Stacking Of Molecules Research Articles

Controlling the Thermoelectric Performance of Doped Naphthobisthiadiazole-Based Donor-Acceptor Conjugated Polymers through Backbone Engineering.

This study investigates backbone engineering and evaluates the thermoelectric properties of FeCl3-doped naphthobisthiadiazole (NTz)-based donor-acceptor (D-A) conjugated polymer films. The NTz acceptor unit is coupled with three distinct donor units, namely dialkylated terthiophene (3T), dialkylated quaterthiophene (4T), and dialkylated bisthienyl thienothiophene (2T-TT) to yield copolymers designated as PNTz3T, PNTz4T, and PNTzTT. The difference in donor units leads to diverse molecule stacking and electronic properties, which can be systematically discovered via the three polymers. The linear structure of PNTz4T enables an orderly arrangement of side chains, thereby promoting dopant intercalation for enhanced carrier concentration. Additionally, this linear structure leads to an edge-on stacking mode, thereby improving the in-plane carrier mobility. As a result, the doped PNTz4T exhibits the highest electrical conductivity (σ) of 88.3 S cm-1 along with a Seebeck coefficient (S) of 62.2 µV K-1, thereby achieving the highest power factor (PF) of 34.2 µW m-1 K-2. These results highlight the relationship between the molecular design, microstructure, and doping effects in manipulating the thermoelectric performance of doped NTz-based D-A polymers.

Cryo-EM structure of a natural prion: chronic wasting disease fibrils from deer

Chronic wasting disease (CWD) is a widely distributed prion disease of cervids with implications for wildlife conservation and also for human and livestock health. The structures of infectious prions that cause CWD and other natural prion diseases of mammalian hosts have been poorly understood. Here we report a 2.8 Å resolution cryogenic electron microscopy-based structure of CWD prion fibrils from the brain of a naturally infected white-tailed deer expressing the most common wild-type PrP sequence. Like recently solved rodent-adapted scrapie prion fibrils, our atomic model of CWD fibrils contains single stacks of PrP molecules forming parallel in-register intermolecular β-sheets and intervening loops comprising major N- and C-terminal lobes within the fibril cross-section. However, CWD fibrils from a natural cervid host differ markedly from the rodent structures in many other features, including a ~ 180° twist in the relative orientation of the lobes. This CWD structure suggests mechanisms underlying the apparent CWD transmission barrier to humans and should facilitate more rational approaches to the development of CWD vaccines and therapeutics.

Small molecule π-π stacking promotes efficient photoelectrocatalytic splitting of aqueous hydrogen production from polyaniline.

The efficiency of photoelectrocatalysis is fundamentally dependent on the sufficient absorption of light and efficient utilisation of photogenerated carriers, but is largely limited by the reactivity from the inefficient charge transfer and surface sites of the catalyst. In this study, π-π stacking of polar small molecules on aromatic ring-rich polyaniline (PANI) was carried out to improve its photoelectrocatalytic splitting of water for hydrogen production. Detailed photoelectrochemical experiments and density-functional theory (DFT) calculations show that small molecules of p-aminobenzoic acid (PABA) and PANI have the best π-π stacking (compared to p-toluenesulfonic acid (PTA)), which promotes the separation of carriers on the PANI surface. In addition, the polar effect of the small molecules also improves the reactivity of the PANI surface and also reduces the potential barrier for H2 evolution. The current density of PANI-PABA reached -0.12 mA/cm2 (1.23 V vs. RHE) 2.53 times higher than that of pure PANI in linear voltammetric scanning tests under light. This strategy of introducing polar small molecules into organocatalysts via π-π stacking will provide new ideas for the preparation of efficient organic photoelectrocatalysis.

Boosting disassembly of π–π stacked supramolecular nanodrugs under tumor microenvironment by introducing stimuli‐responsive drug‐mates

AbstractNumerous reports have demonstrated the construction of supramolecular nanodrugs (SNDs) via the π–π stacking of drug molecules for antitumor applications because most drugs possess aromatic rings or other planar conjugate units. However, the destruction of π–π stacking and the subsequent disassembly of SNDs under tumor microenvironment (TME), which is the precondition for drug release, have not been clearly described. In this work, based on a disassembly model of π–π stacked naphthoquinone SNDs, the influence of co‐assembled drugs on disassembly is delineated. Both the experimental observation and computational simulation indicate that the disassembly of SNDs under simulated TME highly depends on the disassembly activation energy (ΔEdis) of neighboring π–π stacked molecules. Owing to the high ΔEdis, the disassembly of self‐assembled naphthoquinone SNDs is greatly restricted. Meaningfully, the ΔEdis is the sum of a series of activation energy according to the specific stimuli of TME. Thus, a concept of stimuli‐responsive drug‐mates is proposed for boosting the disassembly of π–π stacked SNDs, namely the foremost co‐assembly of π‐conjugated drugs with additional drug molecules that possess relatively weak π–π interaction but high TME responsiveness. Further computational simulation reveals that the introduction of stimuli‐responsive drug‐mates significantly lowers the ΔEdis, thus accelerating the disassembly of SNDs and the release of drug payloads. Holding the advantages of π‐conjugated drug library, the concept of stimuli‐responsive drug‐mates gives an extensive design of π–π stacked SNDs toward heterogeneous nidus microenvironment responsiveness, which highlights the superiority of widely used drug co‐assembly strategy in constructing multifunctional SNDs.

(Invited) Computational Analysis of the Excited States in the Film States of Non-Fullerene Acceptors

Non-fullerene acceptors are currently widely used as the acceptors of organic thin film solar cells due to their high efficiency. However, the molecular mechanism is still unclear. We have studied the excited states in the film states of non-fullerene acceptors together with experimental collaborators by using theoretical methods. In this presentation, we will present recent progress of our research. For example, we will talk about the excited states in the film states of ITIC. ITIC is a popular acceptor-donor-acceptor-type non-fullerene acceptor. Recently, our collaborator, Prof. Yamakata at Okayama University, Japan, found that the charge separation can take place in ITIC acceptor film even without donor molecules. We investigated this phenomenon by using MD simulations and quantum chemical calculations. MD simulations of the ITIC film showed that the acceptor parts of ITIC are stacked with each other. The dominant angle between two stacked ITIC was found to be ~180 degrees, making J-type dimer. On the other hand, it was also found that there are quite a few V-type dimers with the angles less than 90 degrees. Quantum chemical calculations revealed that the dipole moment in the excited state of J-type dimer is almost zero whereas that of V-type dimer is quite large, indicating strong charge-transfer excited state. Therefore, it is considered that the charge separation of ITIC film can take place in the V-type dimers. We also investigated the excited states in the film states of ITIC analogs. Recently, our collaborator, Prof. Ie at Osaka University, Japan, synthesized several ITIC analogs with different sidechains and found the different efficiency of solar cells. We theoretically investigated the excited states in the film sates of ITIC analogs as in the case of ITIC. It is found that the modification of side chains can change the distributions of angles between two stacked molecules and excited-state properties. These findings highlight the importance of controlling stacking structures in the film state for the efficiency of organic thin film solar cells.

Crystal structure of 4-bromo-5,7-dimeth-oxy-2,3-di-hydro-1H-inden-1-one.

In the title mol-ecule, C11H11BrO3, the di-hydro-indene moiety is essentially planar but with a slight twist in the saturated portion of the five-membered ring. The meth-oxy groups lie close to the above plane. In the crystal, π-stacking inter-actions between six-membered rings form stacks of mol-ecules extending along the a-axis direction, which are linked by weak C-H⋯O and C-H⋯Br hydrogen bonds. A Hirshfeld surface analysis was performed showing H⋯H, O⋯H/H⋯O and Br⋯H/H⋯Br contacts make the largest contributions to inter-molecular inter-actions in the crystal.

Radical cations of chalcogenanthrenes with halogenido metalate anions. Part I: tetramethoxythianthrene

Abstract The electron-rich molecule tetramethoxythianthrene TMO-TA can readily be oxidized to the radical cation using various transition metal halides in acetonitrile as solvent. Reactions with CuBr2, FeCl3, AuCl3, NbCl5, and CuCl2 yield dark blue or black crystals of [TMO-TA]2[CuBr4] (2), [TMO-TA][FeCl4] · CH3CN (3), [TMO-TA][AuCl4] (4), [TMO-TA][NbCl6] · CH3CN (6), and [TMO-TA]5[Cu2Cl6]2 · 2 CH3CN (7). [TMO-TA]2[Ta2OF10] (5) was obtained by anodic oxidation of TMO-TA in the presence of (Nbu4)2[Ta2OF10] as electrolyte. Using mercury(II) bromide, no redox reaction occurs. Instead, the colorless complex [HgBr2(TMO-TA)] (1) is formed. In the crystal structures of the compounds 2–7, the almost planar radical cations show different types of arrangements. Pair formation of the [TMO-TA]•+ radicals to [TMO-TA]2 2+ dimers with the typical intra-pair S⋯S bonds of 3.1–3.2 Å lengths is predominant. Compounds 6 and 7 contain stacks of planar TMO-TA molecules in equidistant arrangement without pair formation and the unique feature of rotation of each adjacent cation by about 30°. Compounds 2, 5, and 7 are electrical semiconductors with band gaps between 0.62 and 1.4 eV, reflecting the arrangement of the radical cations. While 5 is diamagnetic, the magnetic momenta of 2 and 7 correspond only to the expected paramagnetic momenta of magnetically dilute Cu2+ ions. Electrons on the organic radicals are strongly paired in all compounds.

Paper Spray Mass Spectrometry with On‐Paper Electrokinetic Manipulations: Part‐Per‐Trillion Detection of Per/Polyfluoroalkyl Substances in Water and Opioids in Urine

AbstractWe developed a simple, paper‐based device that enables sensitive detection by mass spectrometry (MS) without solid phase extraction or other sample preparation. Using glass fiber filter papers within a 3D printed holder, the device employs electrokinetic manipulations to stack, separate, and desalt charged molecules on paper prior to spray into the MS. Due to counter‐balanced electroosmotic flow and electrophoresis, charged analytes stack on the paper and desalting occurs in minutes. One end of the paper strip was cut into a sharp point and positioned near the inlet of a MS. The stacked analyte bands move toward the paper tip with the EOF where they are ionized by paper spray. The device was applied to analysis of PFAS in tap water with sub part‐per‐trillion detection limits in less than ten minutes with no sample pretreatment. Analysis of opioids in urine also occurs in minutes. The crucial parameters to enable stacking, separation, and MS ionization of both positively and negatively charged analytes were determined and optimized. Experimental and computational modeling studies confirm the electrokinetic stacking and analyte transport mechanisms. On‐paper separations were carried out by stacking analyte bands at different locations depending on their electrophoretic mobility, achieving baseline separation in some cases.

Paper Spray Mass Spectrometry with On-Paper Electrokinetic Manipulations: Part-Per-Trillion Detection of Per/Polyfluoroalkyl Substances in Water and Opioids in Urine.

We developed a simple, paper-based device that enables sensitive detection by mass spectrometry (MS) without solid phase extraction or other sample preparation. Using glass fiber filter papers within a 3D printed holder, the device employs electrokinetic manipulations to stack, separate, and desalt charged molecules on paper prior to spray into the MS. Due to counter-balanced electroosmotic flow and electrophoresis, charged analytes stack on the paper and desalting occurs in minutes. One end of the paper strip was cut into a sharp point and positioned near the inlet of a MS. The stacked analyte bands move toward the paper tip with the EOF where they are ionized by paper spray. The device was applied to analysis of PFAS in tap water with sub part-per-trillion detection limits in less than ten minutes with no sample pretreatment. Analysis of opioids in urine also occurs in minutes. The crucial parameters to enable stacking, separation, and MS ionization of both positively and negatively charged analytes were determined and optimized. Experimental and computational modeling studies confirm the electrokinetic stacking and analyte transport mechanisms. On-paper separations were carried out by stacking analyte bands at different locations depending on their electrophoretic mobility, achieving baseline separation in some cases.

Crystal structure of alectinib hydrochloride Type I, C30H35N4O2Cl

The crystal structure of alectinib hydrochloride has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Alectinib hydrochloride crystallizes in space group P21/n (#14) with the following parameters: a = 12.67477(7), b = 10.44076(5), c = 20.38501(12) Å, β = 93.1438(7)°, V = 2693.574(18) Å3, and Z = 4 at 295 K. The crystal structure consists of stacks of molecules along the b-axis, and the stacks contain chains of strong N–H⋯Cl hydrogen bonds. One density functional theory calculation moved a proton from an N atom to the Cl, but another calculation yielded a more chemically reasonable result. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®)

Delaying crystallization and anchoring the grain boundaries defects via π-π stacked molecules for efficient and stable wide-bandgap perovskite solar cells

Owing to the easy migration of halogen ions in wide-bandgap perovskite, it will lead to the formation of a large number of uncoordinated Pb2+ to form deep-level defects, which seriously affects the power conversion efficiency (PCE) and stability of wide-bandgap perovskite solar cells (PSCs). The introduction of additives has been recognized as an effective method to improve these defects, especially Lewis acid-base additives. Herein, Lewis base molecule dibenzofuran (DBF) with π-conjugated system, which can form π-π stacked dimer, is used as a perovskite additive. The detailed crystallization process of perovskite main precursor triggered by DBF is measured by using laser scanning confocal microscopy. It is demonstrated that the addition of DBF in perovskite samples resulted in a deceleration of the crystallization process, which is due to the formation of Lewis acid-base complexes between DBF π-π stacked dimer and perovskite, which can obtain perovskite films with reduced defect density. As a result, the champion PCE of the wide-bandgap (1.68 eV) perovskite device reaches 20.18 %, significantly higher than the control device (17.79 %). Additionally, the device with no encapsulation demonstrates better stability, as it maintains over 90 % of the initial PCE under an air environment with 30–40 % relative humidity (RH) and 25 °C for 1200 h.

Effect of isopropyl chloride addition in AlCl3 catalytic system on the formation of coal tar pitch-based mesophases

Mesophase pitch is a high-quality precursor for the synthesis of high-performance pitch-based carbon fibers. The mesophase content, texture and softening point are the most important factors for the structure, properties and spinnability of mesophase pitch (MP). Herein, we report a novel approach for the preparation of mesophase pitch with high anisotropic content and low softening point by AlCl3 catalytic pyrolysis in the presence of isopropyl chloride (PrCl). The variation of anisotropic content and mesophase texture under different PrCl additions and the effect of the introduction of isopropyl on the molecular stacking of aromatic lamellar molecules were investigated. The results confirmed that, except for their role in improving catalytic activity, carbocation co-catalysts can improve the structure and molecular assembly of aromatic molecules through the introduction of alkyl groups. The reaction of isopropyl chloride (PrCl) as a co-catalyst catalyzed pyrolysis of medium-temperature coal pitch at 370 ℃ for 8 h produced a bulk mesophase with a content close to 100 %. Compared to the AlCl3 system (without PrCl), the AlCl3-PrCl system can catalyze the preparation of mesophases at lower temperatures. In addition, it is logical that the introduction of isopropyl group significantly increases the stacking spacing of the mesophase pitch layer molecules, which can effectively improve the mobility of the aromatic layer molecules resulting in the growth of mesophase. The fusion texture and anisotropic content of mesophase pitch were significantly improved by replacing the nucleophilic reagent of the AlCl3-catalyzed system. This work provides feasible ideas for the preparation of high-performance coal tar based mesophase pitch.

Crystal structure of nicarbazin, (C13H10N4O5)(C6H8N2O)

The crystal structure of nicarbazin has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Nicarbazin is a co-crystal of 4,4′-dinitrocarbanilide (DNC) and 2-hydroxy-4,6-dimethylpyrimidine (HDP) molecules. Nicarbazin crystallizes in space group P-1 (#2) with a = 6.90659(8), b = 12.0794(4), c = 13.5040(7) Å, α = 115.5709(11), β = 102.3658(6), γ = 91.9270(4)°, V = 982.466(5) Å3, and Z = 2. The DNC and HDP molecules are linked by two strong N–H⋯O and N–H⋯N hydrogen bonds, and the HDP molecules are linked into centrosymmetric dimers by another N–H⋯O hydrogen bond. These strong hydrogen bonds link the molecules into layers parallel to the ab-plane and parallel stacking of both DNC and HDP molecules is prominent in the structure. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Crystal structure of anthraquinone-2-carboxylic acid, C15H8O4

The crystal structure of anthraquinone-2-carboxylic acid has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Anthraquinone-2-carboxylic acid crystallizes in space group P-1 (#2) with a = 3.7942(2), b = 13.266(5), c = 22.835(15) Å, α = 73.355(30), β = 89.486(6), γ = 86.061(1)°, V = 1098.50(7) Å3, and Z = 4. The crystal structure contains two independent molecules of anthraquinone-2-carboxylic acid. Although the expected hydrogen-bonded dimers are present, the dimers are not centrosymmetric. The dimer contains one molecule of each planar low-energy conformation. The crystal structure consists of a herringbone array of centrosymmetric pairs of molecules parallel to the bc-plane. The molecules stack along the short a-axis. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

Polymorphism-Dependent Organic Room Temperature Phosphorescent Scintillation for X-Ray Imaging.

Organic phosphorescent scintillating materials have shown great potential for applications in radiography and radiation detection due to their efficient utilization of excitons. However, revealing the relationship between molecule stacking and the phosphorescent radioluminescence of scintillators is still challenging. This study reports on two phenothiazine derivatives with polymorphism-dependent phosphorescence radioluminescence. The experiments reveal that molecule stacking significantly affects the non-radiation decay of the triplet excitons of scintillators, which further determines the phosphorescence scintillation performance under X-ray irradiation. These phosphorescent scintillators exhibit high radio stability and have a low detection limit of 278 nGys-1. Additionally, the potential application of these scintillators in X-ray radiography, based on their X-ray excited radioluminescence properties, is demonstrated. These findings provide a guideline for obtaining high-performance phosphorescent scintillating materials by shedding light on the effect of crystal packing on the radioluminescence of organic molecules.

Theoretical study on molecular charge populations of 1D π-stacked multimers in neutral and electron oxidation states

Abstract We theoretically investigated molecular charge populations of 1D π-stacked multimers consisting of π-conjugated molecules in the neutral and electron oxidation states based on the valence-bond (VB) theory. Qualitative analysis for a π-stacked trimer model based on the VB mixing diagram suggested that the inner monomer site tends to be more positively charged than the outer sites in the monocationic π-stacked trimer. Spatial expansion of each molecular site orbital toward the stacking direction is predicted to enhance the difference of positive charge populations between the inner and outer monomers. In contrast, an opposite tendency for the site charges was expected in the dicationic π-stacked trimer, primarily due to the hole–hole Coulomb repulsions. To generalize the results of the trimer to π-stacked N-mers, 1D N-site VB configuration interaction models were constructed considering the orbital expansion effects between the sites. We examined how the number of monomers (N), stacking distance (R), and characteristic orbital exponent for the monomers (ζ) affected the molecular charge populations in the monocationic and dicationic π-stacked N-mers through the parameters χij characterizing the orbital expansion effect. The results are expected to help establish design strategies for novel electronic functional materials based on discrete stacks of π-conjugated molecules.

Mesomorphism Modulation of Perfluorinated Janus Triphenylenes by Inhomogeneous Chain Substitution Patterns.

Two isomeric series of compounds with "inverted" chains' substitution patterns, 7,10-dialkoxy-1,2,3,4-tetrafluoro-6,11-dimethoxytriphenylene and 6,11-dialkoxy-1,2,3,4-tetrafluoro-7,10-dimethoxytriphenylene, labelled respectively p-TPFn and m-TPFn, and two non-fluorinated homologous isomers, 3,6-dibutoxy-2,7-dimethoxytriphenylene and 2,7-dibutoxy-3,6-dimethoxytriphenylene, p-TP4 and m-TP4, respectively, were synthesized in three steps and obtained in good yields by the efficient transition-metal-free, fluoroarene nucleophilic substitution via the reaction of appropriate 2,2'-dilithium biphenylenes with either perfluorobenzene, C6 F6 , to yield p-TPFn and m-TPFn, or o-difluorobenzene, C6 H4 F2 , for p-TP4 and m-TP4, respectively. The single-crystal structures of p-TPF4, m-TPF4 and p-TP4, unequivocally confirmed that the cyclization reactions occurred at the expected positions, and that the fluorinated molecules stack up into columns with short separation, a propitious situation for the emergence of columnar mesophases. The mesomorphous properties were found to be greatly affected by both chains' length and positional isomerism: a Colhex phase is found for p-TPF4 and m-TPF4, but mesomorphism vanishes in p-TPF6, and changes for the isomeric homologs m-TPFn, with the induction for n≥6 of a lamello-columnar phase, LamColrec . As expected, both non-fluorinated compounds are deprived of mesomorphism. These compounds emit blue-violet colour in solution, independently of the chains' substitution pattern, and the absolute fluorescence quantum yields can reach up to 46 %. In thin films, fluorescence is slightly redshifted.

An elegant approach for the synthesis of multisubstituted imidazole via FeCl3/SiO2 catalyzed activation of acetals: a photophysical study of an imidazole-carbazole hybrid.

A simple and solvent-free catalytic system was developed for the direct conversion of multisubstituted imidazoles through the reaction of acetals and benzils with ammonium acetate/amines as the source of nitrogen. The reaction occurred under mild and benign conditions using FeCl3/SiO2 as a heterogeneous catalyst without the requirement of any toxic organic solvents. The easy preparation and recyclability of the catalyst allows the reaction to be simple and highly efficient, resulting in very good yields of imidazoles. Novel imidazole-carbazole hybrid compounds were also synthesised by adopting the present methodology. Single crystal X-ray diffraction study indicated the presence of a CH⋯π supramolecular interaction that renders effective molecular packing in the solid state. The steady-state and spectro-dynamic behaviours of these hybrid molecules were investigated, and it was revealed that a solvent-dependent excimer-coupled ICT phenomenon guided excited state photophysics. Very unusual excimer lifetime was noticed in the solid state of this bis-heterocyclic compound owing to the stacking of molecules via CH⋯π interaction, as evident from the X-ray studies.

Hydrate aggregation in oil-gas pipelines: Unraveling the dual role of asphalt and water

Molecular dynamics was employed to investigate the micro-mechanism of water and asphalt on hydrate aggregation, addressing the mechanism of aggregation caused by hydrates, asphalt, and water droplets in pipelines. In low-water-content pipelines, the oxygen atoms in asphalt form hydrogen bonds with hydrates, anchoring them to the hydrates. Asphalt forms stable molecular films through π-π interactions, effectively preventing hydrate aggregation. In addition to traditional hydrogen bonds (bond energies around 18 kJ/mol), asphalt also form π hydrogen bonds (bond energies around 9 kJ/mol), making it easier to bind with water. The water droplets reduce the face-to-face stacking of asphalt molecules from 35.63 % to 30.63 %. Hydrogen bonds drive asphalt to approach water droplets, and the number of hydrogen bonds between asphalt and water droplets is almost 3 times that between asphalt and hydrates. This greatly disrupts the pre-existing asphalt films between hydrate particles and weakens the anti-aggregation effect. Water bridges between hydrate particles further promote hydrate aggregation. In the HWA model, hydrate particles begin to aggregate at 27.15 ns. Water droplets can easily change the distribution status of asphalt and other anti-agglomeration agents. When designing anti-agglomeration agents, it is necessary to consider maintaining the stability of water droplets to prevent water diffusion.

Exploiting Locality in Full Configuration Interaction Quantum Monte Carlo for Fast Excitation Generation.

In this paper, we propose an improved excitation generation algorithm for the full configuration interaction quantum Monte Carlo method, which is particularly effective in systems described by localized orbitals. The method is an extension of the precomputed heat-bath strategy of Holmes et al., with more effective sampling of double excitations and a novel approach for nonuniform sampling of single excitations. We demonstrate the effectiveness of the algorithm for a chain of 30 hydrogen atoms with atom-localized orbitals, a stack of benzene molecules, and an Fe(II)-porphyrin model complex, whereby we show an overall efficiency gain by a factor of two to four, as measured by variance reduction per wall-clock time.