Electrospray‐Ionization Mass Spectrometry for Screening the Specificity and Stability of Single‐Stranded‐DNA Templated Self‐Assemblies

Supramolecular complexes consisting of a single‐stranded oligothymine ( dTn ) as the host template and an array of guest molecules equipped with a complementary diaminotriazine hydrogen‐bonding unit have been studied with electrospray‐ionization mass spectrometry (ESI‐MS). In this hybrid construct, a supramolecular stack of guest molecules is hydrogen bonded to dTn . By changing the hydrogen‐bonding motif of the DNA host template or the guest molecules, selective hydrogen bonding was proven. We were able to detect single‐stranded‐DNA (ssDNA)–guest complexes for strands with lengths of up to 20 bases, in which the highest complex mass detected was 15 kDa; these complexes constitute 20‐component self‐assembled objects. Gas‐phase breakdown experiments on single‐ and multiple‐guest–DNA assemblies gave qualitative information on the fragmentation pathways and the relative complex stabilities. We found that the guest molecules are removed from the template one by one in a highly controlled way. The stabilities of the complexes depend mainly on the molecular weight of the guest molecules, a fact suggesting that the complexes collapse in the gas phase. By mixing two different guests with the ssDNA template, a multicomponent dynamic library can be created. Our results demonstrate that ESI‐MS is a powerful tool to analyze supramolecular ssDNA complexes in great detail.     

Laser Spectroscopic Study of Cold Gas‐Phase Host‐Guest Complexes of Crown Ethers

The structure, molecular recognition, and inclusion effect on the photophysics of guest species are investigated for neutral and ionic cold host‐guest complexes of crown ethers (CEs) in the gas phase. Here, the cold neutral host‐guest complexes are produced by a supersonic expansion technique and the cold ionic complexes are generated by the combination of electrospray ionization (ESI) and a cryogenically cooled ion trap. The host species are 3n‐crown‐n (3nCn; n = 4, 5, 6, 8) and (di)benzo‐3n‐crown‐n ((D)B3nCn; n = 4, 5, 6, 8). For neutral guests, we have chosen water and aromatic molecules, such as phenol and benzenediols, and as ionic species we have chosen alkali‐metal ions (M⁺). The electronic spectra and isomer‐specific vibrational spectra for the complexes are observed with various laser spectroscopic methods: laser‐induced fluorescence (LIF); ultraviolet‐ultraviolet hole‐burning (UV‐UV HB); and IR‐UV double resonance (IR‐UV DR) spectroscopy. The obtained spectra are analyzed with the aid of quantum chemical calculations. We will discuss how the host and guest species change their flexible structures for forming best‐fit stable complexes (induced fitting) and what kinds of interactions are operating for the stabilization of the complexes. For the alkali metal ion?CE complexes, we investigate the solvation effect by attaching water molecules. In addition to the ground‐state stabilization problem, we will show that the complexation leads to a drastic effect on the excited‐state electronic structure and dynamics of the guest species, which we call a “cage‐like effect”.     

Metal Ion,Light, and Redox Responsive Interaction of Vesicles by a Supramolecular Switch

Chemical, photochemical and electrical stimuli are versatile possibilities to exert external control on self‐assembled materials. Here, a trifunctional molecule that switches between an “adhesive” and a “non‐adhesive” state in response to metal ions, or light, or oxidation is presented. To this end, an azobenzene–ferrocene conjugate with a flexible N,N′‐bis(3‐aminopropyl)ethylenediamine spacer was designed as a multistimuli‐responsive guest molecule that can form inclusion complexes with β‐cyclodextrin. In the absence of any stimulus the guest molecule induces reversible aggregation of host vesicles composed of amphiphilic β‐cyclodextrin due to the formation of intervesicular inclusion complexes. In this case, the guest molecule operates as a noncovalent cross‐linker for the host vesicles. In response to any of three external stimuli (metal ions, UV irradiation, or oxidation), the conformation of the guest molecule changes and its affinity for the host vesicles is strongly reduced, which results in the dissociation of intervesicular complexes. Upon elimination or reversal of the stimuli (sequestration of metal ion, visible irradiation, or reduction) the affinity of the guest molecules for the host vesicles is restored. The reversible cross‐linking and aggregation of the cyclodextrin vesicles in dilute aqueous solution was confirmed by isothermal titration calorimetry (ITC), optical density measurements at 600 nm (OD₆₀₀), dynamic light scattering (DLS), ζ‐potential measurements and cyclic voltammetry (CV). To the best of our knowledge, a dynamic supramolecular system based on a molecular switch that responds orthogonally to three different stimuli is unprecedented.     

A Study of the Interaction Between Cucurbit[8]uril and Alkyl‐Substituted 4‐Pyrrolidinopyridinium Salts

The interaction between cucuribit[8]uril (Q[8]) and a series of 4‐pyrrolidinopyridinium salts bearing aliphatic substituents at the pyridinium nitrogen, namely 4‐(C₄H₈N)C₅H₅NRBr, where R=Et (g1), n‐butyl (g2), n‐pentyl (g3), n‐hexyl (g4), n‐octyl (g5), n‐dodecyl (g6), has been studied in aqueous solution by ¹H NMR spectroscopy, electronic absorption spectroscopy, isothermal titration calorimetry and mass spectrometry. Single crystal X‐ray diffraction revealed the structure of the host–guest complexes for g1, g2, g3, and g5. In each case, the Q[8] contains two guest molecules in a centrosymmetric dimer. The orientation of the guest molecule changes as the alkyl chain increases in length. Interestingly, in the solid state, the inclusion complexes identified are different from those observed in solution, and furthermore, in the case of g3, Q[8] exhibits two different interactions with the guest. In solution, the length of the alkyl chain plays a significant role in determining the type of host–guest interaction present.     

Electrospray ionization mass spectrometry studies of cyclodextrin‐carboxylate ion inclusion complexes

Aqueous solutions containing simple model aliphatic and alicyclic carboxylic acids (surrogates 1–4) were studied using negative ion electrospray mass spectrometry (ESI‐MS) in the presence and absence of α‐, β‐, and γ‐cyclodextrin. Molecular ions were detected corresponding to the parent carboxylic acids and complexed forms of the carboxylic acids; the latter corresponding to non‐covalent inclusion complexes formed between carboxylic acid and cyclodextrin compounds (e.g., β‐CD, α‐CD, and γ‐CD). The formation of 1:1 non‐covalent inclusion cyclodextrin‐carboxylic complexes and non‐inclusion forms of the cellobiose‐carboxylic acid compounds was also observed. Aqueous solutions of Syncrude‐derived mixtures of aliphatic and alicyclic carboxylic acids (i.e. naphthenic acids; NAs) were similarly studied using ESI‐MS, as outlined above. Molecular ions corresponding to the formation of CD‐NAs inclusion complexes were observed whereas 1:1 non‐inclusion forms of the cellobiose‐NAs complexes were not detected. The ESI‐MS results provide evidence for some measure of inclusion selectivity according to the 'size‐fit' of the host and guest molecules (according to carbon number) and the hydrogen deficiency (z‐series) of the naphthenic acid compounds. The relative abundances of the molecular ions of the CD‐carboxylate anion adducts provide strong support for differing complex stability in aqueous solution. In general, the 1:1 complex stability according to hydrogen deficiency (z‐series) of naphthenic acids may be attributed to the nature of the cavity size of the cyclodextrin host compounds and the relative lipophilicity of the guest. Copyright © 2009 John Wiley & Sons, Ltd.     

Structural connectivity of 18-Crown-6/H+/L-tryptophan noncovalent complexes in gas phase and in solution: Delineating host–guest–solvent interactions in solution from gas phase structures

We investigate the structural correlation of noncovalent crown ether/H⁺/L-tryptophan (CR/TrpH⁺) host–guest complexes in the solution phase with those in the gas phase generated through electrospray ionization/mass spectrometry (ESI/MS) techniques. We perform quantum chemical calculations to determine their structures, relative Gibbs free energies, and infrared spectra. We compare the calculated infrared (IR) spectra with the IR multiphoton dissociation (IRMPD) spectra observed for the 18-Crown-6/TrpH⁺ complex by Polfer and co-workers [J. Phys. Chem. A 2013, 117, 1181–1188] for assigning the IR bands. We observe that the carboxyl group remains “naked,” lacking hydrogen bonding with the CR unit in the gas phase, and that this most stable conformer originates from the corresponding lowest Gibbs free energy structure in solution. Based on these findings, we propose that gas phase host–guest complexes directly correlate with those in solution, reinforcing the possibility of obtaining invaluable information about host–guest–solvent interactions in solution from the structure of the host–guest pair in the gas phase.     

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

X‐ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host–guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X‐ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light‐atom‐only crystal. Atomic displacement parameters obtained independently from the X‐ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Ų indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host–guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host–guest interaction (e.g., in protein–drug complexes), at least for polar molecules.     

α‐Cyclodextrin Host–Guest Binding: A Computational Study of the Different Driving Forces

Free‐energy differences govern the equilibrium between bound and unbound states of a host and its guest molecules. The understanding of the underlying entropic and enthalpic contributions, and their complex interplay are crucial for the design of new drugs and inhibitors. In this study, molecular dynamics (MD) simulations were performed with inclusion complexes of α‐cyclodextrin (αCD) and three monosubstituted benzene derivatives to investigate host–guest binding. αCD Complexes are an ideal model system, which is experimentally and computationally well‐known. Thermodynamic integration (TI) simulations were carried out under various conditions for the free ligands in solution and bound to αCD. The two possible orientations of the ligand inside the cavity were investigated. Agreement with experimental data was only found for the more stable orientation, where the substituent resides inside the cavity. The better stability of this conformation results from stronger Van der Waals interactions and a favorable antiparallel host–guest dipole–dipole alignment. To estimate the entropic contributions, simulations were performed at three different temperatures (250, 300, and 350 K) and using positional restraints for the host. The system was found to be insensitive to both factors, due to the large and symmetric cavity of αCD, and the nondirectional nature of the host–guest interactions.     

Recognition of N‐Alkyl and N‐Aryl Acetamides by N‐Alkyl Ammonium Resorcinarene Chlorides

N‐Alkyl ammonium resorcinarene chlorides are stabilized by an intricate array of intra‐ and intermolecular hydrogen bonds that leads to cavitand‐like structures. Depending on the upper‐rim substituents, self‐inclusion was observed in solution and in the solid state. The self‐inclusion can be disrupted at higher temperatures, whereas in the presence of small guests the self‐included dimers spontaneously reorganize to 1:1 host–guest complexes. These host compounds show an interesting ability to bind a series of N‐alkyl acetamide guests through intermolecular hydrogen bonds involving the carbonyl oxygen (C?O) atoms and the amide (NH) groups of the guests, the chloride anions (Cl^?) and ammonium (NH₂⁺) cations of the hosts, and also through CH ??? π interactions between the hosts and guests. The self‐included and host–guest complexes were studied by single‐crystal X‐ray diffraction, NMR titration, and mass spectrometry.     

Inhibition of acid‐induced decomposition of diphenyltriazenes by complexation with cyclodextrins

Acid‐promoted N? N bond cleavage in 1,3‐diphenyltriazenes (X‐Ph‐N=N‐NH‐Ph‐X; X = H, 4‐OCH₃), leading to formation of diazonium ions and anilines, is strongly inhibited in aqueous solutions in the presence of cyclodextrins (CDs). The inhibition is ascribed to the formation of inclusion complexes that render the guest diphenyltriazene significantly less basic as a result of the less polar nature of the CD cavity (a microsolvent effect). Association equilibrium constants for 1:1 host–guest complexes increase in the order α‐CD <β‐CD ～ permethyl‐β‐CD < hydroxypropyl‐β‐CD, with values for X = 4‐OCH₃ being larger than those for X = H. In the case of α‐CD, formation of 2:1 host–guest complexes is also involved. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 567–574, 2010     

Fluorescent Cross‐Linked Supramolecular Polymer Constructed by Orthogonal Self‐Assembly of Metal–Ligand Coordination and Host–Guest Interaction

A new host molecule consists of four terpyridine groups as the binding sites with zinc(II) ion and a copillar[5]arene incorporated in the center as a spacer to interact with guest molecule was designed and synthesized. Due to the 120 ° angle of the rigid aromatic segment, a cross‐linked dimeric hexagonal supramolecular polymer was therefore generated as the result of the orthogonal self‐assembly of metal–ligand coordination and host–guest interaction. UV/Vis spectroscopy, ¹H NMR spectroscopy, viscosity and dynamic light‐scattering techniques were employed to characterize and understand the cross‐linking process with the introduction of zinc(II) ion and guest molecule. More importantly, well‐defined morphology of the self‐assembled supramolecular structure can be tuned by altering the adding sequence of the two components, that is, the zinc(II) ion and the guest molecule. In addition, introduction of a competitive ligand suggested the dynamic nature of the supramolecular structure.     

Unusual covalent bond-breaking reactions of beta-cyclodextrin inclusion complexes of nucleobases/nucleosides and related guest molecules

Host-guest complexes between nucleobases or nucleosides and beta-cyclodextrin can be observed by electrospray ionization mass spectrometry (ESI-MS) and their relative abundances appear to correlate with the condensed-phase binding order. Using Fourier transform ion cyclotron resonance mass spectrometry, the extent of the interactions between the host oligosaccharide and guest species have also been examined for permethylated beta-cyclodextrin : adenine/deoxyadenosine and permethylated maltoheptaose : adenine/deoxyadenosine using gas-phase exchange reactions with the gaseous amines, n-propylamine and ethylenediamine. The ease of guest exchange in the gas-phase follows the order : deoxyadenosine > adenine > deoxycytidine > cytosine, which is in contrast to their relative binding order in solution. Collision-induced dissociation (CID) has been used to probe the fragmentation behavior of oligosaccharide : nucleobase/nucleoside complexes. Under these conditions the inclusion complexes either (a) dissociate, (b) result in cleavage of the host oligosaccharide or (c) result in cleavage of the guest molecule. This study has shown that the preferred dissociation pathway of these complexes depends on the structures of both the cyclodextrin and guest molecule.     

Space filling of permethylated β‐cyclodextrin by volatile hydrophobic and hydrophilic guests in polyethylene glycol

The inclusion of volatile organic compounds of various classes in the permethylated β‐cyclodextrin in an oligomeric solution of polyethylene glycol was investigated by inverse gas–liquid chromatography methods and by a stereochemical approach. It was established that the “guest–host” complexation process is influenced by the geometrical structure of the guest molecules, their chirality, and entropy factors.     

What Happens to Hydrophobic Interactions during Transfer from the Solution to the Gas Phase? The Case of Electrospray-Based Soft Ionization Methods

The disappearance of the hydrophobic effect in the gas phase due to the absence of an aqueous surrounding raises a long-standing question: can noncovalent complexes that are exclusively bound by hydrophobic interactions in solution be preserved in the gas phase? Some reports of successful detection by mass spectrometry of complexes largely stabilized by hydrophobic effect are questionable by the presence of electrostatic forces that hold them together in the gas phase. Here, we report on the MS-based analysis of model supramolecular complexes with a purely hydrophobic association in solution, β-cyclodextrin, and synthetic adamantyl-containing ligands with several binding sites. The stability of these complexes in the gas phase is investigated by quantum chemical methods (DFT-M06). Compared with the free interaction partners, the inclusion complex between β-cyclodextrin and adamantyl-containing ligand is shown to be stabilized in the gas phase by ΔG = 9.6 kcal mol^–1. The host–guest association is mainly enthalpy-driven due to strong dispersion interactions caused by a large nonpolar interface and a high steric complementarity of the binding partners. Interference from other types of noncovalent binding forces is virtually absent. The complexes are successfully detected via electrospray ionization mass spectrometry, although a high dissociation yield is also observed. We attribute this pronounced dissociation of the complexes to the collisional activation of ions in the atmospheric interface of mass spectrometer. The comparison of several electrospray-based ionization methods reveals that cold spray ionization provides the softest ion generation conditions for these complexes.     

Amphiphilic Inclusion Spaces for Various Guests and Regulation of Fluorescence Intensity of 1,8‐Bis(4‐aminophenyl)anthracene Crystals

A host framework for inclusion of various guest molecules was investigated by preparation of inclusion crystals of 1,8‐bis(4‐aminophenyl)anthracene (1,8‐BAPA) with organic solvents. X‐ray crystallographic analysis revealed construction of the same inclusion space incorporating 1,8‐BAPA and eight guest molecules including both non‐polar (benzene) and polar guests (N,N‐dimethylformamide, DMF). Fluorescence efficiencies varied depending on guest molecule polarity; DMF inclusion crystals exhibited the highest fluorescence intensity (Φ_F=0.40), four times as high as that of a benzene inclusion crystal (Φ_F=0.10). According to systematic investigations of inclusion phenomena, strong host–guest interactions and filling of the inclusion space led to a high fluorescence intensity. Temperature‐dependent fluorescence spectral measurements revealed these factors effectively immobilised the host framework. Although hydrogen bonding commonly decreases fluorescence intensity, the present study demonstrated that such strong interactions provide excellent conditions for fluorescence enhancement. Thus, this remarkable behaviour has potential application toward sensing of highly polar molecules, such as biogenic compounds.     

How important is the dispersion interaction for cyclobis(paraquat‐p‐phenylene)‐based molecular “shuttles”? A theoretical study

Inclusion complexes of cyclobis(paraquat‐p‐phenylene) and various aromatic molecules in their neutral and oxidized form were studied at the LMP2/6‐311+G**//BHandHLYP/6‐31G* level of theory, which represents the highest level theoretical study to date for these complexes. The results show that it is dispersion interaction that contributes most to the binding energy. One electron oxidation of a guest molecule leads to complete dissociation of inclusion complex generating strong repulsion potential between guest and host molecules. Electrostatic interactions also can play an important role, provided the guest molecule has a dipole moment; however, dispersion interactions always dominate in binding energy. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Comparing Grubbs‐, Werner‐, and Hofmann‐Type (Carbene)ruthenium Complexes: The Key Role of Pre‐Equilibria for Olefin Metathesis

A gas‐phase comparison of intrinsic olefin metathesis rates for (carbene)ruthenium complexes by means of electrospray‐ionization tandem mass spectrometry reveals a reversal of the reactivity trends observed in solution. The solution‐phase ordering of reactivity is accordingly attributed to a more favorable pre‐equilibrium, producing the metathesis‐active species in the case of the Hofmann‐ and Werner‐type complexes relative to those of the Grubbs type.     

Spectroscopic and thermal characterization of the host–guest interactions between α‐, β‐ and γ‐cyclodextrins and vanadocene dichloride

Host–guest interactions between α‐, β‐ and γ‐cyclodextrins and vanadocene dichloride (Cp₂VCl₂) have been investigated by a combination of thermogravimetric analysis, differential scanning calorimetry, powder X‐ray diffraction and solid‐state and solution electron paramagnetic resonance (EPR) spectroscopy. The solid‐state results demonstrated that only β‐ and γ‐cyclodextrins form 1:1 inclusion complexes, while α‐cyclodextrin does not form an inclusion complex with Cp₂VCl₂. The β‐ and γ‐CD–Cp₂VCl₂ inclusion complexes exhibited anisotropic electron‐⁵¹V (I = 7/2) hyperfine coupling constants whereas the α‐CD–Cp₂VCl₂ system showed only an asymmetric peak with no anisotropic hyperfine constant. On the other hand, solution EPR spectroscopy showed that α‐cyclodextrin (α‐CD) may be involved in weak host–guest interactions in equilibrium with free vanadocene species. Copyright © 2008 John Wiley & Sons, Ltd.     

Complexation between Methyl Viologen (Paraquat) Bis(Hexafluorophosphate) and Dibenzo[24]Crown‐8 Revisited

Paraquat bis(hexafluorophosphate) undergoes stepwise dissociation in acetone. All three species—the neutral molecule, and the mono‐ and dications—are represented significantly under the experimental conditions typically used in host–guest binding studies. Paraquat forms at least four host–guest complexes with dibenzo[24]crown‐8. They are characterized by both 1:1 and 1:2 stoichiometries, and an overall charge of either zero (neutral molecule) or one (monocation). The monocationic 1:1 host–guest complex is the most abundant species under typical (0.5–20 mM ) experimental conditions. The presence of the dicationic 1:1 host–guest complex cannot be excluded on the basis of our experimental data, but neither is it unambiguously confirmed to be present. The two confirmed forms of paraquat that do undergo complexation—the neutral molecule and the monocation—exhibit approximately identical binding affinities toward dibenzo[24]crown‐8. Thus, the relative abundance of neutral, singly, and doubly charged pseudorotaxanes is identical to the relative abundance of neutral, singly, and doubly charged paraquat unbound with respect to the crown ether in acetone. In the specific case of paraquat/dibenzo[24]crown‐8, ion‐pairing does not contribute to host–guest complex formation, as has been suggested previously in the literature.     

Inclusion of chlorophenols by 4,4′‐(cyclohexane‐1,1‐diyl)diphenol: structures and kinetics of decomposition

The structures of the inclusion compounds 4,4′‐(cyclohexane‐1,1‐diyl)diphenol–3‐chlorophenol (1/1) and 4,4′‐(cyclohexane‐1,1‐diyl)diphenol–4‐chlorophenol (1/1), both C₁₈H₂₀O₂·C₆H₅ClO, are isostructural with respect to the host molecule and are stabilized by extensive host–host, host–guest and guest–host hydrogen bonding. The packing is characterized by layers of host and guest molecules. The kinetics of thermal decomposition follow the R2 contracting‐area model, kt = [1 − (1 − α)^½], and yield activation energies of 105 (8) and 96 (8) kJ mol⁻¹, respectively.