isotherms of metal organic framework structures taken at 77 K. Zn benzendicarboxylate (IRMOF-1) and Zn naphthalendicarboxylate (IRMOF-8) linker structures show identical saturation values of 137 hydrogen molecules on a per unit cell basis, despite the higher sorption potential of IRMOF-8 of 6.1 kJ/mol over that of IRMOF-1 of 4.1 kJ/mol. Charge transfer between linker and vertex, as well as surface area, appear to dominate the sorption behavior, over that of linker length in these two systems.     

Synthesis and self‐assembly of rod‐coil molecules with n‐shaped rod building block

The rod‐coil molecules with n‐shaped rod building block, consisting of an anthracene unit and two biphenyl groups linked together with acetylenyl bonds at the 1,8‐position of anthracene as a rigid rod segment, and the alkyl or alkyloxy chains with various length (i.e., methoxy‐ ( 1 ), octyl‐ ( 2 ), hexadecyl‐ ( 3 )) at the 10‐position of anthracene and poly(ethylene oxide) with the number of repeating units of 7 connected with biphenyl as coil segments were synthesized. The molecular structures were characterized by ¹H NMR and MALDI‐TOF mass spectroscopy. The self‐assembling behavior of new type of molecules 1–3 was investigated by means of DSC, POM, and SAXS at the bulk state. These molecules with a n‐shaped rod building block segment self‐assemble into supramolecular structures through the combination of π–π stacking of rigid rod building blocks and microphase separation of the rod and coil blocks. SAXS studies reveal that molecules 1 and 2 show hexagonal columnar and rectangular columnar structures in the liquid crystalline phase, respectively; meanwhile, molecules 1–3 self‐organize into lamellar structures in the crystalline state. In addition, self‐assembling studies of molecules 1–3 by DLS and TEM indicated that these molecules self‐assemble into elongated nanofibers in aqueous medium. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 1415–1422, 2010     

Correlating Pressure‐Induced Emission Modulation with Linker Rotation in a Photoluminescent MOF

Conformational changes of linker units in metal‐organic frameworks (MOFs) are often responsible for gate‐opening phenomena in selective gas adsorption and stimuli‐responsive optical and electrical sensing behaviour. Herein, we show that pressure‐induced bathochromic shifts in both fluorescence emission and UV/Vis absorption spectra of a two‐fold interpenetrated Hf MOF, linked by 1,4‐phenylene‐bis(4‐ethynylbenzoate) ligands ( Hf‐peb ), are induced by rotation of the central phenyl ring of the linker, from a coplanar arrangement to a twisted, previously unseen conformer. Single‐crystal X‐ray diffraction, alongside in situ fluorescence and UV/Vis absorption spectroscopies, measured up to 2.1 GPa in a diamond anvil cell on single crystals, are in excellent agreement, correlating linker rotation with modulation of emission. Topologically isolating the 1,4‐phenylene‐bis(4‐ethynylbenzoate) units within a MOF facilitates concurrent structural and spectroscopic studies in the absence of intermolecular perturbation, allowing characterisation of the luminescence properties of a high‐energy, twisted conformation of the previously well‐studied chromophore. We expect the unique environment provided by network solids, and the capability of combining crystallographic and spectroscopic analysis, will greatly enhance understanding of luminescent molecules and lead to the development of novel sensors and adsorbents.     

Supramolecular nanostructures from self‐assembly of T‐shaped rod building block oligomers

T‐shaped coil–rod–coil oligomers, consisting of a dibenzo[a,c]phenazine unit and phenyl groups linked together with acetylenyl bonds at the 2,7‐position of dibenzo[a,c]phenazine as a rigid segment have been synthesized. The coil segments of these new molecules composed of poly(ethylene oxide) (PEO)–poly(propylene oxide) (PPO) incorporating lateral methyl groups between the rod and coil segment and two flexible alkyl groups connecting with the rigid segment at the 4,6‐position of dibenzo[a,c]phenazine, respectively. The experimental results reveal that the length of the flexible PEO coil chain influence construction of various supra‐nanostructures from lamellar structure to rectangular columnar structure. It is also shown that introduction of different length of alkyl side chain groups in the backbone of the T‐shaped molecules affect the self‐organization behavior to form hexagonal perforate layer or oblique columnar structures. In addition, lateral methyl groups attached to the surface of rod and coil segments, dramatically influence the self‐assembling behavior in the crystalline phase. T‐shaped molecules containing a lateral methyl group at the surface of rod and PEO coil segments, self‐assemble into 3D body‐centered tetragonal structures in the crystalline phase, while molecules without a lateral methyl group based on PEO coil chain self‐organize into 2D oblique columnar crystalline structures. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 5021–5028     

Heterobifunctional isotope‐labeled amine‐reactive photo‐cross‐linker for structural investigation of proteins by matrix‐assisted laser desorption/ionization tandem time‐of‐flight and electrospray ionization LTQ‐Orbitrap mass spectrometry

Chemical cross‐linking combined with a subsequent enzymatic digestion and mass spectrometric analysis of the created cross‐linked products presents an alternative approach to assess low‐resolution protein structures. By covalently connecting pairs of functional groups within a protein or a protein complex a set of structurally defined interactions is built up. We synthesized the heterobifunctional amine‐reactive photo‐cross‐linker N‐succinimidyl p‐benzoyldihydrocinnamate as a non‐deuterated (SBC) and doubly deuterated derivative (SBDC). Applying a 1:1 mixture of SBC and SBDC for cross‐linking experiments aided the identification of cross‐linked amino acids in the mass spectra based on the characteristic isotope patterns of fragment ions. The cross‐linker was applied to the calcium‐binding protein calmodulin with a subsequent analysis of cross‐linked products by nano‐high‐performance liquid chromatography matrix‐assisted laser desorption/ionization tandem time‐of‐flight mass spectrometry (nano‐HPLC/MALDI‐TOF/TOF‐MS) and nano‐HPLC/nano‐electrospray ionization (ESI)‐LTQ‐Orbitrap‐MS. Copyright © 2009 John Wiley & Sons, Ltd.     

Novel designed polymer–acyclovir conjugates with linker‐controlled drug release and hepatoma cell targeting

To develop designed polymer–drug conjugates, where the rate of drug liberation and hepatoma cell targeting function could be rationally and widely controlled, we facilely synthesized a series of novel, galactose‐functionalized polymer–acyclovir conjugates with different linkers and first reported the effect of the linker structure including the type of acyclovir‐linked bond (an ester bond or an amide bond) and relative length of the linker between acyclovir and the polymer main chain on release rate and targeting ability of conjugates. In vitro release studies showed that the cumulative released acyclovir from these polymer–acyclovir conjugates was between 24 and 65% in pH 1.2 glycine solution after 7 days. The ester bond more easily underwent hydrolysis than the amide bond. The longer the relative linker length was, the faster the acyclovir was released. The cell recognition experiments visualized using confocal laser scanning microscopy exhibited that the resultant galactose‐functionalized polymer–acyclovir conjugates had evident targeting to hepG2 cells, and targeting ability was also in connection with the relative length of linker. By choosing appropriate linker, cellular internalization of acyclovir could be well achieved. We consider these results to be helpful for the design of multifunctional polymeric prodrugs, in which the required release rate and targeting ability could be rationally controlled by predetermined molecular architecture. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 117–126, 2008