Reversible Coordinative Bonds in Molecular Recognition

Synthesis and characterization of borohydride rare-earth complexes supported by 2-pyridinemethanamido ligands and their application in the ring-opening polymerization of cyclic esters

The synthesis of 2-pyridinemethanamido borohydride complexes of yttrium and neodymium was achieved through the in situ deprotonation of the protio-ligand 2-pyridinemethanamine C5H3R1N-C(CH3)R2-NH(2,6-iPr2C6H3), denoted as PyAH (with PyAH1: R1 = R2 = H; PyAH2: R1 = CH3, R2 = H; PyAH3: R1 = C(CH3)N-(2,6-iPr2C6H3), R2 = CH3), in the presence of trisborohydride RE(BH4)3(THF)3 (RE = Y and Nd) as a precursor and a base. The isolation of various molecular structures, nine of which were structurally characterized by X-ray diffraction analysis, was achieved and revealed to depend not only on (i) the nature of the 2-pyridinemethanamido ligand and (ii) the rare-earth element but also on (iii) the reaction conditions, notably the type of base used. These include seven mono-substituted species, eventually also comprising the cation derived from the base reagent, such as [(PyA1)Y(BH4)3]2[Mg(THF)6] (1Y), [(PyA1)Nd(BH4)3Mg(PyA1)](THF)4 (1Nd), (PyA1)Nd(BH4)2(THF)2 (1'Nd), [(PyA1)Nd(THF)(BH4)(μ-BH4)]2 (1''Nd), [(PyA2)Nd(BH4)3]2[Mg(THF)6] (3Nd), (PyA2)Nd(BH4)2(THF)2 (3'Nd) and (PyA3)Nd(BH4)2 (4Nd), as well as two bis-substituted complexes (PyA1)2Y(BH4) (2Y) and (PyA1)2Nd(BH4) (2Nd). On the other hand, the unexpected amido/ene-amido derivative [(PyA(EA))Y(BH4)2][Li(THF)4] (5Y) (PyA(EA): R1 = CCH2-N(2,6-iPr2C6H3), R2 = CH3), where the PyAH3 protio-ligand underwent double deprotonation, was recovered from the reaction carried out with nBuLi in the yttrium series. In some cases, the synthesis led to the isolation of borohydride 2-pyridinemethanamido-supported magnesium complexes (PyA2)Mg(BH4)(THF) and (PyA3)Mg(BH4)(THF). In parallel, the PyAH2 pro-ligand could be structurally analyzed, and an unprecedented adduct of the type [KN(SiMe3)2·PyAH1]2 was isolated and characterized by X-ray diffraction analysis. Preliminary investigations of the ring-opening polymerization of L-lactide and ε-caprolactone with some of the complexes synthesized are finally presented, demonstrating moderate to high catalytic activities.

A new biphenol-dipicolylamine based ligand and its dinuclear Zn2+ complex as fluorescent sensors for ibuprofen and ketoprofen in aqueous solution

In this work, the study of the new ligand 3,3'-bis[N,N-bis(pyridine-2-ylmethyl)aminomethyl]-2,2'-dihydroxybiphenyl (L) is reported, where a central 2,2'-biphenol (BPH) fluorophore was functionalized at 3,3'-positions with two dipicolylamine (DPA) side arms as receptor units. Following the synthesis and full chemical-physical characterization, the acid-base and Zn2+-coordination abilities of L were investigated through a combination of potentiometric, UV-Vis, fluorescence, NMR, XRD and DFT measurements. The optical properties of the ligand turned out to be strongly dependent on the pH, being straightforwardly associated with the protonation state of the BPH moiety, whereas its peculiar design allowed to form stable mono and dinuclear Zn2+ complexes. In the latter species, the presence of two Zn2+ ions coordinatively unsaturated and placed at close distance to each other, prompted us to test their usefulness as metallo-receptors for two environmental pollutants of great relevance, ibuprofen and ketoprofen. Potentiometric and fluorescence investigations evidenced that these important non-steroidal anti-inflammatory drugs (NSAIDs) are effectively coordinated by the metallo-receptors and, of relevance, both the stability and the fluorescence properties of the resulting ternary adducts are markedly affected by the different chemical architectures of the two substrates. This study aims at highlighting the promising perspectives arising from the use of polyamino phenolic ligands as chemosensors for H+/Zn2+ and other additional anionic targets in their metal-complexed forms.

Gold-iron oxide (Au/Fe3O4) magnetic nanoparticles as the nanoplatform for binding of bioactive molecules through self-assembly

Nanomedicine plays a crucial role in the development of next-generation therapies. The use of nanoparticles as drug delivery platforms has become a major area of research in nanotechnology. To be effective, these nanoparticles must interact with desired drug molecules and release them at targeted sites. The design of these “nanoplatforms” typically includes a functional core, an organic coating with functional groups for drug binding, and the drugs or bioactive molecules themselves. However, by exploiting the coordination chemistry between organic molecules and transition metal centers, the self-assembly of drugs onto the nanoplatform surfaces can bypass the need for an organic coating, simplifying the materials synthesis process. In this perspective, we use gold-iron oxide nanoplatforms as examples and outline the prospects and challenges of using self-assembly to prepare drug-nanoparticle constructs. Through a case study on the binding of insulin on Au-dotted Fe3O4 nanoparticles, we demonstrate how a self-assembly system can be developed. This method can also be adapted to other combinations of transition metals, with the potential for scaling up. Furthermore, the self-assembly method can also be considered as a greener alternative to traditional methods, reducing the use of chemicals and solvents. In light of the current climate of environmental awareness, this shift towards sustainability in the pharmaceutical industry would be welcomed.

Julolidine-hydrazone based chemosensor for detection of Zn2+: Fluorescent in-situ formed Zn2+ complex discriminates PPi from ADP and ATP

In the present investigation, we have designed and synthesised Zn²⁺ sensitive Julolidine-hydrazone (JSB) based chemosensor, which crystallised in a monoclinic crystal system with P21/c space group. The bare JSB was nonemissive, but in the presence of Zn²⁺ ions in solution it showed emission, ascribed to the chelation enhanced emission process, which is also utilised to detect Zn²⁺ in water samples. Comparing the chromaticity coordinates deduced from the emission colors of the JSB-Zn²⁺ in solution, powder and hybrid polymer thin film, using CIE (Commission Internationale de I'Eclairage 1931) chromaticity diagram, it was found that compared to the emission of the solution, the emission of the powder was red shifted, while that of the thin film was blue shifted. Further, the sensing of Zn²⁺ showed reversibility in the presence of pyrophosphate (PPi), which allowed quantification of PPi. Interestingly, in addition to the detection of PPi using the in-situ formed JSB-Zn²⁺ complex, the process was selective and discriminated PPi from ADP and ATP. The detection of PPi was rationalized via a decomplexation reaction, and translated in the construction of INHIBIT logic gate. Additionally, the possible use of the JSB coated sensor paper for the on-site detection of Zn²⁺ and subsequent JSB-Zn²⁺ complex for PPi ions has been demonstrated. The experimental results showed good correlation with the theoretical calculations wherever possible.

Efficient synthesis of 6,6′-diamido-2,2′-dipicolylamine ligands for potential phosphate anion sensing

Through retrosynthetic analysis, functionalized 6,6′-diamido-2,2′-dipicolylamines (DA-DPAs) have been efficiently synthesized, which may accelerate the development of selective probes towards phosphate anions.

Selective Activation of Aromatic Aldehydes Promoted by Dispersion Interactions: Steric and Electronic Factors of a π-Pocket within Cage-Shaped Borates for Molecular Recognition

Selective bond formations are one of the most important reactions in organic synthesis. In the Lewis acid mediated electrophile reactions of carbonyls, the selective formation of a carbonyl-acid complex plays a critical role in determining selectivity, which is based on the difference in the coordinative interaction between the carbonyl and Lewis acid center. Although this strategy has attained progress in selective bond formations, the discrimination between similarly sized aromatic and aliphatic carbonyls that have no functional anchors to strongly interact with the metal center still remains a challenging issue. Herein, this work focuses on molecular recognition driven by dispersion interactions within some aromatic moieties. A Lewis acid catalyst with a π-space cavity, which is referred to as a π-pocket, as the recognition site for aromatic carbonyls is designed. Cage-shaped borates 1B with various π-pockets demonstrated significant chemoselectivity for aromatic aldehydes 3 b-f over that of aliphatic 3 a in competitive hetero-Diels-Alder reactions. The effectiveness of our catalysts was also evidenced by intramolecular recognition of the aromatic carbonyl within a dicarbonyl substrate. Mechanistic and theoretical studies demonstrated that the selective activation of aromatic substrates was driven by the preorganization step with a larger dispersion interaction, rather than the rate-determining step of the C-C bond formation, and this was likely to contribute to the preferred activation of aromatic substrates over that of aliphatic ones.

Experimental and theoretical substantiation of differences of geometric isomers of copper(II) α-amino acid chelates in ATR-FTIR spectra

Stereo and structural isomerism of the copper(II) chelate complexes define their biological activity. At the same time, the identification of the geometric isomers of such complexes is a nontrivial task of modern coordination chemistry. In the presented work we have studied the trans- and cis-isomers of chelates bis(S-valinato)copper(II), (R,S-valinato)copper(II) and other mixed ligand copper(II) amino acid complexes with the joint use of experimental by ATR-FTIR spectroscopy and DFT simulations. Using DFT simulations (method M06/6 311+G(d)) the optimum conformers of the geometric isomers of copper(II) a-amino acid chelate complexes were found and their characteristic stretching vibrations were established in the mid-wave region of the IR spectra. The experimental ATR-FTIR bands of the compounds well agree with the theoretical estimates. Such a joint use allows to determine of cis- and trans-isomers of copper(II) N,O-amino acid chelates in the mid-wave region of the ATR-FTIR spectrum.

ON/OFF Control of the Flipping Motion of Diuranyl Bis(Salophen) Macrocycle by Extremely Strong Binding with Fluoride Ion

Diuranyl bis(salophen) complex 1 features a relatively slow conformational motion, induced by an intramolecular O═U═O···UO₂ binding motif, which interconverts the two nonsymmetric halves of the ligand. This flipping motion, which constitutes one of the fundamental molecular motions, can be completely halted by addition of fluoride anion, which is bound to 1, reaching one of the highest affinities reported to date. This system represents a model to study flipping dynamics in light of the possibility of developing novel types of molecular machines based on it.

Design and application of a fluorogenic receptor for selective sensing of cations, small neutral molecules, and anions

An unprecedented single multi-analyte fluorogenic receptor, a sodium salt of N-(methyl-2-thiophenyl)-tyrosine (NaHTyrthio), is reported for the selective sensing of cations (Cu²⁺), small neutral molecules (nitrobenzene and aniline) and anions (F⁻) by variable spectral responses.

A Fluorescent Chemosensor for Zn2+ Based on a C3-Symmetrical and Pre-Organized 2,2′,2″-Nitrilotribenzoic Acid Material

A C3-symmetrical 4,4″,4⁗-nitrilotris(2′-methyl-[1,1′-biphenyl]-3-carboxylic acid) (4) derived from nitrilotriacetic acid (NTA) was found to selectively bind Zinc(ii) ions both in DMSO or MeOH. A synergistic effect of the anionic counter ion SO42− on the sensing behaviour of 4 to metal ions was clearly observed in DMSO. Interestingly, 4 showed a rapid hypochromatic shift in emission ascribed to the deprotonation and the concomitant formation of a 4–metal complex upon the addition of Zn2+ ions, instead of the bathochromic shift and emission enhancement attributed to the SO42−-involved hydrogen-bonding interaction for Ni2+, Li+, Mg2+, and Na+ ions at ratios below 1:1 in DMSO. The observed sensing process of sulfate salts associated with the SO42−-involved hydrogen-bonding interaction, deprotonation, and the concomitant complexation can also be clearly monitored by titration methods utilising UV-vis, fluorescence, and NMR spectroscopy in solution. In comparison with 4, compound 1 showed an obvious difference in the binding interaction with zinc sulfate in MeOH, probably owing to the decreased acidity. Anion-induced hydrogen-bonding interactions and deprotonation of the COOH protons in the excited state also endowed 4 versatile spectroscopic properties. The addition of F− and SO42− anions resulted in a remarkable enhancement probably related with a rigidifying effect. 2,2′,2″-Nitrilotribenzoic acid can be utilised as a potential scaffold to build a series of conjugated fluorescent sensors by its chelation effect owing to the rigid cavity pre-organised by the triphenylamine moiety and the carboxylic groups and the conjugation extension in the 4,4′,4″ positions.

A quinoline-based Cu2+ ion complex fluorescence probe for selective detection of inorganic phosphate anion in aqueous solution and its application to living cells

A quinaldine functionalized probe QP has been designed and synthesized. It exhibited selective turn-off fluorescence response toward Cu²⁺ ion over most of the biologically important ions at physiological pH. The binding ratio of the probe QP and Cu²⁺ ion was determined to be 1:1 through fluorescence titration, Job's plot and ESI-MS. The binding constant (K) of Cu²⁺ to probe QP was found to be 2.12×10⁴M^-1. Further, the Cu²⁺ ensemble of probe QP was found to respond H₂PO₄^- and HPO₄^2- among other important biological anions via fluorescence turn-on response at physiological pH. Fluorescence microscopy imaging using living Hela cells showed that probe QP could be used as an effective fluorescent probe for detecting Cu²⁺ cation and H₂PO₄^- and HPO₄^2- anions in living cells.

Deciphering Selectivity in Organic Reactions: A Multifaceted Problem

Computational chemistry has made a sustained contribution to the understanding of chemical reactions. In earlier times, half a century ago, the goal was to distinguish allowed from forbidden reactions (e.g., Woodward-Hoffmann rules), that is, reactions with low or high to very high activation barriers. A great achievement of computational chemistry was also to contribute to the determination of structures with the bonus of proposing a rationalization (e.g., anomeric effect, isolobal analogy, Gillespie valence shell pair electron repulsion rules and counter examples, Wade-Mingos rules for molecular clusters). With the development of new methods and the constant increase in computing power, computational chemists move to more challenging problems, close to the daily concerns of the experimental chemists, in determining the factors that make a reaction both efficient and selective: a key issue in organic synthesis. For this purpose, experimental chemists use advanced synthetic and analytical techniques to which computational chemists added other ways of determining reaction pathways. The transition states and intermediates contributing to the transformation of reactants into the desired and undesired products can now be determined, including their geometries, energies, charges, spin densities, spectroscopy properties, etc. Such studies remain challenging due to the large number of chemical species commonly present in the reactive media whose role may have to be determined. Calculating chemical systems as they are in the experiment is not always possible, bringing its own share of complexity through the large number of atoms and the associated large number of conformers to consider. Modeling the chemical species with smaller systems is an alternative that historically led to artifacts. Another important topic is the choice of the computational method. While DFT is widely used, the vast diversity of functionals available is both an opportunity and a challenge. Though chemical knowledge helps, the relevant computational method is best chosen in conjunction with the nature of the experimental systems and many studies have been concerned with this topic. We will not address this aspect but give references in the text. Usually, a computational study starts with the validation of the method by means of benchmark calculations vs accurate experimental data or state-of-the-art calculations. Finally, computational chemists can bring more than the sole determination of the reaction pathways through the analysis of the electronic structure. In our case, we have privileged the NBO analysis, which has the advantage of describing interactions on the basis of terms and concepts that are shared within the chemical community. In this Account, we have chosen to select representative reactions from our own work to highlight the diversity of situations than can be addressed nowadays. These include selective activation of C(sp(3))-H bonds, selective reactions with low energy barriers, involving closed shell or radical species, the role of noncovalent interactions, and the importance of considering side reactions.

Bioinspired polymer vesicles and membranes for biological and medical applications

Biological membranes play an essential role in living organisms by providing stable and functional compartments, supporting signalling and selective transport. Combining synthetic polymer membranes with biological molecules promises to be an effective strategy to mimic the functions of cell membranes and apply them in artificial systems.

Advantages of anchoring growth factors to materials for neural stem/progenitor cell proliferation

We tried to clarify the mechanisms underlying immobilized-growth factor in NSPC regulation using approaches from materials science and cell biology.

A tetraphenylethene-based zinc complex as a sensitive DNA probe by coordination interaction

We developed a new DNA probe by utilizing the coordination interaction of Zn(2+) with DNA and the consequent emission. Because the coordination interactions do not depend on the length of the DNA, the new probe exhibited much higher sensitivity for the detection of short ssDNA than the corresponding probe based on electrostatic interactions.

Design and synthesis of Tröger's base ditopic receptors: host-guest interactions, a combined theoretical and experimental study

Two flexible Tröger's base ditopic receptors C4TB and C5TB incorporating monoaza crown ether were designed and synthesized for bisammonium ion complexation. A comprehensive study of host-guest interactions was established by (1)H NMR spectroscopy and DFT calculations. Bisammonium chloride (A1) with a shorter alkyl chain spacer showed the highest affinity for the receptors. M06-2X/cc-pVTZ calculations including the solvent effects on host-guest complexes were employed to explain and rationalize the experimental trends. The short N-H···O or N-H···N hydrogen-bond distances observed in the range of 1.71-1.98 Å indicate the existence of a strong charge assisted hydrogen bonding between the host and the guest. The unusual behaviour (higher binding constant) of A5 in (1)H NMR titration is traced to the conformational folding of the guest.

Tris(8-methoxy-2-quinolylmethyl)amine (8-MeOTQA) as a highly fluorescent Zn2+probe prepared by convenient C3-symmetric tripodal amine synthesis

The convenient synthesis ofC₃-symmetric tribenzylamines utilizing acetaldehyde ammonia trimer (1) revealed tris(8-methoxy-2-quinolylmethyl)amine (8-MeOTQA) as a fluorescent zinc sensor with high sensitivity.

Molecular imprinting science and technology: a survey of the literature for the years 2004-2011

Herein, we present a survey of the literature covering the development of molecular imprinting science and technology over the years 2004-2011. In total, 3779 references to the original papers, reviews, edited volumes and monographs from this period are included, along with recently identified uncited materials from prior to 2004, which were omitted in the first instalment of this series covering the years 1930-2003. In the presentation of the assembled references, a section presenting reviews and monographs covering the area is followed by sections describing fundamental aspects of molecular imprinting including the development of novel polymer formats. Thereafter, literature describing efforts to apply these polymeric materials to a range of application areas is presented. Current trends and areas of rapid development are discussed.

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

Stimuli-responsive hydrogel patterns for smart microfluidics and microarrays

In this review, we highlight the properties, functions and applications of stimuli-responsive hydrogel patterns in bioanalytical applications. Stimuli-responsive hydrogel patterns can be realized by well-established micro- and nanofabrication technologies such as photolithography and micromolding, and are currently adopted as active components for manipulation of flow and biosamples in microchannel and microarray systems. We overview the properties of stimuli-responsive hydrogel materials and their fabrication methods along with some representative examples in microfluidics and microarrays.

Selective recognition of anionic cell membranes using targeted liposomes coated with zinc(ii)-bis(dipicolylamine) affinity units

Zinc(ii)-bis(dipicolylamine) (Zn2BDPA) coated liposomes are shown to have high recognition selectivity towards vesicle and cell membranes with anionic surfaces. Robust synthetic methods were developed to produce Zn2BDPA-PEG-lipid conjugates with varying PEG linker chain length. One conjugate (Zn2BDPA-PEG2000-DSPE) was used in liposome formulations doped with the lipophilic near-infrared fluorophore DiR. Fluorescence cell microscopy studies demonstrated that the multivalent liposomes selectively and efficiently target bacteria in the presence of healthy mammalian cells and cause bacterial cell agglutination. The liposomes also exhibited selective staining of the surfaces of dead or dying human cancer cells that had been treated with a chemotherapeutic agent.