Dynamic covalent chemistry

Dynamic covalent chemistry relates to chemical reactions carried out reversibly under conditions of equilibrium control. The reversible nature of the reactions introduces the prospects of "error checking" and "proof-reading" into synthetic processes where dynamic covalent chemistry operates. Since the formation of products occurs under thermodynamic control, product distributions depend only on the relative stabilities of the final products. In kinetically controlled reactions, however, it is the free energy differences between the transition states leading to the products that determines their relative proportions. Supramolecular chemistry has had a huge impact on synthesis at two levels: one is noncovalent synthesis, or strict self-assembly, and the other is supramolecular assistance to molecular synthesis, also referred to as self-assembly followed by covalent modification. Noncovalent synthesis has given us access to finite supermolecules and infinite supramolecular arrays. Supramolecular assistance to covalent synthesis has been exploited in the construction of more-complex systems, such as interlocked molecular compounds (for example, catenanes and rotaxanes) as well as container molecules (molecular capsules). The appealing prospect of also synthesizing these types of compounds with complex molecular architectures using reversible covalent bond forming chemistry has led to the development of dynamic covalent chemistry. Historically, dynamic covalent chemistry has played a central role in the development of conformational analysis by opening up the possibility to be able to equilibrate configurational isomers, sometimes with base (for example, esters) and sometimes with acid (for example, acetals). These stereochemical "balancing acts" revealed another major advantage that dynamic covalent chemistry offers the chemist, which is not so easily accessible in the kinetically controlled regime: the ability to re-adjust the product distribution of a reaction, even once the initial products have been formed, by changing the reaction's environment (for example, concentration, temperature, presence or absence of a template). This highly transparent, yet tremendously subtle, characteristic of dynamic covalent chemistry has led to key discoveries in polymer chemistry. In this review, some recent examples where dynamic covalent chemistry has been demonstrated are shown to emphasise the basic concepts of this area of science.     

离子型共价有机框架材料的制备及对染料吸附性能的研究

茜素红(Alizarin Red,AR)作为蒽醌类染料中的重要组成,由于其具有优异的特性,在染料和酸碱指示剂等方面被广泛使用。但是AR具有毒性高、结构复杂以及化学需氧量(COD)值大等原因,使其成为了主要污染物之一,去除水体中的茜素红染料污染物已经成为了目前亟待解决的问题。共价有机框架材料作为一种新型的多孔有机材料,由于其具有比表面积大,孔径均一和可设计的独特优势,已经广泛应用吸附和分离等方面。因此,以三醛基间苯三酚和溴化乙锭为构筑单元,通过水热的方法合成一种二维离子型共价有机框架材料(TpEB-COF)。对制备的TpEB-COF进行相关表征,包括X射线衍射仪(XRD),扫描电镜(SEM)和能量色散谱仪(EDS)等。然后将制备的TpEB-COF作为固体吸附剂,将其应用对水中AR的吸附,研究了不同吸附时间和不同pH值对吸附过程的影响。实验结果证明制备的离子型共价有机框架材料具有良好的晶型结构。同时,对实验数据分析表明,离子型共价有机框架材料对于茜素红的吸附符合准二级动力学方程和Langmuir吸附模型,吸附效率为82.8%,最大吸附量为828 mg g-1。本研究不仅为共价有机框架材料的设计和合成奠定坚实的基础,而且拓展了离子型共价有机框架材料的应用范围,促进共价有机框架材料的发展。     

Boronic acid building blocks: tools for self assembly

Dynamic covalent functionality has been acknowledged as a powerful tool for the construction of organised architectures, the reversible nature thermodynamically facilitates self-control and self-correction. The use of boronic acids complexation with diols and their congeners has already shown great promise in realising and developing reversible boron-containing multicomponent systems with dynamic covalent functionality. The structure-directing potential has lead to the development of a variety of self-organisation involving not only macrocycles, cages and capsules, but also porous covalent organic frameworks and polymers. Structure controls as well as remarkable synthesis are highlighted in this feature article.     

Covalent radii revisited

A new set of covalent atomic radii has been deduced from crystallographic data for most of the elements with atomic numbers up to 96. The proposed radii show a well behaved periodic dependence that allows us to interpolate a few radii for elements for which structural data is lacking, notably the noble gases. The proposed set of radii therefore fills most of the gaps and solves some inconsistencies in currently used covalent radii. The transition metal and lanthanide contractions as well as the differences in covalent atomic radii between low spin and high spin configurations in transition metals are illustrated by the proposed radii set.     

Charge‐Shift Bonding: A New and Unique Form of Bonding

Charge‐shift bonds (CSBs) constitute a new class of bonds different than covalent/polar‐covalent and ionic bonds. Bonding in CSBs does not arise from either the covalent or the ionic structures of the bond, but rather from the resonance interaction between the structures. This Essay describes the reasons why the CSB family was overlooked by valence‐bond pioneers and then demonstrates that the unique status of CSBs is not theory‐dependent. Thus, valence bond (VB), molecular orbital (MO), and energy decomposition analysis (EDA), as well as a variety of electron density theories all show the distinction of CSBs vis‐à‐vis covalent and ionic bonds. Furthermore, the covalent–ionic resonance energy can be quantified from experiment, and hence has the same essential status as resonance energies of organic molecules, e.g., benzene. The Essay ends by arguing that CSBs are a distinct family of bonding, with a potential to bring about a Renaissance in the mental map of the chemical bond, and to contribute to productive chemical diversity.     

Dynamic covalent gels assembled from small molecules: from discrete gelators to dynamic covalent polymers

Dynamic covalent chemistry has emerged recently to be a powerful tool to construct functional materials. This article reviews the progress in the research and development of dynamic covalent chemistry in gels assembled from small molecules. First dynamic covalent reactions used in gels are reviewed to understand the dynamic covalent bonding. Afterwards the catalogues of dynamic covalent gels are reviewed according to the nature of gelators and the interactions between gelators. Dynamic covalent bonding can be involved to form low molecular weight gelators. Low molecular weight molecules with multiple functional groups react to form dynamic covalent cross-linked polymers and act as gelators. Two catalogues of gels show different properties arising from their different structures. This review aims to illustrate the structure-property relationships of these dynamic covalent gels.     

Complex kinetics of the electron transfer between the photoactive redox label TUPS and the heme of cytochrome c

The photoinduced covalent redox label 8-thiouredopyrene-1,3,6-trisulfonate (TUPS) has been attached to two lysine residues (K8 and K39) at opposite sides of horse heart cytochrome c, as well as to cysteines, at the same positions, introduced by site-directed mutagenesis. Electron transfer between TUPS and the heme of cytochrome c deviates from the expected monoexponential kinetic behavior. Neither the overall rate nor the individual exponential components of electron transfer, as followed by kinetic absorption spectroscopy, correlate with the length of the covalent link connecting the dye with the protein. Molecular dynamics calculations show that TUPS can approach the protein surface and occupy several such positions. This heterogeneity may explain the multiexponential electron-transfer kinetics. The calculated optimal electron-transfer pathways do not follow the covalent link but involve through space jumps from the dye to the protein moiety, effectively decoupling the length of the covalent link and the electron-transfer rates.     

Charge-Shift Bonding: A New and Unique Form of Bonding

Charge-shift bonds (CSBs) constitute a new class of bonds different than covalent/polar-covalent and ionic bonds. Bonding in CSBs does not arise from either the covalent or the ionic structures of the bond, but rather from the resonance interaction between the structures. This Essay describes the reasons why the CSB family was overlooked by valence-bond pioneers and then demonstrates that the unique status of CSBs is not theory-dependent. Thus, valence bond (VB), molecular orbital (MO), and energy decomposition analysis (EDA), as well as a variety of electron density theories all show the distinction of CSBs vis-à-vis covalent and ionic bonds. Furthermore, the covalent–ionic resonance energy can be quantified from experiment, and hence has the same essential status as resonance energies of organic molecules, e.g., benzene. The Essay ends by arguing that CSBs are a distinct family of bonding, with a potential to bring about a Renaissance in the mental map of the chemical bond, and to contribute to productive chemical diversity.     

Template-directed synthesis employing reversible imine bond formation

The imine bond--formed by the reversible condensation of an amine and an aldehyde--and its applications as a dynamic covalent bond in the template-directed synthesis of molecular compounds, will be the focus of this tutorial review. Template-directed synthesis--or expressed another way, supramolecular assistance to covalent synthesis--relies on the use of reversible noncovalent bonding interactions between molecular building blocks in order to preorganise them into a certain relative geometry as a prelude to covalent bond formation to afford the thermodynamically preferred product. The use of this so-called dynamic covalent chemistry (DCC) in templated reactions allows for an additional amount of reversibility, further eliminating potential kinetic products by allowing the covalent bonds that are formed during the template-directed reaction to be 'proofread for errors', thus making it possible for the reaction to search out its thermodynamic minimum. The marriage of template-directed synthesis with DCC has allowed chemists to construct an increasingly complex collection of compounds from relatively simple precursors. This new paradigm in organic synthesis requires that each individual piece in the molecular self-assembly process is preprogrammed so that the multiple recognition events expressed between the pieces are optimised in a highly cooperative manner in the desired product. It offers an extremely simple way of making complex mechanically interlocked compounds--e.g., catenanes, rotaxanes, suitanes, Borromean rings and Solomon knots--from relatively simple precursors.     

共价氢化物发生-光度分析法高选择性的研究与应用——Ⅱ.砷、锡、锑共价氢化物的还原性及锡的高选择性测定

本文在共价氢化物发生-光度分析体系中设置固体氧化剂氢化物气体分离柱,以AsH_3、SbH_3和SnH_4为研究对象探讨了氢化物之间的干扰消除及高选择性测定问题。成功地建立了锡测定时其它共价氢化物元素干扰的消除方法,具有简便、高效、实用的特点。     

Fluorine-19 nuclear magnetic resonance and biochemical characterization of fluorotyrosine-labeled-thymidylate-synthetase

Fluorotyrosine has been incorporated into thymidylate synthetase from Lactobacillus casei by growth of the bacterium in media containing 3-fluorotyrosine. The enzyme exhibited a specific activity 70% of that of the normal enzyme and formed a covalent binary complex with pyrimidine nucleotides, as well as a covalent ternary complex with 5-fluorodeoxyuridylate and 5,10-methylenetetrahydrofolate. ¹⁹F nuclear magnetic resonance spectroscopy has been used to follow the formation of these complexes. 5-Fluorodeoxyuridylate, dUMP, dTMP and dCMP produced identical conformational changes in the enzyme as monitored by the fluorotyrosyl resonances. Ternary complex formation of the fluorotyrosine-containing enzyme with 5-fluorodeoxyuridylate and 5,10-methylenetetrahydrofolate resulted in further spectral changes.     

A New Dynamic Covalent Bond of Se?N: Towards Controlled Self‐Assembly and Disassembly

A new kind of Se? N dynamic covalent bond has been found that can form between the Se atom of a phenylselenyl halogen species and the N atom of a pyridine derivative, such as polystyrene‐b‐poly(4‐vinylpyridine). This Se? N dynamic covalent bond can be reversibly and rapidly formed or cleaved under acidic or basic conditions, respectively. Furthermore, the bond can be dynamically cleaved by heating or treatment with stronger electron‐donating pyridine derivatives. The multiple responses of Se? N bond to external stimuli has enriched the existing family of dynamic covalent bonds. It can be used for controlled and reversible self‐assembly and disassembly, which may find potential applications in a number of areas, including self‐healing materials and responsive assemblies.     

Layer‐by‐Layer Assembly for Surface Tethering of Thin‐Hydrogel Films: Design Strategies and Applications

Manipulation and engineering of the surfaces has a key role in improving the materials properties. Anchoring of thin hydrogels on the materials surface is one of the recently developed methods to achieve surfaces with high potential applications. Layer‐by‐layer (LBL) has been used widely as a strong strategy for immobilization of thin hydrogel films on the surface of various organic/inorganic substrates. Electrostatic LBL and covalent LBL are two main strategies used in this regard. In electrostatic LBL, negatively and positively hydrophilic polymers are sequentially assembled to create a multilayer hydrogel which subsequent covalent crosslinking of multilayers improved the stability of the inserted layers. On the other hand, covalent LBL requires hydrophilic polymers bearing reactive telechelic groups. These reactive polymers are prepared by various polymerization techniques or by post‐functionalization of biopolymers. The principles of hydrogel anchoring have described along with representative examples. Besides, the potential applications of the modified surfaces in specific cases have been addressed and overviewed.     

Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations

Ibrutinib is the first covalent inhibitor of Bruton''s tyrosine kinase (BTK) to be used in the treatment of B-cell cancers. Understanding the mechanism of covalent inhibition will aid in the design of safer and more selective covalent inhibitors that target BTK. The mechanism of covalent inhibition in BTK has been uncertain because there is no appropriate residue nearby that can act as a base to deprotonate the cysteine thiol prior to covalent bond formation. We investigate several mechanisms of covalent modification of C481 in BTK by ibrutinib using combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics reaction simulations. The lowest energy pathway involves direct proton transfer from C481 to the acrylamide warhead in ibrutinib, followed by covalent bond formation to form an enol intermediate. There is a subsequent rate-limiting keto–enol tautomerisation step (ΔG^‡ = 10.5 kcal mol⁻¹) to reach the inactivated BTK/ibrutinib complex. Our results represent the first mechanistic study of BTK inactivation by ibrutinib to consider multiple mechanistic pathways. These findings should aid in the design of covalent drugs that target BTK and other similar targets.

QM/MM simulations show that covalent modification of BTK by ibrutinib proceeds via an intramolecular proton transfer from C481 to the acrylamide warhead of ibrutinib, followed by covalent bond formation and subsequent keto–enol tautomerisation.      

Merging constitutional and motional covalent dynamics in reversible imine formation and exchange processes

The formation and exchange processes of imines of salicylaldehyde, pyridine-2-carboxaldehyde, and benzaldehyde have been studied, showing that the former has features of particular interest for dynamic covalent chemistry, displaying high efficiency and fast rates. The monoimines formed with aliphatic α,ω-diamines display an internal exchange process of self-transimination type, inducing a local motion of either "stepping-in-place" or "single-step" type by bond interchange, whose rate decreases rapidly with the distance of the terminal amino groups. Control of the speed of the process over a wide range may be achieved by substituents, solvent composition, and temperature. These monoimines also undergo intermolecular exchange, thus merging motional and constitutional covalent behavior within the same molecule. With polyamines, the monoimines formed execute internal motions that have been characterized by extensive one-dimensional, two-dimensional, and EXSY proton NMR studies. In particular, with linear polyamines, nondirectional displacement occurs by shifting of the aldehyde residue along the polyamine chain serving as molecular track. Imines thus behave as simple prototypes of systems displaying relative motions of molecular moieties, a subject of high current interest in the investigation of synthetic and biological molecular motors. The motional processes described are of dynamic covalent nature and take place without change in molecular constitution. They thus represent a category of dynamic covalent motions, resulting from reversible covalent bond formation and dissociation. They extend dynamic covalent chemistry into the area of molecular motions. A major further step will be to achieve control of directionality. The results reported here for imines open wide perspectives, together with other chemical groups, for the implementation of such features in multifunctional molecules toward the design of molecular devices presenting a complex combination of motional and constitutional dynamic behaviors.     

Chemically functionalized glassy carbon spheres: a new covalent bulk modified composite electrode for the simultaneous determination of lead and cadmium

A new type of covalent bulk modified glassy carbon composite electrode has been fabricated and utilized in the simultaneous determination of lead and cadmium ions in aqueous medium. The covalent bulk modification was achieved by the chemical reduction of 2-hydroxybenzoic acid diazonium tetrafluroborate in the presence of hypophosphorous acid as a chemical reducing agent. The covalent attachment of the modifier molecule was examined by studying Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy and the surface morphology was examined by scanning electron microscopy images. The electrochemistry of modified glassy carbon spheres was studied by its cyclic voltammetry to decipher the complexing ability of the modifier molecules towards Pb²⁺ and Cd²⁺ ions. The developed sensor showed a linear response in the concentration range 1–10 μM with a detection limit of 0.18 and 0.20 μM for lead and cadmium, respectively. The applicability of the proposed sensor has been checked by measuring the lead and cadmium levels quantitatively from sewage water and battery effluent samples.     

Capillary electrophoresis methods for the determination of covalent polyphenol–protein complexes

The bioactivities and bioavailability of plant polyphenols including proanthocyanidins and other catechin derivatives may be affected by covalent reaction between polyphenol and proteins. Both processing conditions and gastrointestinal conditions may promote formation of covalent complexes for polyphenol-rich foods and beverages such as wine. Little is known about covalent reactions between proteins and tannin, because suitable methods for quantitating covalent complexes have not been developed. We established capillary electrophoresis methods that can be used to distinguish free protein from covalently bound protein-polyphenol complexes and to monitor polyphenol oxidation products. The methods are developed using the model protein bovine serum albumin and the representative polyphenol (-)epigallocatechin gallate. By pairing capillaries with different diameters with appropriate alkaline borate buffers, we are able to optimize resolution of either the protein-polyphenol complexes or the polyphenol oxidation products. This analytical method, coupled with purification of the covalent complexes by diethylaminoethyl cellulose chromatography, should facilitate characterization of covalent complexes in polyphenol-rich foods and beverages such as wine.     

Computational and experimental evidence of through-space NMR spectroscopic J coupling of hydrogen atoms

J coupling in NMR spectroscopy is conventionally associated with covalent bonds. A noncovalent contribution often called through-space coupling (TSC) has been observed for heavy atoms. In this study, the TSC was detected and analyzed for the more common (1)H-(1)H coupling as well. In synthesized model molecules the hydrogen positions could be well controlled. For several coupling constants the through-space mechanism was even found to be the predominant factor. The nature and magnitude of the phenomenon were also analyzed by density functional computations. Calculated carbon- and hydrogen-coupling maps and perturbed electronic densities suggest that the aromatic system strongly participates in the noncovalent contribution. Unlike covalent coupling, which is usually governed by the Fermi contact, TSC is dominated by the diamagnetic term comprising interactions of nuclei with the electron orbital angular momentum. The computations further revealed a strong distance and conformational dependence of TSC. This suggests that the through-space coupling can be explored in molecular structural studies in the same way as the covalent one.     

CYP450 2B4 covalently attached to carbon and gold screen printed electrodes by diazonium salt and thiols monolayers

An easy covalent immobilization method used to develop enzyme biosensors based on carbon and gold screen printed electrodes (SPCEs and gold SPEs) is described. The linkage of biomolecules through 4-nitrobenzenediazonium tetrafluoroborate, mercaptopropionic acid and thioctic acid monolayers has been attempted using bare SPCEs and gold SPEs, as well as gold nanoparticles (AuNPs) modified SPCEs and gold SPEs. Direct covalent attachment of Cytochrome P450 2B4 (CYP450 2B4) to the transducer has been carried out by carbodiimide and hydroxysuccinimide. Experimental variables in the immobilization process and in the chronoamperometric determination of Phenobarbital (PB) have been optimized by the experimental design methodology. Reproducibility of the different biosensors has been checked under the optimum conditions, yielding values lower than 6%. Their performances have been shown by the determination of PB in pharmaceutical drugs.