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/ß 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.

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 AlI and AlIII 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 (FeII)6-coordinated triply interlocked ("Star of David") [2]catenane (612 link) and a (FeII)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 FeII 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 FeII 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 (FeII)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 (FeII)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.

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.

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.

Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices.

The operation of DNA nanodevices is often limited by erroneous strand displacement. Here we demonstrate simple design principles that reduce such leakage by up to two orders of magnitude. Enhanced operational robustness against multiple spurious inputs was obtained by simply relocating toehold overhangs to external locations and strengthening adjacent G-C clamping.

The Importance of 1,5-Oxygen⋠⋠⋠Chalcogen Interactions in Enantioselective Isochalcogenourea Catalysis.

The importance of 1,5-O⋅⋅⋅chalcogen (Ch) interactions in isochalcogenourea catalysis (Ch=O, S, Se) is investigated. Conformational analyses of N-acyl isochalcogenouronium species and comparison with kinetic data demonstrate the significance of 1,5-O⋅⋅⋅Ch interactions in enantioselective catalysis. Importantly, the selenium analogue demonstrates enhanced rate and selectivity profiles across a range of reaction processes including nitronate conjugate addition and formal [4+2] cycloadditions. A gram-scale synthesis of the most active selenium analogue was developed using a previously unreported seleno-Hugerschoff reaction, allowing the challenging kinetic resolutions of tertiary alcohols to be performed at 500 ppm catalyst loading. Density functional theory (DFT) and natural bond orbital (NBO) calculations support the role of orbital delocalization (occurring by intramolecular chalcogen bonding) in determining the conformation, equilibrium population, and reactivity of N-acylated intermediates.

The Energetic Significance of Metallophilic Interactions.

Metallophilic interactions are increasingly recognized as playing an important role in molecular assembly, catalysis, and bio-imaging. However, present knowledge of these interactions is largely derived from solid-state structures and gas-phase computational studies rather than quantitative experimental measurements. Here, we have experimentally quantified the role of aurophilic (AuI ⋅⋅⋅AuI ), platinophilic (PtII ⋅⋅⋅PtII ), palladophilic (PdII ⋅⋅⋅PdII ), and nickelophilic (NiII ⋅⋅⋅NiII ) interactions in self-association and ligand-exchange processes. All of these metallophilic interactions were found to be too weak to be well-expressed in several solvents. Computational energy decomposition analyses supported the experimental finding that metallophilic interactions are overall weak, meaning that favorable dispersion and orbital hybridization contributions from M⋅⋅⋅M binding are largely outcompeted by electrostatic or dispersion interactions involving ligand or solvent molecules. This combined experimental and computational study provides a general understanding of metallophilic interactions and indicates that great care must be taken to avoid over-attributing the energetic significance of metallophilic interactions.

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.

Simultaneous G-Quadruplex DNA Logic.

A fundamental principle of digital computer operation is Boolean logic, where inputs and outputs are described by binary integer voltages. Similarly, inputs and outputs may be processed on the molecular level as exemplified by synthetic circuits that exploit the programmability of DNA base-pairing. Unlike modern computers, which execute large numbers of logic gates in parallel, most implementations of molecular logic have been limited to single computing tasks, or sensing applications. This work reports three G-quadruplex-based logic gates that operate simultaneously in a single reaction vessel. The gates respond to unique Boolean DNA inputs by undergoing topological conversion from duplex to G-quadruplex states that were resolved using a thioflavin T dye and gel electrophoresis. The modular, addressable, and label-free approach could be incorporated into DNA-based sensors, or used for resolving and debugging parallel processes in DNA computing applications.

Nanopore Detection of Single-Molecule Binding within a Metallosupramolecular Cage.

Guest encapsulation is a fundamental property of coordination cages. However, there is a paucity of methods capable of quantifying the dynamics of guest binding processes. Here, we demonstrate nanopore detection of single-molecule binding within metallosupramolecular cages. Real-time monitoring of the ion current flowing through a transmembrane α-hemolysin nanopore resolved the binding of different guests to both cage enantiomers. This enabled the single-molecule kinetics of guest binding to be quantified, whereas the ordering and durations of events were consistent with a guest-exchange mechanism that does not involve ligand dissociation. In addition to providing a new approach for single-molecule interrogation of dynamic supramolecular processes, this work also establishes that cage complexes which are too large to enter the nanopore can be exploited for detecting small molecules, thus constituting a new class of molecular adapter.

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.

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.

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.