Dimers Stack Research Articles

Discrete π-Stacks from Self-Assembled Perylenediimide Analogues.

The formation of well-defined finite-sized aggregates represents an attractive goal in supramolecular chemistry. In particular, construction of discrete π-stacked dye assemblies remains a challenge. Reported here is the design and synthesis of a novel type of discrete π-stacked aggregate from two comparable perylenediimide (PDI) dyads (PEP and PBP). The criss-cross PEP-PBP dimers in solution and (PBP-PEP)-(PEP-PBP) tetramers in the solid state are well elucidated using single-crystal X-ray diffraction, dynamic light scattering, and diffusion-ordered NMR spectroscopy. Extensive π-π stacking between the PDI units of PEP and PBP as well as repulsive interactions of swallow-tailed alkyl substituents are responsible for the selective formation of discrete dimer and tetramer stacks. Our results reveal a new approach to preparing discrete π stacks that are appealing for making assemblies with well-defined optoelectronic properties.

Discrete π‐Stacks from Self‐Assembled Perylenediimide Analogues

AbstractThe formation of well‐defined finite‐sized aggregates represents an attractive goal in supramolecular chemistry. In particular, construction of discrete π‐stacked dye assemblies remains a challenge. Reported here is the design and synthesis of a novel type of discrete π‐stacked aggregate from two comparable perylenediimide (PDI) dyads (PEP and PBP). The criss‐cross PEP‐PBP dimers in solution and (PBP‐PEP)‐(PEP‐PBP) tetramers in the solid state are well elucidated using single‐crystal X‐ray diffraction, dynamic light scattering, and diffusion‐ordered NMR spectroscopy. Extensive π–π stacking between the PDI units of PEP and PBP as well as repulsive interactions of swallow‐tailed alkyl substituents are responsible for the selective formation of discrete dimer and tetramer stacks. Our results reveal a new approach to preparing discrete π stacks that are appealing for making assemblies with well‐defined optoelectronic properties.

Organic conductors with BiIII and SbIII chloride-based anions

New layered organic conductors, (BEDT-TTF)4(BiCl5)1 7 (1), δ-(BEDT-TTF)2BiCl5 (2), and δ-(BEDT-TTF)6Sb3Cl12 (3), were obtained (BEDT-TTF is bis(ethylenedithio)tetrathia-fulvalene). In the crystal structures of 1—3, organic radical cation layers are composed of di-merized stacks. The dimers are formed by BEDT-TTF radical cations rotated through angle ω relative to each other, which results in twisted stacks, giving rise to so-called twisted overlap mode in the layers. These layers alternate with non-conductive inorganic layers consisting of chains in which the Cl, Bi, and Sb sites are partially occupied. This indicates discontinuities in the chains of anions, and, apparently, the absence of continuous polymer chains in the crystal structure. According to measurements of the temperature dependence of the electrical resistance, the compounds are semiconductors.

One Stimulus In Situ Induces Two Sequential Luminescence Switchings in the Same Solvent‐Fuming Process: Anthracene Excimer as the Intermediate

AbstractCommonly, one stimulus only induces one luminescence switching in stimuli‐responsive experiment. Herein, it is reported that one stimulus in situ induces two luminescent switches, resulting from two phase transitions in a solvent‐fuming process. Two phase transitions are in situ composed of a first fast and a subsequent slow process, corresponding to the change of molecular packing from the amorphous state to the π–π dimer crystalline state to the cocrystalline state with the inclusion of solvents, accompanied with luminescent transformation from pure blue to green to deep blue. Theoretical and experimental results reveal that the staggered π–π dimer stacking of anthracenes serves as the intermediate state to bridge the two phase transitions. This finding expands a new horizon in the stimuli‐responsive field and inspires novel applications in information storage and security fields.

Polymorphism and configurational isomerism in 3-(9-anthryl)-1-(3-hydroxyphenyl)prop-2-en-1-one

In this study, 3-(9-anthryl)-1-(3-hydroxyphenyl)prop-2-en-1-one was synthesized and formed two cis isomers (α and β polymorphs) and one trans isomer under different crystallization conditions. Single crystal X-ray diffraction revealed that all the three crystals exhibit the similar crystal structures, in which the two adjacent chalcone molecules form dimers through intermolecular H-bonds between the phenolic hydroxyl and carbonyl groups, and all of the dimers stack parallel to construct their 3D structures. In order to rationalize the configurational phenomenon and investigate the stability of the three crystals, Hirshfeld surface analyses, theoretical calculation and grinding experiments were performed. The results revealed that the coexistence of H-bonds and C–H···π interactions around the two hydrogen atoms on the CC double bond may be crucial for formation of the cis configuration, and the trans isomer is more stable than the other two cis isomers. Moreover, the optical-physical properties of these crystals were also investigated. Due to the similar crystal structures, the similar fluorescence bands were observed in their spectra.

Radical Cation Salts of Cyanobenzene‐Ethylenedithio‐TTF Electron Donors with Halide (Cu and Hg) Binuclear Anions

Three salts of the two isomers of the dissymmetric TTF‐derivative cyanobenzene‐ethylenedithio‐tetrathiafulvalene (CNB‐EDT‐TTF) with binuclear polyhalide complex dianions, namely [4‐CNB‐EDT‐TTF]2 [Cu2Cl6] (1); [5‐CNB‐EDT‐TTF]2 [Cu2Cl6] 2CH2Cl2 (2) and [5‐CNB‐EDT‐TTF]2 [Hg2Br6] (3) were prepared and characterized by single‐crystal X‐ray diffraction and magnetic susceptibility measurements. In spite of the different structural types of these compounds, the three compounds present donors in dimerized stacks. The crystal structures of 1 and 3 consist of segregated head‐to‐tail donor dimer stacks and dianion columns. The structural motif of 2 is mixed columns of alternating head‐to‐tail donor dimers and dianions. The three salts present C–N···H–C interactions, which in 2 and 3 can be described as a R22(10) synthon. The magnetic susceptibility of the salts with the paramagnetic (Cu2Cl6)2– dianion (1 and 2) show that they behave as paramagnets where the Cu2+ atoms of the dianion are antiferromagnetically coupled with magnetic exchange values J/kB of –58.8 and –155.6 K, respectively. The different J values are associated with differences in dianion geometry.

Crystal structure and Hirshfeld surfaces analysis of the nickel(II) complex of the Shiff base ligand 6,6'-{(1E,1'E)-[ethane-1,2-diylbis(aza-nylyl-idene)]bis-(methanylyl-idene)}bis-[2-(tri-fluoro-meth-oxy)phenol

In the title complex, (6,6'-{(1E,1'E)-[ethane-1,2-diylbis(aza-nylyl-idene)]bis(methanylyl-idene)}bis-[2-(tri-fluoro-meth-oxy)phenol]-κ4 O,N,N',O')nickel(II), [Ni(C18H12F6N2O4)], the nickel(II) ion has a square-planar coordination sphere, being ligated by two N and two O atoms of the Schiff base ligand 6,6'-{(1E,1'E)-[ethane-1,2-diylbis(aza-nylyl-idene)]bis-(methanylyl-idene)}bis-[2-(tri-fluoro-meth-oxy)phenol] (L). Inversion-related mol-ecules are linked by a short Ni⋯Ni inter-action of 3.2945 (6) Å forming a dimer. In the crystal, the dimers stack up the a axis, with a closest Ni⋯Ni separation of ca 3.791 Å. There are no other significant inter-molecular inter-actions present. However, the Hirshfeld surface analysis and the two-dimensional fingerprint plots indicate that the packing is dominated by H⋯F/F⋯H, H⋯H, O⋯H/H⋯O and C⋯H/H⋯C contacts.

Unusual temperature-sensitive excimer fluorescence from discrete π-π dimer stacking of anthracene in a crystal.

Herein, an unusual blue shift in excimer fluorescence with increasing temperature was observed from a crystal with a discrete π-π anthracene dimer, originating from the more temperature-sensitive intermolecular geometry of the π-π dimer (e.g., π-π distance) compared to the intramolecular geometry of the monomer, which is confirmed by temperature-dependent single-crystal X-ray diffraction (XRD) measurements.

Alkyl chain-dependent cyano-stilbene derivative's molecular stacking, emission enhancement and fluorescent response to the mechanical force and thermal stimulus

Two cyano-stilbene derivatives with butyl (C4MPA) and octyl groups (C8MPA) were synthesized to investigate the effects of alkyl chains on molecular stacking, emission enhancement, and mechanofluorochromism. The two compounds displayed weak emissions in monomolecular state and emitted an enhanced fluorescence in crystal state. However, the fluorescence quantum yield of C4MPA (19%) was lower than that of C8MPA (76%). Face-to-face dimer stacking was found only in the C4MPA crystal, in which molecules adopted a nonplanar configuration. The C8MPA crystal presented two kinds of antiparallel 1D arrangement. One involved the antiparallel stacking of nonplanar aromatic moieties. The other consisted of coplanar molecules without π-π stacking, which were responsible for the higher luminescence yield. Moreover, the emission of the C4MPA solid was quenched under mechanical force, whereas the C8MPA solid still emitted a strong fluorescence after grinding. C8MPA lost fluorescence when heated at above 60 °C because of its low melting point, and the supercooling viscous liquid without fluorescence was observed even the sample was cooled to room temperature for 10 h, meaning a very slowly crystallization process. Such non-emissive supercooling viscous liquid might rapidly transform into strongly emissive solid under the mechanical force shearing stimulus. Thus, C8MPA films could be used as sensors for mechanical force and thermal stimuli.

Multicentric two-electron covalent bonding (pancake bonding) between semiquinone radicals determines bulk properties

Fine details of stacking interactions in three different types of π-stacked tetrachlorosemiquinone radical anions (Cl4Q) were studied by a combination of X-ray charge density, quantum chemical computation and atoms-in-molecules (AIM) analysis: 1) stacks of pancake-bonded radical dimers in triclinic polymorph of N-MePy·Cl4Q (N-MePy = N-methylpyridinium cation), 2) stacks of trimers of partially charged semiquinones in [4-damp])2[Cl4Q]3 (4-damp = 4-dimethylamino-N-methylpyridinium) and 3) stacks of equidistant radicals in orthorhombic polymorph of N-MePy·Cl4Q. For the first time, we provide experimental evidence (based on X-ray charge density) of two-electron multicentric covalent bonding (pancake bonding) between the radicals. Typical pancake-bonded radical dimers in 1) are characterised by short interplanar distance (2.86 A) and multiple bonding (3, -1) critical points between the rings with maximum electron density exceeding 0.095 e A-3 ; in addition, a (3, +3) critical point (local minimum of electron density) was also found, indicating a cage-like electronic structure [1]. The covalent contribution to total interaction in a dimer was calculated to be -9.4 kcal mol-1. Between the dimers, interplanar separation is 3.60 A and only negligible electron density is found. In trimers there are two electrons shared between three closely interacting rings (interplanar separations are ca. 2.84 A), and (3, -1) bonding critical points are found with maximum electron density of 0.077 e A-3 ; there are also two (3, +3) local minima [2]. The calculated covalent contribution is -6.8 kcal mol-1. Maximum electron density between the rings in a stack of equidistant radicals (interplanar separation of 3.17 A) is much lower, 0.050 e A-3, and there is no local minimum of electron density [1]. However, the HOMO orbitals extend between the rings, and the calculated covalent contribution is -2.9 kcal mol-1. This compound is a 1D semiconductor [3, 4], and its semiconductivity is explained by pancake bonding extending along the stack.

Polymorphism of G4 associates: from stacks to wires via interlocks.

We examined the assembly of DNA G-quadruplexes (G4s) into higher-order structures using atomic force microscopy, optical and electrophoretic methods, NMR spectroscopy and molecular modeling. Our results suggest that parallel blunt-ended G4s with single-nucleotide or modified loops may form different types of multimers, ranging from stacks of intramolecular structures and/or interlocked dimers and trimers to wires. Decreasing the annealing rate and increasing salt or oligonucleotide concentrations shifted the equilibrium from intramolecular G4s to higher-order structures. Control antiparallel and hybrid G4s demonstrated no polymorphism or aggregation in our experiments. The modification that mimics abasic sites (1′,2′-dideoxyribose residues) in loops enhanced the oligomerization/multimerization of both the 2-tetrad and 3-tetrad G4 motifs. Our results shed light on the rules that govern G4 rearrangements. Gaining control over G4 folding enables the harnessing of the full potential of such structures for guided assembly of supramolecular DNA structures for nanotechnology.

5-[Phenyl(pyridin-4-yl)amino]penta-2,4-diyn-1-ol

In the title diacetylene derivative, C16H12N2O, the amino plane makes dihedral angles of 3.90 (4) and 60.53 (4)°, respectively, with the pyridyl and phenyl rings, indicating that an electron-deficient pyridyl ring makes better conjugation with a lone pair of the amino nitrogen atom. In the crystal, molecules form inversion dimersviapairs of hydrogen bonds between the hydroxy and pyridyl groups, with an O...N distance of 2.7765 (16) Å. The dimers stack along theaaxis, but the title compound shows little solid-state polymerization reactivity.

Syntheses, spectroscopy, and crystal structures of 3-(4-bromo-phen-yl)-1,5-di-phenyl-formazan and the 3-(4-bromo-phen-yl)-1,5-di-phenyl-verdazyl radical and the crystal structure of the by-product 5-anilino-3-(4-bromo-phen-yl)-1-phenyl-1H-1,2,4-triazole.

The title compounds, C19H15BrN4, C20H16BrN4 and C20H15BrN4, are nitro-gen-rich organic compounds that are related by their synthesis. The verdazyl radical, in which stacking leads to anti-ferromagnetic inter-actions, was reported previously [Iwase et al. (2013 ▸). Phys. Rev. B, 88, 184431]. For this compound, improved structural data and spectroscopic data are presented. The other two compounds have been crystallized for the first time and form stacks of dimers, roughly along the a-axis direction of the crystal. The formazan mol-ecule shows signs of rapid intra-molecular H-atom exchange typical for this class of compounds and spectroscopic data are provided in addition to the crystal structure. The triazole compound appears to be a side-product of the verdazyl synthesis.

Hybrid Structure of the RagA/C-Ragulator mTORC1 Activation Complex

The lysosomal membrane is the locus for sensing cellular nutrient levels, which are transduced to mTORC1 via the Rag GTPases and the Ragulator complex. The crystal structure of the five-subunit human Ragulator at 1.4 A resolution was determined. Lamtor1 wraps around the other four subunits to stabilize the assembly. The Lamtor2:Lamtor3 dimer stacks upon Lamtor4:Lamtor5 to create a platform for Rag binding. Hydrogen-deuterium exchange was used to map the Rag binding site to the outer face of the Lamtor2:Lamtor3 dimer and to the N-terminal intrinsically disordered region of Lamtor1. EM was used to reconstruct the assembly of the full-length RagAGTP:RagCGDP dimer bound to Ragulator at 16 A resolution, revealing that the G-domains of the Rags project away from the Ragulator core. The combined structural model shows how Ragulator functions as a platform for the presentation of active Rags for mTORC1 recruitment, and might suggest an unconventional mechanism for Rag GEF activity.

Hybrid Structure of the RagA/C-Ragulator mTORC1 Activation Complex

The lysosomal membrane is the locus for sensing cellular nutrient levels, which are transduced to mTORC1 via the Rag GTPases and the Ragulator complex. The crystal structure of the five-subunit human Ragulator at 1.4Å resolution was determined. Lamtor1 wraps around the other four subunits to stabilize the assembly. The Lamtor2:Lamtor3 dimer stacks upon Lamtor4:Lamtor5 to create a platform for Rag binding. Hydrogen-deuterium exchange was used to map the Rag binding site to the outer face of the Lamtor2:Lamtor3 dimer and to the N-terminal intrinsically disordered region of Lamtor1. EM was used to reconstruct the assembly of the full-length RagAGTP:RagCGDP dimer bound to Ragulator at 16Å resolution, revealing that the G-domains of the Rags project away from the Ragulator core. The combined structural model shows how Ragulator functions as a platform for the presentation of active Rags for mTORC1 recruitment, and might suggest an unconventional mechanism for Rag GEF activity.

4-(Prop-2-yn-1-ylsulfanyl)-1H-pyrazolo[3,4-d]pyrimidine

The asymmetric unit of the title compound, C8H6N4S, consists of two independent molecules differing in the orientation of the side chain. In the crystal, molecules form dimers through N—H...N hydrogen bonds. The dimers stack along thea-axis direction with weak π–π stacking interactions [centroid–centroid distances of 3.898 (2) and 3.908 (2) Å]. The crystal studied was refined as a two-component twin.

(3E)-4-(3,4,5-Trimethoxyphenyl)but-3-en-2-one

The asymmetric unit of the title compound, C13H16O4, consists of two independent molecules, which are linked into dimers by four C—H...O hydrogen bonds. In both molecules, the C atoms of themeta-methoxy groups lie close to their respective ring planes, whereas the C atoms ofpara-methoxy groups are significantly displaced. Pairwise C—H...π(ring) interactions form stacks of dimers, which are further associated through additional C—H...O hydrogen bonds.

A Crystalline π-Stack Containing Five Stereoisomers: Insights into Conformational Isomorphism, Chirality Inversion, and Disorder.

An unprecedented crystal-packing arrangement of a tetramethoxy-bay-substituted perylene bisimide (PBI) consists of three crystallographically independent molecules, that is, an achiral (AC) PBI of saddle-shaped geometry along with two pairs of propeller-like twisted (P)- and (M)-enantiomeric PBI frameworks. All these five conformations are observed within a single π-stack revealing an intriguing packing sequence with an inversion of chirality from P to M via AC. Nudged elastic band calculations for the isolated molecule show that AC is a local minimum of the P to M interconversion path. In addition, two minor conformations were observed in the crystal, one of which resembles a transition-state molecule. Theoretical studies of dimeric and trimeric stacks reveal that the coexistence of all these structures in the crystal lattice is aided by the strong dispersion interactions between PBI cores and perfectly interdigitated dodecyl chains which stabilize energetically higher conformations.

A Crystalline π‐Stack Containing Five Stereoisomers: Insights into Conformational Isomorphism, Chirality Inversion, and Disorder

AbstractAn unprecedented crystal‐packing arrangement of a tetramethoxy‐bay‐substituted perylene bisimide (PBI) consists of three crystallographically independent molecules, that is, an achiral (AC) PBI of saddle‐shaped geometry along with two pairs of propeller‐like twisted (P)‐ and (M)‐enantiomeric PBI frameworks. All these five conformations are observed within a single π‐stack revealing an intriguing packing sequence with an inversion of chirality from P to M via AC. Nudged elastic band calculations for the isolated molecule show that AC is a local minimum of the P to M interconversion path. In addition, two minor conformations were observed in the crystal, one of which resembles a transition‐state molecule. Theoretical studies of dimeric and trimeric stacks reveal that the coexistence of all these structures in the crystal lattice is aided by the strong dispersion interactions between PBI cores and perfectly interdigitated dodecyl chains which stabilize energetically higher conformations.

(R*)-1-Benzyl-3-(2-hydroxyphenyl)indoline-2-one

The title compound, C21H17NO2, crystallizes with two independent molecules (AandB) in the asymmetric unit. The indoline ring system is almost planar in both molecules (r.m.s. deviations = 0.020 and 0.024 Å for moleculesAandB, respectively). The benzyl and phenol rings are inclined to the indole ring system by 80.39 (12) and 68.39 (12)° in moleculeA, and by 79.90 (13) and 74.88 (10)° in moleculeB. The aryl rings are inclined to one another by 33.30 (14) and 30.62 (14)° in moleculesAandB, respectively. In the crystal,Amolecules are linked by pairs of O—H...O hydrogen bonds, forming inversion dimers. The same situation is observed for theBmolecules and both sets of inversion dimers encloseR22(14) ring motifs. These dimers stack along thea-axis direction and are linked by offset π–π interactions [intercentroid distance = 3.6802 (13) Å] involvingAandBindole ring systems, forming layers parallel to theabplane.