Structure Of Molecular Assemblies Research Articles

Tuning Surface Organic Structures by Small Gas Molecules through Catassembly and Coassembly.

The field of molecular assembly has seen remarkable advancements across various domains, such as materials science, nanotechnology, and biomedicine. Small gas molecules serve as pivotal modulators, capable of altering the architecture of assemblies via tuning a spectrum of intermolecular forces including hydrogen bonding, dipole-dipole interactions, and metal coordination. Surface techniques, notably scanning tunneling microscopy and atomic force microscopy, have proven instrumental in dissecting the structural metamorphosis and characteristic features of these assemblies at an unparalleled single-molecule resolution. Recent research has spotlighted two innovative approaches for modulating surface molecular assemblies with the aid of small gas molecules: "catassembly" and "coassembly". This Perspective delves into these methodologies through the lens of varying molecular interaction types. The strategies discussed here for regulating molecular assembly structures using small gas molecules can aid in understanding various complex assembly processes and structures and provide guidance for the further fabrication of complex surface structures.

Bidirectional π − π stacking for near-infrared photothermal effects and photo-thermo-electric conversion in a semiconductive hydroxamate coordination polymer

Photo-thermo-electric conversion is an emerging technology for utilizing solar energy. As the main component, photothermal materials play a significant role in achieving high conversion efficiency from sunlight to electrical energy. Organic photothermal materials have attracted intense attention recently due to their excellent photothermal efficiency and recycling capabilities. However, broad sunlight absorption in organics heavily relies on the realization of intramolecular or intermolecular charge transfer. Exploring more versatile and efficient methods to construct materials with broad sunlight absorption remains a great challenge. Herein, we report a novel photothermal compound from the perspective of modulating molecular assembly structure. By combining two distinct metal ions, Ba2+ and Mn2+, with the planar ligand H2ONDI, a new coordination polymer, {[BaMn(ONDI)2(H2O)3]⋅H2O}n (1), can be obtained. This coordination polymer exhibits rare bidirectional π−π stacking columns along both the a and b axis. The tightly bidirectional arrangement of ligands in 1 results in a broad optical absorption from the ultraviolet region to the near-infrared area, leading to intriguing near-infrared photothermal effects under irradiation of a laser of 808 nm with a efficiency of 42.3 %. By integrating with thermoelectric devices, 1 shows good application potential in the field of photo-thermo-electric conversion, with the maximum open circuit voltage reaching 313 mV under the irradiation of 1 sun. Furthermore, 1 displays semiconducting behavior because the presence of bidirectional π−π stacking columns facilitates charge transport along two directions, including hopping and band-like charge transport.

Carrier Transport Switching of Ferroelectric BTBT Derivative.

Alkylamide-substituted [1]benzothieno[3,2-b][1]benzothiophene (BTBT) derivative of BTBT-NHCOC14H29 (1), which has ferroelectric N-H···O= hydrogen-bonding network of alkylamide group and two-dimensional (2D) electric structure of BTBT π-cores, was prepared to design the external electric field-responsive organic semiconductors. The short-chain derivative of BTBT-NHCOC3H7 (1') revealed the coexistence of a 2D electronic band structure based on the herringbone BTBT arrangement and the one-dimensional (1D) hydrogen-bonding chain. 1 formed a smectic E (SmE) liquid crystal phase above 412 K and showed ferroelectric hysteresis in the electric field-polarization (P-E) curves at 403-433 K. The remanent polarization (Pr) and coercive electric field (Ec) of 1 at 408 K, 0.1 Hz were 24.0 μC cm-2 and 5.54 V μm-1, respectively. By thermal annealing of thin-film 1 at 443 K, the molecular assembly structure of 1 changed from a monolayer to a bilayer structure with high crystallinity, resulting in conducting layers of BTBT parallel to the substrate surface. The organic field-effect transistor (OFET) device with thermally annealed thin-film 1 showed p-type semiconducting behavior with the hole mobility of 1.0 × 10-3 cm2 V-1 s-1. Furthermore, device 1 showed switching behavior of semiconducting properties by electric field poling and thermal annealing cycle. The electric field response of ferroelectrics modulated the molecular orientation and conduction properties of organic semiconductors, resulting in external electric field control of carrier transport properties.

Insights into the Rearrangement of the Molecular Assembly Structure of 6-Aminonicotinic Acid in Its Hydrated Environment.

Water, as a ubiquitous and essential component of life, is known to have a significant impact on the structure and function of organic molecules. In this study, we investigate the role of water in the phase transition of organic molecular assembly structures by scanning tunneling microscopy at room temperature. The results show that the -O-H···O hydrogen induced by water molecules can lead to a significant structural transition in the molecular assembly, specifically through selective weakening of -C-H···O between 6-aminonicotinic acid and the formation of new -O-H···O bonds between 6-aminonicotinic acid and water molecules. Subsequent thermal treatment of these molecular assembly structures reveals that the formation of -N-H···O hydrogen bonds induced by water molecules has created a different pathway for the phase transition of the molecular assembly structure. This knowledge has important implications for the design of organic molecules with specific nanostructures that can be controlled through hydration.

Optical and redox properties and molecular assembly structures of π-expanded tetrathienylene isomers

Optical and redox properties and molecular assembly structures of π-expanded tetrathienylene isomers

Wood as a hydrothermally stimulated shape-memory material: mechanisms of shape-memory effect and molecular assembly structure networks

Abstract This study aimed to evaluate the shape-memory effect (SME) of wood (Populus x beijingensis W. Y. Hsu) and identify the net-points and switches in its molecular and morphological structures. During several cycles of deformation and subsequent recovery, a high shape recovery rate and ratio were maintained. The transverse compression tests of wet and dry wood reveal that the hydrothermal coupling stimulation can considerably reduce the strength of wood. The X-ray diffraction characterization of wood under hydrothermal stimulation shows that the role of network nodes in the SME of wood is influenced by temperature. The wavenumber shifting and changes in the intensity ratio of the characteristic Fourier transform infrared peaks showed that hydrogen bonds acted as switches for the water-stimulated shape-memory behavior. By taking into account viscoelastic relaxation, a kinetic model derived from nonequilibrium thermodynamic fluctuation theory was used to describe the shape recovery process. The effects of hydration on recovery kinetics, activation, and dynamic mechanical behaviors were also studied. To explain the shape-memory mechanism of wood under hydrothermal stimulation, a hybrid-structure network model based on a single three-dimensional switch network was proposed in this study.

Ferroelectricity and Phase Change Memory of Bis(tetradecylamide)-Substituted Benzene Derivatives

Interplay between intermolecular interactions including hydrogen bonding, halogen–halogen, and van der Waals interactions in molecular crystals leads to diverse phase transition behaviors and physical properties. Bis(tetradecylamide)-substituted benzene derivatives, terephthalamide (C14-TPA), isophthalamide (C14-IPA), and phthalamide (C14-PA), were examined, and the electric field–polarization curves of the former two crystals indicated ferroelectric hysteresis behavior in high-temperature solid phases. C14-XIPA derivatives where X = CH3, Cl, Br, or I at the 5-position of the IPA molecule were synthesized, and the effects of substituent X on the molecular assembly structure and physical properties were investigated. H- and CH3-substituted C14-IPA and C14-MeIPA formed a crystalline phase in which intermolecular amide-type N–H···O═ hydrogen-bonding interactions were dominant, whereas halogen-substituted C14-XIPAs formed a metastable glass phase upon cooling from the isotropic liquid. The formation of the glass phase is associated with energy competition between hydrogen bonding, halogen–halogen, and van der Waals interactions among the −CONH–, −X, and −CnH2n+1 units. The glass-crystal phase transition of C14-XIPAs (X = Cl, Br, or I) changes the refractive index under polarized optical microscopic observation, which can be utilized for phase-change memory.

Molecular cluster analysis using local order parameters selected by machine learning.

Accurately extracting local molecular structures is essential for understanding the mechanisms of phase and structural transitions. A promising method to characterize the local molecular structure is defining the value of the local order parameter (LOP) for each particle. This work develops the Molecular Assembly structure Learning package for Identifying Order parameters (MALIO), a machine learning package that can propose an optimal (set of) LOP(s) quickly and automatically for a huge number of LOP species and various methods of selecting neighboring particles for the calculation. We applied this package to distinguish between the nematic and smectic phases of uniaxial liquid crystal molecules, and selected candidate LOPs that could be used to precisely observe the nematic-smectic phase transition. The LOP candidates were used to observe the nucleation and subsequent percolation transition, and the effect of the choice of LOP species and neighboring particles on the statistics of local molecular structures (clusters) was examined. The procedure revealed the time evolution of the number of clusters and the dependence of the percolation curve on the number of neighboring particles for each LOP species. The LOP species with the lowest dependence on the number of neighboring particles was the best-performing LOP species in the MALIO screening strategy. These results not only show that machine learning can powerfully screen a huge number of LOP species and suggest only a few promising candidates, but also indicate that MALIO can select the best LOP species.

Conjugated Polymer Nanoparticles: Photothermal and Photodynamic Capabilities According to Molecular Ordering in Their Assembly Structures

We report that conjugated polymer nanoparticles (CPNs) coated with polyethylene glycols (PEGs) exhibit photothermal and photodynamic capabilities according to molecular ordering in their assembly structures. CPN-PEGs were made using three different methods: a dispersion process of phase-separated film assemblies of a conjugated polymer and a phospholipid-conjugated PEG (CPN-I), a dispersion process of a conjugated polymer and a phospholipid followed by surface conjugation with PEGs (CPN-II), and a miniemulsification of the conjugated polymer and the phospholipid-conjugated PEG. Our findings revealed that the ordered molecular assembly structures in CPN-I and CPN-II increased intermolecular interactions and decreased the optical band gap, promoting nonradiative exciton relaxation via the energy-gap law’s internal conversion mechanism and rationalizing CPN-I’s shorter singlet exciton lifetime (13 ps). Meanwhile, CPN-III with a disordered structure generated more singlet oxygen than CPN-I and CPN-II, indicating increased triplet exciton generation upon the polaron recombination. Our findings present that the photothermal and photodynamic properties of CPNs are obviously dependent on the assembly structure order and that CPNs with an ordered assembly of conjugated backbones have a stronger photothermal effect, whereas those with a disordered structure have a better photodynamic effect.

On the influence of water on THz vibrational spectral features of molecular crystals.

The nanoscale structure of molecular assemblies plays a major role in many (μ)-biological mechanisms. Molecular crystals are one of the most simple of these assemblies and are widely used in a variety of applications from pharmaceuticals and agrochemicals, to nutraceuticals and cosmetics. The collective vibrations in such molecular crystals can be probed using terahertz spectroscopy, providing unique characteristic spectral fingerprints. However, the association of the spectral features to the crystal conformation, crystal phase and its environment is a difficult task. We present a combined computational-experimental study on the incorporation of water in lactose molecular crystals, and show how simulations can be used to associate spectral features in the THz region to crystal conformations and phases. Using periodic DFT simulations of lactose molecular crystals, the role of water in the observed lactose THz spectrum is clarified, presenting both direct and indirect contributions. A specific experimental setup is built to allow the controlled heating and corresponding dehydration of the sample, providing the monitoring of the crystal phase transformation dynamics. Besides the observation that lactose phases and phase transformation appear to be more complex than previously thought - including several crystal forms in a single phase and a non-negligible water content in the so-called anhydrous phase - we draw two main conclusions from this study. Firstly, THz modes are spread over more than one molecule and require periodic computation rather than a gas-phase one. Secondly, hydration water does not only play a perturbative role but also participates in the facilitation of the THz vibrations.

Kinetic trapping of 3D-printable cyclodextrin-based poly(pseudo)rotaxane networks

<h2>Summary</h2> Synthetically trapping kinetically varied (super)structures of molecular assemblies and amplifying them to the macroscale is a promising, yet challenging, approach for the advancement of meta-stable materials. Here, we demonstrated a concerted kinetic trapping design to timely resolve a set of transient polypseudorotaxanes in solution and harness a crop of them via micro-crystallization. By installing stopper or speed bump moieties on the polymer axles, meta-stable polypseudorotaxanes with segmented cyclodextrin blocks were hierarchically amplified into crystalline networks of different crosslinking densities at mesoscale and viscoelastic hydrogels with 3D-printability in bulk. We demonstrated simultaneous 3D-printing of two polypseudorotaxane networks from one reactive ensemble and their conversion to heterogeneous polyrotaxane monoliths. Spatially programming the macroscale shapes of these heterogeneous polyrotaxanes enabled the construction of moisture-responsive actuators, in which the shape morphing originated from the different numbers of cyclodextrins interlocked in these polyrotaxane networks.

Room-Temperature Phosphorescence Emitters Exhibiting Red to Near-Infrared Emission Derived from Intermolecular Charge-Transfer Triplet States of Naphthalenediimide-Halobenzoate Triad Molecules.

Room-temperature phosphorescence (RTP) emitters have attracted significant attention. However, purely organic RTP emitters in red to near-infrared region have not been properly investigated. In this study, a series of naphthalenediimide-halobenzoate-linked molecules are synthesized, one of which exhibits efficient RTP properties, showing red to near-infrared emission in solid and aqueous dispersion. Spectroscopic studies and single-crystal X-ray diffraction analysis have shown that the difference in the stacking modes of compounds affects the optical properties, and the formation of intermolecular charge-transfer complexes of naphthalenediimide-halobenzoate moiety results in a bathochromic shift of absorption and RTP properties. The time-dependent density functional theory calculations showed that the formation of charge-transfer triplet states and the external heavy atom effect of the halogen atom enhance the intersystem crossing between excited singlet and triplet states.

Study on Molecular Design and Synthesis of Novel Surfactants, and Physicochemical Properties and Structure of Molecular Assembly

Study on Molecular Design and Synthesis of Novel Surfactants, and Physicochemical Properties and Structure of Molecular Assembly

Steering Effect of Bromine on Intermolecular Dehydrogenation Coupling of Poly(p-phenylene) on Cu(111).

Among the multitudinous methodologies to steer on-surface reactions, less attention has been paid to the effect of externally introduced halogen atoms. Herein, highly selective trans-dehydrogenation coupling at the specific meta-C-H site of two poly(p-phenylene) molecules, p-quaterphenyl (Ph4) and p-quinquephenyl (Ph5), is achieved on Cu(111) by externally introduced bromine atoms. Scanning tunneling microscopy/spectroscopy experiments reveal that the formed molecular assembly structure at a stoichiometric ratio of 4:1 for Br to Ph4 or 5:1 for Br to Ph5 can efficiently promote the reactive collision probability to trigger the trans-coupling reaction at the meta-C-H site between two neighboring Ph4 or Ph5 molecules, leading to an increase in the coupling selectivity. Such Br atoms can also affect the electronic structure and adsorption stability of the reacting molecules. It is conceptually demonstrated that externally introduced halogen atoms, which can provide an adjustable halogen-to-precursor stoichiometry, can be employed to efficiently steer on-surface reactions.

Bicomponent supramolecular self‐assemblies studied with tip‐enhanced Raman spectroscopy

AbstractThe formation of well‐ordered supramolecular self‐assembly based on cytosine and 4,4′‐bipyridine on Ag(111) has been investigated with subnanometer‐resolved tip‐enhanced Raman spectroscopy (TERS) using a low‐temperature ultrahigh‐vacuum scanning tunneling microscope (STM). The co‐deposition of two molecules on the Ag(111) surface held at room temperature results in well‐ordered hydrogen‐bonded monolayer islands, which transform into well‐aligned double‐stranded chains after thermal annealing. Site‐dependent TERS spectra help to identify the packing structures of molecular assemblies. The changes of molecule‐specific vibrational fingerprints across the assemblies can be clearly monitored by combining high‐resolution TERS spectra with advanced multivariate analysis. Furthermore, the peak positions and relative intensities for characteristic vibrational modes of the two molecules are found to vary due to the changes of the local hydrogen bonding and interaction environment in different molecular samples. Our findings demonstrate that TERS is sensitive to the local molecular interactions, provides new potentials to monitor the functionality of molecular architectures on demand, and opens new opportunities to probe surface chemistry at the nanoscale.

Mixed Columnar Assembly of Ferroelectric and Antiferroelectric Benzene Derivatives Bearing Multiple -CONHC14H29 Chains.

The discotic hexagonal columnar (Colh) liquid crystalline phases of simple benzene derivatives bearing -CONHC14H29 chains at the 1-, 3-, and 5-positions (3BC) and 1-, 2-, 4-, and 5-positions (4BC) display ferroelectricity and antiferroelectricity, respectively. The phase transition behavior, molecular assembly structures, dielectric response, and ferroelectric properties of their mixed crystals [(3BC)1-x(4BC)x] were evaluated to clarify the nanoscaling effect on the collective inversion of the one-dimensional (1D) N-H···O═ hydrogen bonding interaction observed in the (3BC)∞ chain. A small quantity of 4BC doped into 3BC (x ≤ 0.03) maintained the ferroelectric polarization-electric field response (P-E) in the (3BC)1-x(4BC)x chains, where the antiferroelectric 4BC molecules in the ferroelectric 3BC column act as a pinning potential site for dipole inversion. On the contrary, a relatively large amount of 4BC doping (x ≥ 0.1) forms a domain separation state between the hydrogen-bonded (3BC)∞ and (4BC)∞ columns, in which the ferroelectric P-E hysteresis completely disappeared. The correlation length for the appearance of ferroelectricity in the 1D column was estimated to be ∼40 nm in the Colh liquid crystalline phase of 3BC.

Primary to quaternary structures of molecular assemblies

Several kinds of molecular assemblies are prepared from polypeptides and cyclic peptides at various levels of structural regularities, which lead to the current proposal to categorize molecular assemblies into primary to quaternary structures. The categorization places a focal point on phase separation in molecular assemblies because highly sophisticated molecular assemblies have hierarchical organizations of molecules that accompany phase separation and the regular arrangement of chromophores, as frequently observed in nature. Examples of the peptide-based molecular assemblies are thus explained in accordance with the primary to quaternary structures with the aim of implementing nanomaterials in the coming era. Categorization of molecular assemblies of primary to quaternary structures is herein proposed with citing typical examples of peptide molecular assemblies for each category. Primary structure; tubes and vesicles, Secondary structure; chimeric morphology, Tertiary structure; phase-separated tubes, Quaternary structure; hierarchical organization of molecular assemblies.

Ferroelectric Alkylamide-Substituted Helicene Derivative with Two-Dimensional Hydrogen-Bonding Lamellar Phase.

Alkylamide (-CONHC nH2 n+1)-substituted benzene and its pyrene derivatives have shown a discotic hexagonal columnar liquid-crystalline phase through a one-dimensional (1D) intermolecular N-H···O═ hydrogen-bonding interaction, the direction of which is inverted through the application of an alternate current voltage. The polar hydrogen-bonding chains and dipole inversion reveal a ferroelectric polarization-electric field ( P- E) hysteresis curve. Non-π-planar helicene derivatives bearing two -CONHC14H29 chains also indicate a ferroelectric response. The racemic helicene derivative shows a bilayer lamellar liquid-crystal phase within a temperature range of 330-420 K, whereas there is no liquid crystallinity for the optically active derivative because of the different molecular assembly structure. The racemic phase is constructed through a two-dimensional (2D) N-H···O═ hydrogen-bonding network, which shows ferroelectric P- E hysteresis curves at above 340 K. The collective dipole inversion in the 2D layer contributes to the ferroelectricity in the lamellar phase. The remanent polarization ( Pr) of 11.1 μC cm-2 is about 6 times higher than those of the π-planar benzene- and pyrene-based 1D ferroelectrics. Both the density of the hydrogen-bonding site and the domain orientation in the 2D system are higher than those of the 1D columnar system.

Molecular Assemblies of Tetrahedral Triphenylmethanol and Triphenylamine Derivatives Bearing −NHCOCnH2n+1 Chains

Nonplanar three-fold symmetrical triphenylmethanol (1: n = 10 and 2: n = 3) and triphenylamine (3: n = 10 and 4: n = 3) derivatives bearing three alkylamide (−NHCOCnH2n+1) chains were studied in terms of their phase transitions, molecular assemblies, nano- or meso-structures, and dielectric responses. Slight modification of the structural core from a hydroxyl moiety (C–OH in 1) to a nitrogen atom (N in 3) drastically changed the molecular assembly structures and physical properties in solids. The molecular assembly of 1 showed a glass–plastic crystal phase transition at ∼340 K, whereas 3 only displayed a direct solid–liquid phase transition. Uniform microscale spheres and nanowires with average diameters of 2 μm and 200 nm, respectively, were observed for the molecular assemblies of 1 and 3 on substrate surfaces, respectively, corresponding to amorphous glass and one-dimensional hydrogen-bonding columnar structures. An α-type frequency- and temperature-dependent dielectric relaxation was observed in amorp...

Phase transition and molecular assembly structure of ellagic acid ester derivatives

Ellagic acid and its esters were examined in terms of phase transition, electronic structure, dielectric constant, and molecular assembly.