Flat Molecules Research Articles

Wet spinning of a library of carbohydrate low molecular weight gels

HypothesisRecently, a low molecular weight hydrogel based on a carbohydrate alkyl amide has been successfully used as biomaterial for neuron cell culture and for 3D printing. Varying the molecular structure should make it possible to extend the library of carbohydrate low molecular weight hydrogels available for these applications and to improve their performances. ExperimentsThirteen molecules easy to synthetize and designed to be potentially biocompatible were prepared. They are based on gluconamide, glucoheptonamide, galactonamide, glucamide, aliphatic chains and glycine. Their gelation in water was investigated in thermal conditions and wet spinning conditions, namely by dimethylsulfoxide-water exchange under injection. FindingsNine molecules give hydrogels in thermal conditions. By wet spinning, six molecules self-assemble fast enough, within few seconds, to form continous hydrogel filaments. Therefore, the method enables to shape by injection these mechanically fragile hydrogels, notably in the perspective of 3D printing. Depending on the molecular structure, persistent or soluble gel filaments are obtained. The microstructures are varied, featuring entangled ribbons, platelets or particles. In thermal gelation, molecules with a symmetrical polar head (galacto, glucoheptono) give flat ribbons and molecules with an asymmetrical polar head (gluco) give helical ribbons. The introduction of an extra glycine linker disturbs this trend.

Symmetry mediated tunable molecular magnetism on a 2D material

Symmetries in nanoscale structures can be decisive for their structural, electronic, and magnetic properties, particularly in systems with reduced dimensions. Here we show that the symmetries of a flat metal-organic molecule adsorbed on a transition metal dichalcogenide, a 2-dimensional layered material, have a dramatic effect on the total spin and the intramolecular spin-spin interactions. Using a scanning probe microscope, we find two different molecular spin states by modifying the symmetry of the molecules via the twist angle to the substrate. Additionally, we observe significant non-collinear Dzyaloshinskii–Moriya interaction between two electron spins on the molecule induced by the spin-orbit coupling of the van der Waals coupled layered material with broken inversion symmetry. Our work opens a path for modifying the spin by exploiting symmetries and for studying the nature of surface-induced non-collinear spin-spin interaction within a single molecule which might allow the realization of more complex topological spin structures.

Cyclization Strategies for the Concurrent Installation of Multiple Quaternary Stereogenic Centers

AbstractIn this review we highlight the general cyclization strategies currently available to organic chemists for the concurrent and stereoselective installation of multiple Quaternary Stereogenic Centers (QSC) atoms in cyclic or polycyclic architectures. QSCs embedded in rigid cyclic architectures are motifs found in many blockbuster drugs and important bioactive natural product classes, and yet, direct access to these structures stereoselectively from simple precursors remains a significant challenge. Underscoring the difficulty associated with their synthesis, such topologically three‐dimensional molecules are underrepresented in existing small molecule compound libraries, which are instead dominated by linear or flat molecules. This review focuses on methods disclosed in both natural product synthesis and methodology studies since the turn of the 21st century. The cases to be examined successfully achieve these challenging transformations: (1) one‐step assembly of the cyclized architecture; and (2) concurrent stereoselective installation of multiple (≥2) new QSCs. These cyclization strategies, which address the aforementioned fundamental challenges in complex molecule synthesis, have been categorized into five broad groups: i) Biomimetic Polyene Cyclization Cascades; ii) Cyclization Cascades of Prochiral Alkenes; iii) Cycloadditions; iv) Dearomatizations; v) Electrocyclizations.

Heavy doped organic crystals ordering

The simple model that can describe structure and charge ordering in complex doped organic crystals is proposed. We consider the quasione-dimensional model of a crystal with chains (stacks) of flat BEDT-TTF molecules. In a chain of large molecules, small molecules fill every space between large molecules. The interaction between all molecules is described by the Lennard-Jones potential. It is shown that the small dopant molecules are in the double-well potential. It is shown that in case of the electrically neutral molecules at low temperatures, there is a fluctuating structural ordering: the small molecules group in pairs near a large molecule, and the lattice period in the fluctuation domain doubles. The structure of the boundary between the fluctuation domains is defined. In case of the charged molecules, correction to electric dipole interaction makes the system essentially three-dimensional, and there is ferroelectric ordering in a chain and an antiferroelectric one between the chains. Structure of the charge domains and domain boundaries are described.

Application of multi-active center organic quinone molecular functionalized graphene in fully pseudocapacitive asymmetric supercapacitors

5, 7, 12, 14-pentacenetetrone (PT), polycyclic quinone derivatives, are rich in carbonyl, which were investigated as a novel organic electrode material for supercapacitors. PT with a π conjugated system, is a flat molecule, generating strong π–π interactions between molecules. PT molecules were uniformly fixed on conductive reduced graphene oxide (rGO) through π–π interaction by one-step solvothermal method, forming a three-dimensional cross-linked PT@rGO hydrogel. This composite structure was conducive to reducing the charge transfer resistance and promoting the Faraday reaction of electrode, which achieved the superposition of electric double-layer capacitance and pseudocapacitance. Appropriate organic molecular loading can effectively improve electrochemical performance. The optimal PT@rGO electrode material displayed the specific capacitance of 433.2 F g−1 at 5 mV s−1 with an excellent rate capability in 1 mol l−1 H2SO4 electrolyte. Finally, the fully pseudocapacitive asymmetric supercapacitor has been assembled by using PT@rGO as positive electrode and benz[a]anthracene-7,12-quinone (BAQ) modified rGO(BAQ/rGO)as negative electrode, which exhibited the good energy storage performance in a cell voltage of 1.8 V.

Catalytic asymmetric reductive hydroalkylation of enamides and enecarbamates to chiral aliphatic amines

To increase the reliability and success rate of drug discovery, efforts have been made to increase the C(sp3) fraction and avoid flat molecules. sp3-Rich enantiopure amines are most frequently encountered as chiral auxiliaries, synthetic intermediates for pharmaceutical agents and bioactive natural products. Streamlined construction of chiral aliphatic amines has long been regarded as a paramount challenge. Mainstream approaches, including hydrogenation of enamines and imines, C–H amination, and alkylation of imines, were applied for the synthesis of chiral amines with circumscribed skeleton structures; typically, the chiral carbon centre was adjacent to an auxiliary aryl or ester group. Herein, we report a mild and general nickel-catalysed asymmetric reductive hydroalkylation to effectively convert enamides and enecarbamates into drug-like α-branched chiral amines and derivatives. This reaction involves the regio- and stereoselective hydrometallation of an enamide or enecarbamate to generate a catalytic amount of enantioenriched alkylnickel intermediate, followed by C–C bond formation via alkyl electrophiles.

Nanoscale ordering of planar octupolar molecules for nonlinear optics at higher temperatures

We develop scenarios for orientational ordering of an in-plane system of small flat octupolar molecules at the low-concentration limit, aiming towards nonlinear-optical (NLO) applications at room temperatures. The octupoles interact with external electric poling fields and intermolecular interactions are neglected. Simple statistical-mechanics models are used to analyze the orientational order in the very weak poling limit, sufficient for retrieving the NLO signals owing to the high sensitivity of NLO detectors and measurement chains. Two scenarios are discussed. Firstly, the octupolar poling field is imparted by a system of point charges; the setup is subject to cell-related constraints imposed by mechanical strength and dielectric breakdown limit. The very weak octupolar order of benchmarking TATB molecules is shown to emerge at Helium temperatures. The second scenario addresses the dipoling of octupolar molecules with a small admixture of electric dipolar component. It requires a strong field regime to become effective at Nitrogen temperature range. An estimation of the nonlinear susceptibility coefficient matrix for both scenarios is done in the high-temperature (weak interaction) limit formalism. We argue that moderate modifications of the system like, e.g., an increase of the size of the octupole, accompanied by dipole-assisted octupoling, can increase the poling temperature above Nitrogen temperatures.

From groove binding to intercalation: unravelling the weak interactions and other factors modulating the modes of interaction between methylated phenanthroline-based drugs and duplex DNA.

Several antitumor drugs base their cytotoxicity on their capacity to intercalate between base pairs of DNA. Nevertheless, it has been established that the mechanism of intercalation of drugs in DNA starts with the prior groove binding mode of interaction of the drug with DNA. Sometimes, for some kind of flat small molecules, groove binding does not produce any cytotoxic effect and the fast transition of such flat small molecules to the cytotoxic intercalation mode is desirable. This is the case of methylated phenanthroline (phen) derivatives, where, changes in the substitution in the position and number of methyl groups determine their capability as cytotoxic compounds and, therefore, it is a way for the modulation of cytotoxic effects. In this work, we studied this modulation by means of the interaction of the [Pt(en)(phen)]2+ complex and several derivatives by methylation of phen in different number and position and the d(GTCGAC)2 DNA hexamer via groove binding using PM6-DH2 and DFT-D methods. The analysis of the geometries, electronic structure and energetics of the studied systems was compared to experimental works to gain insight into the relation structure-interaction for the studied systems with cytotoxicity. The trends are explained by means of the Non-Covalent Interaction (NCI) index, the Energy Decomposition Analysis (EDA) and solvation contributions. Our results are in agreement with the experiments, in which the methylation of position 4 of phen seems to favour the interaction via groove binding thus making the transition to the intercalation cytotoxic mode difficult. Looking at the NCI results, these interactions come not only from the CH/π and CH/n interactions of the methyl group in position 4 but also from the ethylenediamine (en) ligand, whose orientation in the Pt complex was found in such a way that it produces a high number of weak interactions with DNA, especially with the sugar and phosphate backbone.

Crystal structures and dielectric properties of 4,4′-dimethyl-6,6′-dichlorothioindigo (Pigment Red 181)

The structures of the red polymorph (space group P 1) and the black polymorph (space group P21/c) of 4,4′-dimethyl-6,6′-dichlorothioindigo were solved from single-crystal samples. For both polymorphs, the spatial stacking of the flat molecules is driven by π-stacking and noncovalent interactions within the layers. Spectroscopic (UV–vis, IR and photoluminescence) and thermal properties of the red polymorph were investigated experimentally. The bandgap of this polymorph was estimated as 2.08 eV at room temperature. It is demonstrated that the electric conductivity of the red polymorph follows the hopping mechanism.

Flat crown ethers with planar tetracoordinate carbon atoms

AbstractNovel flat crown ether molecules have been characterized in silico using density functional theory. Monomer units of Si2C3 with a planar tetracoordinate carbon (ptC) atom have been used as building blocks. Alkali (Li+, Na+, K+, Rb+, and Cs+) and alkaline‐earth (Be2+, Mg2+, Ca2+, Sr2+, and Ba2+) metal ions, and uranyl (UO) ion selective complexes have also been theoretically identified. The high symmetry and higher structural rigidity of the host molecules may likely impart higher selectivity in chelation. The potential energy surface of the parent elemental composition, Si2C3H2, has been investigated using coupled‐cluster (CC) approximation. The molecule with a ptC atom within the latter is a low‐lying isomer lying 12.41 kcal mol−1 above the global minimum at the CCSD(T)/cc‐pVTZ level. The crown ether molecules identified here could theoretically be considered the derivatives of the ptC atom isomer. Theoretical binding energies (ΔE; 0 K) and thermally corrected Gibbs free energies (ΔG; 298.15 K) for crown ether molecules have been computed to gauge their binding affinities.

Suppressing π–π stacking interactions for enhanced solid-state emission of flat aromatic moleculesviaedge functionalization with picket-fence-type groups

Picket-fence-type substituents effectively suppress the π–π stacking interaction of flat aromatic molecules and enhance solid-state emission for application in organic light-emitting diodes.

A peculiar chromatographic selectivity of porous graphitic carbon during the separation of dileucine isomers

Porous graphitic carbon is a versatile stationary phase for high-performance liquid chromatography which performs especially well for isomeric separations. Shape-sensitivity of the stationary phase is caused by a steric effect when a molecule interacts with a flat carbon surface. It follows that branched, non-flat molecules are eluted much earlier than flat or linear molecules. In this short communication we show that if a molecule has a highly ionizable group, the “shape” of a molecule part which is farther from the ionizable group affects retention much more than the “shape” of a molecule part which is closer to the ionizable group. Dipeptides which consist of tert-leucine and norleucine were used as an example. Basic and acidic eluents were used. Retention strongly depends on whether a norleucine or tert-leucine residual is located near the non-ionized side in an eluent for both basic and acidic eluents. A residual located on the opposite side is less important. To investigate the possible causes of this peculiar retention behavior we compared the retention behavior of these dipeptides for porous graphitic carbon with the behavior for other types of stationary phases and with the calculated physicochemical properties. Strong and complex dependence of elution order on a mobile phase composition is demonstrated. The separation of other dileucine isomers is also considered. The applicability of porous graphitic carbon for the separation of complex mixtures of isomeric peptides is discussed.

From Isocyanides to Iminonitriles via Silver-mediated Sequential Insertion of C(sp3)-H Bond.

SummaryHeterocycles are prevalent constituents of many marketing drugs and biologically active molecules to meet modern medical challenges. Isocyanide insertion into C(sp3)–H bonds is challenging especially for the construction of quaternary carbon centers. Herein, we describe an efficient strategy for the synthesis of α-iminonitrile substituted isochromans and tetrahydroisoquinolines (THIQs) with quaternary carbon centers through silver-triflate-mediated sequential isocyanide insertion of C(sp3)–H bonds, where isocyanide acts as the crucial “CN” and “imine” sources. The produced α-iminonitriles have extensive applications as valuable synthetic building blocks for pharmacologically interesting heterocycles. This protocol could be further applied for the synthesis of iminonitrile-decorated phenanthridines and azapyrene. Interestingly, a remarkable aggregation-induced emission (AIE) effect was first observed for an iminonitrile-decorated pyrene derivative, which may open a particular area for iminonitrile applications in materials science.

Two new polymorphs of cis-perinone: crystal structures, physical and electric properties.

The crystal structures of two polymorphs of cis-perinone (bisbenzimidazo[2,1-b:1',2'-j]benzo[lmn][3,8]phenanthroline-6,9-dione, Pigment Red 194) were solved from single crystals obtained solvothermally from 1,2-dichlorobenzene or n-butanol at 220°C. Both crystal structures (space group P21/c) derive from stacking of flat molecules arranged due to π-π interaction. The melting points of these two polymorphs are 471°C and 468°C and their respective optical bandgaps are 1.94 eV and 1.71 eV. One of the polymorphs demonstrates drift and hopping mechanisms of electric conductivity, whereas the other one is dominated by the drift conductivity. The direct current (DC) electric conductivity of the samples are 4.77 × 10-13 S m-1 and 6.84 × 10-10 S m-1 at room temperature. The significant difference in DC conductivities can be explained by the dependence of the mobility and concentration of charge carriers on the structure of the samples.

Strain Effects on the Energy-Level Alignment at Metal/Organic Semiconductor Interfaces.

Flexible and wearable devices are among the upcoming trends in the opto-electronics market. Nevertheless, bendable devices should ensure the same efficiency and stability as their rigid analogs. It is well-known that the energy barriers between the metal Fermi energy and the molecular levels of organic semiconductors devoted to charge transport are key parameters in the performance of organic-based electronic devices. Therefore, it is paramount to understand how the energy barriers at metal/organic semiconductor interfaces change with bending. In this work, we experimentally measure the interface energy barriers between a metallic contact and small semiconducting molecules. The measurements are performed in operative conditions, while the samples are bent by a controlled applied mechanical strain. We determine that energy barriers are not sensitive to bending of the sample, but we observe that the hopping transport of the charges in flat molecules can be tuned by mechanical strain. The theoretical model developed for this work confirms our experimental observations.

How adsorbates alter the metallic behavior of quasi-1D electron systems of the Si(5 5 3)-Au surface

The plasmonic signals of quasi-1D electron systems are a clear and direct measure of their metallic behavior. Due to the finite size of such systems in reality, plasmonic signals from a gold-induced superstructure on Si(5 5 3) can be studied with infrared spectroscopy. The infrared spectroscopic features have turned out to be extremely sensitive to adsorbates. Even without geometrical changes of the surface superstructure, the effects of doping, of the adsorbate induced electronic surface scattering, and of the electronic polarizability changes on top of the substrate surface give rise to measurable changes of the plasmonic signal. Especially strong changes of the plasmonic signal have been observed for gold, oxygen, and hydrogen exposure. The plasmonic resonance gradually disappears under these exposures, indicating the transion to an insulating behavior, which is in accordance with published results obtained from other experimental methods. For C70 and, as shown here for the first time, TAPP-Br, the plasmonic signal almost retains its original intensity even up to coverages of many monolayers. For C70, the changes of the spectral shape, e.g. of electronic damping and of the resonance position, were also found to be marginal. On the other hand, TAPP-Br adsorption shifts the plasmonic resonance to higher frequencies and strongly increases the electronic damping. Given the dispersion relation for plasmonic resonances of 1D electron systems, the findings for TAPP-Br indicate a push-back effect and therefore stronger confinement of the free charge carriers in the quasi-one-dimensonal channel due to the coverage by the flat TAPP-Br molecules. On the gold-doped Si(5 5 3)-Au surface TAPP-Br acts as counter dopant and increases the plasmonic signal.

Surface Coupling of Octaethylporphyrin with Silicon Tetrachloride.

The surface assembly of 2,3,7,8,12,13,17,18-octaethylporphyrin (OEP) using silicon tetrachloride as a coupling agent was investigated using atomic force microscopy (AFM). Nanopatterned films of Si-OEP were prepared by protocols of colloidal lithography to evaluate the morphology, thickness, and molecular orientation for samples prepared on Si(111). The natural self-stacking of porphyrins can pose a challenge for molecular patterning. When making films on surfaces, porphyrins will self-associate to form co-planar configurations of random stacks of molecules. There is a tendency for the flat molecules to orient spontaneously in a side-on arrangement that is mediated by physisorption to the substrate as well as by π–π interactions between macrocycles to form a layered arrangement of packed molecules, analogous to a stack of coins. When silicon tetrachloride is introduced to the reaction vessel, the coupling between the surface and porphyrins is mediated through covalent Si–O bonding. For these studies, surface structures of Si-OEP were formed that are connected with a Si–O–Si motif to a silicon atom coordinated to the center of the porphyrin macrocycles. Protocols of colloidal lithography were used as a tool to prepare surface structures and films of Si-OEP to facilitate surface characterizations. Conceptually, by arranging the macrocycles of porphyrins with defined orientation, local AFM surface measurements can be enabled to help address mechanistic questions about how molecules self-assemble and bind to substrates.

Molecular Simulation of Naphthalene, Phenanthrene, and Pyrene Adsorption on MCM-41.

The adsorption of three typical polycyclic aromatic hydrocarbons (PAHs), naphthalene, phenanthrene, and pyrene with different ring numbers, on a common mesoporous material (MCM-41) was simulated based on a well-validated model. The adsorption equilibriums (isotherms), states (angle distributions and density profiles), and interactions (radial distribution functions) of three PAHs within the mesopores were studied in detail. The results show that the simulated isotherms agreed with previous experimental results. Each of the PAHs with flat molecules showed an adsorption configuration that was parallel to the surface of the pore, in the following order according to the degree of arrangement: pyrene (Pyr) > phenanthrene (Phe) > naphthalene (Nap). In terms of the interaction forces, there were no hydrogen bonds or other strong polar forces between the PAHs and MCM-41, and the O–H bond on the adsorbent surface had a unique angle in relation to the PAH molecular plane. The polarities of different H atoms on the PAHs were roughly the same, while those of the C atoms on the PAHs decreased from the molecular centers to the edges. The increasing area of the π-electron plane on the PAHs with the increasing ring number could lead to stronger adsorption interactions, and thus a shorter distance between the adsorbate and the adsorbent.

Amplification of Chirality by Adenosine Monophosphate-Capped Luminescent Gold Nanoclusters in Nematic Lyotropic Chromonic Liquid Crystal Tactoids.

Amplification of chirality across length scales is a key concept pertinent to many models aiming to unravel the origin of homochirality. Tactoids of lyotropic chromonic liquid crystals formed by DNA, dyes, and other flat ionic molecules in water in the biphasic nematic + isotropic regime turn out to be a particularly relevant system to investigate chirality transfer and amplification. Herein, we present experiments to determine the amplification of chirality by luminescent gold nanoclusters decorated with adenosine monophosphate inducing chiral nematic tactoids formed by disodium cromoglycate in water. Polarized optical microscopy investigations of the induced homochiral tactoids reveal that adenosine monophosphate shows a higher optical activity when bound to the surface of such gold nanoclusters in comparison to free adenosine monophosphate, despite a three-time lower overall concentration. Free adenosine monophosphate also induces the opposite chiral twist both in the bulk nematic phase as shown by induced thin film circular dichroism spectropolarimetry and in the tactoids in comparison to adenosine monophosphate bound to the gold nanocluster. Overall, these experiments demonstrate that lyotropic chromonic liquid crystal tactoids are powerful systems to image and quantify chirality amplification by key biological chiral molecules that would have played a role in the origin of homochirality.

A water-soluble two-dimensional supramolecular organic framework with aggregation-induced emission for DNA affinity and live-cell imaging.

A water-soluble two-dimensional supramolecular organic framework (2D SOF) was prepared via self-assembly of cucurbit[8]uril (CB[8]) and a three-arm flat linker molecule, which contains a benzene ring as the core and three Brooker's merocyanine (BM) analogs as arms. The strong host-guest interactions between BM and CB[8] and the directional head-to-tail stacking modes between the BM arms synergistically led to the formation of a 2D SOF. The structure of the 2D SOF was verified by 1H NMR, 2D 1H NMR NOESY, and DLS characterizations, while the monolayer structure was characterized by Cryo-TEM and AFM measurements. The 2D SOF exhibited an obvious AIE enhancement effect in H2O. In addition, DNA induced photoluminescence enhancement was observed for the monomer. As a result, this AIEgen-based 2D SOF could feature not only as a cell visualizer but also as a tracker for the nucleus in biological imaging due to the dynamic assembly process.