Molecular Rods Research Articles

Engineering Switchable Rotors in Molecular Crystals with Open Porosity

The first example of a porous molecular crystal containing rotors is presented. The permanently porous crystal architecture is sustained by rotor-bearing molecular rods which are connected through charge-assisted hydrogen bonds. The rotors, as fast as 10(8) Hz at 240 K, are exposed to the crystalline channels, which absorb CO2 and I2 vapors at low pressure. The rotor dynamics could be switched off and on by I2 absorption/desorption, showing remarkable change of material dynamics by the interaction with gaseous species and suggesting the use of molecular crystals in sensing and pollutant management.

Synthesis of homochiral tris-indanyl molecular rods.

Homochiral tris-indanyl molecular rods designed for supramolecular surface self-assembly were synthesized. The chiral indanol moiety was constructed via a Ti-mediated alkyne trimerization. Further manipulations resulted in a homochiral indanol monomer. This was employed as the precursor for successive Sonogashira and Ohira-Bestman reactions towards the homochiral tris-indanyl molecular rods. The molecular rods will be applied for scanning tunnelling microscopy studies of their surface self-assembly and chirality.

Theoretical Investigation of the Dependence of Exchange Interaction on Dihedral Angle between Two Aromatic Rings in a Wire Unit

Abstract The dependence of intramolecular exchange interaction on dihedral angle between two aromatic rings in a wire unit was investigated by using broken-symmetry UDFT (BS-UDFT) calculation. Biphenyl rings and 2,2′-bithiophene rings were used for molecular rods and nitronyl nitroxide and verdazyl were chosen as organic radical species. The exchange interaction was proportional to cos2 θ where θ is the dihedral angle between two aromatic rings. This result shows good agreement with the dependence of conductance on dihedral angle between two phenyl rings. Our calculation strongly suggests the similarity of molecular conductance and intramolecular exchange interaction and reinforced the existence of an electron-tunneling mechanism underlying two physical properties.

Ferrocenyl end capped molecular rods: synthesis, structure, and properties

A series of ferrocenyl phenylethynyl rods 1–11 were designed, and synthesized by a Pd catalysed Sonogashira cross-coupling, and oxidative homo-coupling reactions. The ferrocenyl moieties in the rods 1–11 are attached at the para/meta position of phenylethynyl unit or at the acetylenic unit. The effect of enhancing the conjugation, and connectivity (meta/para) on the photonic and electrochemical properties were explored. The para linkage, and butadiynyl linkage lower the band gap in the rods. The meta linked ferrocenyl phenylethynyl rods 2, 4, and 10 show good HOMO–LUMO separation compared to para linked rods 1, 3, 9. The single crystal X-ray structures of rods 2, 4, 10, 14 and 19 are reported. The ferrocene units in rods 2, 4, and 10 are in a trans configuration with respect to the phenyl ring.

Changing gears to neutral in a polymorph of one-dimensional arrays of cogwheel-like pairs of molecular rotors

We report on a polymorph (2) of an amphidynamic crystal of molecular rods with two helical 1,4-bis(ethynyl)bicyclo[2.2.2]octane rotators where half of the rod-like molecules appear to be shifted with respect to their closest neighbours. This translation takes cogwheel-like pairs of rotators apart in the lattice in such a way that their motion becomes uncorrelated. This property is to be contrasted with the highly correlated motion found to govern the rotators in a recently-published polymorph 1 of the same material. As with polymorph 1, this motion is shown to take place independently of mutations in the handedness of the rotators and of the ‘mutamer’-induced second harmonic generation.

Synthesis and Spectroscopic Characterization of Fluorophore‐Labeled Oligospiroketal Rods

AbstractFluorescence probes consisting of well‐established fluorophores in combination with rigid molecular rods based on spirane‐type structures were investigated with respect to their fluorescence properties under different solvent conditions. The attachment of the dyes was accomplished by 1,3‐dipolar cycloaddition between alkynes and azides (‘click’ reaction) and is a prime example for a novel class of sensor constructs. Especially, the attachment of two (different) fluorophores on opposite sides of the molecular rods paves the way to new sensor systems with less bulky (compared to the conventional DNA‐ or protein‐based concepts), nevertheless rigid spacer constructs, e.g., for FRET‐based sensing applications. A detailed photophysical characterization was performed in MeOH (and in basic H2O/MeOH mixtures) for i) rod constructs containing carboxyfluorescein, ii) rod constructs containing carboxyrhodamine, iii) rod constructs containing both carboxyfluorescein and carboxyrhodamine, and iv) rod constructs containing both pyrene and perylene parts. For each dye (pair), two rod lengths with different numbers of spirane units were synthesized and investigated. The rod constructs were characterized in ensemble as well as single‐molecule fluorescence experiments with respect to i) specific roddye and ii) dyedye interactions. In addition to MeOH and MeOH/NaOH, the rod constructs were also investigated in micellar systems, which were chosen as a simplified model for membranes.

Synthesis of closo- and nido-biscarboranes with rigid unsaturated linkers as precursors to linear metallacarborane-based molecular rods

Several biscarborane-type derivatives of 8-iodo-1,2-dicarba-closo-dodecaborane (1), suitable as the precursors of linear metallacarborane-based molecular rods, were prepared. The synthesized closo-compounds contained two carborane moieties connected through a rigid linear unsaturated linker. The linkers were based on ethynylene and para-phenylene fragments and their combinations. The deboronation of all reported closo-compounds was selective and afforded nido-products with open pentagonal faces on opposite sides of the molecule, parallel to each other and perpendicular to the main molecular axis. All of the closo and nido products were characterized by a variety of physical methods (NMR, HRMS, IR). The structures of closo-carboranes 3, 6, 9, and 14 and nido-carboranes 15 and 17 were established by X-ray diffraction.

The synthesis of π-electron molecular rods with a thiophene or thieno[3,2-b]thiophene core unit and sulfur alligator clips

A series of short oligo(p-phenylene-ethynylene)- and oligo(p-phenylenevinylene)-type molecular rods with an electronically rich thiophene or thieno[3,2-b]thiophene core unit and sulfur anchoring groups (AcS−, t-BuS−) at the termini have been synthesised using Sonogashira coupling or Horner–Wadsworth–Emmons (E)-olefination methodology. The collection of linear/bent, conjugated/cross-conjugated systems has been characterised by UV–vis and fluorescence spectroscopy, optical/calculated HOMO–LUMO gaps and calculated excitation energies.

Oligo(naphthylene–ethynylene) Molecular Rods

AbstractMolecular rods designed for surface chirality studies have been synthesized in high yields. The molecules are composed of oligo(naphthylene–ethynylene) skeletons and functionalized at their two termini with carboxylic acids and hydrophobic groups. The molecular skeletons were constructed by means of palladium‐catalyzed Sonogashira reactions between naphthyl halides and acetylenes. The triazene functionality was used as a protected iodine precursor to allow linear extension of the molecular rods during the syntheses. The carboxylic acid groups in the target molecules were protected as esters during the synthesis to keep the large aromatic molecules soluble during their syntheses. These rigid oligomers were designed to form lamella‐like structures when adsorbed on a surface, through which multiple distinguishable surface conformations should be obtainable. Preliminary scanning tunneling microscopy imaging confirmed these properties.

Electron transport through catechol-functionalized molecular rods

The charge transport properties of a catechol-type dithiol-terminated oligo-phenylene-ethynylene was investigated by cyclic voltammetry (CV) and by the scanning tunnelling microscopy break junction technique (STM-BJ). Single molecule charge transport experiments demonstrated the existence of high and low conductance regions. The junction conductance is rather weakly dependent on the redox state of the bridging molecule. However, a distinct dependence of junction formation probability and of relative stretching distances of the catechol- and quinone-type molecular junctions is observed. Substitution of the central catechol ring with alkoxy-moieties and the combination with a topological analysis of possible π-electron pathways through the respective molecular skeletons lead to a working hypothesis, which could rationalize the experimentally observed conductance characteristics of the redox-active nanojunctions.

Molecular Daisy Chains: Synthesis and Aggregation Studies of an Amphiphilic Molecular Rod

A water-soluble cyclophane as the loop subunit, monofunctionalized with a molecular rod, has been synthesized to introduce a new binding motif for mechanically interlinked oligomers. It has been demonstrated that this hermaphroditic compound forms [c2]daisy chains in polar solvent over a wide range of concentrations. Furthermore, evidence for the formation of higher mechanically interlinked oligomers above the critical aggregation concentration has been obtained.

Structure and Dynamics of Molecular Rods in Membranes: Application of a Spin-Labeled Rod

Molecular rods consisting of a hydrophobic backbone and terminally varying functional groups have been synthesized for applications for the functionalization of membranes. In the present study, we employ a spin-labeled analogue of a recently described new class of molecular rods to characterize their dynamic interactions with membranes. By using the different approaches of ESR and NMR spectroscopy, we show that the spin moiety of the membrane-embedded spin-labeled rod is localized in the upper chain/glycerol region of membranes of different compositions. The rod is embedded within the membrane in a tilted orientation to adjust for the varying hydrophobic thicknesses of these bilayers. This orientation does not perturb the membrane structure. The water solubility of the rod is increased significantly in the presence of certain cyclodextrins. These cyclodextrins also allow the rods to be extracted from the membrane and incorporated into preformed membranes. The latter will improve the future applications of these rods in cellular systems as stable membrane-associated anchors for the functionalization of membrane surfaces.

Kinetic theory and simulations of active polar liquid crystalline polymers

A kinetic model is derived for active polar liquid crystalline polymers, that is, ensembles of polar, large molecular weight, rigid rod, “swimmers” in a viscous solvent. The model couples polarity and particle-activation physics to the Doi–Hess theory for passive liquid crystalline polymers (LCP). Our model extends the polar hydrodynamic liquid crystal model of the Marchetti group to active large molecular weight rods at arbitrary equilibrium volume fractions. The Doi–Hess–Smoluchowski equation inherits contributions due to spatial inhomogeneity and translational diffusion of the rod number density, rod polarity and self-propulsion, and the hydrodynamic equations inherit additional extra stress contributions. By suppression of LCP physics, our model recovers kinetic and mesoscopic active suspension theories of athermal, polar and apolar, micron-scale swimmers. The authors' full orientation space, 2D physical space, Smoluchowski–Navier–Stokes solver is generalized to the new model and implemented on the full system of 125 nonlinear PDEs from which we explore the coupling of rotational and translational diffusion, nano-rod density gradients, polarity and self-propulsion, and flow feedback through polar and nematic stresses. For this paper, results are presented for the dilute regime where the stable passive isotropic phase is driven far from equilibrium by activation physics, the analog of non-Brownian active “pusher” suspensions. We present a rich family of excitable and stationary patterns, previously seen in Landau–de Gennes-type coarse-grained models of apolar and polar active nematics and boundary-driven passive nematics at semi-dilute concentrations where the passive isotropic state is unstable. We find fluctuating, periodic and stationary patterns, including 1D banded and diverse 2D patterns, tunable by the relative strengths of rotational and translational diffusivity with all other physical parameters held constant.

Steering supramolecular patterns by nucleobase-terminated molecules

Supramolecular patterns formed by adsorption from a liquid of nucleobase-terminated molecular rods on a graphite surface were investigated by scanning tunneling microscopy.

First-principle-based MD description of azobenzene molecular rods

Extensive density functional theory (DFT) calculations have been performed to develop a force field for the classical molecular dynamics (MD) simulations of various azobenzene derivatives. Besides azobenzene, we focused on a thiolated azobenzene’s molecular rod (4′-{[(1,1′-biphenyl)-4-yl]diazenyl}-(1,1′-biphenyl)-4-thiol) that has been previously demonstrated to photoisomerize from trans to cis with high yields on surfaces. The developed force field is an extension of OPLS All Atoms, and key bonding parameters are parameterized to reproduce the potential energy profiles calculated by DFT. For each of the parameterized molecule, we propose three sets of parameters: one best suited for the trans configuration, one for the cis configuration, and finally, a set able to describe both at a satisfactory degree. The quality of the derived parameters is evaluated by comparing with structural and vibrational experimental data. The developed force field opens the way to the classical MD simulations of self-assembled monolayers (SAMs) of azobenzene’s molecular rods, as well as to the quantum mechanics/molecular mechanics study of photoisomerization in SAMs.

First principle evaluation of the chiroptical activity of the di-phenyl-diazene derivatives

Azobenzene (di-phenyl-diazene) is well-known as a photoisomerisable molecule and has been widely studied as a molecular photoswitcher. Molecular rods, where di-phenyl arms are bound to the diazene moiety, have been also synthesized. In this article we explore by first principle density functional theory calculations the chiroptical properties (electronic circular dichroism spectra, ECD) of azobenzene and its homologues with polyphenyl arms. In particular, we demonstrate that for molecules in the cis configuration the intrinsic chirality of the distorted cis diazene group dominates the ECD response, while for trans species the non-planarity of the polyphenyl arms induces peaks in the ECD spectrum. Finally, the possibility of obtaining a light-controlled chiral switch by proper functionalization is also speculated.

1,3‐Diethynylbicyclo[1.1.1]pentane, a Useful Molecular Building Block

Abstract1,3‐Diethynylbicyclo[1.1.1]pentane (DEBCP) has been found to be a valuable molecular building block mostly for the synthesis of extended, rigid, rod‐like molecules. With its straightforward linear geometry, DEBCP can be used as a nonconjugated alternative to more frequently used π‐conjugated, rod‐like building blocks. Examples of reactions that introduce DEBCP into larger structures are (1) the reaction of DEBCP lithium acetylides with electrophiles such as TMSCl, CO2, and Ph2PCl, (2) Sonogashira–Hagihara cross‐coupling reactions with aryl or heteroaryl iodides or bromides, and (3) umpolung reactions that afford the corresponding dibromo and diiodo derivatives of DEBCP, which then successfully react with tert‐C‐cuprates derived from p‐ and m‐dicarbadodecaboranes or bicyclopentanes. These umpolung reactions afforded a new class of molecular rods that combine carborane or bicyclo[1.1.1]pentane cages with ethynylene linkers. Many of the DEBCP derivatives were studied by single‐crystal X‐ray diffraction. They form well‐organized arrays of molecular rotors, the DEBCP units, and so can be considered as examples of artificial molecular‐size machines.

"Pore-Like" Effects of Super-Molecular Self-Assembly on Molecular Diffusion of Poly(Ethylene Oxide)-Poly(Propylene Oxide)-Poly(Ethylene Oxide) in Water.

Molecular diffusion of triblock copolymers poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) in water was studied with the help of Pulsed Field Gradient NMR in the broad range of polymer weight fractions from 0.09 to 0.8. Owing to amphiphilic nature of the molecules, these block copolymers exhibit rich self-organization properties when mixed with water. In particular, at ambient temperatures they form micelles and three liquid crystalline mesophases: cubic, hexagonal, and lamellar. The corresponding super-molecular structure formations were studied with the same block copolymer and at the same temperature. Self-assembly of molecules was shown to produce “pore-like” effects on their self-diffusion properties by imposing severe constraints on the dimensionality of propagation. Diffusion in the hexagonal phase was shown to be quasi one-dimensional in the direction parallel to the long axis of the ordered molecular rods. In the lamellar phase, diffusion was found to be quasi two-dimensional, in the plane of the lamellar structures. The observed diffusion anisotropy was attributed to the effects of the specific molecular ordering on the mesoscopic length scale.

Building Blocks for Oligospiroketal (OSK) Rods and Evaluation of Their Influence on Rod Rigidity

We report on the synthesis of three new sleeves and their incorporation in OSK rods. The structures of these sleeves are based on neo-inositol, terephthalaldehyde diacetals, and indacene. To quantify the influence of the sleeves on rod rigidity, we applied the worm-like chain (WLC) model on the new rods and found that this approach is rather disappointing. As the chief cause of this result, we assume that the rigidity of typical molecular rods largely exceeds the rigidity of polymers, which were successfully described by the WLC model. Alternatively, we suggest quantifying the rigidity of molecular rods by fitting an empirical function on the end-to-end distance distribution curve obtained by MD simulations. After checking various function types, the Levy-Martin function proved to be most suitable for this purpose. On the basis of this function, we defined the Levy-Martin parameter and suggest using this parameter for the characterization of the rigidity of molecular rods.

An MCBJ case study: The influence of π-conjugation on the single-molecule conductance at a solid/liquid interface

π-Conjugation plays an important role in charge transport through single molecular junctions. We describe in this paper the construction of a mechanically controlled break-junction setup (MCBJ) equipped with a highly sensitive log I–V converter in order to measure ultralow conductances of molecular rods trapped between two gold leads. The current resolution of the setup reaches down to 10 fA. We report single-molecule conductance measurements of an anthracene-based linearly conjugated molecule (AC), of an anthraquinone-based cross-conjugated molecule (AQ), and of a dihydroanthracene-based molecule (AH) with a broken conjugation. The quantitative analysis of complementary current–distance and current–voltage measurements revealed details of the influence of π-conjugation on the single-molecule conductance.