Reinforced molecular recognition as an alternative to rigid receptors

In theory, a perfectly rigid receptor will probably be an unbeatable binder. However, rigidity may not be easy to achieve in practice and it is certainly not Nature’s method to realise high affinity. In many proteins binding affinity is increased through non-covalent interactions within the protein. Thus there is a considerable incentive to follow Nature’s example and start exploring the use of secondary intra-receptor interactions to aid in the binding process. Secondary interactions within a receptor will reinforce host–guest binding when the same conformational rearrangement (or freezing of motion) is required for guest binding as for the formation of the intra-receptor interactions. Introducing secondary interactions will require rather elaborate synthetic receptors to be produced. With the recent developments in dynamic combinatorial chemistry, access to the desired structures should be facilitated. Whether or not this approach will develop into a practical method remains to be established, but even if it does not, efforts along these lines will lead to a better understanding of the complex interplay between molecular recognition, folding and dynamics.

The role of solvent cohesion in nonpolar solvation

<p>Understanding hydrophobic interactions requires a molecular-level picture of how water molecules adjust to the introduction of a nonpolar solute. New insights into the latter process are derived from the observation that the Gibbs energies of solvation of the noble gases and linear alkanes by a wide range of solvents, including water, correlate well with linear combinations of internal pressure (P,) and cohesive energy density (ced) of the solvent. P, and ced are empirical solvent parameters that quantify two different aspects of solvent cohesion: the former reflects the cost of creating a cavity by a subtle rearrangement of solvent molecules, whereas the latter captures the cost of creating a cavity with complete disruption of solvent-solvent interactions. For the solvation of smaller solutes the internal pressure is the dominant parameter, while for larger solutes the ced becomes more important. The intriguing observation that the solubility of alkanes in water decreases with increasing chain length, whereas the solubility of noble gases increases with increasing size, can be understood by considering the different relative influences of the ced and P, on the solvation processes of both classes of compounds. Also the solvation enthalpy, but not the entropy, correlates with linear combinations of solvent ced and P,, albeit poorly, suggesting that the good correlations observed for the Gibbs energy are largely due to enthalpy, most likely that related to cavity formation.</p>

Dynamic Combinatorial Libraries: From Exploring Molecular Recognition to Systems Chemistry

Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

An Approach to the de Novo Synthesis of Life

[Image: see text] As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal. The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or binding-induced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for how life may have originated on earth, and for every-day life by opening up new vistas in the form living technology and materials

Efficient and Mild Microwave-Assisted Stepwise Functionalization of Naphthalenediimide with α-Amino Acids

Microwave dielectric heating proved to be an efficient method for the one-pot and stepwise syntheses of symmetrical and unsymmetrical naphthalenediimide derivatives of α-amino acids. Acid-labile side chain protecting groups are stable under the reaction conditions; protection of the α-carboxylic group is not required. The stepwise condensation of different amino acids resulted in high yields of unsymmetrical naphthalenediimides. The reaction proceeds without racemization and is essentially quantitative.

Tailor-made functionalized self-assembled peptide (nano)fibers and hydrogels, and methods, uses and kits related thereto

The invention relates to self-assembling peptide (nano)fibers, hydrogels, and methods, uses and intermediate products and kits relating thereto. Provided is a method for providing peptide-based functionally modified (nano)fibers, comprising (i) providing a fiber forming solution comprising pseudopeptide building blocks of the formula A-Peptide-B, wherein: Peptide is a moiety of 1 to 8 amino acid residues having a sequence that is predisposed to form a one-dimensional array, such as β-sheet fibrils; A is an aromatic moiety carrying two reactive thiol groups; and B is a reactive α-nucleophile; (ii) exposing the fiber forming solution to oxidizing conditions to induce supramolecular self-assembly of the pseudopeptide building blocks into peptide-based (nano)fibers; and (iii) contacting said (nano)fibers with at least one biologically relevant functional group of interest comprising reactivity C forming a reactive pair with B to obtain covalently functionally modified nanofibers