Molecular clips and tweezers hosting neutral guests

Intense current interest in supramolecular chemistry is devoted to the construction of molecular assemblies displaying controlled molecular motion associated to recognition. On this ground, molecular clips and tweezers have focused an increasing attention. This tutorial review points out the recent advances in the construction of always more sophisticated molecular clips and tweezers, illustrating their remarkably broad structural variety and focusing on their binding ability towards neutral guests. A particular attention is brought to recent findings in dynamic molecular tweezers whose recognition ability can be regulated by external stimuli. Porphyrin-based systems will not be covered here as this very active field has been recently reviewed.     

Molecular clips with extended aromatic sidewalls as receptors for electron-acceptor molecules. Synthesis and NMR, photophysical, and electrochemical properties

We have synthesized molecular clips 1 comprising (i) two benzo[k]fluoranthene sidewalls and (ii) a dimethylene-connected benzene bridge that carries two acetoxy (1a), hydroxy (1b), or methoxy (1c) substituents in the para position. Their NMR spectra, single-crystal structures, and photophysical (fluorescence intensity, lifetime, depolarization) and electrochemical properties are discussed. For the purpose of comparison, similar compounds (2 and 3) containing only one benzo[k]fluoranthene unit have been prepared and studied. The strongly fluorescent clips 1 form stable complexes with electron-acceptor guests because of a highly negative electrostatic potential on the inner van der Waals surface of their cavity. The complexation constants in chloroform solution for a variety of guests, determined by NMR and fluorescence titration, are much larger than those of the corresponding anthracene and naphthalene clips (4 and 5), particularly in the case of extended aromatic guests. The effect of the substituents in the para position of the benzene spacer unit of clips 1 is discussed on the basis of the host-guest complex structures obtained by X-ray analysis and molecular mechanics simulations. In the case of 9-dicyanomethylene-2,4,7-trinitrofluorene (TNF) guest, complex formation with clip 1a causes dramatic changes in the photophysical and electrochemical properties: (i) a new charge-transfer band at 600 nm arises, (ii) a very efficient quenching of the strong benzo[k]fluoranthene fluorescence takes place, (iii) shifts of both the first oxidation (clip-centered) and reduction (TNF-centered) potentials are observed, and (iv) reversible disassembling of the complex can be obtained by electrochemical stimulation.     

Spectroscopy, NMR and DFT studies on molecular recognition of crown ether bridged chiral heterotrinuclear salen Zn(II) complex

A barium-containing crown ether bridged chiral heterotrinuclear salen Zn(II) complex BaZn2L(ClO4)2, where L is a folded dinuclear chiral (R,R)-salen ligand, has been synthesized and characterized by elemental analysis, 1H NMR, UV-vis, IR, circular dichroism (CD) spectra, and mass spectra. As a folded dinuclear chiral host, its recognition with achiral guests (imidazole derivatives), rigid bidentate guest (1,4-diazobicyclo[2,2,2]octane, DABCO) and chiral guests (amino acid methyl esters) was investigated by means of UV-vis spectrophotometric titration, CD spectra. The association constants of D-amino acid methyl esters are found to be higher than those of their L-enantiomer. The sandwich-type binding of BaZn2L(ClO4)2-DABCO supramolecular assembly was specially studied via 1H NMR titration and 1H ROESY. To understand the recognition on molecular level, density functional theory (DFT) calculations on B3LYP/LanL2DZ were performed on the minimal energy conformations of host, guests, and host-guest complexes. The minimal energy conformations were obtained by molecular mechanics (MM) optimization and molecular dynamics (MD) simulation. The results of single point energy, HOMO energy, and charges transfer were analyzed. The results of theoretical calculations are in good agreement with the experimental data.     

A Modular Phosphorylated Glycoluril-Derived Molecular Tweezer for Potent Binding of Aliphatic Diamines

A molecular tweezer based on a glycoluril-derived framework bearing four phosphate groups was synthesized and shown to be capable of binding organic amines in aqueous solution. This work reports the K_a values for 30 complexes of this molecular tweezer and amine guests, determined by means of ¹H NMR titrations. Both the hydrophobic cavity and the phosphate groups contribute to the binding. Bulkier molecules and molecules bearing negatively charged groups like carboxylates in amino acids bind less tightly due to a steric clash and coulombic repulsion. The narrow cavity and the strong ionic interactions of the phosphate groups with ammonium guests favor binding of aliphatic diamines. These binding properties clearly distinguish this system from structurally related molecular clips and tweezers.     

Dendrimer-tetrachloroplatinate precursor interactions. 2. Noncovalent binding in PAMAM outer pockets

Density functional theory is used to investigate the complexation ability of dendrimer outer pockets--in both tertiary amine protonated and unprotonated scenarios--toward molecular guests, particularly tetrachloroplatinate(II) and its mono- and diaquated derivatives as well as competing counterions. The effect of the outer pocket (host) on the binding affinity of guest molecules is analyzed and it is found that is more feasible for the host to accept species, particularly charged ones, inside an unprotonated pocket rather than outside; unlike the protonated pocket where the opposite is more likely to occur. Conformational changes triggered by the hosting of particular guests can have an impact in the global configuration of the larger dendrimer the pockets are part of.     

Synthesis and computational study of two new glycoluril clips containing benzocrown ether side walls

Two new glycoluril-derived molecular clips containing benzocrown ether side walls have been synthesized via reaction of a glycoluril scaffold with two bromomethylated benzocrown ethers. The molecular geometry of their most stable structures were investigated with density functional theory at the B3LYP level of theory using STO-3G, 6-31G, and 6-311G basis sets. Then based on the obtained computer-optimized structures, the binding properties of one clip with some 5-substituted resorcinols have been calculated.     

Lamellar organic thin films through self-assembly and molecular recognition.

Molecular clips possessing U-shaped cavities have been functionalized on their convex side with long aliphatic tails. These molecules form dimers which self-assemble into malleable lamellar thin films. Upon addition of a guest (methyl 3,5-dihydroxybenzoate), a 1:1 host-guest complex is formed, which prohibits clip dimerization. As a result, the lamellar structure of the material is lost. Complexation of 3,5-dihydroxybenzoic acid in the clip results in host-guest complexes which dimerize by hydrogen bonding interactions between the carboxylic acid functions of the bound guests. This dimerization restores the lamellar type architecture of the material.     

Supramolecular recognition. Terpyridyl palladium and platinum molecular clefts and their association with planar platinum complexes

Molecular receptors, consisting of either two parallel cofacially disposed terpyridyl-Pd-Cl+ or terpyridyl-Pt-Cl+ units, are described. Concerted rotation of these units about the molecular spacer can alter their separation between 6.4 and 7.2 A to accommodate the dimensions of molecular guests. Neutral and anionic planar complexes of platinum(II) were investigated as guests to determine if metal-metal interaction between the host and guest metals could stabilize host-guest association. With a neutral guest, it was found that host-guest formation is signaled by a color change from light yellow to deep red. For one of the anionic guests, a visible absorption band appears upon host-guest formation with the platinum receptor that is ascribed to transitions associated with a Pt-Pt interaction. The association constants found for the neutral guest with the palladium and platinum receptors are large, suggesting that metal-metal interaction contributes to the molecular recognition. The structures of the host-(neutral)guest complexes in solution have been determined by 1H NOESY spectra. A crystal structure of the platinum host-(neutral)guest complex is the same as that found in solution and confirms the presence of a Pt-Pt interaction. Temperature-dependent (195)Pt NMR spectra in solution provide a quantitative estimate of the conformational interconversions of the free platinum receptor.     

Molecules with Large Cavities in Supramolecular Chemistry

Supramolecular chemistry is a new area of research that has rapidly developed from pure synthetic chemistry, and its novelty has led to interdisciplinary cooperation between organic and inorganic chemistry, biochemistry, physical and theoretical chemistry, and physics. Whereas molecular chemistry essentially deals with the covalent bonding of atoms, Supramolecular chemistry is predominantly involved in the study of the weaker intermolecular interactions resulting in the association and self-organization of several components to form larger aggregates (supramolecules). The first crown ether discovered by the subsequent Nobel prizewinner Pedersen was more the fortuitous reaction product of an impurity, but nowadays, some twenty-five years later, chemists are able to tailor host molecules to special requirements. Host compounds having a cyclophane skeleton make an important contribution, since their aromatic structural units ensure the necessary rigidity of the molecular structures and thereby improve the preorganization of the coordination sites for the cooperative binding of the guests. During the course of the rapid development of Supramolecular chemistry such a large number of synthetic hosts has been developed and their interaction with guests studied in such depth that we must restrict ourselves here to a discussion of a particular group of host compounds, namely cavity-supporting macrobicyclic and macrooligocyclic phanesu, which bear a similar relation to open-chain and monocyclic hosts as the metal-complexing cryptands to the podands and crown ethers. The molecular architecture of these three-dimensionally bridged macrooligocycles is a challenge for synthetic chemistry. (Not only the size and shape of the intramolecular cavity, but also the provision of the latter with suitable coordination centers have to be included in the synthesis strategy.) The capacity for the envelopment of guests from all sides and the expedient endo functionalization often also produce a particularly strong binding of host and guest, outstanding selectivities with regards to molecular recognition, and special properties of the Supramolecular complexes.     

Cucurbit[8]uril (CB[8])‐Based Supramolecular Switches

The use of cucurbit[8]uril as a molecular host has emerged in the chemical literature as a reliable strategy for the creation of dynamic chemical systems, owing to its ability to form homo‐ and heteroternary complexes in aqueous media with appropriate molecular switches as guests. In this manner, CB[8]‐based supramolecular switches can be designed in a predictable and modular fashion, through the selection of appropriate guests able to condition the redox, photochemical, or pH‐triggered behavior of tailored multicomponent systems. Furthermore, CB[8] allows the implementation of dual/triple and linear/orthogonal stimuli‐dependent properties into these molecular devices by a careful selection of the guests. This versatility in their design gives these supramolecular switches great potential for the rational development of new materials, in which their function is not only determined by the custom‐made stimuli‐responsiveness, but also by the transient aggregation/disaggregation of homo‐ or heteromeric building blocks.     

Tridymite-like host clathrate [K(H2O)n][CuZn(CN)4]: crystal structure, guest molecular motion and properties

A new clathrate [K(H(2)O)(n)][CuZn(CN)(4)] has been synthesized and its host structure has been determined by the single-crystal X-ray diffraction method. It has a [CuZn(CN)(4)](-) tridymite-like 3D framework host, formed with tetrahedral Cu(I) and Zn(II) ions and cyanide bridges and includes water molecules as guests, together with K(+). This tridymite-like structure is the first structural variation of the [CuZn(CN)(4)](-) 3D framework, whose only known structure has been a cristobalite-like structure. The new host shows properties never seen in the previous cristobalite-like structure host. It absorbs and desorbs water as a guest and the water content (n) varies between 1.2 and 11.2 at room temperature, by adjusting the conditions where the clathrate is placed. The desorption of the water causes deformation of the host structure and this deformation is recovered by the absorption of water. The water can be replaced with methanol and acetonitrile by their absorption instead of water. Solid-state (2)H-NMR spectra revealed the molecular motion of the water, methanol and acetonitrile guests in a temperature range between 123 K and 300 K.     

A theoretical study of cohesion, structural deformation, inclusion, and dynamics in porous hydrogen-bonded molecular networks

Molecules with multiple sites of hydrogen bonding attached to suitable cores tend to crystallize as open networks. The resulting crystals can have the following unusual properties: They can include significant amounts of guest molecules; the guests are typically located in channels and can be exchanged without loss of crystallinity; and the geometry of the networks can change in response to new guests. We have found that DFT calculations can provide accurate simulations of the unusual structure and properties of such materials, represented by crystals of prototypic tetrapyridinone 1. These calculations have yielded three key insights that cannot be obtained directly from experiments. (1) The hypothetical porous network obtained by removing guests from crystals of compound 1 is highly flexible, and its deformations are inherently anisotropic, leading to lengthening or shortening of the channels along the c axis and no significant changes along the a and b axes. (2) Quantitative analysis of the total cohesive energy has revealed that hydrogen bonding within the network makes a dominant contribution, along with interactions of guests with the network. (3) Differences in the overall stability of crystals of compound 1 as the guests are varied do not arise primarily from significant changes in the cohesive energy of the network itself; instead, differences in guest-guest interactions play a key role, resulting from the nature of the guests and constraints imposed by the surrounding network. These insights, together with the results of ab initio molecular dynamics, help explain how hydrogen-bonded networks can be robust yet permit molecular movement that underlies the exchange of guests and adaptive porosity. These insights promise to be of general value to scientists studying ordered molecular materials in which strong directional interactions are prominent.     

Host—guest Complementarity and Crystal Packing of Intercalated Layered Structures

Intercalated layered structures are analyzed in order to estimate the rules governing their crystal packing. An overview is given on structural types of layered intercalates based on various types of host structures and guest species. The factors describing the host–guest complementarity in intercalated layered structures like: the character of active sites, the host–guest and guest–guest interactions, the size of guests and topology of layers are investigated and their effect on crystal packing is illustrated on examples. Special attention will be paid to the conditions for the regular ordering of guests in the interlayer space, as the requirement of structure ordering is of great importance in design of intercalates for special applications, where one has to control the interlayer porosity or electronic properties of guest molecules etc. A method of structure analysis based on a combination of molecular modeling and experiments has been worked out for intercalates. Molecular modeling (force field calculations) in conjunction with experiments (diffraction methods and vibration spectroscopy) enables us to analyze the disordered intercalated structures, where the conventional diffraction analysis fails.     

Enthalpy-entropy compensation reveals solvent reorganization as a driving force for supramolecular encapsulation in water

A chiral self-assembled M4L6 host assembly has been shown to be a suitable host for the supramolecular encapsulation of a series of guests in polar solvents, ranging from simple organic ammonium cations to more complex organometallic species. This molecular recognition process creates highly selective reactivity within the host cavity. In order to understand the factors driving the molecular recognition process, the standard thermodynamic parameters for encapsulation were determined for a series of protiated and fluorinated iridium guests in a variety of polar solvents using van't Hoff analysis. The encapsulation process for these guests exhibited enthalpy-entropy compensation effects. In solvents such as water and methanol, error analysis suggests a chemical origin for this behavior. In contrast, error analysis of this compensation behavior in polar aprotic solvents such as dimethyl sulfoxide reveals that this correlation is due to an artifact inherent in the intrinsic correlation between the enthalpy and entropy terms in the van't Hoff analysis. Guest encapsulation in polar protic solvents such as water appears to be driven by initial desolvation of the guest with concomitant rearrangement of the hydrogen bond networks in solution. This behavior shares common characteristics with other synthetic and natural host-guest and molecular recognition processes in aqueous solution, ranging from simple crown ether to complex enzyme-ligand interactions.     

Synthesis and molecular recognition of novel oligo(ethylenediamino) bridged bis(beta-cyclodextrin)s and their copper(II) complexes: enhanced molecular binding ability and selectivity by multiple recognition

Four bridged bis(beta-cyclodextrin)s tethered by different lengths of oligo(ethylenediamine)s have been synthesized and their inclusion complexation behavior with selected substrates elucidated by circular dichroism spectroscopy and fluorescence decay. In order to study their binding ability quantitatively, inclusion complexation stability constants with four dye guests, that is, brilliant green (BG), methyl orange (MO), ammonium 8-anilino-1-naphthalenesulfonic acid (ANS), and sodium 6-(p-toluidino)-2-naphthalenesulfonate (TNS), have been determined in aqueous solution at 25 degrees C with spectrophotometric, spectropolarimetric, or spectrofluorometric titrations. The results obtained indicate that the two tethered cyclodextrin units might cooperatively bind to a guest, and the molecular binding ability toward model substrates, especially linear guests such as TNS and MO, could be extended. The tether length plays a crucial role in the molecular recognition, the binding constants for ANS and TNS decrease linearly with an increase in the tether length of dimeric cyclodextrin. The Gibbs free energy changes (-deltaGo) for the unit increment per ethylene are 0.99 kJ mol(-1) for ANS and 0.44 kJmol(-1) for TNS, respectively. On the other hand, the presence of a copper(II) ion in metallobis(beta-cyclodextrin)s oligo(ethylenediamino) tethers enhances not only the original binding ability, but also the molecular selectivity through triple or multiple recognition, as compared with the parent bis(beta-cyclodextrin)s.     

Enantioselective binding of amino acids and amino alcohols by self-assembled chiral basket-shaped receptors

Amino acid appended diphenylglycoluril-based chiral molecular receptors 2 and 3 have been prepared and their aggregation has been studied in water at various pH's and in chloroform. The binding of several biologically relevant guests with aromatic moieties to these aggregates has been studied with UV-Vis spectroscopy in competition experiments with 4-(4-nitrophenylazo)resorcinol (Magneson) and 2-(4-hydroxyphenylazo)benzoic acid (HABA) as probes. Aggregates of chiral host 2b showed binding of catecholamines and aromatic amino acids in an aqueous environment, as well as discrimination between amino acid enantiomers, and can be considered a mimic for adrenergic receptors.     

Polycationic (mixed) core-shell dendrimers for binding and delivery of inorganic/organic substrates

The convergent synthesis of a series of polycationic aryl ether dendrimers has been accomplished by a convenient procedure involving quantitative quaternarization of aryl(poly)amine core molecules. The series has been expanded to the preparation of the first polycationic, mixed core-shell dendrimer. All these dendrimers consist of an apolar core with a peripheral ionic layer which is surrounded by a less polar layer of dendritic wedges. These cationic, macromolecular species have been investigated for their ability to form assemblies with (anionic) guest molecules. The results obtained from UV/Vis and NMR spectroscopies, and MALDI-TOF-MS demonstrate that all the cationic sites throughout the dendrimer core are involved in ion pair formation with anionic guests giving predefined guest/host ratios up to 24. The large NMR spectroscopic shifts of resonances correlated with the groupings located in the core of the dendrimers, together with the relaxation time data indicate that the anionic guests are associated with the cationic core of these dendrimers. The X-ray molecular structure of the octacationic, tetra-arylsilane model derivative [Si(C6H3[CH2NMe3](2)-3,5)4]8+. 8I- shows that the iodide counterions are primarily located near the polycationic sphere. The new polycationic dendrimers have been investigated for their catalytic phase-transfer behavior and substrate delivery over a nanofiltration membrane.     

Cucurbit[7]uril Inclusion Complexes with Benzimidazole Derivatives: A Computational Study

Molecular dynamics (MD) simulations were carried out to study the host–guest complexation in aqueous solution between cucurbit[7]uril (CB7) and the neutral and protonated forms of benzimidazole derivatives. Complexation occurs via encapsulation of the hydrophobic part (benzene ring) of the guest within the CB7 hydrophobic cavity, and the interactions of the amine group(s) of the imidazole ring of the guest with the CB7 carbonyl portals. The molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) method is used to estimate the host–guest Gibbs energy of binding. The results indicate that CB7 binds the protonated form more strongly than the neutral one, and that the dominant contribution to the Gibbs energy of complexation for the neutral and protonated guests is associated, respectively, with the host–guest van der Waals and electrostatic interactions. Quantum chemical calculations using dispersion-corrected density functional theory (DFT) are used to calculate the binding affinities and to predict the pK_a values of the free and complexed guests. The calculated pK_a values for the free guests reveal excellent agreement with the experimental values, while for the complexed guests, general trends are obtained.     

Supramolecular microcontact printing and dip-pen nanolithography on molecular printboards

The transfer of functional molecules onto self-assembled monolayers (SAMs) by means of soft and scanning-probe lithographic techniques-microcontact printing (muCP) and dip-pen nanolithography (DPN), respectively-and the stability of the molecular patterns during competitive rinsing conditions were examined. A series of guests with different valencies were transferred onto beta-cyclodextrin- (beta-CD-) terminated SAMs and onto reference hydroxy-terminated SAMs. Although physical contact was sufficient to generate patterns on both types of SAMs, only molecular patterns of multivalent guests transferred onto the beta-CD SAMs were stable under the rinsing conditions that caused the removal of the same guests from the reference SAMs. The formation of kinetically stable molecular patterns by supramolecular DPN with a lateral resolution of 60 nm exemplifies the use of beta-CD-terminated SAMs as molecular printboards for the selective immobilization of printboard-compatible guests on the nanometer scale through the use of specific, multivalent supramolecular interactions. Electroless deposition of copper on the printboard was shown to occur selectively on the areas patterned with dendrimer-stabilized gold nanoparticles.     

Oligo Tröger's bases--new molecular scaffolds

Oligo Tr?ger's bases are compounds containing two or more Tr?ger's base subunits (1,5-methanodiareno[b,f][1,5]diazocines) sharing one or more arene parts. Due to their interesting molecular shapes, these compounds are studied as chiral molecular tweezers, clips, cavitands, clefts, calixes, etc. This review includes all available data on oligo Tr?ger's bases, and introduces their preparation and properties to a wide audience.