Context-Dependent Significance of London Dispersion

ConspectusLondon forces constitute an attractive component of van der Waals interactions and originate from transient correlated momentary dipoles in adjacent atoms. The in-depth investigation of London dispersion forces poses notable challenges, especially in solution, owing to their inherently weak and competing character. Our objective in this Account is to shed light on the context-dependent significance of London dispersion forces by contrasting our own experimental findings with those from other research endeavors. Specifically, we will explore how factors such as the choice of system and solvent can influence the apparent role of London dispersion forces in molecular recognition processes. We initiate our Account by scrutinizing the Wilcox balance, which has yielded diverse and occasionally contradictory results. Following that, we provide an overview of the role of London dispersion forces and their context-dependent variations, encompassing alkyl-alkyl, halogen-π, alkyl-π, and aromatic stacking interactions.Several experimental investigations have revealed how difficult it is to measure the significance of London dispersion in solution. Indeed, dispersion forces seldom act as the exclusive driving force in molecular recognition processes, and solvation energetics also strongly influence equilibria and kinetics. Molecular balances that bring apolar functional groups into contact have proven to be instrumental in the experimental measurement of dispersion. The intramolecular approach avoids the need to pay the entropic cost of bringing interacting groups into contact, while also enabling solvent screening. Such experimental studies have found dispersion interactions between functional groups to be very weak (<5 kJ mol-1), meaning that they frequently take backstage to electrostatic contributions and solvophobic effects and are readily damped by competitive dispersion interactions with the solvent. By using such approaches, competitive dispersion interactions with the solvent have been shown to be described by the bulk polarizability of the solvent (perfluoroalkanes have the lowest bulk polarizabilities, while carbon disulfide has one of the highest). Dispersion interactions are also strongly distance-dependent, which results in considerable context-dependent outcomes across different investigations. For example, we caution against the risk of attributing the stability of a "more sterically hindered" isomer as arising from intramolecular dispersion forces. The total energy of the system can reveal other contributions to stability, such as nonintuitive minimization of strain elsewhere in the molecule. Indeed, the delicate distance-dependent balance between sterics and London dispersion means that even subtle changes in size and geometry can lead to disparate behavior. Similarly, solvophobic effects also contribute to stabilizing contacts between bulky functional groups, which can be revealed if there is a correlation with the cohesive energy density of the solvent.

Experimental Quantification of Halogen⋅⋅⋅Arene van der Waals Contacts

Crystallographic and computational studies suggest the occurrence of favourable interactions between polarizable arenes and halogen atoms. However, the systematic experimental quantification of halogen⋅⋅⋅arene interactions in solution has been hindered by the large variance in the steric demands of the halogens. Here we have synthesized molecular balances to quantify halogen⋅⋅⋅arene contacts in 17 solvents and solvent mixtures using 1 H NMR spectroscopy. Calculations indicate that favourable halogen⋅⋅⋅arene interactions arise from London dispersion in the gas phase. In contrast, comparison of our experimental measurements with partitioned SAPT0 energies indicate that dispersion is sufficiently attenuated by the solvent that the halogen⋅⋅⋅arene interaction trend was instead aligned with increasing exchange repulsion as the halogen increased in size (ΔGX ⋅⋅⋅Ph =0 to +1.5 kJ mol-1 ). Halogen⋅⋅⋅arene contacts were slightly less disfavoured in solvents with higher solvophobicities and lower polarizabilities, but strikingly, were always less favoured than CH3 ⋅⋅⋅arene contacts (ΔGMe ⋅⋅⋅Ph =0 to -1.4 kJ mol-1 ).

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.

Functionalised nanopores: chemical and biological modifications

Nanopore technology has established itself as a powerful tool for single-molecule studies. By analysing changes in the ion current flowing through a single transmembrane channel, a wealth of molecular information can be elucidated. Early studies utilised nanopore technology for sensing applications, and subsequent developments have diversified its remit. Nanopores can be synthetic, solid-state, or biological in origin, but recent work has seen these boundaries blurred as hybrid functionalised pores emerge. The modification of existing pores and the construction of novel synthetic pores has been an enticing goal for creating systems with tailored properties and functionality. Here, we explore chemically functionalised biological pores and the bio-inspired functionalisation of solid-state pores, highlighting how the convergence of these domains provides enhanced functionality.

The convergence of chemistry, biology, and solid-state approaches enables the construction hybrid nanopores with enhanced single-molecule applications.

Reversible Reductive Elimination in Aluminum(II) Dihydrides

Oxidative addition and reductive elimination are defining reactions of transition‐metal organometallic chemistry. In main‐group chemistry, oxidative addition is now well‐established but reductive elimination reactions are not yet general in the same way. Herein, we report dihydrodialanes supported by amidophosphine ligands. The ligand serves as a stereochemical reporter for reversible reductive elimination/oxidative addition chemistry involving Al^I and Al^III intermediates.

Quantifying Interactions and Solvent Effects Using Molecular Balances and Model Complexes

Where the basic units of molecular chemistry are the bonds within molecules, supramolecular chemistry is based on the interactions that occur between molecules. Understanding the "how" and "why" of the processes that govern molecular self-assembly remains an open challenge to the supramolecular community. While many interactions are readily examined in silico through electronic structure calculations, such insights may not be directly applicable to experimentalists. The practical limitations of computationally accounting for solvation is perhaps the largest bottleneck in this regard, with implicit solvation models failing to comprehensively account for the specific nature of solvent effects and explicit models incurring a prohibitively high computational cost. Since molecular recognition processes usually occur in solution, insight into the nature and effect of solvation is imperative not only for understanding these phenomena but also for the rational design of systems that exploit them.Molecular balances and supramolecular complexes have emerged as useful tools for the experimental dissection of the physicochemical basis of various noncovalent interactions, but they have historically been underexploited as a platform for the evaluation of solvent effects. Contrasting with large biological complexes, smaller synthetic model systems enable combined experimental and computational analyses, often facilitating theoretical analyses that can work in concert with experiment.Our research has focused on the development of supramolecular systems to evaluate the role of solvents in molecular recognition, and further characterize the underlying mechanisms by which molecules associate. In particular, the use of molecular balances has provided a framework to measure the magnitude of solvent effects and to examine the accuracy of solvent models. Such approaches have revealed how solvation can modulate the electronic landscape of a molecule and how competitive solvation and solvent cohesion can provide thermodynamic driving forces for association. Moreover, the use of simple model systems facilitates the interrogation and further dissection of the physicochemical origins of molecular recognition. This tandem experimental/computational approach has married less common computational techniques, like symmetry adapted perturbation theory (SAPT) and natural bonding orbital (NBO) analysis, with experimental observations to elucidate the influence of effects that are difficult to resolve experimentally (e.g., London dispersion and electron delocalization).

Reversible stimuli-responsive chromism of a cyclometallated platinum(II) complex

We report the reversible chromism and luminescence of a cyclometalated platinum(ii) complex that forms dimers, with close PtPt interactions that can be modulated by solvent and temperature. The precise reversible control may be exploited in future stimuli-responsive chemosensing or optoelectronic devices.

Transmembrane Ion Channels Formed by a Star of David [2]Catenane and a Molecular Pentafoil Knot

A (Fe^II)₆-coordinated triply interlocked ("Star of David") [2]catenane (6₁² link) and a (Fe^II)₅-coordinated pentafoil (5₁) knot are found to selectively transport anions across phospholipid bilayers. Allostery, topology, and building block stoichiometry all play important roles in the efficacy of the ionophoric activity. Multiple Fe^II cation coordination by the interlocked molecules is crucial: the demetalated catenane exhibits no anion binding in solution nor any transmembrane ion transport properties. However, the topologically trivial, Lehn-type cyclic hexameric Fe^II helicates-which have similar anion binding affinities to the metalated Star of David catenane in solution-also display no ion transport properties. The unanticipated difference in behavior between the open- and closed-loop structures may arise from conformational restrictions in the linking groups that likely enhances the rigidity of the channel-forming topologically complex molecules. The (Fe^II)₆-coordinated Star of David catenane, derived from a hexameric cyclic helicate, is 2 orders of magnitude more potent in terms of ion transport than the (Fe^II)₅-coordinated pentafoil knot, derived from a cyclic pentamer of the same building block. The reduced efficacy is reminiscent of multisubunit protein ion channels assembled with incorrect monomer stoichiometries.

Quantifying Through-Space Substituent Effects

The description of substituents as electron donating or withdrawing leads to a perceived dominance of through-bond influences. The situation is compounded by the challenge of separating through-bond and through-space contributions. Here, we probe the experimental significance of through-space substituent effects in molecular interactions and reaction kinetics. Conformational equilibrium constants were transposed onto the Hammett substituent constant scale revealing dominant through-space substituent effects that cannot be described in classic terms. For example, NO2 groups positioned over a biaryl bond exhibited similar influences as resonant electron donors. Meanwhile, the electro-enhancing influence of OMe/OH groups could be switched off or inverted by conformational twisting. 267 conformational equilibrium constants measured across eleven solvents were found to be better predictors of reaction kinetics than calculated electrostatic potentials, suggesting utility in other contexts and for benchmarking theoretical solvation models.

Reconciling Electrostatic and n→π* Orbital Contributions in Carbonyl Interactions

Interactions between carbonyl groups are prevalent in protein structures. Earlier investigations identified dominant electrostatic dipolar interactions, while others implicated lone pair n→π* orbital delocalisation. Here these observations are reconciled. A combined experimental and computational approach confirmed the dominance of electrostatic interactions in a new series of synthetic molecular balances, while also highlighting the distance-dependent observation of inductive polarisation manifested by n→π* orbital delocalisation. Computational fiSAPT energy decomposition and natural bonding orbital analyses correlated with experimental data to reveal the contexts in which short-range inductive polarisation augment electrostatic dipolar interactions. Thus, we provide a framework for reconciling the context dependency of the dominance of electrostatic interactions and the occurrence of n→π* orbital delocalisation in C=O⋅⋅⋅C=O interactions.

Switchable foldamer ion channels with antibacterial activity

Synthetic ion channels may have applications in treating channelopathies and as new classes of antibiotics, particularly if ion flow through the channels can be controlled. Here we describe triazole-capped octameric α-aminoisobutyric acid (Aib) foldamers that "switch on" ion channel activity in phospholipid bilayers upon copper(ii) chloride addition; activity is "switched off" upon copper(ii) extraction. X-ray crystallography showed that CuCl₂ complexation gave chloro-bridged foldamer dimers, with hydrogen bonds between dimers producing channels within the crystal structure. These interactions suggest a pathway for foldamer self-assembly into membrane ion channels. The copper(ii)-foldamer complexes showed antibacterial activity against B. megaterium strain DSM319 that was similar to the peptaibol antibiotic alamethicin, but with 90% lower hemolytic activity.

Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices

Simple design principles improve conformational stability and decrease strand leakage by two orders of magnitude.

Synthetically Diversified Protein Nanopores: Resolving Click Reaction Mechanisms

Nanopores are emerging as a powerful tool for the investigation of nanoscale processes at the single-molecule level. Here, we demonstrate the methionine-selective synthetic diversification of α-hemolysin (α-HL) protein nanopores and their exploitation as a platform for investigating reaction mechanisms. A wide range of functionalities, including azides, alkynes, nucleotides, and single-stranded DNA, were incorporated into individual pores in a divergent fashion. The ion currents flowing through the modified pores were used to observe the trajectory of a range of azide-alkyne click reactions and revealed several short-lived intermediates in Cu(I)-catalyzed azide-alkyne [3 + 2] cycloadditions (CuAAC) at the single-molecule level. Analysis of ion-current fluctuations enabled the populations of species involved in rapidly exchanging equilibria to be determined, facilitating the resolution of several transient intermediates in the CuAAC reaction mechanism. The versatile pore-modification chemistry offers a useful approach for enabling future physical organic investigations of reaction mechanisms at the single-molecule level.

An RNA-dependent mechanism for transient expression of bacterial translocation filaments

The prokaryotic RNA chaperone Hfq mediates sRNA-mRNA interactions and plays a significant role in post-transcriptional regulation of the type III secretion (T3S) system produced by a range of Escherichia coli pathotypes. UV-crosslinking was used to map Hfq-binding under conditions that promote T3S and multiple interactions were identified within polycistronic transcripts produced from the locus of enterocyte effacement (LEE) that encodes the T3S system. The majority of Hfq binding was within the LEE5 and LEE4 operons, the latter encoding the translocon apparatus (SepL-EspADB) that is positively regulated by the RNA binding protein, CsrA. Using the identified Hfq-binding sites and a series of sRNA deletions, the sRNA Spot42 was shown to directly repress translation of LEE4 at the sepL 5' UTR. In silico and in vivo analyses of the sepL mRNA secondary structure combined with expression studies of truncates indicated that the unbound sepL mRNA is translationally inactive. Based on expression studies with site-directed mutants, an OFF-ON-OFF toggle model is proposed that results in transient translation of SepL and EspA filament assembly. Under this model, the nascent mRNA is translationally off, before being activated by CsrA, and then repressed by Hfq and Spot42.

Structural evidence for the covalent modification of FabH by 4,5-dichloro-1,2-dithiol-3-one (HR45)

We use mass spectrometry analysis and molecular modelling to show the established antimicrobial inhibitor 4,5-dichloro-1,2-dithiol-3-one (HR45) acts by forming a covalent adduct with the target β-ketoacyl-ACP synthase III (FabH). The 5-chloro substituent directs attack of the essential active site thiol (C112) via a Michael-type addition elimination reaction mechanism.

In Situ Synthetic Functionalization of a Transmembrane Protein Nanopore

Monitoring current flow through a single nanopore has proved to be a powerful technique for the in situ detection of molecular structure, binding, and reactivity. Transmembrane proteins, such as α-hemolysin, provide particularly attractive platforms for nanopore sensing applications due to their atomically precise structures. However, many nanopore applications require the introduction of functional groups to tune selectivity. To date, such modifications have required genetic modification of the protein prior to functionalization. Here we demonstrate the in situ synthetic modification of a wild-type α-hemolysin nanopore embedded in a membrane. We show that reversible dynamic covalent iminoboronate formation and the resulting changes in the ion current flowing through an individual nanopore can be used to map the reactive behavior of lysine residues within the nanopore channel. Crucially, the modification of lysine residues located outside the nanopore channel was found not to affect the stability or utility of the nanopore. Finally, knowledge of the reactivity patterns enabled the irreversible functionalization of a single, assignable lysine residue within the nanopore channel. The approach constitutes a simple, generic tool for the rapid, in situ synthetic modification of protein nanopores that circumvents the need for prior genetic modification.

The Role of Terminal Functionality in the Membrane and Antibacterial Activity of Peptaibol-Mimetic Aib Foldamers

Peptaibols are peptide antibiotics that typically feature an N-terminal acetyl cap, a C-terminal aminoalcohol, and a high proportion of α-aminoisobutyric acid (Aib) residues. To establish how each feature might affect the membrane-activity of peptaibols, biomimetic Aib foldamers with different lengths and terminal groups were synthesised. Vesicle assays showed that long foldamers (eleven Aib residues) with hydrophobic termini had the highest ionophoric activity. C-terminal acids or primary amides inhibited activity, while replacement of an N-terminal acetyl with an azide group made little difference. Crystallography showed that N₃ Aib₁₁ CH₂ OTIPS folded into a 3₁₀ helix 2.91 nm long, which is close to the bilayer hydrophobic width. Planar bilayer conductance assays showed discrete ion channels only for N-acetylated foldamers. However long foldamers with hydrophobic termini had the highest antibacterial activity, indicating that ionophoric activity in vesicles was a better indicator of antibacterial activity than the observation of discrete ion channels.

The Origin of Chalcogen-Bonding Interactions

Favorable molecular interactions between group 16 elements have been implicated in catalysis, biological processes, and materials and medicinal chemistry. Such interactions have since become known as chalcogen bonds by analogy to hydrogen and halogen bonds. Although the prevalence and applications of chalcogen-bonding interactions continues to develop, debate still surrounds the energetic significance and physicochemical origins of this class of σ-hole interaction. Here, synthetic molecular balances were used to perform a quantitative experimental investigation of chalcogen-bonding interactions. Over 160 experimental conformational free energies were measured in 13 different solvents to examine the energetics of O···S, O···Se, S···S, O···HC, and S···HC contacts and the associated substituent and solvent effects. The strongest chalcogen-bonding interactions were found to be at least as strong as conventional H-bonds, but unlike H-bonds, surprisingly independent of the solvent. The independence of the conformational free energies on solvent polarity, polarizability, and H-bonding characteristics showed that electrostatic, solvophobic, and van der Waals dispersion forces did not account for the observed experimental trends. Instead, a quantitative relationship between the experimental conformational free energies and computed molecular orbital energies was consistent with the chalcogen-bonding interactions being dominated by n → σ* orbital delocalization between a lone pair (n) of a (thio)amide donor and the antibonding σ* orbital of an acceptor thiophene or selenophene. Interestingly, stabilization was manifested through the same acceptor molecular orbital irrespective of whether a direct chalcogen···chalcogen or chalcogen···H-C contact was made. Our results underline the importance of often-overlooked orbital delocalization effects in conformational control and molecular recognition phenomena.

Discrimination of supramolecular chirality using a protein nanopore

Supramolecular chirality may emerge from self-assembly processes to yield architectures that differ only in the topological arrangement of their constituent parts. Since the properties of the resulting enantiomeric assemblies are identical, purification and characterisation can be challenging. Here, we have examined the hypothesis that the intrinsic chirality of a protein nanopore can be exploited to detect supramolecular chirality. Transient blockages in the ion current flowing through a single membrane-spanning α-haemolysin nanopore were shown to discriminate between M4L6 tetrahedral coordination cages of opposing chiralities. The single-molecule nature of the approach facilitated direct access to the rates of association and dissociation with the nanopore, which allowed the concentrations of the enantiomeric supramolecular assemblies to be determined in situ. Thus, we have established that a protein nanopore can be used to discriminate the chiral topologies of supramolecular assemblies, even when they are too large to fully enter the nanopore.

Strong Short-Range Cooperativity in Hydrogen-Bond Chains

Chains of hydrogen bonds such as those found in water and proteins are often presumed to be more stable than the sum of the individual H bonds. However, the energetics of cooperativity are complicated by solvent effects and the dynamics of intermolecular interactions, meaning that information on cooperativity typically is derived from theory or indirect structural data. Herein, we present direct measurements of energetic cooperativity in an experimental system in which the geometry and the number of H bonds in a chain were systematically controlled. Strikingly, we found that adding a second H-bond donor to form a chain can almost double the strength of the terminal H bond, while further extensions have little effect. The experimental observations add weight to computations which have suggested that strong, but short-range cooperative effects may occur in H-bond chains.

Length-Dependent Formation of Transmembrane Pores by 310-Helical α-Aminoisobutyric Acid Foldamers

The synthetic biology toolbox lacks extendable and conformationally controllable yet easy-to-synthesize building blocks that are long enough to span membranes. To meet this need, an iterative synthesis of α-aminoisobutyric acid (Aib) oligomers was used to create a library of homologous rigid-rod 3₁₀-helical foldamers, which have incrementally increasing lengths and functionalizable N- and C-termini. This library was used to probe the inter-relationship of foldamer length, self-association strength, and ionophoric ability, which is poorly understood. Although foldamer self-association in nonpolar chloroform increased with length, with a ∼14-fold increase in dimerization constant from Aib₆ to Aib₁₁, ionophoric activity in bilayers showed a stronger length dependence, with the observed rate constant for Aib₁₁ ∼70-fold greater than that of Aib₆. The strongest ionophoric activity was observed for foldamers with >10 Aib residues, which have end-to-end distances greater than the hydrophobic width of the bilayers used (∼2.8 nm); X-ray crystallography showed that Aib₁₁ is 2.93 nm long. These studies suggest that being long enough to span the membrane is more important for good ionophoric activity than strong self-association in the bilayer. Planar bilayer conductance measurements showed that Aib₁₁ and Aib₁₃, but not Aib₇, could form pores. This pore-forming behavior is strong evidence that Aib_m (m ≥ 10) building blocks can span bilayers.

Man-made molecular machines: membrane bound

This tutorial review charts the development of man-made molecular machines; from solution-phase to transmembrane assemblies.

DNA modulates solvent isotope effects in a nanopore

Here we investigate the modulation of solvent isotope effects by the entry of DNA molecules into individual α-haemolysin nanopores. Solvent isotope effects in D2O versus H2O were enhanced (kH/kD ≈ 1.6) compared to the bulk (kH/kD ≈ 1.2), except when the pore was most blocked (kH/kD ≤ 1.1).

Effect of solvent polarizability on the assembly and ordering of nanoscale polyhedral oligomeric silsesquioxane films

Understanding the factors that affect molecular self-assembly is crucial to building designed nanoscale structures. We have deposited nanoscale films of polyhedral oligomeric silsesquioxane (POSS) onto polished silicon substrates from a range of organic solvents. We studied these films using synchrotron X-ray reflectivity and found that dip-coating from benzene, toluene, or chloroform results in near-substrate ordering only, but when acetone, hexane, or THF is used, self-assembled layers are formed throughout the entire deposited film. We conclude that solvent polarizability is the factor that determines the alignment of the POSS molecules. We have successfully tested this prediction using additional solvents selected on the basis of their calculated polarizabilities.

How much do van der Waals dispersion forces contribute to molecular recognition in solution?

The emergent properties that arise from self-assembly and molecular recognition phenomena are a direct consequence of non-covalent interactions. Gas-phase measurements and computational methods point to the dominance of dispersion forces in molecular association, but solvent effects complicate the unambiguous quantification of these forces in solution. Here, we have used synthetic molecular balances to measure interactions between apolar alkyl chains in 31 organic, fluorous and aqueous solvent environments. The experimental interaction energies are an order of magnitude smaller than estimates of dispersion forces between alkyl chains that have been derived from vaporization enthalpies and dispersion-corrected calculations. Instead, it was found that cohesive solvent-solvent interactions are the major driving force behind apolar association in solution. The results suggest that theoretical models that implicate important roles for dispersion forces in molecular recognition events should be interpreted with caution in solvent-accessible systems.