Recognition,replication and extrabiotic chemistry

Abstract

The subject is how molecules fit together - molecular recognition - and the intriguing specific issue is why molecules fit together. Complementarity and selfcomplementarity are central to these problems, and by complementarity is meant that of molecular size, shape, and charge that gives rise to the reciprocal, weak intermolecular forces that bind host and guest, however temporarily, to one another. One of the unexpected dividends from the study of forces is concerned with ‘extrabiotic’¹ chemistry. This term is intended to define chemical or other systems which show properties reminiscent² of living systems, yet have little or no structural relationship to what is regarded as biological. In our own research hydrogen bonding and aryl stacking interactions have provided the intermolecular forces of recognition. Self-replicating systems appear to be an inevitable consequence of such forces.³     

Supramolecular Strategies for Controlling Reactivity within Confined Nanospaces

Nanospaces are ubiquitous in the realm of biological systems and are of significant interest among supramolecular chemists. Understanding chemical behavior within nanospaces offers new perspectives on biological phenomena in nature and opens the way to highly unusual and selective forms of catalysis. Supramolecular chemistry exploits weak, yet effective, intermolecular interactions such as hydrogen bonding, metal‐ligand coordination, and the hydrophobic effect to assemble nano‐sized molecular architectures, providing reactions with remarkable rate acceleration, substrate specificity, and product selectivity. In this minireview, the focus is on the strategies that supramolecular chemists use to emulate the efficiency of biological processes, and elucidating how chemical reactivity is efficiently controlled within well‐defined nanospaces. Approaches such as orientation and proximity of substrate, transition‐state stabilization, and active‐site incorporation will be discussed.     

From supramolecular chemistry towards constitutional dynamic chemistry and adaptive chemistry

Supramolecular chemistry has developed over the last forty years as chemistry beyond the molecule. Starting with the investigation of the basis of molecular recognition, it has explored the implementation of molecular information in the programming of chemical systems towards self-organisation processes, that may occur either on the basis of design or with selection of their components. Supramolecular entities are by nature constitutionally dynamic by virtue of the lability of non-covalent interactions. Importing such features into molecular chemistry, through the introduction of reversible bonds into molecules, leads to the emergence of a constitutional dynamic chemistry, covering both the molecular and supramolecular levels. It considers chemical objects and systems capable of responding to external solicitations by modification of their constitution through component exchange or reorganisation. It thus opens the way towards an adaptive and evolutive chemistry, a further step towards the chemistry of complex matter.     

Supramolecular coordination chemistry: the synergistic effect of serendipity and rational design

Supramolecular coordination compounds bear exceptional advantages over their organic counterparts. They are available in one-pot reactions and in high yields and display physical properties that are generally inaccessible with organic species. Moreover, their weak, reversible, noncovalent bonding interactions facilitate error checking and self-correction. This Review emphasizes the achievements in supramolecular coordination chemistry initiated by serendipity and their materialization based on rational design. The recognition of similarities in the synthesis of different supramolecular assemblies allows prediction of potential results in related cases. Supramolecular synthesis obeys guidelines comparable to the "lead sheet" used by small jazz ensembles for improvisation and therefore more often leads to unpredicted results. The combination of detailed symmetry considerations with the basic rules of coordination chemistry has only recently allowed for the design of rational strategies for the construction of a variety of nanosized systems with specified size and shape.     

Self-assembly of diorganotin(IV) oxides (R = Me, nBu, Ph) and 2,5-pyridinedicarboxylic acid to polymeric and trinuclear macrocyclic hybrids with porous solid-state structures: influence of substituents and solvent on the supramolecular structure

2,5-Pyridinedicarboxylic acid has been reacted with three different diorganotin(IV) oxides (R = Me, nBu, Ph) to study the molecular and supramolecular structures of the resulting diorganotin(IV) 2,5-pyridinedicarboxylates. It has been found that coordinating solvent molecules can change the supramolecular structure completely. The molecular structures found are either polymeric (zigzag) or cyclotrimeric; the supramolecular arrangements include (i) systems having only loosely bound discrete molecules (van der Waals contacts), (ii) systems having a 2D or 3D hydrogen-bonded structure, and (iii) systems having a 3D polymeric coordination structure. Channels or cavities are formed in several cases. For a particular case, evidence has been provided that molecular aggregation to capsules through hydrogen bonding interactions is possible in solution.     

Bulk chemical shifts in hydrogen-bonded systems from first-principles calculations and solid-state-NMR

We present an analysis of bulk (1)H NMR chemical shifts for a series of biochemically relevant molecular crystals in analogy to the well-known solvent NMR chemical shifts. The term bulk shifts denotes the change in NMR frequency of a gas-phase molecule when it undergoes crystallization. We compute NMR parameters from first-principles electronic structure calculations under full periodic boundary conditions and for isolated molecules and compare them to the corresponding experimental fast magic-angle spinning solid-state NMR spectra. The agreement between computed and experimental lines is generally very good. The main phenomena responsible for bulk shifts are packing effects (hydrogen bonding and pi-stacking) in the condensed phase. By using these NMR bulk shifts in well-ordered crystalline model systems composed of biologically relevant molecules, we can understand the individual spectroscopic signatures of packing effects. These local structural driving forces, hydrogen bonding, pi-stacking, and related phenomena, stand as a model for the forces that govern the assembly of much more complex supramolecular aggregates. We show to which accuracy condensed-phase ab initio calculations can predict structure and structure-property relationships for noncovalent interactions in complex supramolecular systems.     

Hydrothermal Synthesis and Crystal Structure of Manganese（ Ⅱ ） Coordination Polymer Assembled by 4-Sulfophthalate and 4,4＇-Bipyridine

The rational design and synthesis of metal-directed supramolecular framework compounds have received much attention in coordination chemistry because of their potential applications in catalysis, molecular selection, nonlinear optics, ion exchange, and microelectronics. Many high-dimensional coordination complexes have been designed and prepared through molecular self-assembly processes. The open metal organic framework can be produced via two kinds of interactions, i. e. , coordinate covalent bonds and weaker intermolecular forces. For this reason, the most efficient means to synthesize these compounds is to establish possible connections among different units.     

Dynamic imine chemistry

Formation of an imine--from an amine and an aldehyde--is a reversible reaction which operates under thermodynamic control such that the formation of kinetically competitive intermediates are, in the fullness of time, replaced by the thermodynamically most stable product(s). For this fundamental reason, the imine bond has emerged as an extraordinarily diverse and useful one in the hands of synthetic chemists. Imine bond formation is one of a handful of reactions which define a discipline known as dynamic covalent chemistry (DCC), which is now employed widely in the construction of exotic molecules and extended structures on account of the inherent 'proof-reading' and 'error-checking' associated with these reversible reactions. While both supramolecular chemistry and DCC operate under the regime of reversibility, DCC has the added advantage of constructing robust molecules on account of the formation of covalent bonds rather than fragile supermolecules resulting from noncovalent bonding interactions. On the other hand, these products tend to require more time to form--sometimes days or even months--but their formation can often be catalysed. In this manner, highly symmetrical molecules and extended structures can be prepared from relatively simple precursors. When DCC is utilised in conjunction with template-directed protocols--which rely on the use of noncovalent bonding interactions between molecular building blocks in order to preorganise them into certain relative geometries as a prelude to the formation of covalent bonds under equilibrium control--an additional level of control of structure and topology arises which offers a disarmingly simple way of constructing mechanically-interlocked molecules, such as rotaxanes, catenanes, Borromean rings, and Solomon knots. This tutorial review focuses on the use of dynamic imine bonds in the construction of compounds and products formed with and without the aid of additional templates. While synthesis under thermodynamic control is giving the field of chemical topology a new lease of life, it is also providing access to an endless array of new materials that are, in many circumstances, simply not accessible using more traditional synthetic methodologies where kinetic control rules the roost. One of the most endearing qualities of chemistry is its ability to reinvent itself in order to create its own object, as Berthelot first pointed out a century and a half ago.     

肽基超分子胶体

肽基超分子胶体是基于肽分子间超分子作用,自发形成且具有有序分子排布及规整结构,兼具传统胶体及超分子特性的组装体系。利用超分子弱相互作用构筑功能性胶体,不仅是人们对生命组装进程深入理解的有效手段,也是实现优异的超分子材料的重要途径。肽分子具有组成明确、性能可调、生物安全性高及可降解等优势,是超分子化学、胶体与界面化学领域重要的组装基元。基于肽的超分子自组装,能够实现多尺度、多功能的生物胶体的构筑,被广泛应用于医药、催化、能源等领域。如何通过对肽序列的设计及分子间作用力的调控,实现对胶体结构和功能的精确控制,是近年来研究的重要课题之一。从分子尺度研究和揭示超分子胶体的组装过程及物理化学机制,探究胶体结构与功能的关系,是实现超分子结构和功能化的重要内容。本文基于"分子间作用的调控"及"结构与功能的关系"两个基本科学问题,系统地综述了肽基超分子胶体的组装机制、结构与功能,以及研究现状。     

Supramolecular chemistry — Scope and perspectives: Molecules — Supermolecules — Molecular devices

Supramolecular chemistry is the chemistry of the intermolecular bond, covering the structures and functions of the entities formed by association of two or more chemical species. Molecular recognition in the supermolecules formed by receptor-substrate binding rests on the principles of molecular complementarity, as found in spherical and tetrahedral recognition, linear recognition by co-receptors, metallo-receptors, amphilic receptors and anion coordination. Supramolecular catalysis by receptors bearing reactive groups effects bond cleavage reactions as well as synthetic bond formation via co-catalysis. Lipophilic receptor molecules act as selective carriers for various substrates and allow the setting up of coupled transport processes linked to electron and proton gradients or to light. Whereas endo-receptors bind substrates in molecular cavities by convergent interactions, exo-receptors rely on interactions between the surfaces of the receptor and the substrate; thus new types of receptors such as the metallonucleates may be designed. In combination with polymolecular assemblies, receptors, carriers and catalysts may lead to molecular and supramolecular devices, defined as structurally organized and functionally integrated chemical systems built on supramolecular architectures. Their recognition, transfer and transformation features are analyzed specifically from the point of view of molecular devices that would operate via photons, electrons or ions, thus defining the fields of molecular photonics, electronics and ionics. Introduction of photosensitive groups yields photoactive receptors for the design of light conversion and charge separation centres. Redox active polyolefinic chains represent molecular wires for electron transfer through membranes. Tubular mesophases formed by stacking of suitable macrocyclic receptors may lead to ion channels. Molecular self-assembling occurs with acyclic ligands that form complexes with a double helical structure. Such developments in molecular and supramolecular design and engineering open perspectives towards the realization of molecular photonic, electronic and ionic devices, that would perform highly selective recognition, reaction and transfer operations for signal and information processing at the molecular level.     

Metallogels from Coordination Complexes,Organometallic, and Coordination Polymers

A supramolecular gel results from the immobilization of solvent molecules on a 3D network of gelator molecules stabilized by various supramolecular interactions that include hydrogen bonding, π–π stacking, van der Waals interactions, and halogen bonding. In a metallogel, a metal is a part of the gel network as a coordinated metal ion (in a discrete coordination complex), as a cross‐linking metal node with a multitopic ligand (in coordination polymer), and as metal nanoparticles adhered to the gel network. Although the field is relatively new, research into metallogels has experienced a considerable upsurge owing to its fundamental importance in supramolecular chemistry and various potential applications. This focus review aims to provide an insight into the development of designing metallogelators. Because of the limited scope, discussions are confined to examples pertaining to metallogelators derived from discrete coordination complexes, organometallic gelators, and coordination polymers. This review is expected to enlighten readers on the current development of designing metallogelators of the abovementioned class of molecules.     

NMR spectroscopy in coordination supramolecular chemistry: A unique and powerful methodology

Metal-mediated self-assembly is emerging as a very important strategy for the synthesis of supramolecular species. Still, a major challenge in coordination supramolecular chemistry continues to be the characterization of the self-assembled complexes and the investigation of their dynamic behaviour in solution. In this context, NMR spectroscopy appears as a unique and powerful methodology. This practical-oriented review describes the rich variety of NMR techniques which are applied to the investigation of different aspects of the structure and behaviour of supramolecular complexes. “Classic” 1D NMR spectra reflect characteristic chemical shifts due to metal–ligand interactions or encapsulation phenomena, as well as symmetry and chiral properties of host–guest assemblies. Mainstream ¹H, ¹³C, ¹⁹F and ³¹P spectra are eventually complemented by the use of NMR-active metal nuclides. Homo- and heteronuclear 2D correlation experiments are ubiquitous in the literature, providing through-bond and through-space connectivities. Increasingly, diffusion measurements are also gaining popularity in this field, being used to gain information about molecular size, intermolecular interactions and even association constants of supramolecular complexes. Knowledge about the thermodynamic properties and the dynamic behaviour of coordination supramolecular assemblies is essential for the development of their practical applications. The most frequently used NMR methodologies for the calculation of association constants (simple signal integration, NMR titration and diffusion measurements) and for the investigation of dynamic supramolecular equilibria (lineshape analysis, selective inversion recovery experiments and 2D EXSY spectra) are described, together with the use of variable-temperature investigations for the determination of the thermodynamic and activation parameters of self-assembly and encapsulation processes.     

Supramolecular amphiphiles

Supramolecular amphiphiles (SA), also named superamphiphiles, refer to amphiphiles that are formed by non-covalent interactions. This tutorial review focuses on the molecular architectures of SAs, including diversified topologies such as single chain, double chain, bolaform, gemini and rotaxane types. Non-covalent syntheses that have been employed to fabricate SAs are driven by hydrogen bonding, electrostatic attraction, host-guest recognition, charge transfer interaction, metal coordination and so on. It should be noted that SAs can be either small organic molecules or polymers. SAs allow for tuning of their amphiphilicity in a reversible fashion, leading to controlled self-assembly and disassembly. This line of research has been enriching traditional colloid chemistry and current supramolecular chemistry, and the application of SAs in the field of functional supramolecular materials is keenly anticipated.     

Theoretical investigation of the interactions between the π‐systems of molecular organic semiconductors and an analysis of the contributions of repulsion and electrostatics

A concept for the interactions between π‐systems is necessary to understand a number of phenomena in modern material sciences such as supramolecular properties and self‐assembly. In the present article, we investigate the intermolecular interaction energies between organic semiconductors with extended π‐systems using SAPT (symmetry‐adapted perturbation theory), LMO‐EDA (localized molecular orbital energy decomposition analysis), DFT‐D (density functional theory including dispersion corrections), and force‐field approaches. Both apolar organic molecules such as acenes and highly polarized π‐systems of merocyanines and squaraines were used to probe the influence of electrostatics on the shape of the potential energy surfaces (PES) governing the geometric structures of aggregates. Our results reveal that the shapes of the PESs result from variations in the short‐range, highly specific repulsion forces even for highly polar molecules. Using distributed quadrupoles, we show that it is nevertheless possible to mimic the intermolecular potentials with electrostatics. This is also possible with van‐der‐Waals potentials and a simple overlap‐based force‐field ansatz based on the overlap between p‐orbitals. © 2016 Wiley Periodicals, Inc.     

Supramolecular chemistry and crystal engineering

Supramolecular chemistry is the chemistry of molecular ensembles and intermolecular interactions. Currently it is a major, interdisciplinary branch of science dealing with chemical, physical, biological and technological aspects of the creation and study of complex chemical systems based upon non-valent interactions. Crystal engineering is a direction of supramolecular chemistry aimed at the design of periodic structures with a desired supramolecular organization. This paper shortly reviews the goals and research objects of supramolecular chemistry and crystal engineering and lists the most important historical facts and the literature.     

Molecular Recognition with Model Systems

How structures fit together is the principal domain of molecular recognition, and current studies are evolving from the host–guest chemistry of ions to interactions between two molecules. Recent advances in the synthesis of sizable concave molecules, especially those featuring convergent functional groups, make it possible to bind smaller convex structures with considerable selectivity. One result is that hydrogen bonding can be addressed in model systems. The present review emphasizes the use of cleftlike structures as a means of probing the forces involved in nucleic acid recognition. The application of such molecules to the catalysis of chemical reactions, particularly those involved in self-replicating systems, is also described. Some implications for future pharmaceutical agents are suggested as a result of access to synthetic receptors for biologically relevant targets.     

Switching surface chemistry with supramolecular machines

Tethered supramolecular machines represent a new class of active self-assembled monolayers in which molecular configurations can be reversibly programmed using electrochemical stimuli. We are using these machines to address the chemistry of substrate surfaces for integrated microfluidic systems. Interactions between the tethered tetracationic cyclophane host cyclobis(paraquat-p-phenylene) and dissolved pi-electron-rich guest molecules, such as tetrathiafulvalene, have been reversibly switched by oxidative electrochemistry. The results demonstrate that surface-bound supramolecular machines can be programmed to adsorb or release appropriately designed solution species for manipulating surface chemistry.     

Methods of modulating hydrogen bonded interactions in synthetic host-guest systems

Hydrogen bonded interactions are among the most important non-covalent interactions in supramolecular chemistry. The strength, selectivity and directionality inherent in hydrogen bonding processes have allowed the creation of complex and efficient molecular hosts capable of selective binding to a wide variety of complementary guests. Major advances in controlling host-guest complexation have occurred in the last decade, principally through systematic modification of the electrostatic properties and/or geometry of the hosts, thereby fine-tuning the molecular recognition event. More recently, systems have been developed which allow the effectiveness and selectively of hydrogen bonding interactions to be reversibly modulated by an external stimulus, more accurately mimicking biological systems and providing building blocks for the construction of novel advanced materials, sensors and devices. In this review, we highlight some of the methods available for modulating the strength and selectivity of hydrogen bonded interactions in synthetic host-guest systems.     

Integrating Molecular Modeling with Semiempirical Quantum Mechanical Calculations into the Upper-Level Inorganic Chemistry Course

The analysis of chemical bonding and reactivity from the perspective of molecular orbital theory is challenging for students at the undergraduate level. In an attempt to improve the instruction of this material in my upper-level inorganic chemistry course I developed a series of computational experiments using a molecular modeling program that can perform semiempirical quantum mechanical calculations. These exercises explore the chemistry of molecular systems through an analysis of the variation in the attractive and repulsive forces in the system as a function of structure or composition. The exercises challenge the analysis skills of the students by requiring them to consider how two or more factors contribute to the properties of the system. Examples of exercises that demonstrate different types of computational experiments are given. These sample exercises examine the structure of simple molecules, the reactivity of Lewis acids, and the bonding in transition metal complexes.