Molecular Arrangement Research Articles

Synthesis, photophysical, electrochemical, theoretical and self-assembly investigation of tetraphenylethene tethered arylimidazoles

To understand the comparative structure–property relationships, we have designed and synthesized 4,5-diphenyl-2-(4-(1,2,2-triphenylvinyl)phenyl)-1H-imidazole, coded as JR-1 and 4,4′-(2-(4-(1,2,2-triphenylvinyl)phenyl)-1H-imidazole-4,5-diyl)bis(N,Ndimethylalanine)coded as JR-2. Here, we conducted various analyses, including, structural, photophysical, thermal, electrochemical, and computational studies, to gain a deeper understanding of introduction electron releasing N,N-dimethyleamine groups on later one. The molecules exhibit high thermal stability (200 − 300 °C) low band gap (2.75 – 3.26 eV) and comparable HOMO (−4.81 to − 5.35 eV) and LUMO (−2.06 to − 2.09 eV) energy levels with those of calculated and reported ambipolar materials. The UV–vis absorption was observed in the range of 300–400 nm for JR-1 and 300 − 440 nm for JR-2. These compounds exhibit distinct mechanochromism, solvatochromism, aggregation-induced emission, and aggregation-caused quenching and selective sensing. Interestingly, JR-1 exhibits mechanochromism without solvatochromism, while JR-2 is solvatochromic without mechanochromism. Due to incorporation of N,N-Dimethylphenylamine donating groups on imidazole leads to solvatochromicity and aggregation-caused quenching. Moreover, their optical properties differ significantly in dilute solutions compared to its solid state due to distinct molecular arrangements. Consequently, morphological studies reveal the formation of 3D rod and spear-shaped s supramolecular self-assembly structures in different solvent mixtures. This research work offers a fundamental strategy for the design of fluorophores for optoelectronic applications.

The molecular arrangement of ceramides in the unit cell of the long periodicity phase of stratum corneum models shows a high adaptability to different ceramide head group structures

The stratum corneum (SC) lipid matrix, composed primarily of ceramides (CERs), cholesterol and free fatty acids (FFA), has an important role for the skin barrier function. The presence of the long periodicity phase (LPP), a unique lamellar phase, is characteristic for the SC. Insight into the lipid molecular arrangement within the LPP unit cell is imperative for understanding the relationship between the lipid subclasses and the skin barrier function. In this study, the impact of the CER head group structure on the lipid arrangement and barrier functionality was investigated using lipid models forming the LPP. The results demonstrate that the positions of CER N-(tetracosanoyl)-sphingosine (CER NS) and CER N-(tetracosanoyl)-phytosphingosine (CER NP), two essentials CER subclasses, are not influenced by the addition of another CER subclass (N-(tetracosanoyl)-dihydrosphingosine (CER NdS), N-(2R-hydroxy-tetracosanoyl)-sphingosine (CER AS) or D-(2R-hydroxy-tetracosanoyl)-phytosphingosine (CER AP)). However, differences are observed in the lipid organization and the hydrogen bonding network of the three different models. A similar localization of CER NP and CER NS is also observed in a more complex lipid model, with the CER subclass composition mimicking that of human SC. These studies show the adaptability and insensitivity of the LPP unit cell structure to changes in the lipid head group structures of the CER subclasses.

Preparation, thermal properties, and structures of ionic plastic crystals with sandwich and half-sandwich Ru complexes

We have recently been investigating the phase behavior of salts of cationic sandwich complexes in pursuit of novel ionic plastic crystals (IPCs). In this study, we synthesized salts containing sandwich complexes [Ru(Cp)(C6H6)]X ([1]X; X = CPFSA− (1,1,2,2,3,3-hexafluoropropane-1,3-disulfonimide), SbCl6−) and half-sandwich complexes [Ru(Cp)(DMSO)3]X ([2]X; X = CPFSA−, FSA− ((FSO2)2N−), PF6−). In addition, we examined their thermal properties and crystal structures. Among them, [1]CPFSA exhibited an IPC phase between 365 and 630 K, whereas the others did not undergo phase transitions at 123–403 K. The cations and anions were alternately arranged in the crystals of [1]X, whereas [2]X did not exhibit the alternating arrangement except for [2]PF6. The results showed that alternating molecular arrangements are crucial for the IPC formation, although low symmetry of the ion environment and intermolecular steric hindrance may inhibit it.

Hydrogen- and halogen-bonding-directed trimeric supramolecular motifs in dihalogenated 1,2,4-triazoles.

Hydrogen-bonding and halogen-bonding interactions are important noncovalent interactions that play a significant role in the crystal structure of organic molecules. An in-depth analysis is given of the crystal packing of two previously reported crystal structures of dihalogenated 1,2,4-triazole derivatives, namely 3,5-dichloro-1H-1,2,4-triazole and 3,5-dibromo-1H-1,2,4-triazole. This work provides insights into the complex interplay of hydrogen-bonding and halogen-bonding interactions resulting in the formation of multiple trimeric motifs in the crystal structure of 1,2,4-triazole derivatives. Analysis of the crystal packing of these isostructural crystal structures revealed that the molecular arrangement in these molecules is primarily stabilized by the formation of different trimeric motifs stabilized by N-H...N hydrogen bonds, N-H...X (X = Cl/Br) halogen bonds and C-X...X halogen-bonding interactions. Computational studies further revealed that all these trimers are energetically stable. A crystallographic database search further reveals that while the cyclic trimers reported in this study are present in other molecules, structures analyzed in this study are the sole instances where all are present simultaneously.

Algebraic Nexus of Fibonacci Forms and Two-Simplex Topology in Multicellular Morphogenesis

Background: Fibonacci patterns and tubular forms both arose early in the phylogeny of multicellular organisms. Tubular forms offer the advantage of a regulated internal milieu, and Fibonacci forms may offer packing efficiencies. The underlying mechanisms behind the cellular genesis of Fibonacci and tubular forms remain unknown. Methods: In a multicellular organism, cells adhere to form a macrostructure and to coordinate further replication. We propose and prove simple theorems connecting cell replication and adhesion to Fibonacci forms and simplicial topology. Results: We identify some cellular and molecular properties whereby the contact inhibition of replication by adhered cells may approximate Fibonacci growth patterns. We further identify how a component 2→3 cellular multiplication step may generate a multicellular structure with some properties of a two-simplex. Tracking the homotopy of a two-simplex to a circle and to a tube, we identify some molecular and cellular growth properties consistent with the morphogenesis of tubes. We further find that circular and tubular cellular aggregates may be combinatorially favored in multicellular adhesion over flat shapes. Conclusions: We propose a correspondence between the cellular and molecular mechanisms that generate Fibonacci cell counts and those that enable tubular forms. This implies molecular and cellular arrangements that are candidates for experimental testing and may provide guidance for the synthetic biology of hollow morphologies.

Unraveling the influence of aromatic endcaps in peptide self-assembly

Aromatic peptides are an emerging class of building units for molecular self-assembly and creation of functional biomaterials. The strength of aromatic association plays an essential role in the self-assembly of aromatic peptides. Here, we design a series of aromatic peptides with different hydrophobic domains but the same peptide sequence. The hydrophobicity and aromaticity can be carefully regulated by the number of benzene rings and the alkyl spacer between the benzene and peptide regions. Upon the continuous enhancement of aromaticity, diverse supramolecular nanostructures, including nanotubes, nanofibers, and short helical ribbons, were clearly observed. The peptide with diphenyl groups exhibits the highest regularity of molecular packing, due to the synergy of force balance between hydrogen bonding and π–π interactions. In addition, the incorporation of a spacer in between the aromatic and peptide regions facilitates the self-assembly capability, as the interference between aromatic association and hydrogen bonding is hindered. These dramatic results demonstrate that aromaticity serves as an effective and robust parameter in the molecular arrangement, providing a new perspective into the formation and evolution of supramolecular assembly.

Exploring long-range fluorine–carbon J-coupling for conformational analysis of deoxyfluorinated disaccharides: A combined computational and NMR study

In this study, we investigated the potential of long-range fluorine–carbon J-coupling for determining the structures of deoxyfluorinated disaccharides. Three disaccharides, previously synthesized as potential galectin inhibitors, exhibited through-space fluorine–carbon J-couplings. In our independent conformational analysis of these disaccharide derivatives, we employed a combination of density functional theory (DFT) calculations and nuclear magnetic resonance (NMR) experiments. By comparing the calculated nuclear shieldings with the experimental carbon chemical shifts, we were able to identify the most probable conformers for each compound. A model comprising fluoromethane and methane molecules was used to study the relationship between molecular arrangements and intermolecular through-space J-coupling. Our study demonstrates the important effect of internuclear distance and molecular orientation on the magnitude of fluorine–carbon coupling. The experimental values for the fluorine–carbon through-space couplings (TSCs) of the disaccharides corresponded with values calculated for the most probable conformers identified by the conformational analysis. These results unlock the broader application of fluorine–carbon TSCs as powerful tools for conformational analysis of flexible molecules, offering valuable insights for future structural investigations.

Consequences of Vibrational Strong Coupling on Supramolecular Polymerization of Porphyrins.

Supramolecular polymers display interesting optoelectronic properties and, thus, deploy multiple applications based on their molecular arrangement. However, controlling supramolecular interactions to achieve a desirable molecular organization is not straightforward. Over the past decade, light-matter strong coupling has emerged as a new tool for modifying chemical and material properties. This novel approach has also been shown to alter the morphology of supramolecular organization by coupling the vibrational bands of solute and solvent to the optical modes of a Fabry-Perot cavity (vibrational strong coupling, VSC). Here, we study the effect of VSC on the supramolecular polymerization of chiral zinc-porphyrins (S-Zn) via a cooperative effect. Electronic circular dichroism (ECD) measurements indicate that the elongation temperature (Te) of the supramolecular polymerization is lowered by ∼10 °C under VSC. We have also generalized this effect by exploring other supramolecular systems under strong coupling conditions. The results indicate that the solute-solvent interactions are modified under VSC, which destabilizes the nuclei of the supramolecular polymer at higher temperatures. These findings demonstrate that the VSC can indeed be used as a tool to control the energy landscape of supramolecular polymerization. Furthermore, we use this unique approach to switch between the states formed under ON- and OFF-resonance conditions, achieved by simply tuning the optical cavity in and out of resonance.

Heliconical nematic and smectic phases: the synthesis and characterisation of the CB4O.m and CB8O.m series

ABSTRACT The synthesis and characterisation of two series of nonsymmetric dimers belonging to the family of compounds, the 1-(4-cyanobiphenyl-4′-yl)-ω-(4-alkylanilinebenzylidene-4′-oxy)alkanes (CBnO.m) is reported; in the acronym, n refers to the number of carbon atoms in the spacer, and m in the terminal alkyl chain. The two series reported, CB4O.m and CB8O.m, both show twist-bend nematic (NTB) and smectic phases (SmCTB-SH and SmCTB-DH). Their phase behaviour is compared to that of the CB6O.m and CB10O.m series. For each series, locally intercalated molecular packing is observed for short terminal chains and interdigitated packing for long terminal chains. The intercalated anticlinic smectic CA phase is observed for the CB8O.m and CB10O.m series. All four series exhibit the SmCTB-SH and SmCTB-DH phases for the longer terminal chains and all have an interdigitated molecular arrangement. The absence of an intercalated heliconical phase is attributed to the high viscosity associated with the network intercalated structure.

Microscopic solvent-solute interactions, reactivity studies, structure properties and anti cancer activity of 1-(1-benzofuran-5-yl)-N-methylbutan-2-amine

Cancer continues to be a major threat to mankind, as seen by the 19.3 million people who received treatment for the disease in 2020. The study employed quantum mechanical calculations utilising (DFT) B3LYP, using a 6–311++ G(d,p) basis set, to analyse structural characteristics and intramolecular interactions and pharmaceutical aspect of anti-cancer. The study utilised various spectroscopy techniques, including FT-IR, FT-Raman and UV–Vis to examine the molecular arrangements of 1-(1-benzofuran-5-yl)-N-methylbutan-2-amine (1BF5MB).Significant interactions were seen because of the electron-density shift of nitrogen atom's lone pair (LP (O1)) to its antibonding orbital (σ ∗ ) (C13-H30), with an E(2) of 8.51 Kcal/mol. This indicates a substantial degree of electron delocalization. TDM analysis displays graphs that illustrate the capacity to transmit charges. ALIE analysis utilises the colour blue to represent the stable sigma bonds, namely those associated with hydrogen atoms that produce protons. Evaluating the drug-likeness and ADMET assessment enabled the biological features of (1BF5MB). This compound may be deemed a strong anti-tubercular treatment agent due to its relatively low binding affinities for the specific receptors.These results indicate that the drugs block these receptors.

Controlled Molecular Arrangement of Cinnamic Acid in Layered Double Hydroxide through pi-pi Interaction for Controlled Release.

Cinnamic acid (CA) was successfully incorporated into Zn-Al layered double hydroxide (LDH) through coprecipitation. The CA moiety was stabilized in the interlayer space through not only electrostatic interaction but also intermolecular π-π interaction. It was noteworthy that the CA arrangement was fairly independent of the charge density of LDH, showing the important role of the layer-CA and CA-CA interactions in molecular stabilization. Computer simulations using the Monte Carlo method as well as analytical approaches including infrared, UV-vis spectroscopy, and differential scanning calorimetry showed the existence of intermolecular interaction. In order to reinforce molecular stabilization, a neutral derivative of CA, cinnamaldehyde (CAD), was additionally incorporated into LDH. It was clearly shown that CAD played a role as a π-π interaction mediator to enhance the stabilization of CA. The time-dependent release of CA from LDH was first governed by the layer charge density of LDH; however, the existence of CAD provided additional stabilization to the CA arrangement to slow down the release kinetics.

Understanding the Molecular Arrangement and Orientation Characteristics of Mesophase Pitch and Its Fibers via a Polarized Light Microscope.

A polarized light microscope (PLM) was utilized to examine the optical textures of mesophase pitch (MP) and MP-derived fibers, which aimed to reveal the arrangement and orientation characteristics of pitch molecules and to clarify the evolution and transformation mechanism of carbonaceous microcrystalline from pitch fibers to graphitized fibers. The results found that there were distinct optical textures in MP, where one side exhibited a transition from a flattening plane to a mountain-like undulating plane. This transition corresponded to the arrangement of pitch molecules, resembling stacked lamellar structures reminiscent of curved paper. Meanwhile, the optical textures of fibers revealed that the blue substance was wrapped around the red grain-like domains in the longitudinal section and confirmed that the red part belonged to the pyridine insoluble fraction of MP and the blue part belonged to its pyridine-soluble fraction. After graphitization, the red part was transformed into graphite sheets and the blue part was transformed into an amorphous carbon layer which was wrapped around the graphite sheets, forming a carbonaceous microcrystalline package-like bag. Therefore, this study provided a comprehensive interpretation of the structural evolution mechanism of MP and MP-derived fibers based on their macro-optical textures and micro-nanostructures.

Synthesis, Photophysical Properties, Theoretical Studies, and Living Cancer Cell Imaging Applications of New 7-(Diethylamino)quinolone Chalcones.

In this article, three unsymmetrical 7-(diethylamino)quinolone chalcones with D-π-A-D and D-π-A-π-D type push-pull molecular arrangements were synthesized via a Claisen-Schmidt reaction. Using 7-(diethylamino)quinolone and vanillin as electron donor (D) moieties, these were linked together through the α,β-unsaturated carbonyl system acting as a linker and an electron acceptor (A). The photophysical properties were studied, revealing significant Stokes shifts and strong solvatofluorochromism caused by the ICT and TICT behavior produced by the push-pull effect. Moreover, quenching caused by the population of the TICT state in THF-H2O mixtures was observed, and the emission in the solid state evidenced a red shift compared to the emission in solution. These findings were corroborated by density functional theory (DFT) calculations employing the wb97xd/6-311G(d,p) method. The cytotoxic activity of the synthesized compounds was assessed on BHK-21, PC3, and LNCaP cell lines, revealing moderate activity across all compounds. Notably, compound 5b exhibited the highest activity against LNCaP cells, with an LC50 value of 10.89 μM. Furthermore, the compounds were evaluated for their potential as imaging agents in living prostate cells. The results demonstrated their favorable cell permeability and strong emission at 488 nm, positioning them as promising candidates for cancer cell imaging applications.

Variation of Activation Volume as an Indicator of the Difference in Clusterization Phenomenon Induced by H-Bonding and F-Π Stacking Interactions in Enantiomers and a Racemate of Flurbiprofen.

In this paper, X-ray diffraction (XRD), differential scanning calorimetry (DSC), broadband dielectric (BDS), and Fourier transform infrared (FTIR) spectroscopy supported by molecular dynamics (MD) simulations and quantum chemical computations were applied to investigate the structural and thermal properties, molecular dynamics, and H-bonding pattern of R-, S-, and RS-flurbiprofen (FLP). Experimental data indicated various spatial molecular arrangements in crystalline forms of examined systems, which seemed to disappear in the liquid state. Surprisingly, deeper analysis of high-pressure dielectric data revealed unexpected variation in the activation volume of pure enantiomers and a racemate. MD simulations showed that it is an effect of the clusterization phenomenon and a higher population of small associates in the former samples. Moreover, theoretical consideration exposed the particular role of unspecific F-Π interactions as a driving force underlying local molecular arrangements of molecules in the liquid and the crystal lattice of R-, S-, and RS-FLP.

Spiral packing and chiral selectivity in model membranes probed by phase-resolved sum-frequency generation microscopy

Since the lipid raft model was developed at the end of the last century, it became clear that the specific molecular arrangements of phospholipid assemblies within a membrane have profound implications in a vast range of physiological functions. Studies of such condensed lipid islands in model systems using fluorescence and Brewster angle microscopies have shown a wide range of sizes and morphologies, with suggestions of substantial in-plane molecular anisotropy and mesoscopic structural chirality. Whilst these variations can significantly alter many membrane properties including its fluidity, permeability and molecular recognition, the details of the in-plane molecular orientations underlying these traits remain largely unknown. Here, we use phase-resolved sum-frequency generation microscopy on model membranes of mixed chirality phospholipid monolayers to fully determine the three-dimensional molecular structure of the constituent micron-scale condensed domains. We find that the domains possess curved molecular directionality with spiralling mesoscopic packing, where both the molecular and spiral turning directions depend on the lipid chirality, but form structures clearly deviating from mirror symmetry for different enantiomeric mixtures. This demonstrates strong enantioselectivity in the domain growth process and indicates fundamental thermodynamic differences between homo- and heterochiral membranes, which may be relevant in the evolution of homochirality in all living organisms.

Unveiling Nanoscale Heterogeneities at the Bias-Dependent Gold-Electrolyte Interface.

Electrified solid-liquid interfaces (SLIs) are extremely complex and dynamic, affecting both the dynamics and selectivity of reaction pathways at electrochemical interfaces. Enabling access to the structure and arrangement of interfacial water in situ with nanoscale resolution is essential to develop efficient electrocatalysts. Here, we probe the SLI energy of a polycrystalline Au(111) electrode in a neutral aqueous electrolyte through in situ electrochemical atomic force microscopy. We acquire potential-dependent maps of the local interfacial adhesion forces, which we associate with the formation energy of the electric double layer. We observe nanoscale inhomogeneities of interfacial adhesion force across the entire map area, indicating local differences in the ordering of the solvent/ions at the interface. Anion adsorption has a clear influence on the observed interfacial adhesion forces. Strikingly, the adhesion forces exhibit potential-dependent hysteresis, which depends on the local gold grain curvature. Our findings on a model electrode extend the use of scanning probe microscopy to gain insights into the local molecular arrangement of the SLI in situ, which can be extended to other electrocatalysts.

Structures and Dynamics of Complex Guest Molecules in Confinement, Revealed by Solid-State NMR, Molecular Dynamics, and Calorimetry.

This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica materials employing solid-state NMR spectroscopy, supported by calorimetry and molecular dynamics simulations. The combination of steric interactions, hydrogen bonds, and hydrophobic and hydrophilic interactions results in a fascinating phase behavior in the confinement. Combining solid-state NMR and relaxometry, DNP hyperpolarization, molecular dynamics simulations, and general physicochemical techniques, it is possible to monitor these confined molecules and gain deep insights into this phase behavior and the underlying molecular arrangements. In many cases, the competition between hydrogen bonding and electrostatic interactions between polar and non-polar moieties of the guests and the host leads to the formation of ordered structures, despite the cramped surroundings inside the pores.

Molecular Templates on Surfaces by Exploiting Supramolecular Chemistry in Langmuir–Blodgett Monolayers

AbstractAttaining precise control over molecular arrangements is of paramount importance for numerous applications in nanotechnology, particularly in constructing molecular templates to accurately immobilize target materials on surfaces. A strategic combination of supramolecular and interfacial chemistry may serve to build a well‐organized molecular network, enabling the subsequent location of target molecules on specific positions of a surface. A supramolecular complex (compound 1) comprised of a melamine unit forming hydrogen bonds with dendritic arms terminated in a coumarin unit is utilized, which readily undergoes photodimerization. The research demonstrates the formation of well‐organized Langmuir films of compound 1 which can be transferred on substrates at low surface pressures adopting a lying‐flat orientation. Upon irradiation of the pristine films at 365 nm the coumarin units undergo photo‐cross linking, leading to the formation of a compact photo‐crosslinked film. Incubation of these photo‐crosslinked films in a solution containing 1‐hexanethiol results in the withdrawal of the melamine and the chemisorption of two thiol molecules per each melamine unit. The nanopores created by the removal of the melamine core are attributed to the disruption of hydrogen bonds in compound 1 by the thiols. This precisely defined molecular network holds significant promise as a template for orchestrating the arrangement of functional materials on surfaces.

Designing PVdF-HFP/BTO Piezoelectric Sensor based Sensing System for Detecting Volume Expansion of Battery Cell

Piezoelectric sensor can be used to inform the battery safety by detecting the battery swelling induced pressure. In this study, a piezoelectric sensing material, sensor unit, and sensing system were developed using piezoelectric polymer polyvinylidene fluoride-co-hexafluoropropylene(PVdF-HFP) and piezoelectric ceramic BaTiO<sub>3</sub>(BTO). Free-standing PVdF-HFP/BTO composite nanofiber web was retrieved as the sensing material due to the nanofiber web-based flexibility and the molecular arrangement driven piezoelectric performances. The PVdF-HFP/BTO composite nanofiber web-based sensor was employed in the automatic pressure sensing system, which provides the visual and audible signals once the pressure exceeds a certain limit. Our work demonstrates that the design of new piezoelectric sensing system is a fruitful pathway to sensing the battery malfunctions.

Impact of Packing Geometry on Excimer Characteristics and Mobility in Perylene Bisimide Polycrystalline Films.

Efficient exciton transport is essential for high-performance optoelectronics. Considerable efforts have been focused on improving the exciton mobility in organic materials. While it is feasible to improve mobility in organic systems by forming well-ordered stacks, the formation of trap states, particularly the lower-lying states referred to as excimers, remains a significant challenge to enhancing mobility. The mobility of excimer excitons intricately depends on the strength of excitonic coupling in terms of Förster-type diffusive exciton transfer processes. Given that the formation and mobility of excimer excitons are highly sensitive to molecular arrangements (packing geometries), conducting comprehensive investigations into the structure-property relationship in organic systems is crucial. In this study, we prepared three types of polycrystalline films of perylene bisimide (PBI) by varying substituents at the imide and bay positions, which allowed us to tailor the properties of excimer excitons and their mobility based on packing geometries and excitonic coupling strengths. By utilizing femtosecond transient absorption spectroscopy, we observed ultrafast excimer formation in the higher coupling regime, while in the lower coupling regime, the transition from Frenkel to excimer excitons occurs with a time constant of 500 fs. Under high pump-fluence, exciton-exciton annihilation processes occur, indicating the diffusion of excimer excitons. Intriguingly, employing a three-dimensional diffusion model, we derived a diffusion constant that is 3000 times greater in the high coupling regime than in the low coupling regime. To investigate the optoelectronic properties in the form of a bulk system, we fabricated n-type organic field effect transistors and obtained 8000 times higher mobility in the high coupling regime. Furthermore, photocurrent measurements enable us to investigate the charge carrier transport by mobile excimer excitons, suggesting a 230-fold improvement in external quantum efficiency with tightly packing PBI molecules compared to the low coupling regime. These findings not only offer valuable insights into optimizing organic materials for optoelectronic devices but also unveil the intriguing potential of exciton migration within excimers.