Conformational control of molecular tweezers containing a disulfide bond by redox reactions

Molecular tweezers 1b having two alkyl thiol chains were prepared. Intramolecular cyclization of the thiols under oxidative conditions afforded tweezers 2b containing a disulfide bond. X-ray crystal analysis and temperature dependent ¹H NMR spectra analysis revealed that the structure of 1b has a stepped anti arrangement of the three aromatic rings, although that of 2b adopted a cleft conformation because of the intramolecular interaction between the alkyl chain and the terminal naphthalene rings. The thiol-disulfide redox reaction proceeded smoothly and reversibly to control the conformation of the tweezers.     

A conformationally reliable spacer for molecular tweezers

[figure: see text] A reliable and rigid spacer, trans,trans,trans-perhydronaphthacene, for molecular tweezers was designed. A synthesis and molecular recognition study of its 1,14-disubstituted derivatives was carried out.     

Conformational control of flexible molecular tweezers by intramolecular CH/π interaction

The synthesis of new flexible molecular tweezers based on 3,4,8,10,11,13-hexahydro-1H,6H-2,5,9,12-tetraoxa-benzo[1,2:4,5]dicyclooctene bearing two naphthalenes is presented. Intramolecular CH/π interaction between the alkyl ring and the two terminal naphthalenes controls the conformation to give a self-quenched cleft form.     

Calculation of molecular energy indices by the bond interaction method

Conclusions Parameters were determined for an interacting bond model for hydrocarbons and oxygen- and sulfur-containing organic molecules. The parameters obtained were used to calculate the homolytic bond dissociation energies and molecular formation energies.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 7, pp. 1680–1683, July, 1988.     

Synthesis and properties of TTFV-hinged molecular tweezers

Two molecular tweezers containing a tetrathiafulvalene vinylogue (TTFV) core were synthesized via sequential Sonogashira and Horner-Wadsworth-Emmons (HWE) reactions. The electrochemical and spectroscopic properties of these TTFV tweezers were investigated by UV-vis absorption spectroscopy, cyclic voltammetry, and spectro-electrochemical measurements. The property characterizations suggest potential application in electrochemically-actuated molecular switching devices.     

A molecular view of bond rupture

Molecular mechanisms of rupture will be discussed in the light of recent computational studies. Bonds formed by materials as diverse as simple crystalline solids, glassy polymers, and biological ligands and receptors, reveal similar behavior. When these bonds are pulled apart at constant velocity, they rupture through a series of sudden yield events during which the material reorganizes. Yield events are separated by periods of elastic deformation where the stress builds until the system becomes unstable. The nature of the structural change at yield events varies from system to system. Small cavities form in the polymer film, an additional atomic layer is formed in the crystal, and hydrogen binding sites rearrange in the biological system. The work required to rupture these bonds is determined by the full sequence of yield events.     

芳酰胺分子钳对阴离子的识别研究

利用差紫外光谱法考察了新的分子钳1～4对阴离子的识别性能,测定了25 ℃下,在CHCl3中主客体间的结合常数(Ka)和自由能变化(ΔG°). 结果表明,所有分子钳主体对所考察的客体分子显示良好的识别作用,主客体间形成1∶ 1型超分子配合物.识别作用的主要推动力为多重氢键作用.并利用核磁共振氢谱与计算机模拟作为辅助手段对实验结果进行了解释.     

Towards the design of neutral molecular tweezers for anion recognition

Molecular tweezers are simple molecular receptors that can be characterized by the presence of two flat pincers separated by a more or less rigid tether. They have the ability to form complexes with a substrate molecule by gripping the substrate between the tips of the tweezers in a similar manner to that of mechanical tweezers. Kl?rner et al. synthesized one of the structurally simplest molecular tweezers, which is reported to bind electrodeficient aromatic and aliphatic substrates as well as organic cations. Complexes between these molecular tweezers and electron-rich aromatic, aliphatic, or anionic substrates have not been observed. Inspired by several recent reports that describe the interaction of hexafluorobenzene with electron-rich sites of molecules, we conducted a theoretical study to show the possibility of building molecular tweezers, based on those synthesized by Kl?rner, which were able to bind to anions and thus increase their potential as molecular receptors. We characterized complexes formed between several fluorinated derivatives of simple tweezers and an iodine anion, and analyzed the nature of the intermolecular interactions as well as the energetics for the process of complexation. The stabilization trend reflected by the energetic results when fluorine substituents were added to benzene rings confirms our hypothesis about the possibility of obtaining neutral tweezers composed of aromatic rings that can bind anions.     

The measurement of molecular diversity by receptor site interaction simulation

The assembly of large compound libraries for the purpose of screening against various receptor targets to identify chemical leads for drug discovery programs has created a need for methods to measure the molecular diversity of such libraries. The method described here, for which we propose the acronym RESIS (for Receptor Site Interaction Simulation), relates directly to this use. A database is built of three-dimensional representations of the compounds in the library and a set of three-point three-dimensional theoretical receptor sites is generated based on putative hydrophobic and polar interactions. A series of flexible, three-dimensional searches is then performed over the database, using each of the theoretical sites as the basis for one such search. The resulting pattern of hits across the grid of theoretical receptor sites provides a measure of the molecular diversity of the compound library. This can be conveniently displayed as a density map which provides a readily comprehensible visual impression of the library diversity characteristics. A library of 7500 drug compounds derived from the CIPSLINEPC databases was characterized with respect to molecular diversity using the RESIS method. Some specific uses for the information obtained from application of the method are discussed. A comparison was made of the results from the RESIS method with those from a recently published two-dimensional approach for assessing molecular diversity using sets of compounds from the Maybridge database (MAY).     

Van der Waals interaction and hydrogen bond effects on molecular vibrational frequencies

The frequency shift of an AZ two-atomic fragment upon molecule transfer from gas to solution or matrix is investigated. The nearest neighbour ligands are considered to form a cluster. The coupling of the ν_s(AZ) mode with the cluster low-frequency oscillators (ν_Q) is taken into account. One such oscillator can be the ν_σ(AZ…B) intermolecular stretching frequency oscillator in the H-bonded or charge transfer complex. A general expression for the ν_s(AZ) frequency shift (Δω) is obtained, which allows for both the usual van der Waals interaction and the (ν_s, ν_σ) and (ν_s, ν_Q) mode couplings. When the former prevails, the relative frequency shift Δω/ω_f is invariant to the Z → Z* (e.g., H → D) isotopic substitution. When the mode coupling prevails, the quantity Δω/ω²_f is invariant what is typical for H bonds. If the H-bonded or charge transfer complexes are absent, the frequency shift Δω is proportional to α(ϱ_AZ + ϱ_L)⁻⁶ where α is the polarizability of the ligand, ϱ_AZ and ϱ_L are the van der Waals radii of AZ and ligand, respectively. The additional ν_s(AH) frequency shift upon transfer of the AH…B complex from the gas to solution seems to be caused by (ν_s, ν_Q) mode coupling.     

Langmuir and Langmuir-Blodgett monolayers of molecular tweezers and clips

Molecular clips and tweezers are able to selectively bind electron-deficient aromatic and aliphatic substrates. By means of pressure-area isotherms and Brewster angle microscopy (BAM), the self-association process and phase behavior of dimethylene-bridged molecular clips and tetramethylene-bridged molecular tweezers each substituted with two acetoxy groups as polar head groups were investigated. In a series of experiments, we observed that the molecular surface area of the clips and tweezers only depended on the skeletal structure and not on the polar groups. The measured areas agreed with the effective molecular diameters of the molecules if the aromatic side walls of the clips or tweezers were assumed to be aligned perpendicularly to the water surface. We compared the phase behavior of the pure molecular clips and tweezers with that of the host-guest complexes of these molecules, which were formed with 1,2,4,5-tetracyanobenzene (TCNB) as the guest molecule. For the clips with a central benzene (I) and naphthalene spacer unit (II), the complex formation with TCNB had no measurable influence on the phase diagrams of the films. We observed, however, a dramatic difference in the BAM images and pi-A isotherms between the pure molecular tweezers III and its complex with TCNB (TCNB@III). In addition to the pi-A isotherms, we used the surface potential (V)-area (A) isotherms to compare the pure tweezers III with the corresponding complex (TCNB@III). There was a strong difference in the maximum surface potential value for the pure tweezers (450 mV) and that for the complex (300 mV). In additional experiments, we prepared LB layers of such molecules, which were investigated by fluorescence spectroscopy. In comparison to the pure tweezers III, a luminescence emission of charge-transfer (CT) origin was observed for the host-guest complex (TCNB@III) fixed on the solid substrate. It turned out that the spectra were in good agreement with the results observed in chloroform solution.     

Dynamics in host-guest complexes of molecular tweezers and clips

The dynamics in the host-guest complexes of the molecular tweezers 1 a,b and clips 2 a,b with 1,2,4,5-tetracyanobenzene (TCNB, 3) and tropylium tetrafluoroborate (4) as guest molecules were analyzed by temperature-dependent 1H NMR spectroscopy. The TCNB complexes of tweezers 1 a,b were found to be particularly stable (dissociation barrier: DeltaG(++)=16.8 and 15.7 kcal mol(-1), respectively), more stable than the TCNB complexes of clips 2 a,b and the tropylium complex of tweezer 1 b (dissociation barrier: DeltaG(++)=12.4, 11.2, and 12.3 kcal mol(-1), respectively). A detailed analysis of the kinetic and thermodynamic data (especially the negative entropies of activation found for complex dissociation) suggests that in the transition state of dissociation the guest molecule is still clipped between the aromatic tips of the host molecule. The 1H NMR analysis of the TCNB complexes 3@1 b and 3@2 a at low temperatures (T<-80 degrees C) showed that 3 undergoes fast rotation inside the cavity of tweezer 1 b or clip 2 a (rotational barrier: DeltaG( not equal)=11.7 and 8.3 kcal mol(-1), respectively). This rotation of a guest molecule inside the host cavity can be considered to be the dynamic equilibration of noncovalent conformers. In the case of clip complex 3@2 a the association and rotational barriers are smaller by DeltaDeltaG(++)=3-4 kcal mol(-1) than those in tweezer complexes 3@1 a,b. This can be explained by the more open topology of the trimethylene-bridged clips compared to the tetramethylene-bridged tweezers. Finally, the bromo substituents in the newly prepared clip 2 b have a substantial effect on the kinetics and thermodynamics of complex formation. Clip 2 b forms weaker complexes with (TCNB, 3) and tetracyanoquinodimethane (TCNQ, 12) and a more stable complex with 2,4,7-trinitrofluoren-9-ylidene (TNF, 13) than the parent clip 2 a. These results can be explained by a less negative electrostatic potential surface (EPS) inside the cavity and a larger van der Waals contact surface of 2 b compared to 2 a. In the case of the highly electron-deficient guest molecules TCNB and TCNQ the attractive electrostatic interaction is predominant and hence responsible for the thermodynamic complex stability, whereas in the case of TNF with its extended pi system, dispersion forces are more important for host-guest binding.     

Calixarene-based metalloporphyrins: molecular tweezers for complexation of DABCO

We investigated the formation of host-guest complexes between zinc porphyrins covalently attached to calixarenes via amidic bonds and a small bidentate ligand bearing two nitrogen atoms. Depending upon the calixarene structure (S vs CH₂ bridges), the ligand 1,4-diazabicyclo[2.2.2]octane (DABCO) is complexed by metalloporphyrin units by two different ways. While the thiacalix[4]arene prefers an intramolecularly closed cavity with a binding constant of (1.0±0.1)×10⁷ M⁻¹ in CHCl₃ at 294 K (stoichiometry 1:1), the classical calix[4]arene forms a complex by ligation of both porphyrin units separately (stoichiometry 2:1). The differences observed can be rationalized in terms of cavity size and the preorganization due to intramolecular hydrogen bonding of the calixarene lower rim.     

A Bayesian molecular interaction library

We describe a library of molecular fragments designed to model and predict non-bonded interactions between atoms. We apply the Bayesian approach, whereby prior knowledge and uncertainty of the mathematical model are incorporated into the estimated model and its parameters. The molecular interaction data are strengthened by narrowing the atom classification to 14 atom types, focusing on independent molecular contacts that lie within a short cutoff distance, and symmetrizing the interaction data for the molecular fragments. Furthermore, the location of atoms in contact with a molecular fragment are modeled by Gaussian mixture densities whose maximum a posteriori estimates are obtained by applying a version of the expectation-maximization algorithm that incorporates hyperparameters for the components of the Gaussian mixtures. A routine is introduced providing the hyperparameters and the initial values of the parameters of the Gaussian mixture densities. A model selection criterion, based on the concept of a `minimum message length' is used to automatically select the optimal complexity of a mixture model and the most suitable orientation of a reference frame for a fragment in a coordinate system. The type of atom interacting with a molecular fragment is predicted by values of the posterior probability function and the accuracy of these predictions is evaluated by comparing the predicted atom type with the actual atom type seen in crystal structures. The fact that an atom will simultaneously interact with several molecular fragments forming a cohesive network of interactions is exploited by introducing two strategies that combine the predictions of atom types given by multiple fragments. The accuracy of these combined predictions is compared with those based on an individual fragment. Exhaustive validation analyses and qualitative examples (e.g., the ligand-binding domain of glutamate receptors) demonstrate that these improvements lead to effective modeling and prediction of molecular interactions.     

A molecular orbital explanation of bond distance variation caused by hydrogen bond formation

For hydrogen bond systems X–D–HA–Y, a simple molecular orbital model is proposed to understand the mechanism of the bond distance variations caused by the hydrogen bond formation. This model explains the bond distance variations for X–D and A–Y as follows. Electrostatic potential that the electrons in a molecule receive from other molecules causes the changes in atomic orbital energy differences between the bonded atoms. Then, the changes in the orbital energy differences make the bond orders larger or smaller and consequently the bond distances vary. The validity of this model has been confirmed by the effective fragment potential method, using the test systems of (HCOOH)₂, HCONH₂ (formamide) crystal and BF₃·2H₂O crystal.     

Photoactive preorganized subphthalocyanine-based molecular tweezers for selective complexation of fullerenes

The development of new chromophoric receptors capable of binding curved carbon nanostructures is central to the quest for improved fullerene-based organic photovoltaics. We herein report the synthesis and characterization of a subphthalocyanine-based multicomponent ensemble consisting of two electron-rich SubPc-monomers rigidly attached to the convex surface of an electron-poor SubPc-dimer. Such a unique configuration, especially in terms of the two SubPc-monomers, together with the overall stiffness of the linker, endows the multicomponent system with a well-defined tweezer-like topology to efficiently embrace a fullerene in its inner cavity. The formation of a 1 : 1 complex was demonstrated in a variety of titration studies with either C60 or C70. In solution, the underlying association constants were of the order of 10⁵ M⁻¹. Detailed physicochemical experiments revealed a complex scenario of energy- and electron-transfer processes upon photoexcitation in the absence and presence of fullerenes. The close proximity of the fullerenes to the electron-rich SubPcs enables a charge shift from the initially formed reduced SubPc-dimer to either C60 to C70.

A tweezer-like subphthalocyanine-based ensemble has been developed for the selective recognition of fullerenes. The physicochemical properties of both the photoactive receptor and its inclusion complexes with fullerenes have been investigated.     

Sterically controlled recognition of macromolecular sequence information by molecular tweezers

Sequence-specific binding is demonstrated between pyrene-based tweezer molecules and soluble, high molar mass copolyimides. The binding involves complementary pi-pi stacking interactions, polymer chain-folding, and hydrogen bonding and is extremely sensitive to the steric environment around the pyromellitimide binding-site. A detailed picture of the intermolecular interactions involved has been obtained through single-crystal X-ray studies of tweezer complexes with model diimides. Ring-current magnetic shielding of polyimide protons by the pyrene "arms" of the tweezer molecule induces large complexation shifts of the corresponding 1H NMR resonances, enabling specific triplet sequences to be identified by their complexation shifts. Extended comonomer sequences (triplets of triplets in which the monomer residues differ only by the presence or absence of a methyl group) can be "read" by a mechanism which involves multiple binding of tweezer molecules to adjacent diimide residues within the copolymer chain. The adjacent-binding model for sequence recognition has been validated by two conceptually different sets of tweezer binding experiments. One approach compares sequence-recognition events for copolyimides having either restricted or unrestricted triple-triplet sequences, and the other makes use of copolymers containing both strongly binding and completely nonbinding diimide residues. In all cases the nature and relative proportions of triple-triplet sequences predicted by the adjacent-binding model are fully consistent with the observed 1H NMR data.     

Clusteroluminescence: A gauge of molecular interaction

Clusteroluminescence (CL) materials, as an emerging class of luminescent materials with unique photophysical properties, have received increasing attention owing to their great theoretical significance and potential for biological applications. Although much progress has been made in the design, synthesis and application of CL materials, there is still a big challenge in the emission mechanism. So far, through-space interaction has been proposed as the preliminary mechanism of the corresponding clusterization-triggered emission (CTE) effect, but a systematic theory is still needed. This review summarizes the current mechanistic understanding of CL materials including organic/inorganic small molecules, and polymers with/without isolated aromatic structures. In addition, some strategies to achieve high quantum yield, adjustable emission color, and persistent room temperature phosphorescence in CL materials are also summarized. At last, a perspective of the mechanism and application of CL materials are demonstrated, which inspire the researchers working on the development of new kinds of functional materials.     

Synthesis and photophysical,antibacterial studies of some novel molecular tweezers

Zeroth and first generation dendritic wedges with thiophene amide as surface group and 1, 2, 3-triazole as bridging unit which can function as molecular tweezers are synthesised by both convergent and divergent approaches. All the synthesised dendritic wedges displayed the absorbance band between 256 and 294 nm and fluorescence maximum between 357 and 528 nm supporting their self complementary property. Dendritic wedge 5 showed better antibacterial activity than other dendritic wedges in the assay against the human pathogens viz Staphylococcus aureus, Escherichia coli, Bacillus cereus and Klebsiella pneumonia and the dentritic wedge 5 was also effective in the computational molecular docking studies.