Dynamic combinatorial chemistry

Solving chemical problems through the application of evolutionary principles

Molecular evolution has been widely applied in the laboratory to generate novel biological macromolecules. The principles underlying evolution have more recently been used to address problems in the chemical sciences, including the discovery of functional synthetic small molecules, catalysts, materials and new chemical reactions. The application of these principles in dynamic combinatorial chemistry and in efforts involving small molecule-nucleic acid conjugates has facilitated the evaluation of large numbers of candidate structures or reactions for desired characteristics. These early efforts suggest the promise of pairing evolutionary approaches with synthetic chemistry.

Kinetic and Thermodynamic Selectivity in Subcomponent Substitution

Within assemblies prepared by metal-templated imine condensation, one amine residue (subcomponent) may be replaced with another through substitution reactions. Proton transfer from a more to a less acidic amine may be used as the driving force for substitution. Herein, we detail the development of a set of selectivity rules to predict the outcome of subcomponent substitution reactions when several different substrates are present. When both iron and copper complexes were present, substitution occurred preferentially at imines bound to copper. This preference was kinetic in nature in the absence of a chelating amine subcomponent: The different amine residues were found to scramble between the copper and iron complexes following an initial clean substitution at the copper-bound imine. When both chelating and nonchelating amine subcomponents were present, the preference became thermodynamic in nature. Only the nonchelating amine was substituted and no evidence of scrambling was found after the reaction mixture was heated to 50 degrees C for several days. This thermodynamic selectivity, based on the chelate effect, operated in mixtures of Cu(I) and Fe(II) complexes, and in systems containing only Fe(II) complexes.

Dynamic combinatorial libraries of hydrazone-linked pseudo-peptides: dependence of diversity on building block structure and chirality

Expanding on our earlier building block architecture [(MeO)(2)CH-Linker-Pro-X-NHNH(2) where X = Phe, Cha], we have produced a series of new pseudo-dipeptides [(MeO)(2)CH-Linker-Pro-X-NHNH(2) where X = Val, Leu, Ile, Ala] for use in hydrazone-based dynamic combinatorial libraries (DCLs); reverse order analogues [Phe-Pro and Val-Pro] and two enantio-analogues [Pro-Phe and Pro-Val] were also prepared. The behaviours of these building blocks in DCLs, as single components and in mixtures, were studied systematically using HPLC and mass spectrometry in order to gain insight into the relationship between building block structure and good library diversity. Subtle changes in building block structure lead to significant changes in library distribution and in the ability to produce diverse libraries in mixtures.

From supramolecular chemistry towards constitutional dynamic chemistry and adaptive chemistry

Supramolecular chemistry has developed over the last forty years as chemistry beyond the molecule. Starting with the investigation of the basis of molecular recognition, it has explored the implementation of molecular information in the programming of chemical systems towards self-organisation processes, that may occur either on the basis of design or with selection of their components. Supramolecular entities are by nature constitutionally dynamic by virtue of the lability of non-covalent interactions. Importing such features into molecular chemistry, through the introduction of reversible bonds into molecules, leads to the emergence of a constitutional dynamic chemistry, covering both the molecular and supramolecular levels. It considers chemical objects and systems capable of responding to external solicitations by modification of their constitution through component exchange or reorganisation. It thus opens the way towards an adaptive and evolutive chemistry, a further step towards the chemistry of complex matter.

Solvent-modulated reversible conversion of a [2×2]-grid into a pincer-like complex

The triazine derived ligand reacts with one equivalent of Co(II) salts to give complexes whose architecture depends on the solvent employed: the [2 x 2]-grid like tetranuclear complex and the pincer-like mononuclear complex, obtained respectively by crystallization from nitromethane and from acetonitrile may be interconverted reversibly, the grid-pincer conversion being markedly accelerated by adding an amine.

Synthesis, structural characterization and anion binding studies of palladium macrocycles with hydrogen-bonding ligands

The reactions between [Pd(P-P)(OTf)2] (where P-P=dppp or dppf) and two different bipyridyl ligands (=1,3-bis(4-pyridylmethyl)urea and=1,3- bis(pyridinylmethyl)benzenedicarboxamide) containing hydrogen-bonding units have been studied. The X-ray crystal structures of three of these assemblies have been solved showing them to be the [2+2] metallo-macrocycles [Pd(P-P)(n)]2(OTf)4 [P-P=dppp, n=1, (); P-P=dppp, n=2, (); P-P=dppf, n=1, ()]. To confirm whether the dimeric assembly of one of these species () is retained in solution, several investigations have been carried out. 1H NMR studies in DMSO and high resolution ESI mass spectrometry have shown that is in equilibrium with a larger [3+3] metallo-macrocycle. The equilibrium between these two species can be modified by changing the temperature, concentration or solvent. Also, addition of certain anions (e.g. [H2PO4]-) to the mixture shifts the equilibrium favoring the formation of the [2+2] metallo-macrocycle over the [3+3] (initially present in a larger proportion).

Molecular amplification of two different receptors using diastereomeric templates

Two different macrocyclic members of a pseudo-peptide hydrazone dynamic combinatorial library were amplified using the diastereomeric templates quinine and quinidine.

Limitations of the “tethering” strategy for the detection of a weak noncovalent interaction

The success of applying the tethering strategy in a synthetic molecular system strongly depends on the experimental conditions and is related to the strength of the noncovalent interaction and the competition between the 'captured' and unbound ligand for the recognition site.

Synthetic pores with sticky π-clamps

In this report, we describe design, synthesis, evaluation and molecular dynamics simulations of synthetic multifunctional pores with pi-acidic naphthalenediimide clamps. Experimental evidence is provided for the formation of unstable but inert, heterogeneous and acid-insensitive dynamic tetrameric pores that are sensitive to base and ionic strength. Blockage experiments reveal that the introduction of aromatic electron donor-acceptor interactions provides access to the selective recognition of pi-basic intercalators within the pore. This breakthrough is important for the application of synthetic pores as multianalyte sensors.

Driven Evolution of a Constitutional Dynamic Library of Molecular Helices Toward the Selective Generation of [2 × 2] Gridlike Arrays under the Pressure of Metal Ion Coordination

Constitutional dynamics, self-assembly, and helical-folding control are brought together in the efficient Sc(OTf)3/microwave-catalyzed transimination of helical oligohydrazone strands, yielding highly diverse dynamic libraries of interconverting constituents through assembly, dissociation, and exchange of components. The transimination-type mechanism of the ScIII-promoted exchange, as well as its regioselectivity, occurring only at the extremities of the helical strands, allow one to perform directional terminal polymerization/depolymerization processes when starting with dissymmetric strands. A particular library is subsequently brought to express quantitatively [2 x 2] gridlike metallosupramolecular arrays in the presence of ZnII ions by component recombination generating the correct ligand from the dynamic set of interconverting strands. This behavior represents a process of driven evolution of a constitutional dynamic chemical system under the pressure (coordination interaction) of an external effector (metal ions).

Nucleophilic Catalysis of Hydrazone Formation and Transimination: Implications for Dynamic Covalent Chemistry

Aniline accelerates hydrazone formation and transimination through nucleophilic catalysis. To demonstrate the method, unprotected peptides are reacted and then scrambled using a hydrazone reaction under conditions relevant for biological applications. The strong enhancement in the rate of hydrazone equilibration broadens the scope of this stable imine in the field of dynamic covalent chemistry.

High fidelity kinetic self-sorting in multi-component systems based on guests with multiple binding epitopes

The molecular recognition platforms of natural systems often possess multiple binding epitopes, each of which has programmed functional consequences. We report the dynamic behavior of a system comprising CB[6], CB[7], and guests cyclohexanediammonium (1) and adamantanealkylammonium (2) that we refer to as a two-faced guest because it contains two distinct binding epitopes. We find that the presence of the two-faced guest--just as is observed for protein targeting in vivo--dictates the kinetic pathway that the system follows toward equilibrium. The influence of two-faced guest structure, cation concentration, cation identity, and individual rate and equilibrium constants on the behavior of the system was explored by a combination of experiment and simulation. Deconstruction of this system led to the discovery of an anomalous host-guest complex (CB[6].1) whose dissociation rate constant (k(out) = 8.5 x 10(-10) s(-1)) is approximately 100-fold slower than the widely used avidin.biotin affinity pair. This result, in combination with the analysis of previous systems which uncovered extraordinarily tight binding events (K(a) > or = 10(12) M(-1)), highlights the inherent potential of pursuing a systems approach toward supramolecular chemistry.