Anion Binding to Ammonium and Guanidinium Hosts: Implications for the Reverse Hofmeister Effects Induced by Lysine and Arginine Residues.

Anions have a profound effect on the properties of soluble proteins. Such Hofmeister effects have implications in biologics stability, protein aggregation, amyloidogenesis, and crystallization. However, the interplay between the important noncovalent interactions (NCIs) responsible for Hofmeister effects is poorly understood. To contribute to improving this state of affairs, we report on the NCIs between anions and ammonium and guanidinium hosts 1 and 2, and the consequences of these. Specifically, we investigate the properties of cavitands designed to mimic two prime residues for anion-protein NCIs─lysines and arginines─and the solubility consequences of complex formation. Thus, we report NMR and ITC affinity studies, X-ray analysis, MD simulations, and anion-induced critical precipitation concentrations. Our findings emphasize the multitude of NCIs that guanidiniums can form and how this repertoire qualitatively surpasses that of ammoniums. Additionally, our studies demonstrate the ease by which anions can dispense with a fraction of their hydration-shell waters, rearrange those that remain, and form direct NCIs with the hosts. This raises many questions concerning how solvent shell plasticity varies as a function of anion, how the energetics of this impact the different NCIs between anions and ammoniums/guanidiniums, and how this affects the aggregation of solutes at high anion concentrations.

Buffer and Salt Effects in Aqueous Host-Guest Systems: Screening, Competitive Binding, or Both?

There are many open questions regarding the supramolecular properties of ions in water, a fact that has ramifications within any field of study involving buffered solutions. Indeed, as Pielak has noted (Buffers, Especially the Good Kind, Biochemistry, 2021, in press. DOI:10.1021/acs.biochem.1c00200) buffers were conceived of with little regard to their supramolecular properties. But there is a difficulty here; the mathematical models supramolecular chemists use for affinity determinations do not account for screening. As a result, there is uncertainty as to the magnitude of any screening effect and how this compares to competitive salt/buffer binding. Here we use a tetra-cation cavitand to compare halide affinities obtained using a traditional unscreened model and a screened (Debye-Hückel) model. The rule of thumb that emerges is that if ionic strength is changed by >1 order of magnitude─either during a titration or if a comparison is sought between two different buffered solutions─screening should be considered. We also build a competitive mathematical model showing that binding attenuation in buffer is largely due to competitive binding to the host by said buffer. For the system at hand, we find that the effect of competition is approximately twice that of the effect of screening (∼RT at 25 °C). Thus, for strong binders it is less important to account for screening than it is to account for competitive complexation, but for weaker binders both effects should be considered. We anticipate these results will help supramolecular chemists unravel the properties of buffers and so help guide studies of biomacromolecules.

Revisiting Fluorescent Calixarenes: From Molecular Sensors to Smart Materials.

Calix[n]arenes (n = 4, 5, 6, 8) are "chalicelike" phenol-based macrocycles that are among the most fascinating and highly studied scaffolds in supramolecular chemistry. This stems from the functional and tunable diversity at both their upper and lower rims, their preorganized nonpolar cavities and preorganized ion-binding sites, and their well-defined conformations. Conjugation of calixarene scaffolds with various fluorogenic groups has led to the development of smart fluorescent probes that have been utilized as molecular sensors, in bioimaging, for drug and gene delivery, in self-assembly/aggregation, and as smart materials. The fine-tuning and incorporation of different ligating sites in the calix[4]arene scaffold have produced numerous molecular sensors for cations, anions, and biomolecules. Moreover, the aqueous solubility of p-sulfonatocalix[4]arenes has engendered their potential use in drug/gene delivery and enzymatic assays. In addition, because of their strong optical properties, fluorescent calix[4]arenes have been used to develop smart materials, including gels as well as nonlinear optical, organic light-emitting diode, and multiphoton materials. Finally, significant developments in the utility of fluorescent higher calixarenes have been made for bioapplications. This review critically summarizes the recent advances made in all of these different areas.

Single Fluorinated Agent for Multiplexed 19 F-MRI with Micromolar Detectability Based on Dynamic Exchange.

The weak thermal polarization of nuclear spins limits the sensitivity of MRI, even for MR-sensitive nuclei as fluorine-19. Therefore, despite being the source of inspiration for the development of background-free MRI for various applications, including for multiplexed imaging, the inability to map very low concentrations of targets using 19 F-MRI raises the need to further enhance this platform's capabilities. Here, we employ the principles of CEST-MRI in 19 F-MRI to obtain a 900-fold signal amplification of a biocompatible fluorinated agent, which can be presented in a "multicolor" fashion. Capitalizing on the dynamic interactions in host-guest supramolecular assemblies in an approach termed GEST, we demonstrate that an inhalable fluorinated anesthetic can be used as a single 19 F-probe for the concurrent detection of micromolar levels of two targets, with potential in vivo translatability. Further extending GEST with new designs could expand the applicability of 19 F-MRI to the mapping of targets that have so-far remained non-detectable.

Intrinsic and Extrinsic Control of the pKa of Thiol Guests inside Yoctoliter Containers.

Despite decades of research, there are still many open questions surrounding the mechanisms by which enzymes catalyze reactions. Understanding all the noncovalent forces involved has the potential to allow de novo catalysis design, and as a step toward this, understanding how to control the charge state of ionizable groups represents a powerful yet straightforward approach to probing complex systems. Here we utilize supramolecular capsules assembled via the hydrophobic effect to encapsulate guests and control their acidity. We find that the greatest influence on the acidity of bound guests is the location of the acidic group within the yoctoliter space. However, the nature of the electrostatic field generated by the (remote) charged solubilizing groups also plays a significant role in acidity, as does counterion complexation to the outer surfaces of the capsules. Taken together, these results suggest new ways by which to affect reactions in confined spaces.

Electrostatic Control of Macrocyclization Reactions within Nanospaces.

The intrinsic structural complexity of proteins makes it hard to identify the contributions of each noncovalent interaction behind the remarkable rate accelerations of enzymes. Coulombic forces are evidently primary, but despite developments in artificial nanoreactor design, a picture of the extent to which these can contribute has not been forthcoming. Here we report on two supramolecular capsules that possess structurally identical inner-spaces that differ in the electrostatic potential (EP) field that envelops them: one positive and one negative. This architecture means that only changes in the EP field influence the chemical properties of encapsulated species. We quantify these influences via acidity and rates of cyclization measurements for encapsulated guests, and we confirm the primary role of Coulombic forces with a simple mathematical model approximating the capsules as Born spheres within a continuum dielectric. These results reveal the reaction rate accelerations possible under Coulombic control and highlight important design criteria for nanoreactors.

Bright G-Quadruplex Nanostructures Functionalized with Porphyrin Lanterns.

The intricate arrangement of numerous and closely placed chromophores on nanoscale scaffolds can lead to key photonic applications ranging from optical waveguides and antennas to signal-enhanced fluorescent sensors. In this regard, the self-assembly of dye-appended DNA sequences into programmed photonic architectures is promising. However, the dense packing of dyes can result in not only compromised DNA assembly (leading to ill-defined structures and precipitates) but also to essentially nonfluorescent systems (due to π-π aggregation). Here, we introduce a two-step "tether and mask" strategy wherein large porphyrin dyes are first attached to short G-quadruplex-forming sequences and then reacted with per-O-methylated ß-cyclodextrin (PMßCD) caps, to form supramolecular synthons featuring the porphyrin fluor fixed into a masked porphyrin lantern (PL) state, due to intramolecular host-guest interactions in water. The PL-DNA sequences can then be self-assembled into cyclic architectures or unprecedented G-wires tethered with hundreds of porphyrin dyes. Importantly, despite the closely arrayed PL units (∼2 nm), the dyes behave as bright chromophores (up to 180-fold brighter than the analogues lacking the PMßCD masks). Since other self-assembling scaffolds, dyes, and host molecules can be used in this modular approach, this work lays out a general strategy for the bottom-up aqueous self-assembly of bright nanomaterials containing densely packed dyes.

Dynamic Light Scattering - an all-purpose guide for the supramolecular chemist.

Dynamic light scattering (DLS) is a useful tool for the study of the solution-based behavior of colloids and molecular assemblies. The aim of this methods paper is to provide perspective on how this technique can be used by supramolecular chemists. As this technique is not extensively used within the field, we also provide a historical background of its development, summarize data interpretation and the strengths and limitations of the technique, and provide a perspective on some of the important features for supramolecular chemists that can be found in an instrument.

The thermodynamics of guest complexation to octa-acid and tetra-endo-methyl octa-acid: reference data for the sixth statistical assessment of modeling of proteins and ligands (SAMPL6).

Although computer-aided drug design has greatly improved over time, its application in the pharmaceutical industry is still limited by the accuracy of association constant predictions. Towards improving this situation, the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) is a series of community-wide blind challenges aimed to advance computational techniques as standard predictive tools in rational drug design (https://en.wikipedia.org/wiki/SAMPL_Challenge). As an empirical contribution to the sixth assessment (SAMPL6), we report here the association constant (Ka ) and thermodynamic parameters (∆G, ∆H, -T∆S) of eight guests (G0-G7) binding to two subtly different hosts (OA and TEMOA) using ITC. Both hosts contain a unique, well-defined binding pocket capable of storing guests with up to ten non-hydrogen atoms, whilst the selection of amphiphilic guests contain a range of saturated and unsaturated substituents from C6 to C10. The thermodynamic data from this study will allow the challenge participants of SAMPL6 to test the accuracy of their computational protocols for calculating host-guest affinities.

Ion-Hydrocarbon and/or Ion-Ion Interactions: Direct and Reverse Hofmeister Effects in a Synthetic Host.

A combination of 1H NMR spectroscopy, DLS, and turbidity measurements reveal that polarizable anions engender both the Hofmeister and reverse Hofmeister effects in positand 2. Host 2 possesses two principal and distinctly different binding sites: a "soft" nonpolar pocket and a "hard" crown of ammonium cations. NMR spectroscopy reveals that anion affinity to both sites is comparable, with each site showing characteristic selectivities. NMR spectroscopy also reveals that anions competitively bind to the pocket and induce the Hofmeister effect in host-guest binding at very low concentrations (∼2 mM). Furthermore, the suite of techniques utilized demonstrates that anion binding to both sites leads to charge attenuation, aggregation, and finally precipitation (the reverse Hofmeister effect). Anion-induced precipitation generally correlated with affinity, and comparisons between the free host and its adamantane carboxylate (Ada-CO2-) complex reveals that the reverse Hofmeister effect is attenuated by blocking anion binding/charge attenuation at the nonpolar pocket.

Precision Switching in a Discrete Supramolecular Assembly: Alkali Metal Ion-Carboxylate Selectivities and the Cationic Hofmeister Effect.

A cavitand host has been shown to switch from a dimeric assembly to a tetrameric assembly in the presence of cations. Induced by pseudo-specific cation binding attenuating the net negative charge of each host, switching was shown to be highly cation selective. Thus, the concentration of cation required to induce assembly switching ranged from 2 mM in the case of N(n-Bu)4+ to ∼80 mM in the case of Na+ . Overall cation affinity was found to be essentially the reverse of Collins' law of matching water affinities, which predicts Na+ to have the strongest affinity for carboxylate groups. Combined with previous data, these results highlight the point that cation affinity for carboxylates are in large part dictated by context.

Overview of the SAMPL6 host-guest binding affinity prediction challenge.

Accurately predicting the binding affinities of small organic molecules to biological macromolecules can greatly accelerate drug discovery by reducing the number of compounds that must be synthesized to realize desired potency and selectivity goals. Unfortunately, the process of assessing the accuracy of current computational approaches to affinity prediction against binding data to biological macromolecules is frustrated by several challenges, such as slow conformational dynamics, multiple titratable groups, and the lack of high-quality blinded datasets. Over the last several SAMPL blind challenge exercises, host-guest systems have emerged as a practical and effective way to circumvent these challenges in assessing the predictive performance of current-generation quantitative modeling tools, while still providing systems capable of possessing tight binding affinities. Here, we present an overview of the SAMPL6 host-guest binding affinity prediction challenge, which featured three supramolecular hosts: octa-acid (OA), the closely related tetra-endo-methyl-octa-acid (TEMOA), and cucurbit[8]uril (CB8), along with 21 small organic guest molecules. A total of 119 entries were received from ten participating groups employing a variety of methods that spanned from electronic structure and movable type calculations in implicit solvent to alchemical and potential of mean force strategies using empirical force fields with explicit solvent models. While empirical models tended to obtain better performance than first-principle methods, it was not possible to identify a single approach that consistently provided superior results across all host-guest systems and statistical metrics. Moreover, the accuracy of the methodologies generally displayed a substantial dependence on the system considered, emphasizing the need for host diversity in blind evaluations. Several entries exploited previous experimental measurements of similar host-guest systems in an effort to improve their physical-based predictions via some manner of rudimentary machine learning; while this strategy succeeded in reducing systematic errors, it did not correspond to an improvement in statistical correlation. Comparison to previous rounds of the host-guest binding free energy challenge highlights an overall improvement in the correlation obtained by the affinity predictions for OA and TEMOA systems, but a surprising lack of improvement regarding root mean square error over the past several challenge rounds. The data suggests that further refinement of force field parameters, as well as improved treatment of chemical effects (e.g., buffer salt conditions, protonation states), may be required to further enhance predictive accuracy.

The aqueous supramolecular chemistry of cucurbit[n]urils, pillar[n]arenes and deep-cavity cavitands.

This tutorial review summarizes the continuing exploration of three prominent water-soluble hosts: cucurbiturils, pillar[n]arenes and deep-cavity cavitands. As we describe, these hosts are revealing how orchestrating the hydrophobic effect can lead to a broad range of properties and applications, from: nano-reactors, supramolecular polymers, stimuli-responsive biointerfaces, switches, and novel purification devices. We also describe how their study is also revealing more details about the properties of water and aqueous solutions.

Dynamic light scattering studies of the effects of salts on the diffusivity of cationic and anionic cavitands.

Although alkali halide salts play key roles in all living systems, the physical models used to describe the properties of aqueous solutions of salts do not take into account specific ion-ion interactions. To identify specific ion-ion interactions possibly contributing to the aggregation of proteins, we have used dynamic light scattering (DLS) to probe the aggregation of charged cavitands. DLS measurements of negatively charged 1 in the presence of a range of alkali metal halides reveal no significant aggregation of host 1 as a function of the nature of the cation of the added salt. Only at high concentrations could trace amounts of aggregation be detected by 1H NMR spectroscopy. Contrarily, 1 was readily aggregated and precipitated by ZnCl2. In contrast, although fluoride and chloride did not induce aggregation of positively charged host 2, this cavitand exhibited marked aggregation as a function of bromide and iodide concentration. Specifically, bromide induced small but significant amounts of dimerization, whilst iodide induced extreme aggregation. Moreover, in these cases aggregation of host 2 also exhibited a cationic dependence, with an observed trend Na+ > Li+ > K+ ≈ Cs+. In combination, these results reveal new details of specific ion pairings in aqueous solution and how this can influence the properties of dissolved organics.

Molecular Shape and the Hydrophobic Effect.

This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins.

Mapping the Binding Motifs of Deprotonated Monounsaturated Fatty Acids and Their Corresponding Methyl Esters within Supramolecular Capsules.

A suite of NMR techniques revealed that a cavitand (1) formed 2:1 host-guest complexes with a range of monounsaturated fatty carboxylates and their corresponding methyl esters. All of the carboxylates bound to the capsule in a J-shaped motif with the carboxylate at the equatorial region of the dimeric capsule, and the reverse turn of the chain and the methyl terminal in each polar region of the host. Guest exchange was slow on the NMR time scale, while tumbling was slow or close to the NMR time scale depending on the position and stereochemistry of the double bond. In contrast, the methyl esters were found to bind in three motifs depending on the position and stereochemistry of the double bond. Thus, the esters were observed to bind in a J-shaped, U-shaped (the turn in the guest occupying a polar region and the two termini competing for occupancy of the other pole), or a reverse J-shaped motif (ester moiety and turn each occupying a pole and the methyl terminal located near the equator). Relative binding constant (Krel) determinations revealed that the affinity for the capsule was dependent on the position and stereochemistry of the double bond.

Binding of carboxylate and trimethylammonium salts to octa-acid and TEMOA deep-cavity cavitands.

In participation of the fifth statistical assessment of modeling of proteins and ligands (SAMPL5), the strength of association of six guests (3-8) to two hosts (1 and 2) were measured by 1H NMR and ITC. Each host possessed a unique and well-defined binding pocket, whilst the wide array of amphiphilic guests possessed binding moieties that included: a terminal alkyne, nitro-arene, alkyl halide and cyano-arene groups. Solubilizing head groups for the guests included both positively charged trimethylammonium and negatively charged carboxylate functionality. Measured association constants (K a ) covered five orders of magnitude, ranging from 56 M-1 for guest 6 binding with host 2 up to 7.43 × 106 M-1 for guest 6 binding to host 1.

Quantifying Guest Exchange in Supramolecular Systems.

The ability to accurately determine and quantitatively evaluate kinetic phenomena associated with supramolecular assemblies, in real time, is key to a better understanding of their defined architectures and diverse functionalities. Therefore, analytical tools that can precisely assess a wide range of exchange rates within such systems are of considerable importance. This study demonstrates the ability to use an NMR approach based on saturation transfer for the determination of rates of guest exchange from molecular capsules. By using cavitands that assemble into distinct dimeric assemblies, we show that this approach, which we term guest exchange saturation transfer (GEST), allows the use of a conventional NMR setup to study and quantitatively assess a wide range of exchange rates, from 35 to more than 5000 s-1 .

Binding Hydrated Anions with Hydrophobic Pockets.

Using a combination of isothermal titration calorimetry and quantum and molecular dynamics calculations, we demonstrate that relatively soft anions have an affinity for hydrophobic concavity. The results are consistent with the anions remaining partially hydrated upon binding, and suggest a novel strategy for anion recognition.

ITC and NMR Analysis of the Encapsulation of Fatty Acids within a Water-Soluble Cavitand and its Dimeric Capsule.

We report here NMR and ITC studies of the binding of ionizable guests (carboxylate acids) to a deep-cavity cavitand. These studies reveal that the shortest guests favored 1:1 complex formation, but the longer the alkyl chain the more the 2:1 host-guest capsule is favored. For intermediate-sized guests, the equilibrium between these two states is controlled by pH; at low values the capsule containing the carboxylic acid guest is favored, whereas as the pH is raised deprotonation of the guest favors the 1:1 complex. Interestingly, for one host-guest pair the energy required to de-cap the 2:1 capsular complex and form the 1:1 complex is sufficient to shift the pKa of the guest by ~ 3-4 orders of magnitude (4.1-5.4 kcal mol-1). The two largest guests examined form stable 2:1 capsules, with in both cases the guest adopting a relatively high energy J-shaped motif. Furthermore, these 2:1 complexes are sufficiently stable that at high pH guest deprotonation occurs without de-capping of the capsule.