Fuel-Driven Dynamic Combinatorial Peptide Libraries

Dynamic combinatorial chemistry (DCC) creates libraries of molecules that are constantly interchanging in a dynamic combinatorial library. When a library member self-assembles, it can displace the equilibria, leading to emergent phenomena like its selection or even its replication. However, such dynamic combinatorial libraries typically operate in or close to equilibrium. This work introduces a new dynamic combinatorial chemistry fueled by a catalytic reaction cycle that forms transient, out-of-equilibrium peptide-based macrocycles. The products in this library exist out of equilibrium at the expense of fuel and are thus regulated by kinetics and thermodynamics. By creating a chemically fueled dynamic combinatorial library with the vast structural space of amino acids, we explored the liquid-liquid phase separation behavior of the library members. The study advances DCCs by showing that peptide structures can be engineered to control the dynamic library's behavior. The work paves the way for creating novel, tunable material systems that exhibit emergent behavior reminiscent of biological systems. These findings have implications for the development of new materials and for understanding life's chemistry.

Molecular entanglement can strongly increase basicity

Brønsted basicity is a fundamental chemical property featured by several kinds of inorganic and organic compounds. In this Review, we treat a particularly high basicity resulting from the mechanical entanglement involving two or more molecular subunits in catenanes and rotaxanes. Such entanglement allows a number of basic sites to be in close proximity with each other, highly increasing the proton affinity in comparison with the corresponding, non-entangled counterparts up to obtain superbases, properly defined as mechanically interlocked superbases. In the following pages, the development of this kind of superbases will be described with a historical perusal, starting from the initial, serendipitous findings up to the most recent reports where the strong basic property of entangled molecular units is the object of a rational design.

Dissipative Systems Driven by the Decarboxylation of Activated Carboxylic Acids

ConspectusThe achievement of artificial systems capable of being maintained in out-of-equilibrium states featuring functional properties is a main goal of current chemical research. Absorption of electromagnetic radiation or consumption of a chemical species (a "chemical fuel") are the two strategies typically employed to reach such out-of-equilibrium states, which have to persist as long as one of the above stimuli is present. For this reason such systems are often referred to as "dissipative systems". In the simplest scheme, the dissipative system is initially found in a resting, equilibrium state. The addition of a chemical fuel causes the system to shift to an out-of-equilibrium state. When the fuel is exhausted, the system reverts to the initial, equilibrium state. Thus, from a mechanistic standpoint, the dissipative system turns out to be a catalyst for the fuel consumption. It has to be noted that, although very simple, this scheme implies the chance to temporally control the dissipative system. In principle, modulating the nature and/or the amount of the chemical fuel added, one can have full control of the time spent by the system in the out-of-equilibrium state.In 2016, we found that 2-cyano-2-phenylpropanoic acid (1a), whose decarboxylation proceeds smoothly under mild basic conditions, could be used as a chemical fuel to drive the back and forth motion of a catenane-based molecular switch. The acid donates a proton to the catenane that passes from the neutral state A to the transient protonated state B. Decarboxylation of the resulting carboxylate (1acb), generates a carbanion, which, being a strong base, retakes the proton from the protonated catenane that, consequently, returns to the initial state A. The larger the amount of the added fuel, the longer the time spent by the catenane in the transient, out-of-equilibrium state. Since then, acid 1a and other activated carboxylic acids (ACAs) have been used to drive the operation of a large number of dissipative systems based on the acid-base reaction, from molecular machines to host-guest systems, from catalysts to smart materials, and so on. This Account illustrates such systems with the purpose to show the wide applicability of ACAs as chemical fuels. This generality is due to the simplicity of the idea underlying the operation principle of ACAs, which always translates into simple experimental requirements.

Distinctive features and challenges in catenane chemistry

From being an aesthetic molecular object to a building block for the construction of molecular machines, catenanes and related mechanically interlocked molecules (MIMs) continue to attract immense interest in many research areas. Catenane chemistry is closely tied to that of rotaxanes and knots, and involves concepts like mechanical bonds, chemical topology and co-conformation that are unique to these molecules. Yet, because of their different topological structures and mechanical bond properties, there are some fundamental differences between the chemistry of catenanes and that of rotaxanes and knots although the boundary is sometimes blurred. Clearly distinguishing these differences, in aspects of bonding, structure, synthesis and properties, between catenanes and other MIMs is therefore of fundamental importance to understand their chemistry and explore the new opportunities from mechanical bonds.

Self-Assembly of Stimuli-Responsive [2]Rotaxanes by Amidinium Exchange

Advances in supramolecular chemistry are often underpinned by the development of fundamental building blocks and methods enabling their interconversion. In this work, we report the use of an underexplored dynamic covalent reaction for the synthesis of stimuli-responsive [2]rotaxanes. The formamidinium moiety lies at the heart of these mechanically interlocked architectures, because it enables both dynamic covalent exchange and the binding of simple crown ethers. We demonstrated that the rotaxane self-assembly follows a unique reaction pathway and that the complex interplay between crown ether and thread can be controlled in a transient fashion by addition of base and fuel acid. Dynamic combinatorial libraries, when exposed to diverse nucleophiles, revealed a profound stabilizing effect of the mechanical bond as well as intriguing reactivity differences between seemingly similar [2]rotaxanes.

Fine-tuning of the optical output in a dual responsive catenane switch

A [2]catenane switch where the intramolecular pyrene excimer emission can be controlled by orthogonal cation binding and solvent polarity change in various amplitudes and dynamic ranges is reported.

Cross dehydrogenative C-O coupling catalysed by a catenane-coordinated copper(i)

Catalytic activity of copper(i) complexes supported by phenanthroline-containing catenane ligands towards a new C(sp³)–O dehydrogenative cross-coupling of phenols and bromodicarbonyls is reported. As the phenanthrolines are interlocked by the strong and flexible mechanical bond in the catenane, the active catalyst with an open copper coordination site can be revealed only transiently and the stable, coordinatively saturated Cu(i) pre-catalyst is quickly regenerated after substrate transformation. Compared with a control Cu(i) complex supported by non-interlocked phenanthrolines, the catenane-supported Cu(i) is highly efficient with a broad substrate scope, and can be applied in gram-scale transformations without a significant loss of the catalytic activity. This work demonstrates the advantages of the catenane ligands that provide a dynamic and responsive copper coordination sphere, highlighting the potential of the mechanical bond as a design element in transition metal catalyst development.

The use of a catenane-supported copper(i) complex for the cross dehydrogenative C–O coupling of phenols and bromodicarbonyls is described.

Controlling the liberation rate of the in situ release of a chemical fuel for the operationally autonomous motions of molecular machines

Second-order rate constants of the aminolysis of 2-cyano-2-phenylpropanoic anhydride 3 by a series of N-methylanilines differently substituted in the aromatic moiety (4a-d) were measured in dichloromethane. The common reaction product of aminolysis is 2-cyano-2-phenylpropanoic acid 1, which is known to be an effective fuel for acid-base driven molecular machines, but cannot be used in molar excess with respect to the machine. The motivation behind the kinetic study has been the prospect of using the aminolysis of 3 to supply the machine with fuel at a rate that is never so high as to overfeed the system, thus avoiding the malfunction of the machine with concomitant waste of fuel. Knowledge of the kinetic parameters dictated the choice of 4c as the best nucleophile in the lot for feeding acid 1 into a catenane-based molecular machine at a rate that ensured a correct operation.

The canonical behavior of the entropic component of thermodynamic effective molarity. An attempt at unifying covalent and noncovalent cyclizations

The statistically corrected entropic component of effective molarity (EM_S*) complies with the “canonical” values expressed by the log plot of EM_S* vs. the number n of single bonds in the ring product.

Control over the macrocyclisation pathway and product topology in a copper-templated catenane synthesis

Strategies to control building block intertwining and the efficient assembly of a linear [4]catenane are presented.

Photoinduced Release of a Chemical Fuel for Acid-Base-Operated Molecular Machines

Back and forth motions of the acid-base-operated molecular switch 1 are photo-controlled by irradiation of a solution, which also contains the photolabile pre-fuel 4. The photo-stimulated deprotection of the pre-fuel produces controlled amounts of acid 2, the base-promoted decarboxylation of which fuels the back and forth motions of the Sauvage-type [2]-catenane-based molecular switch. Because switch 1 and pre-fuel 4 do not interact in the absence of irradiation, an excess of the latter with respect to 1 can be added to the solution from the beginning. In principle, photocontrol of the back and forth motions of any molecular machine, the operation of which is guided by protonation/deprotonation, could be attained by use of pre-fuel 4, or of any other protected acid that undergoes deprotection by irradiation with light at a proper wavelength, followed by decarboxylation under conveniently mild conditions.

Olefin metathesis reaction as a locking tool for macrocycle and mechanomolecule construction

The present review deals with an updated visit to the olefin metathesis reaction as a powerful tool for the construction of sophisticated macromolecular architectures.

Variations in the fuel structure control the rate of the back and forth motions of a chemically fuelled molecular switch

Moderate variations in the fuel structure cause large changes in the rate of the back and forth motions experienced by a chemically fuelled catenane-based switch.

This work deals with the use of 2-cyano-2-arylpropanoic acids as chemical fuels for an acid–base operated molecular switch that consists of a Sauvage-type catenand composed of two identical macrocycles incorporating a phenanthroline unit. When used as a base promoter of the decarboxylation of propanoic acid derivatives, the switch undergoes large amplitude motion from the neutral catenand to a protonated catenate and back again to the neutral state. The rate of back proton transfer, which determines the rate of the overall process, was markedly affected by para-substituents in the order Cl > H > CH₃ > OCH₃ (ρ = +5.2). Thus, the time required to complete a full cycle was almost two days for the OCH₃ derivative and dropped to a few minutes for the Cl derivative. These results show for the first time that the rate of operation of a molecular switch can be regulated by variations in the fuel structure.

Supramolecular polymerization of a ureidopyrimidinone-based [2]catenane prepared via ring-closing metathesis

The synthesis and supramolecular polymerization of a ureidopyrimidinone‐based Sauvage‐type [2]catenane is reported. The monomer synthesis explores many routes using the elegant metathesis catalysts of Bob Grubbs, yielding a catenane with one ureidopyrimidinone in each cycle. The supramolecular polymer obtained features both mechanical bonds and quadruple hydrogen bonding connections.

Coupling of the Decarboxylation of 2-Cyano-2-phenylpropanoic Acid to Large-Amplitude Motions: A Convenient Fuel for an Acid-Base-Operated Molecular Switch

The decarboxylation of 2-cyano-2-phenylpropanoic acid is fast and quantitative when carried out in the presence of 1 molar equivalent of a [2]catenane composed of two identical macrocycles incorporating a 1,10-phenanthroline unit in their backbone. When decarboxylation is over, all of the catenane molecules have experienced large-amplitude motions from neutral to protonated catenane, and back again to the neutral form, so that they are ready to perform another cycle. This study provides the first example of the cyclic operation of a molecular switch at the sole expenses of the energy supplied by the substrate undergoing chemical transformation, without recourse to additional stimuli.

Experimental Binding Energies in Supramolecular Complexes

On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.

Discoveries from a phenanthroline-based dynamic combinatorial library: catenane from a copper(i) or copper(ii) template?

We report here a DCL study of a phenanthroline-based building block focusing on catenane formation with copper templates.

Applications of dynamic combinatorial chemistry for the determination of effective molarity

A new strategy for determining thermodynamic effective molarities (EM) for macrocylisation reactions using dynamic combinatorial chemistry under dilute conditions is presented. At low concentrations, below the critical value, Dynamic Libraries (DLs) of bifunctional building blocks contain only cyclic species, so it is not possible to quantify the equilibria between linear and cyclic species. However, addition of a monofunctional chain stopper can be used to promote the formation of linear oligomers allowing measurement of EM for all cyclic species present in the DL. The effectiveness of this approach was demonstrated for DLs generated from mixtures of 1,3-diimine calix[4]arenes, linear diaminoalkanes and monoaminoalkanes. For macrocycles deriving from one bifunctional calixarene and one diamine, there is an alternating pattern of EM values with the number of methylene units in the diamine: odd numbers give significantly higher EMs than even numbers. For odd numbers of methylene units, the alkyl chain can adopt an extended all anti conformation, whereas for even numbers of methylene units, gauche conformations are required for cyclisation, and the associated strain reduces EM. The value of EM for the five-carbon linker indicates that this macrocycle is a strainless ring.