Allosteric effects in organic chemistry: binding cooperativity in a model for subunit interactions

Recognition of Amino Acid Salts by Temperature-Dependent Allosteric Binding with Stereodynamic Urea Receptors

Positive homotropic artificial allosteric systems are important for the regulation of cooperativity, selectivity and nonlinear amplification. Stereodynamic homotropic allosteric receptors can transmit and amplify induced chirality by the first ligand binding to axial chirality between two chromophores. We herein report stereodynamic allosteric urea receptors consisting of a rotational shaft as the axial chirality unit, terphenyl units as structural transmission sites and four urea units as binding sites. NMR titration experiments revealed that the receptor can bind two carboxylate guests in a positive homotropic allosteric manner attributed to the inactivation by intramolecular hydrogen-bonding between urea units within the receptor. In addition, the VT-CD spectra observed upon binding of the urea receptor with l- or D-amino acid salts in MeCN showed interesting temperature-dependent Cotton effects, based on the differences of the receptor shaft unit and the guest structure. The successful discrimination of hydrocarbon-based side chains of amino acid salts indicated that the input of chiral and steric information for the guest was amplified as outputs of the Cotton effect and the temperature-dependence of VT-CD spectra through cooperativity of positive allosteric binding.

Reversible hydrogen-bonded polymerization regulated by allosteric metal templation

A stable quadruple hydrogen bonded cyclic dimer assisted by metal templation was successfully self-assembled and its reversible transformation to supramolecular polymer was investigated.

Temperature-induced large amplitude conformational change in the complex of oxatub[4]arene revealed via rotaxane synthesis

Oxatub[4]arene was revealed via rotaxane synthesis to show a large amplitude conformational response to temperature change.

Guest control of a hydrogen bond-catalysed molecular rotor

Herein, the control of a molecular rotor using hydrogen bonding guests is demonstrated. With a properly positioned phenol substituent, the N-arylimide rotors can form an intramolecular hydrogen bond that catalyses the rotational isomerization process. The addition of the guests disrupts the hydrogen bond and raises the rotational barrier, slowing the rotation by two orders of magnitude.

Two-step modulation of ion recognition using a bis(saloph)-macrocyclic host having a 24-crown-8-like cavity

Precise modulation of cation binding affinity was accomplished by the efficient two-step conversion of a newly synthesized macrocyclic ligand H₄L² having a 24-crown-8-like cavity and two saloph moieties. The conversion of H₄L² into L²Ni₂ resulted in a 120-fold enhancement in the binding affinity towards Cs⁺. The electrochemical reduction of L²Ni₂ further enhanced the recognition ability by 3 orders of magnitude.

Cu2+ recognition by N,N'-benzylated bis(amino amides)

Two new C₂-symmetric N,N'-benzylated bis(amino amides) have been synthesised and their interaction with different transition metals studied using a variety of techniques including UV-Vis and CD spectroscopy or ESI-MS. The determination of the corresponding stability constants with Cu²⁺ has been possible, in H₂O/CH₃CN 7/3 v/v, for one of these ligands (4) using potentiometric titrations. The results obtained reveal that N-benzylation affords significant changes to their properties and is accompanied by an appreciable decrease in the corresponding complexation stability constants. However, this, along with the low kinetics associated to Ni²⁺, facilitates the recognition of Cu²⁺ by 4 that can be followed by the naked-eye up to the submillimolar range. Very interestingly, the chiral nature of this ligand provides an intense and well defined CD curve for the corresponding Cu²⁺ complex, very sensitive to the coordination geometry, facilitating the analysis of this interaction even at the μM range. The formation by both ligands (3 and 4) of square planar complexes with Cu²⁺ and Ni²⁺ displaying a 1 : 1 stoichiometry was confirmed by their X-ray crystal structures.

Assessing cooperativity in supramolecular systems

In this tutorial review, different aspects of cooperativity in supramolecular chemistry and their thermodynamic analysis are discussed.

Control of the cavity size of flexible covalent cages by silver coordination to the peripheral binding sites

The synthesis of covalent cages consisting of two porphyrins connected by four flexible spacers each incorporating two 1,2,3-triazolyl ligands is reported. Binding of four silver(I) to the peripheral ligands induces conformational changes in solution and locks the porphyrins in a face-to-face disposition.

Biphenyl appended BODIPY derivatives showing combined environmental polarity and heavy metal cation sensing functionality

Novel BODIPY derivatives exhibiting environmental polarity and combined environmental polarity/Hg²⁺ and Pb²⁺ fluorescence sensing properties have been prepared. The sensing properties are the result of a switchable photoinduced electron transfer (PeT) quenching mechanism.

Collective behaviours: from biochemical kinetics to electronic circuits

In this work we aim to highlight a close analogy between cooperative behaviors in chemical kinetics and cybernetics; this is realized by using a common language for their description, that is mean-field statistical mechanics. First, we perform a one-to-one mapping between paradigmatic behaviors in chemical kinetics (i.e., non-cooperative, cooperative, ultra-sensitive, anti-cooperative) and in mean-field statistical mechanics (i.e., paramagnetic, high and low temperature ferromagnetic, anti-ferromagnetic). Interestingly, the statistical mechanics approach allows a unified, broad theory for all scenarios and, in particular, Michaelis-Menten, Hill and Adair equations are consistently recovered. This framework is then tested against experimental biological data with an overall excellent agreement. One step forward, we consistently read the whole mapping from a cybernetic perspective, highlighting deep structural analogies between the above-mentioned kinetics and fundamental bricks in electronics (i.e. operational amplifiers, flashes, flip-flops), so to build a clear bridge linking biochemical kinetics and cybernetics.

Oligopyrrole macrocycles: receptors and chemosensors for potentially hazardous materials

Oligopyrroles represent a diverse class of molecular receptors that have been utilized in a growing number of applications. Recently, these systems have attracted interest as receptors and chemosensors for hazardous materials, including harmful anionic species, high-valent actinide cations, and nitroaromatic explosives. These versatile molecular receptors have been used to develop rudimentary colorimetric and fluorimetric assays for hazardous materials.

Size selective recognition of small esters by a negative allosteric hemicarcerand

A bis(resorcinarene) substituted 2,2′-bipyridine was found to bind weakly to small esters like ethyl acetate whereas more bulky esters were not recognized by this hemicarcerand. This size selective molecular recognition could be controlled by a negative cooperative allosteric effect: coordination of a triscarbonyl rhenium chloride fragment to the bipyridine causes a conformational rearrangement that orientates the resorcinarene moieties in different directions so that they cannot act cooperatively in the binding of the substrate.