Dissipative Dynamic Libraries (DDLs) and Dissipative Dynamic Combinatorial Chemistry (DDCC)

Spatola, Emanuele; Valentini, Matteo; Ercolani, Gianfranco; Stefano, Stefano Di

doi:10.1002/syst.202200023

Cited by 16 publications

(13 citation statements)

References 105 publications

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“…The study of such ensembles of compounds (Dynamic Combinatorial Chemistry, DCC) has led in the last quarter of a century to important results in the fields of recognition, self-assembly, catalysis, and, more generally, systems chemistry. 32 Very recently, we and other groups have explored the possibility of achieving dissipative dynamic combinatorial libraries (DDCLs), 10 that are dynamic libraries of compounds maintained out-of-equilibrium by the consumption of a fuel. Variation of the nature or the amount of added fuel allows regulation of the duration of the out-of-equilibrium state of the library making available time-control of the library composition and of the related chemical–physical properties.…”

Section: Dissipative Systems Driven By Acasmentioning

confidence: 99%

“…9 Throughout this Account, we will use the term dissipative to indicate a system whose out-of-equilibrium state 7 is maintained by fuel consumption; in other words, a system constituted by a catalyst for the conversion of a fuel into waste, which therefore is able to transitorily divert the free energy associated with the consumption of a fuel toward valuable processes (system operation). 10 Many of the dissipative artificial systems reported so far are driven by bioinspired fuels such as nucleoside triphosphates (ATP and the like) or fragments of RNA/DNA and often take advantage of the presence of enzymes for their operation. 11 However, a number of abiotic fuels have been also used to drive man-made dissipative systems.…”

Section: ■ Introductionmentioning

confidence: 99%

“…The systems whose operation requires the consumption of chemical fuels are often defined as “dissipative” . Throughout this Account, we will use the term dissipative to indicate a system whose out-of-equilibrium state is maintained by fuel consumption; in other words, a system constituted by a catalyst for the conversion of a fuel into waste, which therefore is able to transitorily divert the free energy associated with the consumption of a fuel toward valuable processes (system operation) …”

Section: Introductionmentioning

confidence: 99%

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Dissipative Systems Driven by the Decarboxylation of Activated Carboxylic Acids

Stefano

2023

Acc. Chem. Res.

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Conspectus The 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.

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Section: Dissipative Systems Driven By Acasmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Dissipative Systems Driven by the Decarboxylation of Activated Carboxylic Acids

Stefano

2023

Acc. Chem. Res.

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“…In this work, we introduce templation in chemically fueled dynamic combinatorial libraries to study kinetic selection in dynamic combinatorial libraries. [17][18][19][20] Unlike dynamic combinatorial libraries, chemically fueled libraries are in a non-equilibrium state where bonds form at the expense of high-energy molecules, which we refer to these as fuels. The newly formed bonds revert spontaneously through hydrolysis (Fig.…”

Section: Introductionmentioning

confidence: 99%

Template-based information transfer in chemically fueled dynamic combinatorial librar-ies

Kriebisch¹,

Burger²,

Zozulia³

et al. 2023

Preprint

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One of science’s greatest challenges is how life can spontaneously emerge from a mixture of abiotic molecules. A complicating factor is that life is inherently unstable, and, by extension, so are its molecules—RNA and proteins are prone to hydrolysis and denaturation. For the synthesis of life or to better understand its emergence at its origin, selection mechanisms are needed for such inherently unstable molecules. Here, we present a chemically-fueled dynamic combinatorial library as a model for RNA oligomerization and deoligomerization that shines new light on selection and purification mechanisms under kinetic control. In the experiments, nucleotide oligomers can only sustain by continuous production. We find that hybridization is a powerful tool for selecting unstable molecules as it offers feedback on oligomerization and deoligomerization rates. Template-based copying can thereby select molecules of specific lengths and sequences. Moreover, we find that templation can also be used to purify libraries of oligomers. Further, template-based copying within coacervate-based protocells changes its compartment’s physical properties, like their ability to fuse. Such reciprocal coupling between information sequences and physical properties is a key step toward synthetic life.

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“…Supramolecular interactions are noncovalent interactions responsible for forming highly ordered, self-assembled complex molecular structures in nature. , These interactions involve hydrogen bonds, van der Waals forces, π–π interactions, electrostatic forces, coordination bonds, and hydrophobic interactions. – Their combined bond strength reaches comparable levels of covalent bonds when they act complementarily to form a supramolecular complex. – , Among them, hydrogen and ionic bonds, which bring specificity in the form of directionality and cooperativity among interacting components, are considered strong noncovalent interactions . Overall, supramolecular interactions govern the assembly/disassembly dynamics of natural and synthetic supramolecular systems such as DNA base pairs, micelles, interpolyelectrolyte complexes, hydrogels, fibers, virus-like particles, π-conjugated polymers (CPs), and many more. , An in-depth understanding of these interactions is crucial to designing tailor-utilizing synthetic systems for specific applications. CPs are versatile tools to monitor and study supramolecular interactions .…”

Section: Introductionmentioning

confidence: 99%

Effect of UV Irradiation Time and Headgroup Interactions on the Reversible Colorimetric pH Response of Polydiacetylene Assemblies

Beliktay,

Shaikh,

Koca

et al. 2023

ACS Omega

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Polydiacetylenes are chromatic conjugated polymers formed upon the photopolymerization of self-assembled diacetylenes. They exhibit conformation-dependent colorimetric responses, usually irreversible, to external triggers. Here, we presented an approach to obtain a reversible colorimetric response to a pH change through structural modifications on the monomer and extended photopolymerization time. Both factors, enhanced hydrogen bond forming headgroups and longer UV exposure, impacted the rotational freedom of polydiacetylene conformation. Such a restricted conformation state reduced colorimetric response efficiency but enabled reversible colorimetric response to a pH change. These results highlight the possibility of obtaining a reversible colorimetric pH response of polydiacetylenes for customized sensing applications through monomer-level tailoring combined with tuning the photopolymerization time.

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Dissipative Dynamic Libraries (DDLs) and Dissipative Dynamic Combinatorial Chemistry (DDCC)

Cited by 16 publications

References 105 publications

Dissipative Systems Driven by the Decarboxylation of Activated Carboxylic Acids

Dissipative Systems Driven by the Decarboxylation of Activated Carboxylic Acids

Template-based information transfer in chemically fueled dynamic combinatorial librar-ies

Effect of UV Irradiation Time and Headgroup Interactions on the Reversible Colorimetric pH Response of Polydiacetylene Assemblies

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