Musketeer: a software tool for the analysis of titration data.

Musketeer is a powerful open-source software tool for the analysis of titration data, featuring a simple cross-platform graphical interface for importing data directly from UV-vis, fluorescence and NMR spectrometers, or from spreadsheets. The fast data analysis algorithm can be used to obtain equilibrium constants for simple binding isotherms, as well as for more complicated systems with multiple competing equilibria. Applications of Musketeer for the analysis of a range of different supramolecular and biomolecular systems are illustrated, including titrations with multiple spectroscopically active species, competitive binding assays, denaturation experiments, optimisation of concentrations as variables.

Efficient automated solid-phase synthesis of recognition-encoded melamine oligomers.

Recognition-encoded melamine oligomers (REMO) are synthetic polymers with an alternating 1,3,5-triazine-piperazine backbone and side chains equipped with either a phenol or phosphine oxide recognition unit. Here, we describe an automated method for highly efficient solid-phase synthesis (SPS) of REMO of any specified length and sequence. These SPS protocols are amongst the most robust reported to date, as demonstrated by the synthesis of a mixed-sequence 42-mer, which was obtained in excellent crude purity on a 100 mg scale.

An atomic surface site interaction point description of non-covalent interactions.

Molecular electrostatic potential surfaces (MEPS) calculated using density functional theory have been used to develop a simplified description of the non-covalent interaction properties of organic molecules. The Atomic Interaction Point (AIP) model introduced here represents an evolution of the Surface Site Interaction Point (SSIP) model described previously, in which a molecule is represented by a discrete set of interaction points that define sites of interaction with other molecules. The interaction sites are described by interaction parameters that are equivalent to the experimentally determined H-bond donor and acceptor parameters and .

Replication of synthetic recognition-encoded oligomers by ligation of trimer building blocks.

The development of methods for replication of synthetic information oligomers will underpin the use of directed evolution to search new chemical space. Template-directed replication of triazole oligomers has been achieved using a covalent primer in conjunction with non-covalent binding of complementary building blocks. A phenol primer equipped with an alkyne was first attached to a benzoic recognition unit on a mixed sequence template selective covalent ester base-pair formation.

Polarisation effects on the H-bond acceptor properties of secondary amides.

H-bonding interactions in networks are stabilised by cooperativity, but the relationship between the chemical structures of the interacting functional groups and the thermodynamic consequences is not well-understood. We have used compounds with an intramolecular H-bond between a pyridine H-bond acceptor and an amide NH group to quantify cooperative effects on the H-bond acceptor properties of the amide carbonyl group. H NMR experiments in -octane confirm the presence of the intramolecular H-bond and show that this interaction is intact in the 1 : 1 complex formed with perfluoro--butanol (PFTB).

Supramolecular template-directed synthesis of triazole oligomers.

Sandwich complexes formed by two zinc porphyrins and a diamine ligand (DABCO) have been used as a supramolecular template to direct the synthesis of triazole oligomers. Monomer units equipped with two polymerizable functional groups, an alkyne and an azide, were attached to the template ester bonds between a phenol unit on the monomer and benzoic acid units on the porphyrin. Self-assembly of the zinc porphyrins by addition of DABCO led to a supramolecular complex containing four of the monomer units, two on each porphyrin.

H-bond cooperativity: polarisation effects on secondary amides.

Formation of a H-bond with an amide carbonyl oxygen atom increases the strength of subsequent H-bonds formed by the amide NH, due to polarisation of the bond. The magnitude of this effect has been quantified by measuring association constants for the formation of 1 : 1 complexes of 2-hydroxylbenzamides with tri--butyl phosphine oxide. In 2-hydroxybenzamides, there is an intramolecular H-bond between the phenol OH group and the carbonyl oxygen atom.

Artificial transmembrane signal transduction mediated by dynamic covalent chemistry.

Reversible formation of covalent adducts between a thiol and a membrane-anchored Michael acceptor has been used to control the activation of a caged enzyme encapsulated inside vesicles. A peptide substrate and papain, caged as the mixed disulfide with methane thiol, were encapsulated inside vesicles, which contained Michael acceptors embedded in the lipid bilayer. In the absence of the Michael acceptor, addition of thiols to the external aqueous solution did not activate the enzyme to any significant extent.

An empirical model for solvation based on surface site interaction points.

Surface site interaction points (SSIP) provide a quantitative description of the non-covalent interactions a molecule makes with the environment based on specific intermolecular contacts, such as H-bonds. Summation of the free energy of interaction of each SSIP across the surface of a molecule allows calculation of solvation energies and partition coefficients. A rule-based approach to the assignment of SSIPs based on chemical structure has been developed, and a combination of experimental data on the formation of 1 : 1 H-bonded complexes in non-polar solvents and partition of solutes between different solvents was used to parameterise the method.

Transmembrane signal transduction by cofactor transport.

Information processing and cell signalling in biological systems relies on passing chemical signals across lipid bilayer membranes, but examples of synthetic systems that can achieve this process are rare. A synthetic transducer has been developed that triggers catalytic hydrolysis of an ester substrate inside lipid vesicles in response to addition of metal ions to the external vesicle solution. The output signal generated in the internal compartment of the vesicles is produced by binding of a metal ion cofactor to a head group on the transducer to form a catalytically competent complex.

Folding and duplex formation in mixed sequence recognition-encoded -phenylene ethynylene polymers.

Oligomers equipped with complementary recognition units have the potential to encode and express chemical information in the same way as nucleic acids. The supramolecular assembly properties of -phenylene ethynylene polymers equipped with H-bond donor ( = phenol) and H-bond acceptor ( = phosphine oxide) side chains have been investigated in chloroform solution. Polymerisation of a bifunctional monomer in the presence of a monofunctional chain stopper was used for the one pot synthesis of families of -phenylene ethynylene polymers with sequences or ( = 1-5), which were separated by chromatography.

Mapping the binding site topology of amyloid protein aggregates using multivalent ligands.

A key process in the development of neurodegenerative diseases such as Alzheimer's and Parkinson's diseases is the aggregation of proteins to produce fibrillary aggregates with a cross β-sheet structure, amyloid. The development of reagents that can bind these aggregates with high affinity and selectivity has potential for early disease diagnosis. By linking two benzothiazole aniline (BTA) head groups with different length polyethylene glycol (PEG) spacers, fluorescent probes that bind amyloid fibrils with low nanomolar affinity have been obtained.

Cooperative assembly of H-bonded rosettes inside a porphyrin nanoring.

The melamine·barbiturate H-bonded rosette motif is of comparable dimensions and symmetry to the cavity of a butadiyne-linked 6-porphyrin nanoring. Functionalisation of each of the barbiturate components and the pyrimidine components of a H-bonded rosette with a pyridine ligand leads to a self-assembled hexapyridine ligand, which binds cooperatively to the zinc porphyrin nanoring. UV-vis-NIR and H NMR experiments show that the 7-component assembly forms at concentrations at which neither the H-bonding interactions nor the zinc porphyrin-pyridine interactions are formed in the absence of one of the three components.

Controlled mutation in the replication of synthetic oligomers.

Replication of sequence information with mutation is the molecular basis for the evolution of functional biopolymers. Covalent template-directed synthesis has been used to replicate sequence information in synthetic oligomers, and the covalent base-pairs used in these systems provide an opportunity to manipulate the outcome of the information transfer process through the use of traceless linkers. Two new types of covalent base-pair have been used to introduce mutation in the replication of an oligotriazole, where information is encoded as the sequence of benzoic acid and phenol monomer units.

Template effects of vesicles in dynamic covalent chemistry.

Vesicle lipid bilayers have been employed as templates to modulate the product distribution in a dynamic covalent library of Michael adducts formed by mixing a Michael acceptor with thiols. In methanol solution, all possible Michael adducts were obtained in similar amounts. Addition of vesicles to the dynamic covalent library led to the formation of a single major product.

Supramolecular catalysis by recognition-encoded oligomers: discovery of a synthetic imine polymerase.

All key chemical transformations in biology are catalysed by linear oligomers. Catalytic properties could be programmed into synthetic oligomers in the same way as they are programmed into proteins, and an example of the discovery of emergent catalytic properties in a synthetic oligomer is reported. Dynamic combinatorial chemistry experiments designed to study the templating of a recognition-encoded oligomer by the complementary sequence have uncovered an unexpected imine polymerase activity.

Functional group interaction profiles: a general treatment of solvent effects on non-covalent interactions.

Solvation has profound effects on the behaviour of supramolecular systems, but the effects can be difficult to predict even at a qualitative level. Functional group interaction profiles (FGIPs) provide a simple visual method for understanding how solvent affects the free energy contribution due to a single point interaction, such as a hydrogen bond, between two solute functional groups. A generalised theoretical approach has been developed, which allows calculation of FGIPs for any solvent or solvent mixture, and FGIPs for 300 different solvents have been produced, providing a comprehensive description of solvent effects on non-covalent chemistry.