Structural characterisation methods for supramolecular chemistry that go beyond crystallography

Exploring the Conformational Landscape of Poly(l-lysine) Dendrimers Using Ion Mobility Mass Spectrometry

Ion mobility mass spectrometry (IM-MS) measures the mass, size, and shape of ions in the same experiment, and structural information is provided via collision cross-section (CCS) values. The majority of commercially available IM-MS instrumentation relies on the use of CCS calibrants, and here, we present data from a family of poly(l-lysine) dendrimers and explore their suitability for this purpose. In order to test these compounds, we employed three different IM-MS platforms (Agilent 6560 IM-QToF, Waters Synapt G2, and a home-built variable temperature drift tube IM-MS) and used them to investigate six different generations of dendrimers in two buffer gases (helium and nitrogen). Each molecule gives a highly discrete CCS distribution suggestive of single conformers for each m/z value. The DTCCSN2 values of this series of molecules (molecular weight: 330-16,214 Da) range from 182 to 2941 Å2, which spans the CCS range that would be found by many synthetic molecules including supramolecular compounds and many biopolymers. The CCS values for each charge state were highly reproducible in day-to-day analysis on each instrument, although we found small variations in the absolute CCS values between instruments. The rigidity of each dendrimer was probed using collisionally activated and high-temperature IM-MS experiments, where no evidence for a significant CCS change ensued. Taken together, this data indicates that these polymers are candidates for CCS calibration and could also help to reconcile differences found in CCS measurements on different instrument geometries.

Modern Electrospray Ionization Mass Spectrometry Techniques for the Characterization of Supramolecules and Coordination Compounds

Mass spectrometry is routinely used for myriad applications in clinical, industrial, and research laboratories worldwide. Developments in the areas of ionization sources, high-resolution mass analyzers, tandem mass spectrometry, and ion mobility have significantly extended the repertoire of mass spectrometrists; however, for coordination compounds and supramolecules, mass spectrometry remains underexplored and arguably underappreciated. Here, the reader is guided through different tools of modern electrospray ionization mass spectrometry that are suitable for larger inorganic complexes. All steps, from sample preparation and technical details to data analysis and interpretation are discussed. The main target audience of this tutorial is synthetic chemists as well as technicians/mass spectrometrists with little experience in characterizing labile inorganic compounds.

Structural studies of supramolecular complexes and assemblies by ion mobility mass spectrometry

Recent advances in instrumentation and development of computational strategies for ion mobility mass spectrometry (IM-MS) studies have contributed to an extensive growth in the application of this analytical technique to comprehensive structural description of supramolecular systems. Apart from the benefits of IM-MS for interrogation of intrinsic properties of noncovalent aggregates in the experimental gas-phase environment, its merits for the description of native structural aspects, under the premises of having maintained the noncovalent interactions innate upon the ionization process, have attracted even more attention and gained increasing interest in the scientific community. Thus, various types of supramolecular complexes and assemblies relevant for biological, medical, material, and environmental sciences have been characterized so far by IM-MS supported by computational chemistry. This review covers the state-of-the-art in this field and discusses experimental methods and accompanying computational approaches for assessing the reliable three-dimensional structural elucidation of supramolecular complexes and assemblies by IM-MS.

Studying Cation Exchange in {Cr7Co} Pseudorotaxanes: Preparatory Studies for Making Hybrid Molecular Machines

In the design of dynamic supramolecular systems used in molecular machines, it is important to understand the binding preferences between the macrocycle and stations along the thread. Here, we apply 1H NMR spectroscopy to investigate the relative stabilities of a series of linear alkylammonium templated pseudorotaxanes with the general formula [H2NRR'][Cr7CoF8(O2CCH2 tBu)16] by exchanging the cation in solution. Our results show that the pseudorotaxanes are able to exchange threads via a dissociative mechanism. The position of equilibrium is dependent upon the ammonium cation and solvent used. Short chain primary ammonium cations are shown to be far less favourable macrocycle stations than secondary ammonium cations. Collision-induced dissociation mass spectrometry (CID-MS) has been used to look at disassembly of the pseudorotaxanes in a solvent-free environment and stability trends compared to those in acetone-d6. The energy needed to induce 50 % of the precursor ion loss (E50) is used and shows a similar trend to the equilibria measured by NMR. The relative stabilities of these hybrid inorganic-organic pseudo-rotaxanes are different to those of host-guest compounds involving crown ethers and this may be valuable for the design of molecular machines.

Ion Mobility Mass Spectrometry for Large Synthetic Molecules: Expanding the Analytical Toolbox

Understanding the composition, structure and stability of larger synthetic molecules is crucial for their design, yet currently the analytical tools commonly used do not always provide this information. In this perspective, we show how ion mobility mass spectrometry (IM-MS), in combination with tandem mass spectrometry, complementary techniques and computational methods, can be used to structurally characterize synthetic molecules, make and predict new complexes, monitor disassembly processes and determine stability. Using IM-MS, we present an experimental and computational framework for the analysis and design of complex molecular architectures such as (metallo)supramolecular cages, nanoclusters, interlocked molecules, rotaxanes, dendrimers, polymers and host-guest complexes.

Automated Structural Activity Screening of β-Diketonate Assemblies with High-Throughput Ion Mobility-Mass Spectrometry

Embracing complexity in design, metallo-supramolecular self-assembly presents an opportunity for fabricating materials of economic significance. The array of accessible supramolecules is alluring, along with favourable energy requirements. Implementation is hampered by an inability to efficiently characterise complex mixtures. The stoichiometry, size, shape, guest binding properties and reactivity of individual components and combinations thereof are inherently challenging to resolve. A large combinatorial library of four transition metals (Fe, Cu, Ni and Zn), and six β-diketonate ligands at different molar ratios and pH was robotically prepared and directly analysed over multiple timepoints with electrospray ionisation travelling wave ion mobility-mass spectrometry. The dataset was parsed for self-assembling activity without first attempting to structurally assign individual species. Self-assembling systems were readily categorised without manual data-handling, allowing efficient screening of self-assembly activity. This workflow clarifies solution phase supramolecular assembly processes without manual, bottom-up processing. The complex behaviour of the self-assembling systems was reduced to simpler qualities, which could be automatically processed.

Hexanuclear Ln6 L6 Complex Formation by Using an Unsymmetric Ligand

Multinuclear, self-assembled lanthanide complexes present clear opportunities as sensors and imaging agents. Despite the widely acknowledged potential of this class of supramolecule, synthetic and characterization challenges continue to limit systematic studies into their self-assembly restricting the number and variety of lanthanide architectures reported relative to their transition metal counterparts. Here we present the first study evaluating the effect of ligand backbone symmetry on multinuclear lanthanide complex self-assembly. Replacement of a symmetric ethylene linker with an unsymmetric amide at the center of a homoditopic ligand governs formation of an unusual Ln6 L6 complex with coordinatively unsaturated metal centers. The choice of triflate as a counterion, and the effect of ionic radii are shown to be critical for formation of the Ln6 L6 complex. The atypical Ln6 L6 architecture is characterized using a combination of mass spectrometry, luminescence, DOSY NMR and EPR spectroscopy measurements. Luminescence experiments support clear differences between comparable Eu6 L6 and Eu2 L3 complexes, with relatively short luminescent lifetimes and low quantum yields observed for the Eu6 L6 structure indicative of non-radiative decay processes. Synthesis of the Gd6 L6 analogue allows three distinct Gd⋯Gd distance measurements to be extracted using homo-RIDME EPR experiments.

Hydrogen atoms in supramolecular chemistry: a structural perspective. Where are they, and why does it matter?

Hydrogen bonding interactions are ubiquitous across the biochemical and chemical sciences, and are of particular interest to supramolecular chemists. They have been used to assemble hydrogen bonded polymers, cages and frameworks, and are the functional motif in many host-guest systems. Single crystal X-ray diffraction studies are often used as a key support for proposed structures, although this presents challenges as hydrogen atoms interact only weakly with X-rays. In this Tutorial Review, we discuss the information that can be gleaned about hydrogen bonding interactions through crystallographic experiments, key limitations of the data, and emerging techniques to overcome these limitations.

Regulating supramolecular interactions in dimeric macrocycles

Supramolecular behavior is highly dependent on many factors, including complicated microenvironments and weak interactions. Herein, we describe tuning supramolecular architectures of rigid macrocycles by synergistic effects of their geometric configurations, sizes, and guests. Two paraphenylene-based macrocycles are anchored onto different positions in a triphenylene derivative, resulting in dimeric macrocycles with different shapes and configurations. Interestingly, these dimeric macrocycles show tunable supramolecular interactions with guests. In solid state, a 2 : 1 host-guest complex was observed between 1a and C₆₀/C₇₀, while an unusual 2 : 3 host-guest complex 3C₆₀@(1b)₂ can be observed between 1b and C₆₀. This work expands the scope of the synthesis of novel rigid bismacrocycles and provides a new strategy to construct different supramolecular systems.

Supramolecular Chemistry of Carbon-Based Dots Offers Widespread Opportunities

Carbon dots are an emerging class of nanomaterials that has recently attracted considerable attention for applications that span from biomedicine to energy. These photoluminescent carbon nanoparticles are defined by characteristic sizes of <10 nm, a carbon-based core and various functional groups at their surface. Although the surface groups are widely used to establish non-covalent bonds (through electrostatic interactions, coordinative bonds, and hydrogen bonds) with various other (bio)molecules and polymers, the carbonaceous core could also establish non-covalent bonds (ππ stacking or hydrophobic interactions) with π-extended or apolar compounds. The surface functional groups, in addition, can be modified by various post-synthetic chemical procedures to fine-tune the supramolecular interactions. Our contribution categorizes and analyzes the interactions that are commonly used to engineer carbon dots-based materials and discusses how they have allowed preparation of functional assemblies and architectures used for sensing, (bio)imaging, therapeutic applications, catalysis, and devices. Using non-covalent interactions as a bottom-up approach to prepare carbon dots-based assemblies and composites can exploit the unique features of supramolecular chemistry, which include adaptability, tunability, and stimuli-responsiveness due to the dynamic nature of the non-covalent interactions. It is expected that focusing on the various supramolecular possibilities will influence the future development of this class of nanomaterials.

Influence of β-Cyclodextrin Methylation on Host-Guest Complex Stability: A Theoretical Study of Intra- and Intermolecular Interactions as Well as Host Dimer Formation

Understanding the non-covalent interactions in host-guest complexes is crucial to their stability, design and applications. Here, we use density functional theory to compare the ability of β-cyclodextrin (β-CD) and heptakis(2,6-di-O-methyl)-β-cyclodextrin (DM-β-CD) to encapsulate the model guest phenol. For both macrocycles, we quantify the intramolecular interactions before and after the formation of the complex, as well as the intermolecular host-guest and host-host dimer interactions. These are individually classified as van der Waals interactions or hydrogen bonds, respectively. The results show a stronger intramolecular binding energy of β-CD, with the absolute difference being −5.53 kcal/mol relative to DM-β-CD. Consequently, the intermolecular interactions of both cyclodextrins with phenol are affected, such that the free binding energy calculated for the DM-β-CD/phenol complex (−5.23 kcal/mol) is ≈50% more negative than for the complex with β-CD (−2.62 kcal/mol). The latter is in excellent agreement with the experimental data (−2.69 kcal/mol), which validates the level of theory (B97-3c) used. Taken together, the methylation of β-CD increases the stability of the host-guest complex with the here studied guest phenol through stronger van der Waals interactions and hydrogen bonds. We attribute this to the disruption of the hydrogen bond network in the primary face of β-CD upon methylation, which influences the flexibility of the host toward the guest as well as the strength of the intermolecular interactions. Our work provides fundamental insights into the impact of different non-covalent interactions on host-guest stability, and we suggest that this theoretical framework can be adapted to other host-guest complexes to evaluate and quantify their non-covalent interactions.

Adduct Ions as Diagnostic Probes of Metallosupramolecular Complexes Using Ion Mobility Mass Spectrometry

Following electrospray ionization, it is common for analytes to enter the gas phase accompanied by a charge-carrying ion, and in most cases, this addition is required to enable detection in the mass spectrometer. These small charge carriers may not be influential in solution but can markedly tune the analyte properties in the gas phase. Therefore, measuring their relative influence on the target molecule can assist our understanding of the structure and stability of the analyte. As the formed adducts are usually distinguishable by their mass, differences in the behavior of the analyte resulting from these added species (e.g., structure, stability, and conformational dynamics) can be easily extracted. Here, we use ion mobility mass spectrometry, supported by density functional theory, to investigate how charge carriers (H⁺, Na⁺, K⁺, and Cs⁺) as well as water influence the disassembly, stability, and conformational landscape of the homometallic ring [Cr₈F₈(O₂C^tBu)₁₆] and the heterometallic rotaxanes [NH₂RR'][Cr₇MF₈(O₂C^tBu)₁₆], where M = Mn^II, Fe^II, Co^II, Ni^II, Cu^II, Zn^II, and Cd^II. The results yield new insights on their disassembly mechanisms and support previously reported trends in cavity size and transition metal properties, demonstrating the potential of adduct ion studies for characterizing metallosupramolecular complexes in general.

Intermolecular contributions, filtration effects and signal composition of SIFTER (single-frequency technique for refocusing)

To characterize structure and molecular order in the nanometre range, distances between electron spins and their distributions can be measured via dipolar spin-spin interactions by different pulsed electron paramagnetic resonance experiments. Here, for the single-frequency technique for refocusing dipolar couplings (SIFTER), the buildup of dipolar modulation signal and intermolecular contributions is analysed for a uniform random distribution of monoradicals and biradicals in frozen glassy solvent by using the product operator formalism for electron spin S = 1 / 2 . A dipolar oscillation artefact appearing at both ends of the SIFTER time trace is predicted, which originates from the weak coherence transfer between biradicals. The relative intensity of this artefact is predicted to be temperature independent but to increase with the spin concentration in the sample. Different compositions of the intermolecular background are predicted in the case of biradicals and in the case of monoradicals. Our theoretical account suggests that the appropriate procedure of extracting the intramolecular dipolar contribution (form factor) requires fitting and subtracting the unmodulated part, followed by division by an intermolecular background function that is different in shape. This scheme differs from the previously used heuristic background division approach. We compare our theoretical derivations to experimental SIFTER traces for nitroxide and trityl monoradicals and biradicals. Our analysis demonstrates a good qualitative match with the proposed theoretical description. The resulting perspectives for a quantitative analysis of SIFTER data are discussed.

Light-switched selective catalysis with NADH mimic functionalized metal-organic capsules

By incorporating an active site model of nicotinamide adenine dinucleotide (NADH) as an electron regulator, a redox-active metal-organic capsule as an efficient photocatalyst was obtained for the light switchable synthesis of a series of aromatic azoxy and amino compounds from their corresponding nitroaromatics under either purple (420 nm) or blue (455 nm) LED light irradiation.

Disassembly Mechanisms and Energetics of Polymetallic Rings and Rotaxanes

Understanding the fundamental reactivity of polymetallic complexes is challenging due to the complexity of their structures with many possible bond breaking and forming processes. Here, we apply ion mobility mass spectrometry coupled with density functional theory to investigate the disassembly mechanisms and energetics of a family of heterometallic rings and rotaxanes with the general formula [NH₂RR'][Cr₇MF₈(O₂C^tBu)₁₆] with M = Mn^II, Fe^II, Co^II, Ni^II, Cu^II, Zn^II, Cd^II. Our results show that their stability can be tuned both by altering the d-metal composition in the macrocycle and by the end groups of the secondary ammonium cation [NH₂RR']⁺. Ion mobility probes the conformational landscape of the disassembly process from intact complex to structurally distinct isobaric fragments, providing unique insights to how a given divalent metal tunes the structural dynamics.

Seeing the complete picture: proteins in top-down mass spectrometry

Top-down protein mass spectrometry can provide unique insights into protein sequence and structure, including precise proteoform identification and study of protein–ligand and protein–protein interactions. In contrast with the commonly applied bottom-up approach, top-down approaches do not include digestion of the protein of interest into small peptides, but instead rely on the ionization and subsequent fragmentation of intact proteins. As such, it is fundamentally the only way to fully characterize the composition of a proteoform. Here, we provide an overview of how a top-down protein mass spectrometry experiment is performed and point out recent applications from the literature to the reader. While some parts of the top-down workflow are broadly applicable, different research questions are best addressed with specific experimental designs. The most important divide is between studies that prioritize sequence information (i.e., proteoform identification) versus structural information (e.g., conformational studies, or mapping protein–protein or protein–ligand interactions). Another important consideration is whether to work under native or denaturing solution conditions, and the overall complexity of the sample also needs to be taken into account, as it determines whether (chromatographic) separation is required prior to MS analysis. In this review, we aim to provide enough information to support both newcomers and more experienced readers in the decision process of how to answer a potential research question most efficiently and to provide an overview of the methods that exist to answer these questions.

Cyclodextrin-pillar[n]arene hybridized macrocyclic systems

Cyclodextrin (CD) and pillar[n]arene are significant macrocyclic host molecules in supramolecular chemistry, and have either similar or contrasting physicochemical properties, for example, both can provide capable cavities available for recognizing various favorite guest molecules, while they usually possess different solubility in aqueous solutions, and exhibit diverse chiral characteristics. To balance their similarity and differences inherited from each chemical structure and incorporate both advantages, the CD-pillar[n]arene hybrid macrocyclic system was recently developed. In this review, we will focus on the preparation and application of CD-pillar[n]arene hybrid macrocyclic systems. Both noncovalent interactions and covalent bonds were employed in the synthesis strategies of building the hybrid macrocyclic system, which was in the form of host-guest inclusion, self-assembly, conjugated molecules, and polymeric structures. Furthermore, the CD-pillar[n]arene hybrid macrocyclic system has been primarily applied for the removal of organic pollutants from water, induced chirality, as well as photocatalysis due to the integration of both cavities from CD and pillar[n]arene as hybrid hosts and chiral characteristics inherited from their chemical structures.

Metallosupramolecular cages: from design principles and characterisation techniques to applications

Although metallosupramolecular cages are self-assembled from seemingly simple building blocks, metal ions and organic ligands, architectures of increasingly large size and complexity are accessible and exploited in applications from catalysis to the stabilisation of reactive species. This Tutorial Review gives an introduction to the principles for designing metallosupramolecular cages and highlights advances in the design of large and lower symmetry cages. The characterisation and identification of cages relies on a number of complementary techniques with NMR spectroscopy, mass spectrometry, X-ray crystallography and computational methods being the focus of this review. Finally, examples of cages are discussed where these design principles and characterisation techniques are put into practice for an application or function of the cage.