Quantification of the effect of conformational restriction on supramolecular effective molarities

Dissecting Solvent Effects on Hydrogen Bonding

The experimental isolation of H-bond energetics from the typically dominant influence of the solvent remains challenging. Here we use synthetic molecular balances to quantify amine/amide H-bonds in competitive solvents. Over 200 conformational free energy differences were determined using 24 H-bonding balances in 9 solvents spanning a wide polarity range. The correlations between experimental interaction energies and gas-phase computed energies exhibited wild solvent-dependent variation. However, excellent correlations were found between the same computed energies and the experimental data following empirical dissection of solvent effects using Hunter's α/β solvation model. In addition to facilitating the direct comparison of experimental and computational data, changes in the fitted donor and acceptor constants reveal the energetics of secondary local interactions such as competing H-bonds.

Quantification of cooperativity in the self-assembly of H-bonded rosettes

The self-assembly of triaminopyrimidines with barbiturates and with cyanates was investigated in chloroform solution. Equimolar mixtures of two complementary components form stable macrocyclic 3 : 3 complexes (rosettes). The thermodynamics of self-assembly were quantified by using 1H NMR titrations to measure the strength of pairwise H-bonding interactions between two rosette components (K), allosteric cooperativity associated with formation of a second H-bonding interaction with each component, and the effective molarity for cyclisation of the rosette motif (EM). Pyrimidine-cyanurate interactions are an order of magnitude more favourable than pyrimidine-barbiturate interactions, so the cyanurate rosettes are significantly more stable than barbiturate rosettes. There is no allosteric cooperativity associated with rosette formation, but the chelate cooperativity quantified by the product K EM is exceptionally high (102-104), indicating that there are no other species present that compete with rosette assembly. The values of EM for rosette formation are approximately 2 M for all four rosettes studied and are not affected by differences in peripheral substituents or intrinsic H-bond strength.

Conformationally adaptable macrocyclic receptors for ditopic anions: analysis of chelate cooperativity in aqueous containing media

The effect of chelate cooperativity on the binding of several ditopic anions to two tetrathiourea macrocycles has been analysed in competitive solvent mixtures (H2O : DMSO 1 : 9 v/v). The semi-flexible receptors bind dicarboxylates with high affinity dependent on the length and flexibility of the guest. Chemical double mutant cycle (DMC) analysis allowed the chelate cooperativity effects to be measured in detail and revealed both positive and negative cooperativity effects which were dependent on guest size, flexibility and spacer interactions between guest and macrocycle. 1H NMR and crystallographic studies confirmed the macrocycle hosts are adaptable, changing conformation to match their pore size to a selected guest.

Conformational Entropy as a Means to Control the Behavior of Poly(diketoenamine) Vitrimers In and Out of Equilibrium

Control of equilibrium and non-equilibrium thermomechanical behavior of poly(diketoenamine) vitrimers is shown by incorporating linear polymer segments varying in molecular weight (MW) and conformational degrees of freedom into the dynamic covalent network. While increasing MW of linear segments yields a lower storage modulus at the rubbery plateau after softening above the glass transition (T_g ), both T_g and the characteristic time of stress relaxation are independently governed by the conformational entropy of the embodied linear segments. Activation energies for bond exchange in the solid state are lower for networks incorporating flexible chains; the network topology freezing temperature decreases with increasing MW of flexible linear segments but increases with increasing MW of stiff segments. Vitrimer reconfigurability is therefore influenced not only by the energetics of bond exchange for a given network density, but also the entropy of polymer chains within the network.

Neurotransmitter selection by monoamine oxidase isoforms, dissected in terms of functional groups by mixed double mutant cycles

Double mutant cycles were constructed using neurotransmitters and synthetic substrates that measure their selective binding to one monoamine oxidase (MAO) enzyme isoform over another as a function of structural change. This work measures a reduction in selectivity for the MAOB isoform of 3 to 9.5 kJ mol^-1 upon the addition of hydroxy functional groups to a phenethylamine scaffold. Replacement of hydroxy functional groups on the phenethylamine scaffold by hydrophobic substituents measures an increase in selectivity for MAOB of -1.1 to -6.9 kJ mol^-1. The strategies presented here can be applied to the development of competitive reversible inhibitors of MAO enzymes and other targets with structurally related isoforms.

Inverse Mixed-Mode Chromatography for the Evaluation of Multivalency and Cooperativity of Host-Guest Complexation in Porous Materials

A new separation-based analytical method was developed to evaluate the multivalency and cooperativity of supramolecular host-guest complexation in porous materials. The method is based on inverse mixed-mode chromatography in which a porous material with a multivalent functional group is packed into a column and bound with a complementary guest molecule to form a multivalent complex. The bound guest molecules are eluted in the mobile phase and detected by appropriate methods such as UV absorption. The retention factor of the guest molecule is determined and broken down into the contributions of noncovalent interactions between binding sites (e.g., hydrophobic and ionic components), thereby calculating the effective molarity and cooperativity factor of the complexation. Two model systems denoted as RP/SCX and RP/SAX were analyzed by the established method. On average, the RP/SCX system has an effective molarity (EM) of 0.14 M and a cooperativity factor (β) of 0.86, while the RP/SAX system has an EM value of 0.18 M and a β value of 2.3. Interestingly, experiments have shown that these values do not change with changes in the intrinsic binding strength of the constituent sites. In summary, the developed method allows for quantitative assessment of multivalency and cooperativity effects in porous materials, providing a valuable complement to the analytical toolbox for supramolecular chemists and materials scientists.

Axial coordination reactions with nitrogenous bases and determination of equilibrium constants for zinc tetraarylporphyrins containing four β,β′-fused butano and benzo groups in nonaqueous media

The axial coordination properties of six zinc tetraarylporphyrins with seven different nitrogenous bases were examined in CH2Cl2 for derivatives containing four [Formula: see text],[Formula: see text]-fused butano or benzo groups and the equilibrium constants (log[Formula: see text] determined using spectral titration methods. The examined compounds are represented as butano(YPh)4PorZn and benzo(YPh)4PorZn, where Por is the porphyrin dianion and Y is a CH3, H or Cl substituent on the para-position of each meso-phenyl ring of the macrocycle. The initial four-coordinate butano- and benzoporphyrins will axially bind one nitrogenous base to form five-coordinate derivatives in CH2Cl2 and this leads to a 4–22 nm red-shift of the Soret and Q bands. The log[Formula: see text] values range from 1.98 to 4.69 for butano(YPh)4PorZn and from 3.42 to 5.36 for benzo(YPh)4PorZn, with the exact value depending upon the meso and [Formula: see text]-substituents of the porphyrin and the conjugate acid dissociation constants (p[Formula: see text] of the nitrogenous base.

Guidelines for the assembly of hydrogen-bonded macrocycles

This article highlights selected examples on the synthesis of hydrogen-bonded macrocycles from ditopic molecules and analyze the main factors, often interrelated, that influence the equilibrium between ring and chain species.

Understanding coordination equilibria in solution and gel-phase [2]rotaxanes

An active-metal template approach has been use to synthesise solution and surface bound addressable [2]rotaxanes giving unique insights into thermodynamic equilibria in interlocked structures.

Enhanced Chelate Cooperativity in Polar Solvents

High-throughput UV-vis titrations in combination with chemical double-mutant cycles (DMCs) have been used to study the competition of a polar solvent for formation of intramolecular H-bonds. Twenty-four different zinc porphyrin-pyridine complexes were investigated in mixtures of toluene and phenol. DMCs were used to determine effective molarities (EM) for the formation of intramolecular phenol-amide H-bonds as a function of solvent composition. The values of EM increase by an order of magnitude with increasing concentrations of the more polar solvent, phenol. Phenol solvates the amide groups on the ligands strongly, increasing the steric bulk and destabilizing the complexes. These adverse steric interactions are removed when intramolecular H-bonds are formed and therefore provide an increased driving force for formation of cooperative interactions. The result is that the effects of competitive interactions with polar solvents that reduce binding affinity are attenuated to a significant extent by a corresponding increase in EM in multivalent complexes.

H-Bond Self-Assembly: Folding versus Duplex Formation

Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.

Assessing cooperativity in supramolecular systems

In this tutorial review, different aspects of cooperativity in supramolecular chemistry and their thermodynamic analysis are discussed.

Mix and match recognition modules for the formation of H-bonded duplexes

Oligomeric molecules equipped with complementary H-bond recognition sites form stable duplexes in non-polar solvents. The use of a single H-bond between a good H-bond donor and a good H-bond acceptor as the recognition motif appended to a non-polar backbone leads to an architecture with interchangeable recognition alphabets. The interactions of three different families of H-bond acceptor oligomers (pyridine, pyridine N-oxide or phosphine oxide recognition module) with a family of H-bond donor oligomers (phenol recognition module) are compared. All three donor-acceptor combinations form stable duplexes, where the stability of the 1 : 1 complex increases with increasing numbers of recognition modules. The effective molarity for formation of intramolecular H-bonds that lead to zipping up of the duplex (EM) increases with decreasing flexibility of the recognition modules: 14 mM for the phosphine oxides which are connected to the backbone via a flexible linker; 40 mM for the pyridine N-oxides which have three fewer degrees of torsional freedom, and 80 mM for the pyridines where the geometry of the H-bond is more directional. However, the pyridine-phenol H-bond is an order of magnitude weaker than the other two types of H-bond, so overall the pyridine N-oxides form the most stable duplexes with the highest degree of cooperativity. The results show that it is possible to use different recognition motifs with the same duplex architecture, and this makes it possible to tune overall stabilities of the complexes by varying the components.

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.

The Role of Conformational Changes in Molecular Recognition

Conformational changes of molecules are crucial elements in many biochemical processes, and also in molecular recognition. Here, we present a novel exact mathematical equation for the binding free energy of a receptor-ligand pair. It shows that the energetic contribution due to conformational changes upon molecular recognition is defined by the so-called Kullback-Leibler (KL) divergence between the probability distributions of the conformational ensemble of the biomolecule in the bound and free states. We show that conformational changes always contribute positively to the change in free energy and therefore disfavor the association process. Using the example of ligands binding to a flexible cavity of T4 lysozyme, we illustrate that, due to enthalpy-entropy compensation, the conformational entropy is a misleading quantity for assessing the conformational contribution to the binding free energy, in contrast to the KL divergence, which is the correct quantity to use in this context.

Mix and match backbones for the formation of H-bonded duplexes

The formation of well-defined supramolecular assemblies involves competition between intermolecular and intramolecular interactions, which is quantified by effective molarity. Formation of a duplex between two oligomers equipped with recognition sites displayed along a non-interacting backbone requires that once one intermolecular interaction has been formed, all subsequent interactions take place in an intramolecular sense. The efficiency of this process is governed by the geometric complementarity and conformational flexibility of the backbone linking the recognition sites. Here we report a series of phosphine oxide H-bond acceptor AA 2-mers and phenol H-bond donor DD 2-mers, where the two recognition sites are connected by isomeric backbone modules that vary in geometry and flexibility. All AA and DD combinations form stable AA·DD duplexes, where two cooperative H-bonds lead to an increase in stability of an order of magnitude compared with the corresponding A·D complexes that can only form one H-bond. For all six possible backbone combinations, the effective molarity for duplex formation is approximately constant (7-20 mM). Thus strict complementarity and high degrees of preorganisation are not required for efficient supramolecular assembly. Provided there is some flexibility, quite different backbone modules can be used interchangeably to construct stable H-bonded duplexes.

Hydrogen-Bonded Macrocyclic Supramolecular Systems in Solution and on Surfaces

Cyclization into closed assemblies is the most recurrent approach to realize the noncovalent synthesis of discrete, well-defined nanostructures. This review article particularly focuses on the noncovalent synthesis of monocyclic hydrogen-bonded systems that are self-assembled from a single molecule with two binding-sites. Taking advantage of intramolecular binding events, which are favored with respect to intermolecular binding in solution, can afford quantitative amounts of a given supramolecular species under thermodynamic control. The size of the assembly depends on geometric issues such as the monomer structure and the directionality of the binding interaction, whereas the fidelity achieved relies largely on structural preorganization, low degrees of conformational flexibility, and templating effects. Here, we discuss several examples described in the literature in which cycles of different sizes, from dimers to hexamers, are studied by diverse solution or surface characterization techniques.

Selective complexation of di-n-hexylammonium salts by tailed porphyrin host

A di-n-hexylammonium ion was selectively encapsulated in the cavity of tailed porphyrins due to induced fit and lipophilic interactions.

Six-Coordinate Zinc Porphyrins for Template-Directed Synthesis of Spiro-Fused Nanorings

Five-coordinate geometry is the standard binding mode of zinc porphyrins with pyridine ligands. Here we show that pseudo-octahedral six-coordinate zinc porphyrin complexes can also be formed in solution, by taking advantage of the chelate effect. UV–vis–NIR titrations indicate that the strength of this second coordination is ca. 6–8 kJ mol^–1. We have used the formation of six-coordinate zinc porphyrin complexes to achieve the template-directed synthesis of a 3D π-conjugated spiro-fused array of 11 porphyrin units, covalently connected in a nontrivial topology. Time-resolved fluorescence anisotropy experiments show that electronic excitation delocalizes between the two perpendicular nanorings of this spiro-system within the experimental time-resolution of 270 fs.

Cooperative duplex formation by synthetic H-bonding oligomers

Flexible phenol-phosphine oxide oligomers show promise as a new class of synthetic information molecule.

A series of flexible oligomers equipped with phenol H-bond donors and phosphine oxide H-bond acceptors have been synthesised using reductive amination chemistry. H-bonding interactions between complementary oligomers leads to the formation of double-stranded complexes which were characterised using NMR titrations and thermal denaturation experiments. The stability of the duplex increases by one order of magnitude for every H-bonding group added to the chain. Similarly, the enthalpy change for duplex assembly and the melting temperature for duplex denaturation both increase with increasing chain length. These observations indicate that H-bond formation along the oligomers is cooperative despite the flexible backbone, and the effective molarity for intramolecular H-bond formation (14 mM) is sufficient to propagate the formation of longer duplexes using this approach. The product K EM, which is used to quantify chelate cooperativity is 5, which means that each H-bond is more than 80% populated in the assembled duplex. The modular design of these oligomers represents a general strategy for the design of synthetic information molecules that could potentially encode and replicate chemical information in the same way as nucleic acids.

Influence of receptor flexibility on intramolecular H-bonding interactions

Atropisomers of a series of zinc tetraphenyl porphyrins were synthesized and used as supramolecular receptors. Rotation around the porphyrin-meso phenyl bonds is restricted by installing ortho-chlorine substituents on the phenyl groups. The chlorine substituents allowed chromatographic separation of atropisomers, which did not interconvert at room temperature. The porphyrin meso phenyl groups were also equipped with phenol groups, which led to the formation of intramolecular H-bonds when the zinc porphyrins were bound to pyridine ligands equipped with ester or amide side arms. Binding of the pyridine ligands with the conformationally locked chloroporphyrins was compared with the corresponding unsubstituted porphyrins, which are more flexible. The association constants of 150 zinc porphyrin-pyridine complexes were measured in two different solvents, toluene and 1,1,2,2-tetrachloroethane (TCE). These association constants were then used to construct 120 chemical double mutant cycles to quantify the influence of chlorine substitution on the free energy of intramolecular H-bonds formed between the phenol side arms of the porphyrins and the ester or amide side arms of the pyridine ligands. Conformational restriction leads to increases in the stability of some complexes and decreases in the stability of others with variations in the free energy contribution due to intramolecular H-bonding of -5 to +6 kJ mol(-1).

The flexibility-complementarity dichotomy in receptor-ligand interactions

Synthetic supramolecular complexes provide an opportunity for quantitative systematic exploration of the relationship between chemical structure and molecular recognition phenomena. A family of closely related zinc porphyrin-pyridine complexes was used to examine the interplay of conformational flexibility and geometric complementarity in determining the selectivity of molecular recognition events. The association constants of 48 zinc porphyrin-pyridine complexes were measured in two different solvents, toluene and 1,1,2,2-tetrachloroethane (TCE). These association constants were used to construct 32 chemical double mutant cycles to dissect the free energy contributions of intramolecular H-bonds between the phenol side arms of the porphyrins and the ester or amide side arms of the pyridine ligands. Effective molarities (EM) for the intramolecular interactions were determined by comparison with the corresponding intermolecular H-bonding interactions. The values of EM do not depend on the solvent and are practically identical for amide and ester H-bond acceptors located at the same site on the ligand framework. However, there are variations of an order of magnitude in EM depending on the flexibility of the linker used to connect the H-bond acceptors to the pyridine ligands. Rigid aromatic linkers give values of EM that are an order of magnitude higher than the values of EM for the corresponding ester linkers, which have one additional torsional degree of freedom. However, the most flexible ether linkers give values of EM that are also higher than the values of EM for the corresponding ester linkers, which have one less torsional degree of freedom. Although the penalty for conformational restriction on binding is higher for the more flexible ether linkers, this flexibility allows optimization of the geometric complementarity of the ligand for the receptor, so there is a trade off between preorganization and fit.

Influence of non-covalent preorganization on supramolecular effective molarities

Formation of H-bonding interactions, which restrict the conformational mobility of a flexible linker, have no effect on chelate cooperativity in a family of porphyrin-pyridine complexes.

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.

Cyclodextrin-templated porphyrin nanorings

α- and β-Cyclodextrins have been used as scaffolds for the synthesis of six- and seven-legged templates by functionalizing every primary CH₂OH with a 4-pyridyl moiety. Although these templates are flexible, they are very effective for directing the synthesis of macrocyclic porphyrin oligomers consisting of six or seven porphyrin units. The transfer of chirality from the cyclodextrin templates to their nanoring hosts is evident from NMR and circular dichroism spectroscopy. Surprisingly, the mean effective molarity for binding the flexible α-cyclodextrin-based template within the six-porphyrin nanoring (74 m) is almost as high as for the previously studied rigid hexadentate template (180 m). The discovery that flexible templates are effective in this system, and the availability of a template with a prime number of binding sites, open up many possibilities for the template-directed synthesis of larger macrocycles.

Role of a guanidinium cation-phosphodianion pair in stabilizing the vinyl carbanion intermediate of orotidine 5'-phosphate decarboxylase-catalyzed reactions

The side chain cation of Arg235 provides a 5.6 and 2.6 kcal/mol stabilization of the transition states for orotidine 5'-monophosphate (OMP) decarboxylase (OMPDC) from Saccharomyces cerevisiae catalyzed reactions of OMP and 5-fluoroorotidine 5'-monophosphate (FOMP), respectively, a 7.2 kcal/mol stabilization of the vinyl carbanion-like transition state for enzyme-catalyzed exchange of the C-6 proton of 5-fluorouridine 5'-monophosphate (FUMP), but no stabilization of the transition states for enzyme-catalyzed decarboxylation of truncated substrates 1-(β-d-erythrofuranosyl)orotic acid and 1-(β-d-erythrofuranosyl) 5-fluorouracil. These observations show that the transition state stabilization results from formation of a protein cation-phosphodianion pair, and that there is no detectable stabilization from an interaction between the side chain and the pyrimidine ring of substrate. The 5.6 kcal/mol side chain interaction with the transition state for the decarboxylation reaction is 50% of the total 11.2 kcal/mol transition state stabilization by interactions with the phosphodianion of OMP, whereas the 7.2 kcal/mol side chain interaction with the transition state for the deuterium exchange reaction is a larger 78% of the total 9.2 kcal/mol transition state stabilization by interactions with the phosphodianion of FUMP. The effect of the R235A mutation on the enzyme-catalyzed deuterium exchange is expressed predominantly as a change in the turnover number kex, whereas the effect on the enzyme-catalyzed decarboxylation of OMP is expressed predominantly as a change in the Michaelis constant Km. These results are rationalized by a mechanism in which the binding of OMP, compared with that for FUMP, provides a larger driving force for conversion of OMPDC from an inactive open conformation to a productive, active, closed conformation.

Relationship between chemical structure and supramolecular effective molarity for formation of intramolecular H-bonds

Effective molarity (EM) is a key parameter that determines the efficiency of a range of supramolecular phenomena from the folding of macromolecules to multivalent ligand binding. Coordination complexes formed between zinc porphyrins equipped H-bond donor sites and pyridine ligands equipped with H-bond acceptor sites have allowed systematic quantification of EM values for the formation of intramolecular H-bonds in 240 different systems. The results provide insights into the relationship of EM to supramolecular architecture, H-bond strength, and solvent. Previous studies on ligands equipped with phosphonate diester and ether H-bond acceptors were inconclusive, but the experiments described here on ligands equipped with phosphine oxide, amide, and ester H-bond acceptors resolve these ambiguities. Chemical double-mutant cycles were used to dissect the thermodynamic contributions of individual H-bond interactions to the overall stabilities of the complexes and hence determine the values of EM, which fall in the range 1-1000 mM. Solvent has little effect on EM, and the values measured in toluene and 1,1,2,2-tetrachloroethane are similar. For H-bond acceptors that have similar geometries but different H-bond strengths (amide and ester), the values of EM are very similar. For H-bond acceptors that have different geometries but similar H-bond strengths (amide and phosphonate diester), there is little correlation between the values of EM. These results imply that supramolecular EMs are independent of solvent and intrinsic H-bond strength but depend on supramolecular architecture and geometric complementarity.