Simultaneous Determination of Binding Constants for Multiple Carbohydrate Hosts in Complex Mixtures

Amylose Dimerization in Solution Can Be Studied Using a Model System

Amylose, the linear polymer of α-1,4-linked glucopyranose units, is known to crystallize as a parallel double helix, but evidence of this duplex forming in solution has remained elusive for decades. We show how the dimerization of short amylose chains can be detected in solution using NMR spectroscopy when the glucans are labeled at the reducing-end with an aromatic moiety that overcomes chemical shift degeneracy leading to distinct signals for the single-stranded and duplex amylose. A set of α-1,4 glucans with varying lengths of 6, 12, 18, and 22 glucose units and a 4-aminobenzamide label were synthesized, enabling the first systematic thermodynamic study of the association of amylose in solution. The dimerization is enthalpically driven, entropically unfavorable and beyond a minimum length of 12, each additional pair of glucose residues stabilizes the duplex by 0.85 kJ mol-1 . This fundamental knowledge provides a basis for a quantitative understanding of starch structure, gelation and enzymatic digestion, and lays the foundations for the strategic use of α-1,4-glucans in the development of self-assembled materials.

Quantitative determination of the binding capabilities of individual large-ring cyclodextrins in complex mixtures

Large-ring cyclodextrins (CDs) are a comparatively unexplored family of macrocycles. We use high-resolution 1H-13C HSQC NMR experiments to resolve the anomeric signals of at least 13 different size CDs in a mixture. Using a single titration experiment, we can quantify the individual binding capabilites of these structurally-related hosts, avoiding the need for cumbersome isolation.

Light-controlled enzymatic synthesis of γ-CD using a recyclable azobenzene template

Cyclodextrins (CDs) are important molecular hosts for hydrophobic guests in water and extensively employed in the pharmaceutical, food and cosmetic industries to encapsulate drugs, flavours and aromas. Compared with α- and β-CD, the wide-scale use of γ-CD is currently limited due to costly production processes. We show how the yield of γ-CD in the enzymatic synthesis of CDs can be increased 5-fold by adding a tetra-ortho-isopropoxy-substituted azobenzene template irradiated at 625 nm (to obtain the cis-(Z)-isomer) to direct the synthesis. Following the enzymatic reaction, the template can then be readily recovered from the product mixture for use in subsequent reaction cycles. Heating induces thermal cis-(Z) to trans-(E) relaxation and consequent dissociation from γ-CD whereupon the template can then be precipitated by acidification. For this study we designed and synthesised a set of three water-soluble azobenzene templates with different ortho-substituents and characterised their photoswitching behaviour using UV/vis and NMR spectroscopy. The templates were tested in cyclodextrin glucanotransferase-mediated dynamic combinatorial libraries (DCLs) of cyclodextrins while irradiating at different wavelengths to control the cis/trans ratios. To rationalise the behaviour of the DCLs, NMR titrations were carried out to investigate the binding interactions between α-, β- and γ-CD and the cis and trans isomers of each template.

Templated Enzymatic Synthesis of δ-Cyclodextrin

While α-, β-, and γ-cyclodextrin (CD) are ubiquitous hosts employed by supramolecular chemists, δ-CD (formed from nine α-1,4-linked glucopyranose units) has received very little attention. α-, β-, and γ-CD are the major products of the enzymatic breakdown of starch by cyclodextrin glucanotransferase (CGTase), but δ-CD forms only transiently in this reaction, as a minor component of a complex mixture of linear and cyclic glucans. In this work, we show how δ-CD can be synthesized in unprecedented yields by employing a bolaamphiphile template in an enzyme-mediated dynamic combinatorial library of cyclodextrins. NMR spectroscopy studies revealed that δ-CD can thread up to three bolaamphiphiles forming [2]-, [3]-, or [4]-pseudorotaxanes, depending on the size of the hydrophilic headgroup and the length of the alkyl chain axle. Threading of the first bolaamphiphile occurs in fast exchange on the NMR chemical shift time scale, while subsequent threading occurs in slow exchange. To extract quantitative information for 1:2 and 1:3 binding events occurring in mixed exchange regimes, we derived equations for nonlinear curve fitting that take into consideration both the chemical shift changes for species in fast exchange and the integrals for species in slow exchange to determine K_a1, K_a2, and K_a3. Template T1 could be used to direct the enzymatic synthesis of δ-CD due to the cooperative formation of a 1:2 complex─the [3]-pseudorotaxane δ-CD·T1₂. Importantly, T1 is recyclable. It can be readily recovered from the enzymatic reaction by precipitation and reused in subsequent syntheses enabling preparative-scale synthesis of δ-CD.

Foldaxanes: Rotaxane-like Architectures from Foldamers

Mechanically interlocked molecules such as rotaxanes and catenanes contain free-moving components that cannot dissociate and have enabled the investigation and control of various translational and rotational molecular motions. The architecture of pseudo-rotaxanes and of some kinetically labile rotaxanes is comparable to that of rotaxanes but their components are reversibly associated and not irreversibly interlocked. In other words, pseudo-rotaxanes may fall apart. This Account focuses on a peculiar family of rotaxane-like architectures termed foldaxanes.Foldaxanes consist of a helically folded oligomer wound around a rod-like dumbbell-shaped guest. Winding of the helix around the rod thus entails an unwinding-rewinding process that creates a kinetic barrier. It follows that foldaxanes, albeit reversibly assembled, have significant lifetimes and may not fall apart while defined molecular motions are triggered. Foldaxanes based on helically folded aromatic oligoamide hosts and oligo(alkyl carbamate) guests can be designed rationally through the inclusion of complementary binding motifs on the rod and at the inner rim of the helix so that helix length and rod length match. Single helical foldaxanes (bimolecular species) and double helical foldaxanes (trimolecular species) have thus been produced as well as poly[n]foldaxanes, in which several helices bind to long rods with multiple binding stations. When the binding stations differ and are organized in a certain sequence, a complementary sequence of different stacked helices, each matching with their binding station, can be assembled, thus reproducing in an artificial system a sort of translation process.Foldaxane helix handedness may be controlled by stereogenic centers on the rod-like guest. Handedness can also be transmitted from helix to helix in polyfoldaxanes. Foldaxane formation has drastic consequences for the rod properties, including its stiffening and the restriction of the mobility of a macrocycle already interlocked on the rod. Fast translation (without dissociation) of helices along rod-like guests has been demonstrated. Because of the helical nature of the hosts, translation may be accompanied by rotation in various sorts of screw-like motions. The possibility, on longer time scales, for the helix to dissociate from and reassociate to the rod has allowed for the design of complex, kinetically controlled supramolecular pathways of a helix on a rod. Furthermore, the design of helices with a directionality, that is, with two distinct termini, that bind to nonsymmetrical rod-like guests in a defined orientation makes it possible to also control the orientation of molecular motion. Altogether, foldaxanes constitute a distinct and full-of-potential family of rotaxane-like architectures that possess designer structures and allow orchestration of the time scales of various supramolecular events.

Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing

The power of sensing molecules is often characterized in part by determining their thermodynamic/dynamic properties, in particular the binding constant of a guest to a host. In many studies, traditional nonlinear regression analysis has been used to determine the binding constants, which cannot be applied to complex systems and limits the reliability of such calculations. Supramolecular sensor systems include many interactions that make such chemical systems complicated. The challenges in creating sensing molecules can be significantly decreased through the availability of detailed mathematical models of such systems. Here, we propose uncovering accurate thermodynamic parameters of chemical reactions using better-defined mathematical modeling-fitting analysis is the key to understanding molecular assemblies and developing new bio/sensing agents. The supramolecular example we chose for this investigation is a self-assembled sensor consists of a synthesized receptor, DPA (DPA = dipicolylamine)-appended phenylboronic acid (1) in combination with Zn2+(1.Zn) that forms various assemblies with a fluorophore like alizarin red S (ARS). The self-assemblies can detect multi-phosphates like pyrophosphate (PPi) in aqueous solutions. We developed a mathematical model for the simultaneous quantitative analysis of twenty-seven intertwined interactions and reactions between the sensor (1.Zn-ARS) and the target (PPi) for the first time, relying on the Newton-Raphson algorithm. Through analyzing simulated potentiometric titration data, we describe the concurrent determination of thermodynamic parameters of the different guest-host bindings. Various values of temperatures, initial concentrations, and starting pHs were considered to predict the required measurement conditions for thermodynamic studies. Accordingly, we determined the species concentrations of different host-guest bindings in a generalized way. This way, the binding capabilities of a set of species can be quantitatively examined to systematically measure the power of the sensing system. This study shows analyzing supramolecular self-assemblies with solid mathematical models has a high potential for a better understanding of molecular interactions within complex chemical networks and developing new sensors with better sensing effects for bio-purposes.

A review of NMR analysis in polysaccharide structure and conformation: Progress, challenge and perspective

Nuclear magnetic resonance (NMR) has been widely used as an analytical chemistry technique to investigate the molecular structure and conformation of polysaccharides. Combined with 1D spectra, chemical shifts and coupling constants in both homo- and heteronuclear 2D NMR spectra are able to infer the linkage and sequence of sugar residues. Besides, NMR has also been applied in conformation, quantitative analysis, cell wall in situ, degradation, polysaccharide mixture interaction analysis, as well as carbohydrates impurities profiling. This review summarizes the principle and development of NMR in polysaccharides analysis, and provides NMR spectra data collections of some common polysaccharides. It will help to promote the application of NMR in complex polysaccharides of biochemical interest, and provide valuable information on commercial polysaccharide products.

Light-controlled out-of-equilibrium assembly of cyclodextrins in an enzyme-mediated dynamic system

We show that the selective enzymatic synthesis of specific cyclodextrins can be modulated using light. We use enzyme-mediated dynamic combinatorial chemistry to generate a mixture of interconverting linear and cyclic α-1,4-glucans, and employ an azobenzene photoswitch as a template. Using UV or blue light to switch between photostationary states with different azobenzene cis/trans isomeric ratios, we can promote the out-of-equilibrium assembly of either α-cyclodextrin or β-cyclodextrin.

Sequential molecule-triggered-release system based on acetylated amylose helix aggregates

We developed a molecule-triggered-release system based on acetylated amylose helix aggregates, in which the triggered conditions and duration time can be adjusted. The system could even be customized to meet specific demands.

Supramolecular chemical shift reagents inducing conformational transitions: NMR analysis of carbohydrate homooligomer mixtures

Supramolecular chemical shift reagents improve signal resolution for NMR analysis of homooligosaccharides by inducing conformational transitions upon binding.

Anion binding by biotin[6]uril in water

We show that the newly discovered 6 + 6 biotin-formaldehyde macrocycle Biotin[6]uril binds a variety of anionic guest molecules in water. We discuss how and why the anions are bound based on data obtained using NMR spectroscopy, mass spectrometry, isothermal titrations calorimetry (ITC), computational calculations and single crystal X-ray crystallography.

Metabonomics: analytical techniques and associated chemometrics at a glance

Without any prior knowledge, it can be an overwhelming task to get an overview of and insight into the field of metabonomics. This chapter introduces the concept of metabonomics, the most commonly applied techniques, and the inevitably indispensable multivariate statistical analyses in an easily digestible yet comprehensive manner.