Overcoming barriers with non-covalent interactions: supramolecular recognition of adamantyl cucurbit[n]uril assemblies for medical applications.

Adamantane, a staple in medicinal chemistry, recently became a cornerstone of a supramolecular host-guest drug delivery system, ADA/CB[n]. Owing to a good fit between the adamantane cage and the host cavity of the cucurbit[n]uril macrocycle, formed strong inclusion complexes find applications in drug delivery and controlled drug release. Note that the cucurbit[n]uril host is not solely a delivery vehicle of the ADA/CB[n] system but rather influences the bioactivity and bioavailability of drug molecules and can tune drug properties. Namely, as host-guest interactions are capable of changing the intrinsic properties of the guest molecule, inclusion complexes can become more soluble, bioavailable and more resistant to metabolic conditions compared to individual non-complexed molecules. Such synergistic effects have implications for practical bioapplicability of this complex system and provide a new viewpoint to therapy, beyond the traditional single drug molecule approach. By achieving a balance between guest encapsulation and release, the ADA/CB[n] system has also found use beyond just drug delivery, in fields like bioanalytics, sensing assays, bioimaging, etc. Thus, chemosensing in physiological conditions, indicator displacement assays, in vivo diagnostics and hybrid nanostructures are just some recent examples of the ADA/CB[n] applicability, be it for displacements purposes or as cargo vehicles.

Direct in situ measurement of polymorphic transition temperatures under thermo-mechanochemical conditions.

For the first time, we directly measured the onset and completion temperatures of polymorphic transitions under thermo-mechanochemical conditions by simultaneous in situ synchrotron powder X-ray diffraction and temperature monitoring. We determined the thermo-mechanochemical polymorphic transition temperature in 1-adamantyl-1-diamantyl ether to be 31 °C lower than the transition temperature determined by DSC. Our findings highlight the uniqueness of thermo-mechanochemical conditions, with potential applications in polymorph screening.

Increasing Complexity in Adamantyl Thioethers Characterized by Rotational Spectroscopy.

We report on the synthesis and characterization using high-resolution rotational spectroscopy of three bulky thioethers that feature an adamantyl group connected to a sulfur atom. Detailed experimental and theoretical structures are provided and compared with the 1,1'-diadamantyl ether. In addition, we expand on previous findings concerning microsolvation of adamantyl derivatives by investigating the cluster formation between these thioethers and a water molecule. The investigation of such clusters provides valuable insights into the sulfur-centered hydrogen bonding in thioethers with increasing size and steric repulsion.

Nanostructured supramolecular networks from self-assembled diamondoid molecules under ultracold conditions.

Diamondoid molecules and their derivatives have attracted attention as fascinating building blocks for advanced functional materials. Depending on the balance between hydrogen bonds and London dispersion interactions, they can self-organize in different cluster structures with functional groups tailored for various applications. Here, we present a new approach to supramolecular aggregation where self-assembly of diamondoid acids and alcohols in the ultracold environment of superfluid helium nanodroplets (HNDs) was analyzed by a combination of time-of-flight mass spectrometry and computational tools. Experimentally observed magic numbers of the assembled cluster sizes were successfully identified and computed cluster structures gave valuable insights into a different conglomeration mode when compared to previously explored less-polar diamondoid derivatives. We have confirmed that functional groups acting as good hydrogen bond donors completely take over the self-organization process, resulting in fascinating pair-wise or cyclic supramolecular assemblies. Particularly noteworthy is that mono- and bis-substituted diamondoid derivatives of both series engage in completely different modes of action, which is reflected in differing non-covalent cluster geometries. Additionally, formed cyclic clusters with a polar cavity in the center and a non-polar diamondoid outer layer can be of high interest in porous material design and provide insights into the structural requirements needed to produce bulk materials with desired properties.

Diamondoid ether clusters in helium nanodroplets.

Diamondoid ethers were introduced into superfluid helium nanodroplets and the resulting clusters were analyzed by time-of-flight mass spectrometry. Clusters of higher abundances (magic number clusters) were identified and the corresponding potential cluster geometries were obtained from GFN2-xTB and DFT computations. We found that the studied diamondoid ethers readily self-assemble in helium nanodroplets and that London dispersion attraction between hydrocarbon subunits acts as a driving force for cluster formation. On the other hand, hydrogen bonding between ether oxygens and trace water molecules fosters the eventual breakdown of the initial supramolecular aggregate.

Preparation and characterization of non-aromatic ether self-assemblies on a HOPG surface.

On-surface self-assemblies of aromatic organic molecules have been widely investigated, but the characterization of analogous self-assemblies consisting of fully sp3-hybridized molecules remains challenging. The possible on-surface orientations of alkyl molecules not exclusively comprised of long alkyl chains are difficult to distinguish because of their inherently low symmetry and non-planar nature. Here, we present a detailed study of diamondoid ethers, structurally rigid and fully saturated molecules, which form uniform 2D monolayers on a highly oriented pyrolytic graphite (HOPG) surface. Using scanning tunneling microscopy, various computational tools, and x-ray structural analysis, we identified the most favorable on-surface orientations of these rigid ethers and accounted for the forces driving the self-organization process. The influence of the oxygen atom and London dispersion interactions were found to be responsible for the formation of the observed highly ordered 2D ether assemblies. Our findings provide insight into the on-surface properties and behavior of non-aromatic organic compounds and broaden our understanding of the phenomena characteristic of monolayers consisting of non-planar molecules.

Photogeneration of quinone methide from adamantylphenol in an ultrafast non-adiabatic dehydration reaction.

The ultrafast photochemical reaction of quinone methide (QM) formation from adamantylphenol was monitored in real time using femtosecond transient absorption spectroscopy and fluorescence upconversion in solution at room temperature. Experiments were complemented by theoretical studies simulating the reaction pathway and elucidating its mechanism. Excitation with sub-20 fs UV pulses and broadband probing revealed ultrafast formation of the long-lived QM intermediate directly in the ground state, occurring with a time constant of around 100 fs. UV-vis transient absorption data covering temporal dynamics from femtoseconds to hundreds of milliseconds revealed persistence of the absorption band assigned to QM and partially overlapped with other contributions tentatively assigned to triplet excited states of the adamantyl derivative and the phenoxyl radical that are clearly distinguished by their evolution on different time scales. Our data, together with the computations, provide evidence of a non-adiabatic photodehydration reaction, which leads to the formation of QM in the ground state via a conical intersection, circumventing the generation of a transient QM excited state.

London dispersion dominating diamantane packing in helium nanodroplets.

Diamantane clusters formed inside superfluid helium nanodroplets were analyzed by time-of-flight mass spectrometry. Distinct cluster sizes were identified as "magic numbers" and the corresponding feasible structures for clusters consisting of up to 19 diamantane molecules were derived from meta-dynamics simulations and subsequent DFT computations. The obtained interaction energies were attributed to London dispersion attraction. Our findings demonstrate that diamantane units readily form assemblies even at low pressures and near-zero Kelvin temperatures, confirming the importance of the intermolecular dispersion effect for condensation of matter.

Do Docking Sites Persist Upon Fluorination? The Diadamantyl Ether-Aromatics Challenge for Rotational Spectroscopy and Theory.

Fluorinated derivatives of biological molecules have proven to be highly efficient at modifying the biological activity of a given protein through changes in the stability and the kind of docking interactions. These interactions can be hindered or facilitated based on the hydrophilic/hydrophobic character of a particular protein region. Diadamantyl ether (C20 H30 O) possesses both kinds of docking sites, serving as a good template to model these important contacts with aromatic fluorinated counterparts. In this work, an experimental study on the structures of several complexes between diadamantyl ether and benzene as well as a series of fluorinated benzenes is reported to analyze the effect of H→F substitution on the interaction and structure of the resulting molecular clusters using rotational spectroscopy. All experimentally observed complexes are largely dominated by London dispersion interactions with the hydrogen-terminated surface areas of diadamantyl ether. Already single substitution of one hydrogen atom with fluorine changes the preferred docking site of the complexes. However, the overall contributions of the different intermolecular interactions are similar for the different complexes, contrary to previous studies focusing on the difference in interactions using fluorinated and non-fluorinated molecules.

London Dispersion and Hydrogen-Bonding Interactions in Bulky Molecules: The Case of Diadamantyl Ether Complexes.

Diadamantyl ether (DAE, C20 H30 O) represents a good model to study the interplay between London dispersion and hydrogen-bond interactions. By using broadband rotational spectroscopy, an accurate experimental structure of the diadamantyl ether monomer is obtained and its aggregates with water and a variety of aliphatic alcohols of increasing size are analyzed. In the monomer, C-H⋅⋅⋅H-C London dispersion attractions between the two adamantyl subunits further stabilize its structure. Water and the alcohol partners bind to diadamantyl ether through hydrogen bonding and non-covalent Owater/alcohol ⋅⋅⋅H-CDAE and C-Halcohol ⋅⋅⋅H-CDAE interactions. Electrostatic contributions drive the stabilization of all the complexes, whereas London dispersion interactions become more pronounced with increasing size of the alcohol. Complexes with dominant dispersion contributions are significantly higher in energy and were not observed in the experiment. The results presented herein shed light on the first steps of microsolvation and aggregation of molecular complexes with London dispersion energy donor (DED) groups and the kind of interactions that control them.

Lipophilic Guanylhydrazone Analogues as Promising Trypanocidal Agents: An Extended SAR Study.

In this report, we extend the SAR analysis of a number of lipophilic guanylhydrazone analogues with respect to in vitro growth inhibition of Trypanosoma brucei and Trypanosoma cruzi. Sleeping sickness and Chagas disease, caused by the tropical parasites T. brucei and T. cruzi, constitute a significant socioeconomic burden in low-income countries of sub-Saharan Africa and Latin America, respectively. Drug development is underfunded. Moreover, current treatments are outdated and difficult to administer, while drug resistance is an emerging concern. The synthesis of adamantane-based compounds that have potential as antitrypanosomal agents is extensively reviewed. The critical role of the adamantane ring was further investigated by synthesizing and testing a number of novel lipophilic guanylhydrazones. The introduction of hydrophobic bulky substituents onto the adamantane ring generated the most active analogues, illustrating the synergistic effect of the lipophilic character of the C1 side chain and guanylhydrazone moiety on trypanocidal activity. The n-decyl C1-substituted compound G8 proved to be the most potent adamantane derivative against T. brucei with activity in the nanomolar range (EC50=90 nM). Molecular simulations were also performed to better understand the structure-activity relationships between the studied guanylhydrazone analogues and their potential enzyme target.

Formation of Quinone Methides by Ultrafast Photodeamination: A Spectroscopic and Computational Study.

Formation of quinone methides (QMs) by photoelimination of an ammonium salt from cresol derivatives was investigated by femtosecond transient absorption spectroscopy (fs-TA) and computationally by time-dependent density functional theory using the PCM(water)/(TD-)B3LYP/6-311++G(d,p) level of theory. The photoelimination takes place in an adiabatic ultrafast reaction on the S1 potential energy surface delivering the corresponding QMs(S1), which were detected by fs-TA. Computations predicted a high-energy cation intermediate in the pathway between the Franck-Condon state of a monoammonium salt and the corresponding QM(S1) that was not detected by fs-TA. On the other hand, elimination from a disalt in H2O takes place in one step, giving directly the QM(S1). The combined experimental and theoretical investigation fully disclosed the formation of QMs by the deamination reaction mechanism, which is important in the application of cresols or similar molecules in biological systems.

Photoelimination of nitrogen from adamantane and pentacycloundecane (PCU) diazirines: a spectroscopic study and supramolecular control.

Photochemical reactivity of pentacycloundecane (PCU) and adamantane diazirines was investigated by preparative irradiation in different solvents, laser flash photolysis (LFP) and quantum chemical computations. In addition, formation of inclusion complexes for diazirines with cucurbit[7]uril, ß- and γ-cyclodextrin (ß- and γ-CD) was investigated by 1H NMR spectroscopy, isothermal microcalorimetry and circular dichroism spectroscopy, followed by the investigation of photochemical reactivity of the formed complexes. Diazirines undergo efficient photochemical elimination of nitrogen (ΦR > 0.5) and deliver the corresponding singlet carbenes. Singlet carbenes react in intra- and intermolecular reactions and we found a rare singlet carbene pathway in CH3OH involving protonation and formation of a carbocation, detected due to the specific rearrangement of the pentacycloundecane skeleton. Singlet diazirines undergo intersystem crossing and deliver triplet carbenes that react with oxygen to form ketones which were isolated after irradiation. Our main finding is that the formation of diazirine inclusion complexes with ß-CD and γ-CD changes the relative ratio of singlet vs. triplet pathways, with singlet carbene products being dominant from the chemistry of the irradiated complexes. Our combined theoretical and experimental studies provide new insights into the supramolecular control of carbene reactivity which has possible applications for the control of product distribution by solvent effects and the choice of constrained media.

Functional self-assembled nanovesicles based on ß-cyclodextrin, liposomes and adamantyl guanidines as potential nonviral gene delivery vectors.

Multicomponent self-assembled supramolecular nanovesicles based on an amphiphilic derivative of ß-cyclodextrin and phosphatidylcholine liposomes (PC-liposomes) functionalized with four structurally different adamantyl guanidines were prepared and characterized. Incorporation efficiency of the examined adamantyl guanidines as well as size and surface charge of the prepared supramolecular nanovesicles was determined. Changes in the surface charge of the prepared nanovesicles confirmed that guanidinium groups were exposed on the surface. ITC and 1H NMR spectroscopy complemented by molecular dynamics (MD) simulations were used to elucidate the structural data and stability of the inclusion complexes of ß-cyclodextrin and adamantyl guanidines (AG1-5). The results are consistent and point to a significant contribution of the guanylhydrazone residue to the complexation process for AG1 and AG2 with ß-cyclodextrin. In order to evaluate the potential of the self-assembled supramolecular nanomaterial as a nonviral gene delivery vector, fluorescence correlation spectroscopy was used. It showed that the prepared nanovesicles functionalized with adamantyl guanidines AG1-4 effectively recognize and bind the fluorescently labelled DNA. Furthermore, gel electrophoretic assay confirmed the formation of nanoplexes of functionalized nanovesicles and plasmid DNA. These findings together suggest that the designed supramolecular nanovesicles could be successfully applied as nonviral gene delivery vectors.

Diamantane Suspended Single Copper Atoms.

Single chains of metal atoms are expected to be perfect one-dimensional nanowires in nanotechnology, due to their quantum nature including tunable electronic or spin coupling strengths. However, it is still rather difficult to fabricate such nanowires with metallic atoms under directional and separation control. Here, we succeeded in building higher-order single diamondoid-chains from the lower-order chains using a chemically well-controlled approach that employs diamondoids on metal surfaces. This approach results in higher-order diamondoid double chains by linking two neighboring single chains, and ultimately forms a central chain consisting of single Cu atoms suspended by the diamantane framework. The suspended Cu atoms are placed above the metal surface with a periodic distance of 0.67 ± 0.01 nm. Our bottom-up approach will allow detailed experimental investigations of the properties of these exciting suspended metal atoms (for example, quantized conductance, spin coupling, as well as transfer, etc.). Furthermore, we also identified different spatial configurations on the metal surfaces in on-surface reaction processes using high-resolution AFM imaging and density functional theory computations. Our findings broaden the on-surface synthesis concept from 2D planar aromatic molecules to 3D bulky aliphatic molecules.

Tuning the Reactivity of Peroxo Anhydrides for Aromatic C-H Bond Oxidation.

Phenol moieties are key structural motifs in many areas of chemical research from polymers to pharmaceuticals. Herein, we report on the design and use of a structurally demanding cyclic peroxide (spiro[bicyclo[2.2.1]heptane-2,4'-[1,2]dioxolane]-3',5'-dione, P4) for the direct hydroxylation of aromatic substrates. The new peroxide benefits from high thermal stability and can be synthesized from readily available starting materials. The aromatic C-H oxidation using P4 exhibits generally good yields (up to 96%) and appreciable regioselectivities.

Assigning the absolute configuration of single aliphatic molecules by visual inspection.

Deciphering absolute configuration of a single molecule by direct visual inspection is the next step in compound identification, with far-reaching implications for medicinal chemistry, pharmacology, and natural product synthesis. We demonstrate the feasibility of this approach utilizing low temperature atomic force microscopy (AFM) with a CO-functionalized tip to determine the absolute configuration and orientation of a single, adsorbed [123]tetramantane molecule, the smallest chiral diamondoid. We differentiate between single enantiomers on Cu(111) by direct visual inspection, and furthermore identify molecular dimers and molecular clusters. The experimental results are confirmed by a computational study that allowed quantification of the corresponding intermolecular interactions. The unique toolset of absolute configuration determination combined with AFM tip manipulation opens a route for studying molecular nucleation, including chirality-driven assembly or reaction mechanisms.

London Dispersion Directs On-Surface Self-Assembly of [121]Tetramantane Molecules.

London dispersion (LD) acts between all atoms and molecules in nature, but the role of LD interactions in the self-assembly of molecular layers is still poorly understood. In this study, direct visualization of single molecules using atomic force microscopy with CO-functionalized tips revealed the exact adsorption structures of bulky and highly polarizable [121]tetramantane molecules on Au(111) and Cu(111) surfaces. We determined the absolute molecular orientations of the completely sp3-hybridized tetramantanes on metal surfaces. Moreover, we demonstrate how LD drives this on-surface self-assembly of [121]tetramantane hydrocarbons, resulting in the formation of a highly ordered 2D lattice. Our experimental findings were underpinned by a systematic computational study, which allowed us to quantify the energies associated with LD interactions and to analyze intermolecular close contacts and attractions in detail.

Adamantane in Drug Delivery Systems and Surface Recognition.

The adamantane moiety is widely applied in design and synthesis of new drug delivery systems and in surface recognition studies. This review focuses on liposomes, cyclodextrins, and dendrimers based on or incorporating adamantane derivatives. Our recent concept of adamantane as an anchor in the lipid bilayer of liposomes has promising applications in the field of targeted drug delivery and surface recognition. The results reported here encourage the development of novel adamantane-based structures and self-assembled supramolecular systems for basic chemical investigations as well as for biomedical application.

Unraveling the Structure-Affinity Relationship between Cucurbit[n]urils (n = 7, 8) and Cationic Diamondoids.

We report the measurement of the binding constants (Ka) for cucurbit[n]uril (n = 7, 8) toward four series of guests based on 2,6-disubstituted adamantanes, 4,9-disubstituted diamantanes, 1,6-disubstituted diamantanes, and 1-substituted adamantane ammonium ions by direct and competitive 1H NMR spectroscopy. Compared to the affinity of CB[7]·Diam(NMe3)2, the adamantane diammonium ion complexes (e.g., CB[7]·2,6-Ad(NH3)2 and CB[7]·2,6-Ad(NMe3)2) are less effective at realizing the potential 1000-fold enhancement in affinity due to ion-dipole interactions at the second ureidyl C═O portal. Comparative crystallographic investigation of CB[7]·Diam(NMe3)2, CB[7]·DiamNMe3, and CB[7]·1-AdNMe3 revealed that the preferred geometry positions the +NMe3 groups ≈0.32 Å above the C═O portal; the observed 0.80 Å spacing observed for CB[7]·Diam(NMe3)2 reflects the simultaneous geometrical constraints of CH2···O═C close contacts at both portals. Remarkably, the CB[8]·IsoDiam(NHMe2)2 complex displays femtomolar binding affinity, placing it firmly alongside the CB[7]·Diam(NMe3)2 complex. Primary or quaternary ammonium ion looping strategies lead to larger increases in binding affinity for CB[8] than for CB[7], which we attribute to the larger size of the carbonyl portals of CB[8]; this suggests routes to develop CB[8] as the tightest binding host in the CB[n] family. We report that alkyl group fluorination (e.g., CB[7]·1-AdNH2Et versus CB[7]·1-AdNH2CH2CF3) does not result in the expected increase in Ka value. Finally, we discuss the role of solvation in nonempirical quantum mechanical computational methodology, which is used to estimate the relative changes in Gibbs binding free energies.