Packing Of Dimers Research Articles

Total absorption spectrum of benzene aggregates obtained from two different approaches.

The study of molecular aggregation effects on the electronic spectrum is essential for the development of optoelectronic devices. However, investigating the entire valence absorption spectrum of aggregates using quantum mechanical methods is a challenging task. In this work, we perform systematic simulations of the absorption spectrum of benzene molecular clusters up to 35 eV applying two approaches based on time-dependent density functional theory. The results show that depending on the dimer packing, different energy shifts occur for the symmetry allowed [Formula: see text] transition, in comparison to the monomer. The transition intensity increases for the band around 6 eV for larger aggregates from the monomer to dimers and tetramer, indicating the occurrence of the symmetry forbidden (in [Formula: see text] point group) [Formula: see text] [Formula: see text] transition. The benzene crystal exhibits a large redshift following the experimental spectrum. Also, the continuum regions of all spectra show a good agreement with the experiments both in gas and solid phases. Geometry optimization of the monomer was carried out with Gaussian 09 software using the PBE0/def2-TZVP level of theory. We used dimers and tetramer molecular geometries extracted from the experimental crystal structure. The absorption spectra were directly obtained by the Liouville-Lanczos TDDFT approach with plane waves basis set or indirectly by TDDFT pseudo-spectra calculated in a [Formula: see text] basis followed by analytic continuation procedure to obtain complex polarizability. The former is available at Quantum ESPRESSO, and the latter was calculated using Gaussian 09 with the post-processing performed with a code previously developed in our group.

Molecular "backbone surgery" of electron-deficient heteroarenes based on dithienopyrrolobenzothiadiazole: conformation-dependent crystal structures and charge transport properties.

Electron-deficient heteroarenes based on dithienopyrrolobenzothiadiazole (BTP) have been highly attractive due to their fascinating packing structures, broad absorption profiles, and promising applications in non-fullerene organic solar cells. However, the control of their crystal structures for superior charge transport still faces big challenges. Herein, a conformation engineering strategy is proposed to rationally manipulate the single crystal structure of BTP-series heteroarenes. The parent molecule BTPO-c has a 3D network crystal structure, which originates from its banana-shaped conformation. Subtracting one thiophene moiety from the central backbone leads to a looser brickwork crystal structure of the derivative BTPO-z because of its interrupted angular-shaped conformation. Further subtracting two thiophene moieties results in the derivative BTPO-l with a compact 2D-brickwork crystal structure due to its quasi-linear conformation with a unique dimer packing structure and short π-π stacking distance (3.30 Å). Further investigation of charge-transport properties via single-crystal organic transistors demonstrates that the compact 2D-brickwork crystal structure of BTPO-l leads to an excellent electron mobility of 3.5 cm2 V-1 s-1, much higher than that of BTPO-c with a 3D network (1.9 cm2 V-1 s-1) and BTPO-z with a looser brickwork structure (0.6 cm2 V-1 s-1). Notably, this study presents, for the first time, an elegant demonstration of the tunable single crystal structures of electron-deficient heteroarenes for efficient organic electronics.

A New Charge-Ordered Molecular Conductor: κ-(BEDT-TTF)2K+(18-crown-6)[CoII(NCS)4]∙(H2O)

A new molecular conductor, i.e., κ-(BEDT-TTF)2K+(18-crown-6)[CoII(NCS)4]∙(H2O), is semiconductive with substantial charge gap values (ΔE) of 0.57 eV (measured) and 0.37 eV (calculated). There is a full band separation despite formal average charge on BEDT-TTF of +0.5 and κ(kappa)-type packing of BEDT-TTF dimers that favors high conductivity. X-ray crystal structure analysis reveals complete charge ordering with full Coulomb charge on unique BEDT-TTF radical cations A (QA = +1), while unique molecules B are uncharged (QB = 0). Geometries of A (flat) and B (bent) differ considerably and are in accordance with the ascribing charges. Charge segregation is enhanced by forming tight face-to-face BEDT-TTF dimers AA (QAA = +2) and BB (QBB = 0). Strongly interacting double-charged dimers AA form “superstripes” running along a that are interleaved along b with chains of neutral dimers BB. Peculiar extremely thick (13.7 Å) four-decker insulating anion layers cast strong Coulomb potential onto the conductive layers predetermining charge localization in the latter.

Synthesis, Molecular Packing and Semiconductor Properties of V-ShapedN-Heteroacene Dimers.

This article presents two groups of V-shaped π-scaffolds that consist of two N-heteroacene units fused with either a rigid or flexible eight-membered ring. These rigid and flexible N-heteroacene dimers were synthesized through the condensation of tetraphenylenetetraone with the corresponding diamine and the Pd-catalyzed cross-coupling of tetrabromodibenzo[a,e]cyclooctatetraene with the corresponding diamine, respectively. A comparison of electronic structures and properties of the two groups of V-shaped N-heteroacene dimers shows subtle difference between the rigid and flexible eight-membered ring linkers in forming extended π-systems. X-ray crystallography of these V-shaped molecules has revealed interesting π-π interaction modes, which are dependent on the central connecting units and substituting groups. These π-π interactions between the V-shaped π-scaffolds have enabled the molecules to function as organic semiconductors in solution-processed field effect transistors.

Controlled Self-Assembly of Gold Nanotetrahedra into Quasicrystals and Complex Periodic Supracrystals.

The self-assembly of shape-anisotropic nanocrystals into large-scale structures is a versatile and scalable approach to creating multifunctional materials. The tetrahedral geometry is ubiquitous in natural and manmade materials, yet regular tetrahedra present a formidable challenge in understanding their self-assembly behavior as they do not tile space. Here, we report diverse supracrystals from gold nanotetrahedra including the quasicrystal (QC) and the dimer packing predicted more than a decade ago and hitherto unknown phases. We solve the complex three-dimensional (3D) structure of the QC by a combination of electron microscopy, tomography, and synchrotron X-ray scattering. Nanotetrahedron vertex sharpness, surface ligands, and assembly conditions work in concert to regulate supracrystal structure. We also discover that the surface curvature of supracrystals can induce structural changes of the QC tiling and eventually, for small supracrystals with high curvature, stabilize a hexagonal approximant. Our findings bridge the gap between computational design and experimental realization of soft matter assemblies and demonstrate the importance of accurate control over nanocrystal attributes and the assembly conditions to realize increasingly complex nanopolyhedron supracrystals.

Achieving 19% Power Conversion Efficiency in Planar-Mixed Heterojunction Organic Solar Cells Using a Pseudosymmetric Electron Acceptor.

A record power conversion efficiency (PCE) of over 19% is realized in planar-mixed heterojunction (PMHJ) organic solar cells (OSCs) by adopting the asymmetric selenium substitution strategy in making a pseudosymmetric electron acceptor, BS3TSe-4F. The combined molecular asymmetry with more polarizable selenium substitution increases the dielectric constant of the D18/BS3TSe-4F blend, helping lower the exciton binding energy. On the other hand, dimer packing in BS3TSe-4F is facilitated to enable free charge generation, helping more efficient exciton dissociation and lowering the radiative recombination loss (ΔE2 ) of OSCs. As a result, PMHJ OSCs based on D18/BS3TSe-4F achieve a PCE of 18.48%. By incorporating another mid-bandgap acceptor Y6-O into D18/BS3TSe-4F to form a ternary PMHJ, a higher open-circuit voltage (VOC ) can be achieved to realize an impressive PCE of 19.03%. The findings of using pseudosymmetric electron acceptors in enhancing device efficiency provides an effective way to develop highly efficient acceptor materials for OSCs.

Structural Phase Transitions in Anthracene Crystals.

Anthracene (C14 H10 ) and its derivatives, π-conjugated molecules in acenes, have been widely researched in terms of their reactions, physical properties, and self-assembly (or crystal engineering). These molecules can be functionalized to tune reactivities, optoelectronic properties, and self-assembling abilities. Structural changes in the molecular assemblies, solid states, and crystals have recently been discovered. Therefore, a systematic discussion of anthracene's molecular structure, packing, and optical properties based on its intermolecular structure and phase transitions is important for future chemical and structural design. In the present review, we discuss anthracene's molecular design, dimer packing, and crystal structure, focusing on the structural phase transitions of its crystals. We also provide examples of the phase transitions of anthracene crystals. Changes to edge-to-face of CH-π interaction and face-to-face packing of π-π interaction affect the thermodynamic stabilities of various crystal structures. These structures can inform the prediction of structural and physical properties.

Exploring optimal multimode vibronic pathways in singlet fission of azaborine analogues of perylene.

The development of new singlet fission chromophores is a vibrant area of research to explore the possibility of efficient photovoltaic devices. Using high-level ab-initio density matrix renormalization group calculations, we present a systematic analysis of BN-doped perylenes for their potential application as singlet fission candidates. Four singlet fission chromophores are identified considering the monomer-based properties and their excitonic characters are further analyzed in a dimer configuration optimized in a six-dimensional space for local maxima of fission rates. Furthermore, a multistate multimode vibronic Hamiltonian is employed to identify intra- and interstate vibrational pathways for excitation energy modulation. Several photophysical properties such as Davydov splitting, activation energy and vibronic admixture of multiexcitonic and charge-transfer states are calculated for physically accessible dimers. The optimal dimer packing results in appropriate vibrational relaxation of singlet fission states and promotes significant population transfer which would be more attenuated without such couplings. This work not only identifies potential singlet fission systems with favorable electronic properties but also highlights the sensitivity of dimer packings with respect to the substitution patterns in singlet fission chromophores.

Red to near-infrared piezochromism from AIE-active luminophores: isolated dimers facilitating a wide-range redshift

An AIE-activity architecture with HLCT and highly bright fluorescence was developed and it was the dispersed dimer packing found to be attributable to cholesteryl units. During compression, the dispersed dimers presented a remarkable redshift (157 nm) and high sensitivity (22.1 nm GPa−1).

Alkoxycarbonylphenyl 4-alkoxycinnamate liquid crystals with antiparallel packing

ABSTRACT A series of cinnamates with two flexible chains, one as alkoxy and the other as alkoxycarbonyl, has been synthesised to investigate mesomorphic behaviour. Single crystal X-ray measurements demonstrated the crystalline structure and a dimer packing was predicted due to H-bonding interactions. Most of the compounds show SmA phase only on cooling. Only the member with shortest chains exhibited nematic along with SmA phase. A monotropic SmC phase was observed for compounds with octyloxy group. However, X-ray diffraction studies demonstrated that the SmA to SmC phase transition is not accompanied by a significant interlayer spacing reduction, which was associated to strong intermolecular interactions within the layers. In all the compounds, the mesophase supercools prior to crystallisation.

N-terminal Backbone Pairing Shifts in CCL5-12AAA14 Dimer Interface: Structural Significance of the FAY Sequence.

CC-type chemokine ligand 5 (CCL5) has been known to regulate immune responses by mediating the chemotaxis of leukocytes. Depending on the environment, CCL5 forms different orders of oligomers to interact with targets and create functional diversity. A recent CCL5 trimer structure revealed that the N-terminal conversed F12-A13-Y14 (12FAY14) sequence is involved in CCL5 aggregation. The CCL5-12AAA14 mutant with two mutations had a deficiency in the formation of high-order oligomers. In the study, we clarify the respective roles of F12 and Y14 through NMR analysis and structural determination of the CCL5-12AAA14 mutant where F12 is involved in the dimer assembly and Y14 is involved in aggregation. The CCL5-12AAA14 structure contains a unique dimer packing. The backbone pairing shifts for one-residue in the N-terminal interface, when compared to the native CCL5 dimer. This difference creates a new structural orientation and leads to the conclusion that F12 confines the native CCL5 dimer configuration. Without F12 anchoring in the position, the interfacial backbone pairing is permitted to slide. Structural plasticity occurs in the N-terminal interaction. This is the first case to report this structural rearrangement through mutagenesis. The study provides a new idea for chemokine engineering and complements the understanding of CCL5 oligomerization and the role of the 12FAY14 sequence.

Olanzapine Form IV: Discovery of a New Polymorphic Form Enabled by Computed Crystal Energy Landscapes

Olanzapine is a polymorphic drug molecule that has been extensively studied, with over 60 structures reported in the Cambridge Structural Database. All anhydrous and solvated forms of olanzapine known to date contain the SC0 dimer packing motif. In this study, a new screening approach was adopted involving heat-induced forced crystallization from a polymer-based molecular dispersion of olanzapine. Simultaneous differential scanning calorimetry–powder X-ray diffraction was used to heat the amorphous dispersion and to identify a novel physical form from diffraction and heat flow data. Comparison of the diffraction data with those from a computed crystal energy landscape allowed the crystal structure to be determined. The result was the discovery of a new polymorph, form IV, which does not use the SC0 motif. Hence, while dimer formation is the dominant process that defines crystal packing for olanzapine formed from solution, it seems that molecularly dispersing the drug in a polymeric matrix permits crystallization of alternative motifs. Having identified form IV, it proved possible to scale up the synthesis and demonstrate its enhanced dissolution properties over form I.

Probing Optical Anisotropy and Polymorph-Dependent Photoluminescence in [Ln2 ] Complexes by Hyperspectral Imaging on Single Crystals.

Two homodinuclear and one heterodinuclear lanthanide (Ln)-based complexes of the general formula [Ln2 (bpm)(tfaa)6 ] (Ln=Eu (1), Tb (2), Eu-Tb (3), bpm=2,2'-bipyrimidine, tfaa- =1,1,1-trifluoroacetylacetonate) were synthesized and characterized by single-crystal photoluminescence spectroscopy and hyperspectral imaging. Complexes 1 and 2 crystallize in two polymorphic structures, while three polymorphs were isolated for 3, namely having needle-, plate-, and block-like morphologies. Single-crystal photoluminescence spectroscopy and imaging on Eu3+ -containing 1 and 3 revealed polymorph-dependent J-splitting of the hypersensitive 5 D0 →7 F2 Eu3+ transition as well as electric-to-magnetic dipole emission intensity ratios. According to these observations, the lowest symmetry chemical environment was attributed to the Eu3+ ions present in the needle-like polymorph, also in agreement with single-crystal X-ray diffraction analysis. More importantly, hyperspectral imaging on all three single-crystal polymorphs of 3 exhibits optical anisotropy with photoluminescence enhancement at specific crystallographic faces. This behavior was ascribed to the distinct molecular packing of the Ln-Ln dimers in each polymorphic crystal as well as to face-specific local symmetry of the Eu3+ centers. Overall, opto-structural relationships of three Ln-Ln dimers and their single-crystal polymorphs were established as a particularly promising avenue for control of photoluminescence by chemical crystal engineering.

Structural and biophysical characterization of Rv3716c, a hypothetical protein from Mycobacterium tuberculosis

Latent tuberculosis (TB) is the main hurdle in reaching the goal of “Stop TB 2050”. Tuberculin skin and Interferon-gamma release assay tests used currently for the diagnosis of TB infection cannot distinguish between active disease and latent tuberculosis infection (LTBI) and hence new and sensitive protein markers need to be identified for the diagnosis. A protein Rv3716c from Mycobacterium tuberculosis (MtbRv3716c) has been identified as a potential surrogate marker for the diagnosis of LTBI. Here, we present characterization of MtbRv3716c (∼13 kDa) using both biophysical and X-Ray crystallographic methods. EMSA study showed that MtbRv3716c binds to double stranded DNA. X-ray diffraction data collected on a crystal of MtbRv3716c at 1.9 Å resolution was used for structure determination using the molecular replacement method. Significant electron density was not observed for the N-terminal 21 and C-terminal 41 residues in the final electron density map. The C- terminal disordered region is proline rich and displays characteristics of intrinsically disordered proteins. Although the crystal asymmetric unit contained a protomer, a tight dimer could be generated by the application of the crystal two-fold symmetry parallel to the b axis. Packing of dimers in the crystal is mediated by a cadmium ion (Cd2+) occurring at the interface of two dimers. Molecular packing analysis reveals large cavities that are probably occupied by the disordered segments of the N- and C-termini. Structural comparison with other homologous hypothetical DNA binding proteins (PDB codes: 1PUG, 1YBX) highlights structural features that might be significant for DNA binding.

Comparative Structural Studies of Four Homologous Thioamidic Unclosed Crytpands: Self-Encapsulation of Lariat Arm, Odd–Even Effects, Anomalously Short S···S Chalcogen Bonding, and More

Unclosed cryptands (UCs) 4a–d containing flexible (CH2)n spacers (n = 2–5) and a fixed p-nitrophenyl thioamide substituent (lariat arm) were synthesized and characterized by single crystal X-ray analysis. Comparative analysis of their crystal structures provided an opportunity to recognize that conformation of 4a–d and occurrence of lattice solvent strictly depend on the length and parity of aliphatic linkers. Namely, the degree of self-inclusion of the lariat arm within the macrocyclic cavity was found to increase with greater elongation of the CH2 spacer. Odd-membered UCs (4b and 4d) showed a tendency to crystallize without lattice solvent, while even-membered UCs (4a and 4c) crystallized as various solvates. For two solvates of UC 4c anomalously short and highly directional C═S···S═C chalcogen interactions (dS···S = 3.21–3.35 A) were observed between adjacent UC molecules, forming a dimeric cube-like supramolecular assembly. Packing of dimers and the length of homo-chalcogen interaction were affected b...

Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis.

Metabotropic glutamate receptor 1 (mGlu1), which belongs to class C G protein-coupled receptors (GPCRs), can be coupled with G protein to transfer extracellular signal by dimerization and allosteric regulation. Unraveling the dimer packing and allosteric mechanism can be of great help for understanding specific regulatory mechanism and designing more potential negative allosteric modulator (NAM). Here, we report molecular dynamics simulation studies of the modulation mechanism of FITM on the wild type, T815M and Y805A mutants of mGlu1 through weak interaction analysis and free energy calculation. The weak interaction analysis demonstrates that van der Waals (vdW) and hydrogen bonding play an important role on the dimer packing between six cholesterol molecules and mGlu1 as well as the interaction between allosteric sites T815, Y805 and FITM in wild type, T815M and Y805A mutants of mGlu1. Besides, the results of free energy calculations indicate that secondary binding pocket is mainly formed by the residues Thr748, Cys746, Lys811 and Ser735 except for FITM-bound pocket in crystal structure. Our results can not only reveal the dimer packing and allosteric regulation mechanism, but also can supply useful information for the design of potential NAM of mGlu1.

Shape-controlled percolation transition in 2D random packing of asymmetric dimers

In this paper, we report on an experimental investigation of a shape-controlled percolation transition in two-dimensional (2D) amorphous packing of dimers without long-range order. In the maximally random jammed (MRJ) packing of asymmetric dimers consisting of head and body, a dramatic increase in the connectivity of heads upon increasing the head-to-body size ratio γ leads to a percolation transition of the heads at the well-defined percolation threshold. In comparison with binary disks, the existence of a bond in dimers causes the heads to be homogeneously distributed over a system by inhibiting the local segregation. Interestingly, we found, however, that the cluster structure at the percolation threshold is insensitive to the bond, even though the existence of the bonds affects the percolation threshold as well as the head distribution. The fractal dimensions at the percolation threshold obey the universal law of the 2D percolation theory independently of the existence of bonds. Our finding can provide us with a new perspective of interesting applications of randomly assembled binary composites by using the homogeneous particle distribution and the sensitively tunable connectivity under particle shape control.

Conformation Dynamics and Polarization Effect of α,α-Trehalose in a Vacuum and in Aqueous and Salt Solutions

Conformational changes of α,α-trehalose in a vacuum, water, and 0-20 wt % NaCl solutions were investigated by means of molecular dynamics (MD) simulations at different levels of density function theory (DFT) and with fixed-charge nonpolarizable and variable-charge force fields (FFs), respectively. The relative thermodynamic stability of trehalose is enhanced by the formation of intercycle and/or intracycle hydrogen bonds, but some thermodynamically unfavorable structures can be sampled in the DFT-based ab initio MD simulation. The polarization effects of polar trehalose molecule in aqueous and NaCl solutions were studied by a series of MD simulations with both the conventional nonpolarizable and polarizable force field models. In the polarizable model, the partial charges of trehalose were updated every 2 ps using DFT calculations and fused with the other FF parameters for the energy calculation and MD simulation. Around the trehalose, water molecules located in an asymmetry model and trehalose have a stronger tendency to bind with water molecules than Na(+) and Cl(-) ions. When the trehalose concentration is increased from 3.26 to 6.31 wt % in salt aqueous solution, the two trehalose molecules periodically approach each other in a nearly anhydrate state and leave a way to keep the favorable hydration structure with the mean trehalose-trehalose distance of 8.6 Å. The similarity between the solvated dimer packing styles (shoulder-by-shoulder or head-to-head) and crystal stacking can be used to make an extrapolation to higher sugar concentrations and to rationalize the bioprotection function of trehalose in high salt concentration.

The good host: formation of discrete one-dimensional fullerene "channels" in well-ordered poly(2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene) oligomers.

Due to the unique crystallinity of poly(2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT), it is an excellent model polymer to study the structure-property relationship in organic devices, especially those relying on junctions of electron- and hole-transporting materials. Here, we report the synthesis and characterization of a series of monodisperse PBTTT oligothiophenes (n = 1-5) and systematically examine the evolution of crystalline behavior, morphology, and interaction with [6,6]-phenyl C61-butyric acid methyl ester (PCBM) as the molecular conjugation length increases. We discovered that fullerene intercalation occurs when there is enough free volume between the side chains to accommodate the fullerene molecule. The intercalation of PCBM is observed beyond BTTT-2 and longer oligomers, likely similar to that of PBTTT. Interestingly, both experiments and molecular simulations show that PCBM intercalation also appears to "catalyze" a more efficient packing of the BTTT-2 dimers. Crystal structure analysis revealed that the straight BTTT-2 side chains form one-dimensional (1D) channels that could perfectly host PCBM but, in the pure material, accommodate the interdigitated side chains from adjacent layers. In the blend with PCBM, these channels are maintained and enable the cocrystallization and intercalation of PCBM. This is the first time the actual sublattice cell of PCBM has been determined from the X-ray data, and demonstration the utility of the oligomers as model systems for their polymer counterparts. Among the organic photovoltaic devices (OPVs) made from the BTTT oligomers and [6,6]-phenyl C71-butyric acid methyl ester (PC71BM) blends, the ones containing the BTTT-2 dimer exhibit the highest performance.

Photocurrent enhancement of BODIPY-based solution-processed small-molecule solar cells by dimerization via the meso position.

Three 4,4-difluoro-4-bora-3a,4a-diaza-s-indancene (BODIPY)-based small molecule donors H-T-BO, Br-T-BO, and DIMER were synthesized and fully characterized. Although modification at the meso position has a subtle influence on the light-harvesting ability, energy levels, and phase sizes, it has a striking effect on the packing behavior in solid film as two-dimension grazing incidence X-ray diffraction (2D GIXRD) and X-ray diffraction (XRD) confirm. Br-T-BO exhibits better packing ordering than H-T-BO in pristine film, which is beneficial from reinforced intermolecular interaction from halogen atoms. However, when [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) is blended, no diffraction patterns corresponding to the monomeric donor can be seen from the XRD data and both H-T-BO- and Br-T-BO-based blend films give a slightly blue-shifting absorption peak with respect to their neat ones, both of which imply destruction of the crystalline structure. As for DIMER, the enhancement of the intermolecular interaction arises not only from the expansion of the backbone but the "steric pairing effect" brought on by its twisted structure. When blended with PC71BM, the diffraction patterns of DIMER are, however, kept well and the absorption peak position remains unchanged, which indicates the ordered packing of DIMER is held well in blend film. In coincidence with the fact that packing ordering improves from H-T-BO to Br-T-BO and DIMER in pristine films and the ordered packing of DIMER even in blend film, DIMER-based devices show the highest and most balanced hole/electron mobility of 1.16 × 10(-3)/0.90 × 10(-3) cm(2) V(-1) s(-1)with respect to Br-T-BO (4.71 × 10(-4)/2.09 × 10(-4) cm(2) V(-1) s(-1)) and H-T-BO (4.27 × 10(-5)/1.00 × 10(-5) cm(2) V(-1) s(-1)) based ones. The short-circuit current density of the three molecule-based cells follows the same trend from H-T-BO (6.80) to Br-T-BO (7.62) and then to DIMER (11.28 mA cm(-2)). Finally, the H-T-BO-, Br-T-BO-, and DIMER-based optimal device exhibits a power conversion efficiency of 1.56%, 1.96%, and 3.13%, respectively.