Intramolecular Space Research Articles

Triazole-based pyrene-sugar analogues for selective detection of picric acid in water medium and paper strips

Triazole-linked pyrene-appended inexpensive sensors 1 and 2 were synthesized from carbohydrates to instantly recognize picric acid (PA) based on a charge-transfer mechanism in the semi-water medium. Both sensors showed good selectivity and sensitivity towards PA over a wide variation of nitroaromatics in the absorbance and fluorescence methods. Moreover, sensors 1 and 2 were used for quick finding of picric acids using test strips. Interestingly, it was found that the sensitivity of 2 (LOD: 0.012 µM) is higher than 1 (LOD: 0.093 µM) might be explained by the close intramolecular space of the triazole/sugar residue and pyrene in sensor 2. The fluorescence quenching and structural features of the complexes (1-PA, 2-PA) were supported by density functional theory (DFT) calculations and spectroscopic studies.

Efficient circularly polarized thermally activated delayed fluorescence hetero-[4]helicene with carbonyl-/sulfone-bridged triarylamine structures

This work presents the first circularly polarized thermally activated delayed fluorescence hetero-[4]helicene with a carbonyl-/sulfone-bridged triarylamine structure (QPO-PhCz), demonstrating circularly polarized light emission through effective intramolecular steric hindrance and intramolecular space charge transfer.

Structural and theoretical study of (4E,5Z)‐4,5‐dibenzylidene‐1,2,3,6,7,8‐hexahydroacridine

AbstractThe crystal and molecular structure of (4E,5Z)‐4,5‐dibenzylidene‐1,2,3,6,7,8‐hexahydroacridine as a biologically active substance with potential antioxidant, anti‐inflammatory and anti‐microbial activity is reported. The title compound is found to be non‐planar. The rings are twisted around the central fragment of the molecule by 54.0 and 32.5°. The dihedral angle between the two phenyl rings is 23°. In crystal, the molecules are packed in head‐to‐head stacks along the b‐axis with no intermolecular H‐bonds. DFT B3LYP theoretical modeling with the LANL2DZ basis is performed and a topological analysis of the electron density distribution is carried out in the framework of the Bader QTAIM theory for both isolated molecules and dimeric associates forming stacks in the crystal. It is found that some intermolecular and intramolecular non‐valent interactions are to some extent related to the formation of weak covalent interactions in the intermolecular and intramolecular space.

Impact of Molecular Architecture and Adsorption Density on Adhesion of Mussel-Inspired Surface Primers with Catechol-Cation Synergy.

Marine mussels secrete proteins rich in residues containing catechols and cationic amines that displace hydration layers and adhere to charged surfaces under water via a cooperative binding effect known as catechol-cation synergy. Mussel-inspired adhesives containing paired catechol and cationic functionalities are a promising class of materials for biomedical applications, but few studies address the molecular adhesion mechanism(s) of these materials. To determine whether intramolecular adjacency of these functionalities is necessary for robust adhesion, a suite of siderophore analog surface primers was synthesized with systematic variations in intramolecular spacing between catechol and cationic functionalities. Adhesion measurements conducted with a surface forces apparatus (SFA) allow adhesive failure to be distinguished from cohesive failure and show that the failure mode depends critically on the siderophore analog adsorption density. The adhesion of these molecules to muscovite mica in an aqueous electrolyte solution demonstrates that direct intramolecular adjacency of catechol and cationic functionalities is not necessary for synergistic binding. However, we show that increasing the catechol-cation spacing by incorporating nonbinding domains results in decreased adhesion, which we attribute to a decrease in the density of catechol functionalities. A mechanism for catechol-cation synergy is proposed based on electrostatically driven adsorption and subsequent binding of catechol functionalities. This work should guide the design of new adhesives for binding to charged surfaces in saline environments.

Activity-Based Sensing and Theranostic Probes Based on Photoinduced Electron Transfer.

Fluorescent probes have become powerful tools in detection, imaging and disease diagnosis due to their high sensitivity, specificity, fast response, and technical simplicity. In the last decades, researchers have made remarkable progress in developing signaling mechanisms to design fluorescent probes such as photoinduced electron transfer (PET), intramolecular charge transfer (ICT), and fluorescence resonance energy transfer (FRET). Typical PET is composed of a multicomponent system in which a fluorophore (electron acceptor) is separately linked with a recognition group (electron donor) via a short spacer. PET probes normally feature a low fluorescence background and significant fluorescence enhancement in response to targets. Recent research revealed that PET probes have also been used as theranostic agents, whose fluorescence and toxicity can be simultaneously activated by cancer-specific parameters. In this Account, we highlight the recent advances of rational design and applications of PET probes, focusing primarily on studies from our research group. For example, different from the case of the traditional single-atom electron donor (O, S, N, Se, Te, etc.) in typical PET, we used more a electron-rich pyrrole ring to "switch off" the fluorescence of the fluorophore more efficiently through an "enhanced PET" effect which provided a lower background fluorescence and higher signal-to-noise ratio. Furthermore, normal PET represents the main principle behind the design of small molecule "off-on" fluorescent sensors. We developed new PET platform through intramolecular space folding (folding PET) to overcome the difficulty of designing PET enzyme-targeting probes. Therefore, based on typical PET and these new PET concepts, we, for instance, reported PET probes for the detection of Zn2+ without proton interference, a BODIPY-based d-PET probe for reporting local hydrophilicity within lysosomes, and an "enhanced PET" fluorescent probe for imaging HClO in cancer cells. We also developed COX-2-specific probe for identifying cancer cells and quantifying cancer-related events, and a KIAA1363-sensitive probe for tracking solid tumors in living mice. Furthermore, we first applied an aminopeptidase N (APN)-sensitive probe based on PET for cancer diagnosis and therapy. We anticipate that further development of PET fluorescent probes providing more sensitivity and selectivity to analytes of interest will be equipped with more functions and play indispensable roles in the studies of pathology, diagnostics, and cancer therapies.

Bulk Inclusions of Double Pyridazine Molecular Rotors in Hexagonal Tris( o-phenylene)cyclotriphosphazene.

A new generation of double pyridazine molecular rotors differing in intramolecular dipole-dipole spacing was synthesized. All rotor molecules formed bulk inclusions in a tris( o-phenylenedioxy)cyclotriphosphazene (TPP) host. Results of dielectric spectroscopy were fitted to a pair of nine-state models that accounted for interactions of neighboring dipoles at either an aligned or opposed possible orientation of the local threefold dipole rotation potentials within a channel of the TPP host. The results indicate dipole-dipole interaction strengths at the 100 to 200 K scale that lead dipoles to preferentially populate a subset of low-energy configurations. They also reveal that pyridazines with ethynyl substituents in 3- and 6-positions have slightly higher rotational barriers (3.2-3.5 kcal/mol) than those carrying one ethynyl and one tert-butyl group (1.9-3.0 kcal/mol). Upon cooling, these barriers reduce the rate of thermal transitions between the potential wells so much that the inclusions cannot achieve ordered dipolar ground states.

Highly Efficient Ultralong Organic Phosphorescence through Intramolecular-Space Heavy-Atom Effect.

Metal-free organic phosphorescent materials have attracted considerable attention in the fields of organic electronics and bioelectronics. However, it remains a great challenge to achieve organic phosphors with high quantum efficiency in a single-component system. We designed and synthesized two organic phosphors (PDCz and PDBCz) with an ultralong organic phosphorescence (UOP) feature. Both molecules showed ultralong emission lifetime of >200 ms. For PDBCz crystal, it was found that the absolute phosphorescence quantum efficiency reaches up to 38.1%. Combining the experimental and theoretical studies, the highly efficient UOP was mainly attributed to the intramolecular space heavy-metal effect, which facilitates the spin-orbit coupling between singlet and triplet excited states to effectively promote the intersystem crossing. This study will provide a new platform to rationally design highly efficient UOP materials and show its potential in the field of flexible electronics.

Unravelling the Secrets of Catechol-Cation Binding Synergy

Aqueous electrolyte solutions, including physiological fluids and seawater, limit polymer adhesion to surfaces, yet the marine mussel produces protein glues that adhere robustly under water, even in highly adverse, such as contaminated, conditions. Adhesive mussel foot proteins commonly contain adjacent catecholic 3,4-dihydroxyphenylalanine (Dopa) and cationic lysine residues. Previous work has shown that the pairing of these residues results in significantly higher adhesion energies on inorganic surfaces than either Dopa or lysine alone. Two mechanisms for synergistic binding have been proposed: either lysine evicts adsorbed cations on the substrate, enabling subsequent binding of Dopa to the substrate; or paired Dopa and lysine residues bind simultaneously to the substrate. To evaluate the validity of these two mechanisms, a series of synthetic analogs of siderophores (bacterial iron chelators) was synthesized. The intramolecular spacing between catecholic and cationic moieties was systematically varied across the series. Adhesion forces/energies of monolayers of siderophore analogs confined between symmetrical mica surfaces were measured using a Surface Forces Apparatus (SFA). Our results show no statistically significant dependence of adhesion energy on intramolecular spacing. These results support the surface cation eviction mechanism for catechol-cation synergy, and suggest that proteins incorporating Dopa and lysine residues will display elevated adhesion energies even when the groups are not directly adjacent. The knowledge that catechol-cation binding synergy operates even when the moieties are spatially separated will guide future design of biologically inspired adhesives for medical, dental, and marine applications.

Impact of biogenic amine molecular weight and structure on surfactant adsorption at the air–water interface

The oligoamines, such as ethylenediamine to pentaethylenetetramine, and the aliphatic biogenic amines, such as putrescine, spermidine and spermine, strongly interact with anionic surfactants, such as sodium dodecylsulfate, SDS. It has been shown that this results in pronounced surfactant adsorption at the air–water interface and the transition from monolayer to multilayer adsorption which depends upon solution pH and oligoamine structure. In the neutron reflectivity, NR, and surface tension, ST, results presented here the role of the oligoamine structure on the adsorption of SDS is investigated more fully using a range of different biogenic amines. The effect of the extent of the intra-molecular spacing between amine groups on the adsorption has been extended by comparing results for cadavarine with putrescine and ethylenediamine. The impact of more complex biogenic amine structures on the adsorption has been investigated with the aromatic phenethylamine, and the heterocyclic amines histamine and melamine. The results provide an important insight into how surfactant adsorption at interfaces can be manipulated by the addition of biogenic amines, and into the role of solution pH and oligoamine structure in modifying the interaction between the surfactant and oligoamine. The results impact greatly upon potential applications and in understanding some of the important biological functions of biogenic amines.

Synthesis of a Double-Spanned Resorc[4]arene via Ring-Closing Metathesis and Calculation of Aggregation Propensity

Ring-closing metathesis (RCM) catalyzed by a second-generation Grubbs catalyst has been used to synthesize resorc[4]arenes 2b-5b starting from undecenyl resorc[4]arene 1b fixed in the cone conformation. X-ray diffraction analysis of the major metathesis product, 3b (50% yield), revealed a cavity-shaped architecture resembling a basket, endowed with a large intramolecular space (∼10 Å) and a strong propensity to self-assemble as a supramolecular trio of heterochiral dimers. This prompted us to investigate the aggregation propensity of basket 3b in THF/water solution by UV-visible spectroscopy. The cavitation Gibbs free-energy change (ΔΔGcav = 4.78 kcal mol(-1)) associated with the self-assembly of macrocycle 3b was calculated as a measure of the solvophobic interactions involved in the process.

Backbone‐Directed Perylene Dye Self‐Assembly into Oligomer Stacks

Arm wrestling: Backbone-directed "arm-to-arm" aggregation of a newly designed perylene bisimide (PBI) dyad with a defined intramolecular space leads to the growth of kinetically stable extended PBI π-stacks. This PBI dyad was shown to assemble into oligomers up to 21 units in length.

Investigation of Coordination Interaction of Trigonal Schiff Base Compound with Zn(II) Ions in Organized Molecular Films

In order to investigate the supramolecular assembly and coordination interaction of special amphiphile, a trigonal Schiff base compound with long alkyl chains was designed and synthesized, and its supramolecular assembly and interaction properties were investigated by spectral and morphological measurements. It was found that the Schiff base compound can be spread on water surface to form stable monolayer. When on the Zn(II) ions subphase, an in situ coordination can occur for all ligands. As a result, a 1:2 complex was formed for the trigonal chain Schiff base with Zn(II) ions through the coordination interaction. Due to the directionality and strong matching of coordination, two Zn(II) ions can be encapsulated into intramolecular space of the trigonal Schiff base compound.

Identifying individual DNA species in a complex mixture by precisely measuring the spacing between nicking restriction enzymes with atomic force microscope

We discuss a novel atomic force microscope-based method for identifying individual short DNA molecules (<5000 bp) within a complex mixture by measuring the intra-molecular spacing of a few sequence-specific topographical labels in each molecule. Using this method, we accurately determined the relative abundance of individual DNA species in a 15-species mixture, with fewer than 100 copies per species sampled. To assess the scalability of our approach, we conducted a computer simulation, with realistic parameters, of the hypothetical problem of detecting abundance changes in individual gene transcripts between two single-cell human messenger RNA samples, each containing roughly 9000 species. We found that this approach can distinguish transcript species abundance changes accurately in most cases, including transcript isoforms which would be challenging to quantitate with traditional methods. Given its sensitivity and procedural simplicity, our approach could be used to identify transcript-derived complementary DNAs, where it would have substantial technical and practical advantages versus established techniques in situations where sample material is scarce.

The Crystal and Molecular Structure of (2Z)-2-[3-(4-Methoxybenzoyl)-4,4-dimethyl-1,2-oxazolidin-2-ylidene]-1-(4-methoxyphenyl)ethanone

The crystal and molecular structure of the title compound, viz., (2Z)-2-[3-(4-methoxybenzoyl)-4,4-dimethyl-1,2,-oxazolidin-2-ylidene]-1-(4-methoxyphenyl)ethanone (4), is reported. Compound 4 crystallises from toluene/hexanes mixtures in the P21/c space group with eight molecules in the unit cell. The unit cell parameters are: a = 20.9410(11) Å, b = 8.7523(5) Å, c = 21.2291(9) Å; β = 93.529(3)° and V = 3883.5(3) Å3. There are two structurally distinct molecules of 4 found in the solid-state which differ primarily in terms of the observed torsion angles and the overall intramolecular spacing between the aromatic groups. Bond lengths and angles of this tertiary amide are otherwise typical. This is the first crystallographically characterised example of this class of oxazoline precursors, which have previously found application in the syntheses of other heterocycles. Density functional theory (b3lyp 6-311++G** level of sophistication) has likewise been applied to estimate the gas-phase structure of the title compound.

Research on Hydrogen Bonding Interaction of Trigonal Schiff Base Compound with Barbituric Acid in Organized Molecular Films

In order to investigate the supramolecular assembly and intermolecular hydrogen bonding of special amphiphile, a trigonal Schiff base compound was designed and synthesized, and it supramolecular assembly and interaction properties were investigated by spectral measurements. It was found that the Schiff base compound can be spread on water surface to form stable monolayer. When it was spread on the subphase containing barbituric acid, it can show hydrogen bonding interaction with barbituric acid. Due to the directionality and strong matching of hydrogen bond, two barbituric acid molecules can be encapsulated into intramolecular space of the trigonal Schiff base compound through intermolecular H-bonding to form a 1:2 complex. A rational complex mode was proposed.

Probing the early stages of solvent evaporation and relaxation in solvent‐cast polymer thin films by spectroscopic ellipsometry

AbstractThe formation of solvent‐cast, poly(methyl methacrylate) (PMMA) thin films from dilute bromobenzene solutions was studied using an ellipsometry technique. Bromobenzene has a relatively high refractive index (compared to PMMA), which provides contrast in ellipsometry, allowing the concentration to be determined. The solvent also has a relatively low evaporation rate, which makes the film formation slow enough to capture via the technique. The formation of the glassy film is thus studied in situ, and information on solvent and void concentration in the thin film during the film formation process is obtained. There is evidence that nanovoids (representing intramolecular space) develop in the film when solvent evaporates. Copyright © 2011 John Wiley &amp; Sons, Ltd.

Voltage-gated Na+ channel ligands and ATP: relative molecular similarity and implications for channel function

The voltage-gated sodium channel (VGNC) is targeted by naturally occurring ligands and drugs of diverse structure. ATP modulates VGNC current in-vitro but is given little prominence in models describing channel function. This computational study uses superimposition and molecular fitting to investigate relative molecular similarity within the structures of ATP and VGNC ligands. A motif of 3 linked atoms (C-N-C) in the adenine ring of ATP satisfies the fitting of a wide range of anticonvulsant structures. An alternative group (N-C-N) provides one fitting motif for the ester and amide groups of local anaesthetic drugs; protonated amine and aromatic groups in the same conformers fit to a second motif in the adenine ring. Analogous structures from other drug classes with VGNC blocking activity give the same molecular fits to ATP. Structures fitted to the adenine ring of ATP occlude the intra-molecular space between the nucleoside and triphosphate chain in approximation to their established blocking, activating or neutral effects on Na+ current. The findings are discussed in terms of drug preferences for VGNC states and channel requirements for ATP.

Thermodynamic and spectrographic studies on the interactions of ct-DNA with 5-fluorouracil and tegafur

The interactions of calf thymus deoxyribonucleic acid (ct-DNA) with two antitumour drugs (5-fluorouracil and tegafur) in aqueous buffer solution (pH 7.40) have been investigated using nano-watt-scale isothermal titration calorimetry (ITC), circular dichroism (CD), ultraviolet absorption (UV) and fluorescence spectroscopy. Thermodynamic parameters, i.e., binding proportions and constants, standard changes of enthalpy (Δ H°), Gibbs free energy (Δ G°) and entropy (Δ S°) have been derived from the calorimetric data. The binding ratios of 5-fluorouracil and tegafur with base pairs in ct-DNA are 1:3 and 1:4, respectively. The thermodynamic parameters have been discussed according to the influence of drugs on molecular structure of the DNA shown spectrogram. The results indicate that molecule of 5-fluorouracil or tegafur can intercalate itself into the intra-molecular space formed by DNA double helix and cause some changes in the secondary structure of DNA molecule.

Synthesis and characterization of new cholesteric monomers and smectic polymers containing menthyl groups

New cholesteric monomers (M2−M5) and the corresponding smectic homopolymers (P2−P5) based on menthyl groups were synthesized. The chemical structures were characterized by Fourier transform infrared and 1H NMR. The specific optical rotations were evaluated with a polarimeter. The structure–property relationships of the new compounds are discussed. The mesomorphism was investigated by differential scanning calorimetry, thermogravimetric analysis, polarizing optical microscopy, and X-ray diffraction. The selective reflection property of light was studied with UV/Visible/NIR. The monomers M2−M5 formed the cholesteric or blue phase when a flexible link chain was inserted between the mesogenic core and the terminal menthyl groups by reducing the steric effect. M1 showed no mesomorphism, while M2−M5 revealed enantiotropic cholesteric phase. In addition, M2 and M3 also showed a cubic blue phase on cooling. The selective reflection of light for M2−M5 shifted to the short reciprocal wavelength region with increasing the temperature or intramolecular spacer length. P2−P5 exhibited the smectic A phase. The melting, clearing, and glass transition temperatures increased when increasing the aryl number in the mesogenic core or decreasing the intramolecular spacer length.

Assess the Intramolecular Cavity of a PAMAM Dendrimer in Aqueous Solution by Small-Angle Neutron Scattering

We present a contrast variation small-angle neutron scattering (SANS) study of a series of neutral PAMAM dendrimers in aqueous solutions using three different generations (G4−6) at a concentration of about 10 mg/mL. Varying the solvent hydrogen−deuterium ratio, the scattering contributions from the water molecules and the constituent components of PAMAM dendrimer can be determined. Using an analytical model of the scattering cross section I(Q) incorporating the effect of water penetration, we have quantified the intramolecular space of PAMAM dendrimer by evaluating the number of guest water molecules, and we draw a direct comparison to computational predictions. As expected, the overall available internal cavity was seen to increase as a function of increasing dendrimer generation. However, the fraction of water accessible volume of a dendrimer was found to remain invariant for the three generation PAMAM dendrimers studied in this report. We have also estimated the average water density inside a dendrimer, which is found to be higher than that of bulk water.