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The self-assembling morphologies of proteins, nucleic acids, and peptides are well correlated with their functioning in biological systems. In spite of extensive studies for the morphologies regulating, the directional control of the assembly morphology structure for the peptides still remains challenging. Here, the directional structure control of a bola-like peptide Ac-KIIF-CONH2 (KIIF) was realized by introducing different amount of acetonitrile to the system. The morphologies were characterized by transmission electron microscopy (TEM) and atomic force microscopy (AFM), and the secondary structure was evaluated by circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR). The results demonstrated that the introducing of different amount of acetonitrile has significantly tuned the hydrophobic interactions amongst the side chains, thus affecting the self-assembling morphologies. As acetonitrile content increased, the assemblies changed from nanotubes to helical/twisted ribbons and then to thin fibrils, with a steady decrease in the width. In contrast, the assemblies changed from thin fibrils to helical/twisted ribbons, and then to matured nanotubes, exhibiting a steady increase in the width with peptide concentration increasing. Complementary molecular dynamics (MD) simulations demonstrated the important role of acetonitrile in controlling the hydrophobic interactions, providing microscopic evidence for the structure transition process. We believe such observations provide important insights into the design and fabrication of functional materials with controlled shape and size.
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Interações Hidrofóbicas e Hidrofílicas , Simulação de Dinâmica Molecular , Peptídeos/química , Conformação Proteica em Folha beta , Acetonitrilas/química , Tamanho da Partícula , Propriedades de SuperfícieRESUMO
Supramolecular polymers are able to change their structure, morphology and function in response to external stimuli. However, controlling the independence of stimuli-responses in these systems is challenging. Herein, we exploit halogen bonding (XB) as a reversible network element to regulate the photoresponsive and adaptive behavior of supramolecular polymers. To this end, we have designed a system comprising an amphiphilic XB acceptor with the ability to self-assemble in aqueous media (OPE-Py) and a molecule with a dual photoresponsive and XB donor function [(E)-Azo-I]. OPE-Py self-assembles in aqueous media into supramolecular polymers, which transform into nanoparticle assemblies upon co-assembly with (E)-Azo-I. Interestingly, a third type of assembly (2D sheets) is obtained if OPE-Py is treated with (E)-Azo-I and exposed to photoirradiation. At ambient conditions, both nanoparticles and 2D sheets remain invariant over time. However, heating dissociates the XB interactions present in both assemblies, resulting in their transformation to the original fiber-like morphology of OPE-Py. Thus, breaking the communication between self-assembly and the stimuli-responses upon heating restores the original state of the system, drawing parallels to feedback loops in programming language. This work broadens the still limited scope of XB in solution assemblies and paves the way for multifunctional adaptive supramolecular systems.
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Metalloporphyrins modified carbon-based materials, owing to the excellent acid-base resistance, optimal electron transfer rates, and superior catalytic performance, have shown great potential in energy electrocatalysis. Recently, numerous efforts have concentrated on employing carbon-based substrates as platforms to anchor metalloporphyrins, thereby fabricating a diverse array of composite catalysts tailored for assorted electrocatalytic processes. However, the interplay through bonding regulation of metalloporphyrins with carbon materials and the resultant enhancement in catalyst performance remains inadequately elucidated. Gaining an in-depth comprehension of the synergistic interactions between metalloporphyrins and carbon-based materials within the realm of electrocatalysis is imperative for advancing the development of innovative composite catalysts. Herein, the review systematically classifies the binding modes (i.e., covalent grafting and non-covalent interactions) between carbon-based materials and metalloporphyrins, followed by a discussion on the structural characteristics and applications of metalloporphyrins supported on various carbon-based substrates, categorized according to their binding modes. Additionally, this review underscores the principal challenges and emerging opportunities for carbon-supported metalloporphyrin composite catalysts, offering both inspiration and methodological insights for researchers involved in the design and application of these advanced catalytic systems.
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Diaryliodonium(III) salts have been established as powerful halogen-bond donors in recent years. Herein, a new structural motif for this compound class was developed: iodoloisoxazolium salts, bearing a cyclic five-membered iodolium core fused with an isoxazole ring. A derivative of this class was synthesized and investigated in the solid state by X-ray crystallography. Finally, the potential as halogen-bonding activator was benchmarked in solution in the gold-catalyzed cyclization of a propargyl amide.
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Arachin (ARA) and resveratrol (RES) are the primary protein and bioactive compound in peanuts and their processed products. However, the mechanism of interaction between these two substances remained unclear. To investigate protein structural changes, conformational variations, and molecular mechanisms in the interaction between them, multispectral analysis and computational chemistry methods were employed. Experimental results confirmed that RES quenched ARA's intrinsic fluorescence through static quenching, indicating their interaction. Thermodynamic analysis revealed the interaction between them was endothermic, spontaneous, and primarily hydrophobic. Molecular dynamics (MD) simulations highlighted strong affinity between RES and ARA, with key amino acids (His425, Val426, Phe405, and Phe464) facilitating their interaction. RES binding increased stability without significant protein conformational changes. The independent gradient model based on Hirshfeld partition (IGMH) validated their interaction, emphasizing van der Waals (VDW) interactions and hydrogen bonds (H-bonds) as crucial for stable binding. This research lays a theoretical foundation for potential applications of ARA-RES complex products in the food industry.
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The Protein Data Bank (PDB) was scrutinized for the presence of noncovalent O···Al Triel Bonding (TrB) interactions, involving protein residues (e.g. GLU and GLN), adenosine/guanine diphosphate moieties (ADP and GDP), water molecules and two aluminum fluorides (AlF3 and AlF4-). The results were statistically analyzed, revealing a vast number of O···Al contacts in the active sites of phosphoryl transfer enzymes, with a marked directionality towards the Al σ-/π-hole. The physical nature of the TrBs studied herein was analyzed using Molecular Electrostatic Potential (MEP) maps, the Quantum Theory of Atoms in Molecules (QTAIM), the Non Covalent Interaction plot (NCIplot) visual index and Natural Bonding Orbital (NBO) studies. As far as our knowledge extends, it is the first time that O···Al TrBs are analyzed within a biological context, participating in protein trapping mechanisms related to phosphoryl transfer enzymes. Moreover, since they are involved in the stabilization of aluminum fluorides inside the protein's active site, we believe the results reported herein will be valuable for those scientists working in supramolecular chemistry, catalysis and rational drug design.
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CONTEXT: The CO 2 activation by low-valent group 14 catalysts encompasses the rupture of varied covalent bonds in a single transition state through a concerted pathway. The bond between the central main group atom and the hydride in the complex is elongated to trigger the formation of the C-H bond with CO 2 accompanied by the concomitant formation of the E-O bond between the complex and CO 2 to lead the corresponding formate product. Prior studies have established that besides the apolar nature of CO 2 , its initial interaction with the complex is primarily governed by electrostatic interactions. Notably, other stabilizing interactions and the transfer of charge between catalysts and CO 2 during the initial phases of the reaction have been ignored. In this study, we have quantified the non-covalent interactions and charge transfer that facilitate the activation of CO 2 by group 14 main group complex. Our findings indicate that electrostatic interactions predominantly stabilize the complex and CO 2 in the reactant region. However, induction energy becomes the main stabilizing force as the reaction progresses towards the transition state, surpassing electrostatics. Induction contributes about 50% to the stabilization at the transition state, followed by electrostatics (40%) and dispersion interactions (10%). Atomic charges calculated with the minimal basis iterative stockholder (MBIS) method reveal larger charge transfer for the back-side reaction path in which CO 2 approaches the catalysts in contrast to the front-side approach. Notably, it was discovered that a minor initial bending of CO 2 to approximately 176 ∘ initiates the charge transfer process for all systems. Furthermore, our investigation of group 14 elements demonstrates a systematic reduction in both activation energies and charge transfer to CO 2 while descending in group 14. METHODS: All studied reactions were characterized along the reaction coordinate obtained with the intrinsic reaction coordinate (IRC) methodology at the M06-2X/6-31 g(d,p) level of theory. Gibbs free energy in toluene was computed using electronic energies at the DLPNO-CCSD(T)/cc-pVTZ-SSD(E) level of theory. Vibrational and translational entropy corrections were applied to provide a more accurate description of the obtained Gibbs free energies. To better characterize the changes in the reaction coordinate for all reactions, the reaction force analysis (RFA) has been employed. It enables the partition of the reaction coordinate into the reactant, transition state, and product regions where different stages of the mechanism occur. A detailed characterization of the main non-covalent driving forces in the initial stages of the activation of CO 2 by low-valent group 14 complexes was performed using symmetry-adapted perturbation theory (SAPT). The SAPT0-CT/def2-SVP method was employed for these computations. Charge transfer descriptors based on atomic population using the MBIS scheme were also obtained to complement the SAPT analyses.
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CONTEXT: We perform density functional theory calculations to study the dependence of the structural and electronic properties of the amino acid sarcosine crystal structure on hydrostatic pressure application. The results are analyzed and compared with the available experimental data. Our findings indicate that the crystal structure and properties of sarcosine calculated using the Grimme dispersion-corrected PBE functional (PBE-D3) best agree with the available experimental results under hydrostatic pressure of up to 3.7 GPa. Critical structural rearrangements, such as unit cell compression, head-to-tail compression, and molecular rotations, are investigated and elucidated in the context of experimental findings. Band gap energy tuning and density of state shifts indicative of band dispersion are presented concerning the structural changes arising from the elevated pressure. The calculated properties indicate that sarcosine holds great promise for application in electronic devices that involve pressure-induced structural changes. METHODS: Three widely used generalized gradient approximation functionals-PBE, PBEsol, and revPBE-are employed with Grimme's D3 dispersion correction. The non-local van der Waals density functional vdW-DF is also evaluated. The calculations are performed using the projector-augmented wave method in the Quantum Espresso software suite. The geometry optimization results are visualized using VMD. The Multiwfn and NCIPlot programs are used for wavefunction and intermolecular interaction analyses.
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The importance of anions in various processes has led to a search for molecules that can effectively recognize and interact with these anions. This study explores how the tetraglycine (Gly)4 peptide in its zwitterionic, neutral, and terminally capped forms acts as a receptor for H2PO4- and HSO4- anions within the framework of supramolecular host-guest chemistry. Using molecular dynamics (MD) simulations, we obtained the conformations of the receptor-anion complexes. Density functional theory (DFT), quantifies the complexes' interaction energies in both gas and solvent phases. Proton transfer within the zwitterionic complex with H2PO4- anion alters peptide charge distribution, affecting its conformation and binding site arrangement, as analysed by quantum mechanics/molecular mechanics (QM/MM) methods. Symmetry-adapted perturbation theory (SAPT) and noncovalent interactions analysis highlight the role of electrostatic interactions in these receptor-anion complexes. It emphasizes the key interactions such as N-H···O and O-H···O=C between the peptide backbone and anions and elucidates the molecular recognition mechanism driven by crucial noncovalent interactions. The termination of the peptide's end groups modulates anion binding sites from the backbone to the charged N-terminal, resulting in distinct binding sites. Our findings provide insights for designing peptides tailored to function as anion receptors in diverse supramolecular chemistry applications.
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A new pyridine-fused seleno-diazo-lium salt, 3-(phenyl-selan-yl)[1,2,4]selena-diazolo[4,5-a]pyridin-4-ylium chloride di-chloro-methane 0.352-solvate, C12H9N2Se2 +·Cl-·0.352CH2Cl2, was obtained from the reaction between 2-pyridyl-selenenyl chloride and phenyl-seleno-cyanate. Single-crystal structural analysis revealed the presence of C-Hâ¯N, C-Hâ¯Cl-, C-Hâ¯Se hydrogen bonds as well as chalcogen-chalcogen (Seâ¯Se) and chalcogen-halogen (Seâ¯Cl-) inter-actions. Non-covalent inter-actions were explored by DFT calculations followed by topological analysis of the electron density distribution (QTAIM analysis). The structure consists of pairs of seleno-diazo-lium moieties arranged in a head-to-tail fashion surrounding disordered di-chloro-methane mol-ecules. The assemblies are connected by C-Hâ¯Cl- and C-Hâ¯N hydrogen bonds, forming layers, which stack along the c-axis direction connected by bifurcated Seâ¯Cl-â¯H-C inter-actions.
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Two-dimensional imine covalent organic frameworks (2D imine-COFs) are crystalline porous materials with broad application prospects. Despite the efforts into their design and synthesis, the mechanisms of their formation are still not fully understood. Herein, a one-pot two-step mechanochemical cocrystal precursor synthetic strategy is developed for efficient construction of 2D imine-COFs. The mechanistic investigation demonstrated that the cocrystal precursors of 4,4',4''-(1,3,5-triazine-2,4,6-triyl)trianiline (TAPT) and p-toluenesulphonic acid (PTSA) sufficiently regulate the crystalline structure of COF. Evidenced by characterizations and theoretical studies, a helical hydrogen-bond network was constructed by the N-H···O supramolecular synthons between amine and sulfate in TAPT-PTSA, demonstrating the role of cocrystals in promoting the organized stacking of interlayer π-π interactions, layer arrangement, and interlayer spacing, thus facilitating the orderly assembly of COFs. Moreover, the protonation degree of TAPT amines, which tuned nucleophilic directionality, enabled the sequential progression of intra- and interlayer imine condensation reactions, inhibiting the formation of amorphous polymers. The transformation from cocrystal precursors to COFs was achieved through comprehensive control of hydrogen bond and covalent bond sites. This work significantly advances the concept of hydrogen-bond-regulated COF assembly and its mechanochemical method in the design and synthesis of 2D imine-COFs, further elucidating the mechanistic aspects of their mechanochemical synthesis.
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Intramolecular noncovalent interaction (INCI), a crucial strategy for effectively enhancing molecular planarity and extending π-electron delocalization in organic semiconductors (OSCs), has played an increasingly important role in optoelectronic applications. However, though the INCI formation is regularly considered to improve the device performance by literature, there is no feasible approach to directly and reliably characterizing its formation in practical-OSC films thus far. Here in this study, by theoretical analysis and calculation, the generation of INCIs in OSCs is found, normally consisting of relatively heavy elements, such as O···Se, O···S, N···S interactions, etc., can induce enhanced strength of spin-orbit coupling, the primary factor dominating spin lifetime in OSCs. Based on this newly discovered theory, spin lifetime is creatively employed as a probe for sensitively detecting INCIs in OSC films via spin valves or field-induced electron paramagnetic resonance, respectively. This study will highly promote academic and applicable developments of the cross-cutting frontier research field between organic spintronics and electronics.
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Keratin, as a promising bioresource, possesses significant potential for diverse biological applications due to its favorable biocompatibility, low toxicity, biodegradability, and cell adhesion ability. However, there are few studies on the cell-penetrating ability of keratin peptides (KEPs) for biomolecule delivery. Therefore, this study explored the cell-penetrating ability of KEPs with different molecular weights (Mw) on Caco2 cells using fluorescein-labeled insulin (FITC-INS) as the target intracellular biomolecule. The potential cell-penetrating mechanism was elaborated by combining cellular investigation with the physicochemical characterization of KEPs. The result shows that the KEPs <3 kDa (KEP1) exhibited the highest cell-penetrating ability at 2 mg/mL, allowing efficient delivery of FITC-INS into Caco2 cells without covalent bonding. The cellular uptake mechanism was energy-dependent, mainly involving macropinocytosis. The further fractionation of KEP1 reveals that the most effective components consisted of 8-19 amino acids, including specific hydrophobic peptides (e.g., RVVIEPSPVVV and IIIQPSPVVV), PPII amphipathic peptides (e.g., PPPVVVTFP and FIQPPPVVV), and Cys-rich peptides (e.g., LCAPTPCGPTPL and CLPCRPCGPTPL). Additionally, analysis of the secondary and tertiary structure and amino acid composition illustrated that KEP1 exhibited rich hydrophobic residues and disulfide bonds, which probably contributed to its cell-penetrating ability, as opposed to its small particle size and electrostatic interactions. This study reveals the cell-penetrating ability of KEPs, thus highlighting their potential as biomaterials for noncovalently delivering biomolecules.
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Peptídeos Penetradores de Células , Queratinas , Humanos , Células CACO-2 , Queratinas/química , Queratinas/farmacologia , Peptídeos Penetradores de Células/química , Peptídeos Penetradores de Células/farmacologia , Insulina/química , Insulina/metabolismo , Insulina/administração & dosagem , Insulina/farmacologia , Peptídeos/química , Peptídeos/farmacologia , Fluoresceína-5-Isotiocianato/química , Sistemas de Liberação de MedicamentosRESUMO
Once inhaled, organic compounds in ambient PM2.5 permeate the bloodstream, resulting in internal exposure. The intricate composition of these internalized organic molecules complicates the processes of source attribution and toxicity assessment. A systematic framework to assess the health impacts of water-soluble organic molecules (WSOMs) originating from diverse sources is still undeveloped. This study aims to comprehensively analyze the source-specific health effects of internalized organics in urban PM2.5 through human serum albumin (HSA) non-covalent adductomes with WSOMs. Using high-resolution mass spectrometry, surface plasmon resonance, and machine learning, we mapped HSA-WSOM interactions, uncovering WSOM's potential internal exposure through its HSA adductome. The study identified eight distinct sources of internalized WSOMs, primarily from biogenic emissions, gasoline exhaust, and biomass combustion. Notably, WSOMs from these sources exhibited a predominant interaction with HSA residues ARG257, LEU238, and TRP150, substantially altering the functional dynamics of fatty acid binding site two and the hydrophobic cavity via hydrogen bonding and hydrophobic interactions. The primary health impacts of internalized WSOMs were identified as neurotoxicity and respiratory toxicity. WSOMs originating from biogenic sources and ocean emissions were mainly responsible for neurotoxic effects, whereas those from biomass burning and gasoline exhaust predominantly caused respiratory toxicity. Using the HSA adductome framework, our study identifies source-specific profiles and health effects of internally exposed WSOMs in urban PM2.5, emphasizing the importance of targeted mitigation strategies.
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Green fluorescent protein (GFP) is widely utilized as a fluorescent tag in biochemical fields. Whereas the intermediate (I) state has been proposed in the photoreaction cycle in addition to the A and B states, until now the structure of I has only been estimated by computational studies. In this paper, we report the crystal structures of the I stabilizing variants of GFP at high resolutions where respective atoms can be observed separately. Comparison with the structures in the other states highlights the structural feature of the I state. The side chain of one of the substituted residues, Val203, adopts the gauche- conformation observed for Thr203 in the A state, which is different from the B state. On the other hand, His148 interacts with the chromophore by ordinary hydrogen bonding with a distance of 2.85 Å, while the weaker interaction by longer distances is observed in the A state. Therefore, it was indicated that it is possible to distinguish three states A, B and I by the two hydrogen bond distances Oγ-Thr203···Oη-chromophore and Nδ1-His148···Oη-chromophore. We discuss the characteristics of the I intermediate of wild-type GFP on the bases of the structure estimated from the variant structures by quantum chemical calculations.
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Proteínas de Fluorescência Verde , Ligação de Hidrogênio , Modelos Moleculares , Proteínas de Fluorescência Verde/química , Proteínas de Fluorescência Verde/metabolismo , Cristalografia por Raios X , Conformação ProteicaRESUMO
Silk fibroin is a fiber-forming protein derived from the thread of Bombyx mori silkworm cocoons. This biocompatible protein, under the kosmotropic influence of potassium phosphate, can undergo supramolecular self-assembly driven by a random coil to ß-sheet secondary structure transition. By leveraging concurrent nonspecific adsorption and self-assembly of silk fibroin, we demonstrate an interfacial phenomenon that yields adherent, defect-free nanothin protein coatings that grow continuously in time, without observable saturation in mass deposition. This noncovalent growth of silk fibroin coatings is a departure from traditionally studied protein adsorption phenomena, which generally yield adsorbed layers that saturate in mass with time and often do not completely cover the surface. Here, we explore the fundamental mechanisms of coating growth by examining the effects of coating solution parameters that promote or inhibit silk fibroin self-assembly. Results show a strong dependence of coating kinetics and structure on solution pH, salt species, and salt concentration. Moreover, coating growth was observed to occur in two stages: an early stage driven by protein-surface interactions and a late stage driven by protein-protein interactions. To describe this phenomenon, we developed a kinetic adsorption model with Langmuir-like behavior at early times and a constant steady-state growth rate at later times. Structural analysis by FTIR and photoinduced force microscopy show that small ß-sheet-rich structures serve as anchoring sites for absorbing protein nanoaggregates, which is critical for coating formation. Additionally, ß-sheets are preferentially located at the interface between protein nanoaggregates in the coating, suggesting their role in forming stable, robust coatings.
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Bombyx , Fibroínas , Fosfatos , Fibroínas/química , Bombyx/química , Animais , Fosfatos/química , Adsorção , Nanoestruturas/química , Materiais Revestidos Biocompatíveis/química , Propriedades de Superfície , Cinética , Concentração de Íons de HidrogênioRESUMO
As part of a much larger study on non-covalent interactions in binary adducts, we have explored the solid-state structures of bromopentafluorobenzene (C6F5Br) using differential scanning calorimetry (DSC), variable-temperature powder X-ray diffraction (VT-PXRD), and single-crystal X-ray diffraction (SXD). DSC data initially indicated a single solid-state phase below the freezing point, but revealed additional weak transitions upon heating. The crystal structures of three solid-state phases have been solved. The SXD data showed that phases I and IV are centrosymmetric, whilst phase II is polar. However, the structure of phase III remains elusive due to the changing phase behaviour of C6F5Br that is determined as much as by kinetics as thermodynamics. The results underline the need for multiple analytical techniques to study non-covalent interactions and offer valuable data for refining computational models in crystal structure prediction and machine learning. A comparison with the iodinated counterpart is also made.
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The building block Pyra-Chol has been designed and synthesized, which exhibits different achiral morphologies in good solvents, forming nanospheres in THF and nanoflowers in 1,4-dioxane. In the presence of water as a poor cosolvent, Pyra-Chol demonstrates an agnostic behavior, generating left-handed superhelices in the water:THF (80:20) solvent system. However, when the good solvent is switched to 1,4-dioxane, a change in chirality is observed in the water:1,4-dioxane (30:70) solvent system, resulting in the formation of fused nanospheres. Interestingly, when the poor cosolvent is changed from water to MCH in THF, the chiral pattern remains unchanged, but the morphology changes completely. Supported by the collective spectroscopic and microscopic analysis, the present study efficaciously demonstrates the remarkable control of hydrophobic building block over the chiral sense and also highlights the fascinating influence of good as well as poor cosolvent in supporting the distinct molecular packing.
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Hole transport materials (HTMs) have a critical impact on the performance of perovskite solar cells (PSCs). Especially, the dopant-free HTMs could avoid the usage of hygroscopic dopants and reduce costs, which are important for device stability. Most of the current organic dopant-free HTMs are polycyclic aromatic hydrocarbons-based planar conjugated structures. Yet, the synthesis of conjugated fused heterocycles is often complicated. In this work, intramolecular non-covalent interaction is introduced to construct two organic HTMs (DCT and DTC), which can be facilely obtained through simple reactions. Compared to DTC with hexyl chain on the central benzene ring, DCT with hexyloxy chains shows better planarity in the core structure, as a result of the intramolecular non-covalent interactions between oxygen on hexyloxy and sulfur atom on the adjacent thiophene, as reflected from its single crystal structure. Moreover, DCT in a pristine state shows a decent hole mobility comparable to the doped Spiro-OMeTAD. Ultimately, conventional devices using dopant-free DCT as HTM show a high efficiency of 22.50%, with excellent long-term stability, and light and thermal stability. The results show that the noncovalent interaction is a useful and simple design strategy for dopant-free HTMs, that can effectively improve the efficiency and stability of PSCs.
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Herein, we report the synthesis of double-walled noncovalent carbon nanotubes (CNTs) through host-guest complexation of nanotube fragments and tube-forming crystal engineering. As the smallest fragment of double-walled CNTs, a host-guest complex of perfluorocycloparaphenylene (PFCPP) and carbon nanobelt (CNB) was synthesized by mixing them in solvents. The immediate complexation of the PF[12]CPPâ(6,6)CNB complex with a remarkably high association constant (Ka) of 2×105 L/mol was observed. Time-dependent 1H NMR and thermogravimetry measurements revealed that the stability of (6,6)CNB was significantly improved by encapsulation. X-ray crystallography confirmed the robust belt-in-ring structure of this complex. As indicated by the short distance between PF[12]CPP and (6,6)CNB (2.8 Å), intermolecular orbital interactions exist between the belt and the ring, which were further supported by theoretical calculation and phosphorescence quenching experiments. While the PF[12]CPPâ(6,6)CNB complex adopts various crystal packing structures, chloroform was discovered to be a magic "glue" solvent inducing one-dimensional alignment of the PF[12]CPPâ(6,6)CNB complex to build an unprecedented double-walled noncovalent CNT structure.