Misfolding and aggregation of transthyretin (TTR) causeseveralamyloid diseases. Besides being an amyloidogenic protein, TTR hasan affinity for bicyclic small-molecule ligands in its thyroxine (T4)binding site. One class of TTR ligands are trans-stilbenes. The trans-stilbenescaffold is also widely applied for amyloid fibril-specific ligandsused as fluorescence probes and as positron emission tomography tracersfor amyloid detection and diagnosis of amyloidosis. We have shownthat native tetrameric TTR binds to amyloid ligands based on the trans-stilbenescaffold providing a platform for the determination of high-resolutionstructures of these important molecules bound to protein. In thisstudy, we provide spectroscopic evidence of binding and X-ray crystallographicstructure data on tetrameric TTR complex with the fluorescent salicylicacid-based pyrene amyloid ligand (Py1SA), an analogue of the Congored analogue X-34. The ambiguous electron density from the X-ray diffraction,however, did not permit Py1SA placement with enough confidence likelydue to partial ligand occupancy. Instead, the preferred orientationof the Py1SA ligand in the binding pocket was determined by moleculardynamics and umbrella sampling approaches. We find a distinct preferencefor the binding modes with the salicylic acid group pointing intothe pocket and the pyrene moiety outward to the opening of the T4binding site. Our work provides insight into TTR binding mode preferencefor trans-stilbene salicylic acid derivatives as well as a frameworkfor determining structures of TTR-ligand complexes.

Electronic transitions in molecules due to the absorption or emission of light is a complex quantum mechanical process. Their study plays an important role in the design of novel materials. A common yet challenging task in the study is to determine the nature of electronic transitions, namely which subgroups of the molecule are involved in the transition by donating or accepting electrons, followed by an investigation of the variation in the donor-acceptor behavior for different transitions or conformations of the molecules. In this paper, we present a novel approach for the analysis of a bivariate field and show its applicability to the study of electronic transitions. This approach is based on two novel operators, the continuous scatterplot (CSP) lens operator and the CSP peel operator, that enable effective visual analysis of bivariate fields. Both operators can be applied independently or together to facilitate analysis. The operators motivate the design of control polygon inputs to extract fiber surfaces of interest in the spatial domain. The CSPs are annotated with a quantitative measure to further support the visual analysis. We study different molecular systems and demonstrate how the CSP peel and CSP lens operators help identify and study donor and acceptor characteristics in molecular systems.

Enhancing low-energy emitting Cu(I)-ionic transition metal complexes (iTMCs) light-emitting electrochemical cells (LECs) is of utmost importance towards Cu(I)-iTMC-based white-emitting LECs. Here, the ancillary ligand design includes (i) extension of & pi;-systems and (ii) insertion of S-bridge between heteroaromatics rings. This led to two novel heteroleptic Cu(I)-iTMCs: 2-(pyridin-2-yl-l2-azanyl)quinoline (CuN2) and 2-(naphthalen-2-ylthio)quinoline (CuS2) as N<^>N and bis[(2-diphenylphosphino)phenyl] ether as P<^>P, exhibiting improved photoluminescence quantum yields (& phi;) and thermally activated delayed fluorescence processes compared to their reference Cu(I)-iTMCs: di(pyridin-2-yl)-l2-azane (CuN1) and di(pyridin-2-yl)sulfane (CuS1). Despite CuS2 stands out with the highest & phi; (38% vs 17 / 14 / 1% for CuN1 / CuN2 / CuS1), only CuN2-LECs show the expected enhanced performance (0.35 cd A(-1) at luminance of 117 cd m(-2)) compared to CuN1-LECs (0.02 cd A(-1) at6 cd m(-2)), while CuS2-LECs feature low performances (0.04 cd A(-1) at 10 cd m(-2)). This suggests that conventional chemical design rules are not effective towards enhancing device performance. Herein, nonconventional multivariate statistical analysis and electrochemical impedance spectroscopy studies allow to rationalize the mismatch between chemical design and device performance bringing to light a hidden design rule: polarizability of the ancillary ligand is key for an efficient Cu(I)-iTMC-LECs. All-in-all, this study provides fresh insights for the design of Cu-iTMCs fueling research on sustainable ion-based lighting sources.

Tunable dynamic networks of cellulose nanofibrils (CNFs) are utilized to prepare high-performance polymer gel electrolytes. By swelling an anisotropically dewatered, but never dried, CNF gel in acidic salt solutions, a highly sparse network is constructed with a fraction of CNFs as low as 0.9%, taking advantage of the very high aspect ratio and the ultra-thin thickness of the CNFs (micrometers long and 2-4 nm thick). These CNF networks expose high interfacial areas and can accommodate massive amounts of the ionic conductive liquid polyethylene glycol-based electrolyte into strong homogeneous gel electrolytes. In addition to the reinforced mechanical properties, the presence of the CNFs simultaneously enhances the ionic conductivity due to their excellent strong water-binding capacity according to computational simulations. This strategy renders the electrolyte a room-temperature ionic conductivity of 0.61 +/- 0.12 mS cm(-1) which is one of the highest among polymer gel electrolytes. The electrolyte shows superior performances as a separator for lithium iron phosphate half-cells in high specific capacity (161 mAh g(-1) at 0.1C), excellent rate capability (5C), and cycling stability (94% capacity retention after 300 cycles at 1C) at 60 degrees C, as well as stable room temperature cycling performance and considerably improved safety compared with commercial liquid electrolyte systems.

We investigate the gas-phase structure of the neutral pentaalanine peptide. The IR spectrum in the 340-1820 cm-1 frequency range is obtained by employing supersonic jet cooling, infrared multiphoton dissociation, and vacuum-ultraviolet action spectroscopy. Comparison with quantum chemical spectral calculations suggests that the molecule assumes multiple stable conformations, mainly of two structure types. In the most stable conformation theoretically found, the N-terminus forms a C5 ring and the backbone resembles that of an 310-helix with two beta-turns. Additionally, the conformational preferences of pentaalanine have been evaluated using Born-Oppenheimer molecular dynamics, showing that a nonzero simulation time step causes a systematic frequency shift.

Interfacing electronics with neural tissue is crucial for understanding complex biological functions, but conventional bioelectronics consist of rigid electrodes fundamentally incompatible with living systems. The difference between static solid-state electronics and dynamic biological matter makes seamless integration of the two challenging. To address this incompatibility, we developed a method to dynamically create soft substrate-free conducting materials within the biological environment. We demonstrate in vivo electrode formation in zebrafish and leech models, using endogenous metabolites to trigger enzymatic polymerization of organic precursors within an injectable gel, thereby forming conducting polymer gels with long-range conductivity. This approach can be used to target specific biological substructures and is suitable for nerve stimulation, paving the way for fully integrated, in vivo-fabricated electronics within the nervous system.

We present Moliverse, an integration of the molecular visualization framework VIAMD into the astronomical visualization software OpenSpace, allowing us to bridge the two extreme ends of the scale spectrum to show, for example, the gas composition in a planets atmosphere or molecular structures in comet trails and can empower the creation of educational exhibitions. For that purpose we do not use a linear scale traversal but break the scale continuity and show molecular simulations as focus in the context of celestial bodies. We demonstrate the application of our concept in two storytelling scenarios and envision the application both for science presentations to lay audiences and for dedicated exploration, potentially also in a molecule-only environment.

Biomimetic chiral optoelectronic materials can be utilized in electronic devices, biosensors and artificial enzymes. Herein, this work reports the chiro-optical properties and architectural arrangement of optoelectronic materials generated from self-assembly of initially nonchiral oligothiophene-porphyrin derivatives and random coil synthetic peptides. The photo-physical- and structural properties of the materials were assessed by absorption-, fluorescence- and circular dichroism spectroscopy, as well as dynamic light scattering, scanning electron microscopy and theoretical calculations. The materials display a three-dimensional ordered helical structure and optical activity that are observed due to an induced chirality of the optoelectronic element upon interaction with the peptide. Both these properties are influenced by the chemical composition of the oligothiophene-porphyrin derivative, as well as the peptide sequence. We foresee that our findings will aid in developing self-assembled optoelectronic materials with dynamic architectonical accuracies, as well as offer the possibility to generate the next generation of materials for a variety of bioelectronic applications.

A detailed insight about the molecular organization behind spider silk assembly is valuable for the decoding of the unique properties of silk. The recombinant partial spider silk protein 4RepCT contains four poly-alanine/glycine-rich repeats followed by an amphiphilic C-terminal domain and has shown the capacity to self-assemble into fibrils on hydrophobic surfaces. We herein use molecular dynamic simulations to address the structure of 4RepCT and its different parts on hydrophobic versus hydrophilic surfaces. When 4RepCT is placed in a wing arrangement model and periodically repeated on a hydrophobic surface, fi-sheet structures of the poly-alanine repeats are preserved, while the CT part is settled on top, presenting a fibril with a height of similar to 7 nm and a width of similar to 11 nm. Both atomic force microscopy and cryo-electron microscopy imaging support this model as a possible fibril formation on hydrophobic surfaces. These results contribute to the understanding of silk assembly and alignment mechanism onto hydrophobic surfaces.

Self-assembled nanotubesexhibit impressive biologicalfunctionsthat have always inspired supramolecular scientists in their effortsto develop strategies to build such structures from small moleculesthrough a bottom-up approach. One of these strategies employs moleculesendowed with self-recognizing motifs at the edges, which can undergoeither cyclization-stacking or folding-polymerizationprocesses that lead to tubular architectures. Which of these self-assemblypathways is ultimately selected by these molecules is, however, oftendifficult to predict and even to evaluate experimentally. We showhere a unique example of two structurally related molecules substitutedwith complementary nucleobases at the edges (i.e., G:C and A:U) for which the supramolecular pathway takenis determined by chelate cooperativity, that is, by their propensityto assemble in specific cyclic structures through Watson-Crickpairing. Because of chelate cooperativities that differ in severalorders of magnitude, these molecules exhibit distinct supramolecularscenarios prior to their polymerization that generate self-assemblednanotubes with different internal monomer arrangements, either stackedor coiled, which lead at the same time to opposite helicities andchiroptical properties.

Poly(3,4-ethylenedioxythiophene) polystyrene sulfonate(PEDOT:PSS)is one of the most important mixed electron-ion conducting polymers,where the efficiency of the ion transport is crucial for many of itsapplications. Despite the impressive experimental progress in thedetermination of ionic mobilities in PEDOT:PSS, the fundamentals ofion transport in this material remain poorly understood, and the theoreticalinsight into the ion diffusion on the microscopical level is completelymissing. In the present paper, a Martini 3 coarse-grained moleculardynamics (MD) model for PEDOT:PSS is developed and applied to calculatethe ion diffusion coefficients and ion distribution in the film. Wefind that the ion diffusion coefficients for Na+ ions arepractically the same in the PEDOT-rich and PSS-rich regions and donot show sensitivity to the oxidation level. We compare the calculateddiffusion coefficients with available experimental results. Basedon this comparison and based on the MD morphology simulation of PEDOT:PSSrevealing the formation of pores inside the film, we revise a commonlyaccepted granular morphological model of PEDOT:PSS. Namely, we arguethat PEDOT:PSS films, in addition to PEDOT-rich and PSS-rich regions,must contain a network of pores where the ion diffusion takes place.

We present a pipeline for the interactive visual analysis and exploration of molecular electronic transition ensembles. Each ensemble member is specified by a molecular configuration, the charge transfer between two molecular states, and a set of physical properties. The pipeline is targeted towards theoretical chemists, supporting them in comparing and characterizing electronic transitions by combining automatic and interactive visual analysis. A quantitative feature vector characterizing the electron charge transfer serves as the basis for hierarchical clustering as well as for the visual representations. The interface for the visual exploration consists of four components. A dendrogram provides an overview of the ensemble. It is augmented with a level of detail glyph for each cluster. A scatterplot using dimensionality reduction provides a second visualization, highlighting ensemble outliers. Parallel coordinates show the correlation with physical parameters. A spatial representation of selected ensemble members supports an in-depth inspection of transitions in a form that is familiar to chemists. All views are linked and can be used to filter and select ensemble members. The usefulness of the pipeline is shown in three different case studies.

In molecular analysis, Spatial Distribution Functions (SDF) are fundamental instruments in answering questions related to spatial occurrences and relations of atomic structures over time. Given a molecular trajectory, SDFs can, for example, reveal the occurrence of water in relation to particular structures and hence provide clues of hydrophobic and hydrophilic regions. For the computation of meaningful distribution functions, the definition of molecular reference structures is essential. Therefore we introduce the concept of an internal frame of reference (IFR) for labeled point sets that represent selected molecular structures, and we propose an algorithm for tracking the IFR over time and space using a variant of Kabschs algorithm. This approach lets us generate a consistent space for the aggregation of the SDF for molecular trajectories and molecular ensembles. We demonstrate the usefulness of the technique by applying it to temporal molecular trajectories as well as ensemble datasets. The examples include different docking scenarios with DNA, insulin, and aspirin.

Anionic pentameric thiophene acetates can be used for fluorescence detection and diagnosis of protein amyloid aggregates. Replacing the central thiophene unit by benzothiadiazole (BTD) or quinoxaline (QX) leads to large emission shifts and basic spectral features have been reported [Chem. Eur. J. 2015, 21, 15133-13137]. Here we present new detailed experimental results of solvent effects, time-resolved fluorescence and examples employing multi-photon microscopy and lifetime imaging. Quantum chemical response calculations elucidate how the introduction of the BTD/QX groups changes the electronic states and emissions. The dramatic red-shift follows an increased conjugation and quinoid character of the pi-electrons of the thiophene backbone. An efficient charge transfer in the excited states S-1 and S-2 compared to the all-thiophene analogue makes these more sensitive to the polarity and quenching by the solvent. Taken together, the results guide in the interpretation of images of stained Alzheimer disease brain sections employing advanced fluorescence microscopy and lifetime imaging, and can aid in optimizing future fluorescent ligand development.

Cellulose nanomaterial (CNM)-based foams and aerogels with thermal conductivities substantially below the value for air attract significant interest as super-insulating materials in energy-efficient green buildings. However, the moisture dependence of the thermal conductivity of hygroscopic CNM-based materials is poorly understood, and the importance of phonon scattering in nanofibrillar foams remains unexplored. Here, we show that the thermal conductivity perpendicular to the aligned nanofibrils in super-insulating icetemplated nanocellulose foams is lower for thinner fibrils and depends strongly on relative humidity (RH), with the lowest thermal conductivity (14 mW m(-1) K-1) attained at 35% RH. Molecular simulations show that the thermal boundary conductance is reduced by the moisture-uptake-controlled increase of the fibril-fibril separation distance and increased by the replacement of air with water in the foam walls. Controlling the heat transport of hygroscopic super-insulating nanofibrillar foams by moisture uptake and release is of potential interest in packaging and building applications.

Foams made from cellulose nanomaterials are highly porous and possess excellent mechanical and thermal insulation properties. However, the moisture uptake and hygroscopic properties of these materials need to be better understood for their use in biomedical and bioelectronics applications, in humidity sensing and thermal insulation. In this work, we present a combination of hybrid Grand Canonical Monte Carlo and Molecular Dynamics simulations and experimental measurements to investigate the moisture uptake within nanocellulose foams. To explore the effect of surface modification on moisture uptake we used two types of celluloses, namely TEMPO-oxidized cellulose nanofibrils and carboxymethylated cellulose nanofibrils. We find that the moisture uptake in both the cellulose nanomaterials increases with increasing relative humidity (RH) and decreases with increasing temperature, which is explained using the basic thermodynamic principles. The measured and calculated moisture uptake in amorphous cellulose (for a given RH or temperature) is higher as compared to crystalline cellulose with TEMPO- and CM-modified surfaces. The high water uptake of amorphous cellulose films is related to the formation of water-filled pores with increasing RH. The microscopic insight of water uptake in nanocellulose provided in this study can assist the design and fabrication of high-performance cellulose materials with improved properties for thermal insulation in humid climates or packaging of water sensitive goods.

The synthesis, structures, and properties of [4]cyclonaphthodithiophene diimides ([4]C-NDTIs) are described. NDTIs as important n-type building blocks were catenated in the alpha-positions of thiophene rings via an unusual electrochemical-oxidation-promoted macrocyclization route. The thiophene-thiophene junction in [4]C-NDTIs results in an ideal pillar shape. This interesting topology, along with appealing electronic and optical properties inherited from the NDTI units, endows the [4]C-NDTIs with both near-infrared (NIR) light absorptions, strong excitonic coupling, and tight encapsulation of C-60. Stable orientations of the NDTI units in the nanopillars lead to stable inherent chirality, which enables detailed circular dichroism studies on the impact of isomeric structures on pi-conjugation. Remarkably, the [4]C-NDTIs maintain the strong pi-pi stacking abilities of NDTI units and thus adopt two-dimensional (2D) lattice arrays at the molecular level. These nanopillar molecules have great potential to mimic natural photosynthetic systems for the development of multifunctional organic materials.

Despite great challenges, the development of new molecular structures with multiple and even conflicting characteristics are eagerly pursued for exploring advanced applications. To develop high-performance chiral organic semiconducting molecules, a distorted -system is required for strong coupling with circularly polarized light (CPL), whereas planar pi -stacking systems are necessary for high charge-carrier mobility. To address this dilemma, in this work, we introduce a skeleton merging approach through distortion of a perylene diimide (PDI) core with four fused heteroaromatics to form an ortho-pi -extended PDI double-[7]heterohelicene. PDI double helicene inherits a high dissymmetry factor from the helicene skeleton, and the extended pi -planar system concurrently maintains a high level of charge transport properties. In addition, ortho-pi -extension of the PDI skeleton brings about near-infrared (NIR) light absorption and ambipolar charge transport abilities, endowing the corresponding organic phototransistors with high photoresponsivity of 450 and 120mAW(-1) in p- and n-type modes respectively, along with a high external quantum efficiency (89%) under NIR light irradiations. Remarkably, these multiple characteristics enable high-performance broadband CPL detections up to NIR spectral region with chiral organic semiconductors. In organic semiconducting molecules materials, distorted pi -systems enable strong coupling with circular polarized light while planar pi -stacking systems are necessary for high charge-carrier mobility. Here, the authors address this dilemma by introducing a skeleton merging approach through distortion of a perylene diimide core with four fused heteroaromatics to form a pi -extended double helicene.

Electronic transitions in molecules due to absorption or emission of light is a complex quantum mechanical process. Their study plays an important role in the design of novel materials. A common yet challenging task in the study is to determine the nature of those electronic transitions, i.e. which subgroups of the molecule are involved in the transition by donating or accepting electrons, followed by an investigation of the variation in the donor-acceptor behavior for different transitions or conformations of the molecules. In this paper, we present a novel approach towards the study of electronic transitions based on the visual analysis of a bivariate field, namely the electron density in the hole and particle Natural Transition Orbital (NTO). The visual analysis focuses on the continuous scatter plots (CSPs) of the bivariate field linked to their spatial domain. The method supports selections in the CSP visualized as fiber surfaces in the spatial domain, the grouping of atoms, and the segmentation of the density fields to peel the CSP. This peeling operator is central to the visual analysis process and helps identify donors and acceptors. We study different molecular systems, identifying local excitation and charge transfer excitations to demonstrate the utility of the method.

Protein nanofibrils (PNFs) represent a promising class of biobased nanomaterials for biomedical and materials science applications. In the design of such materials, a fundamental understanding of the structure-function relationship at both molecular and nanoscale levels is essential. Here we report investigations of the nanoscale morphology and molecular arrangement of amyloid-like PNFs of a synthetic peptide fragment consisting of residues 11-20 of the protein beta-lactoglobulin (beta-LG(11-20)), an important model system for PNF materials. Nanoscale fibril morphology was analysed by atomic force microscopy (AFM) that indicates the presence of polymorphic self-assembly of protofilaments. However, observation of a single set of C-13 and N-15 resonances in the solid-state NMR spectra for the beta-LG(11-20) fibrils suggests that the observed polymorphism originates from the assembly of protofilaments at the nanoscale but not from the molecular structure. The secondary structure and inter-residue proximities in the beta-LG(11-20) fibrils were probed using NMR experiments of the peptide with C-13- and N-15-labelled amino acid residues at selected positions. We can conclude that the peptides form parallel beta-sheets, but the NMR data was inconclusive regarding inter-sheet packing. Molecular dynamics simulations confirm the stability of parallel beta-sheets and suggest two preferred modes of packing. Comparison of molecular dynamics models with NMR data and calculated chemical shifts indicates that both packing models are possible.

The bi-thiophene-vinylene-benzothiazole (bTVBT4) ligand developed for Alzheimers disease (AD)-specific detection of amyloid tau has been studied by a combination of several theoretical methods and experimental spectroscopies. With reference to the cryo-EM tau structure of the tau protofilament (Nature 2017, 547, 185), a periodic model system of the fibril was created, and the interactions between this fibril and bTVBT4 were studied with nonbiased molecular dynamics simulations. Several binding sites and binding modes were identified and analyzed, and the results for the most prevailing fibril site and ligand modes are presented. A key validation of the simulation work is provided by the favorable comparison of the theoretical and experimental absorption spectra of bTVBT4 in solution and bound to the protein. It is conclusively shown that the ligand-protein binding occurs at the hydrophobic pocket defined by the residues Ile360, Thr361, and His362. This binding site is not accessible in the Picks disease (PiD) fold, and fluorescence imaging of bTVBT4-stained brain tissue samples from patients diagnosed with AD and PiD provides strong support for the proposed tau binding site.

The synthesis and characterization of a family of copper(i) complexes bearing a bridged bis-pyridyl ancillary ligand is reported, highlighting how the bridge nature impacts the photo- and electro-luminescent behaviours within the family. In particular, the phosphonium bridge led to copper(i) complexes featuring good electrochemical stability and high ionic conductivity, as well as a stark blue-to-orange luminescence shift compared to the others. This resulted in high performance light-emitting electrochemical cells reaching stabilities of 10 mJ at ca. 40 cd m(-2) that are one order of magnitude higher than those of the other complexes. Overall, this work sheds light onto the crucial role of the bridge nature of the bis-pyridyl ancillary ligand on the photophysical features, film forming and, in turn, on the final device performances.

Two-component organogels and xerogels based on a C-3-symmetric pyrene-containing gelator have been deeply characterized through a wide range of techniques. Based on the formation of charge transfer complexes, the gelation phenomenon proved to be highly dependent on the nature of the electron poor dopant. This parameter significantly influenced the corresponding gelation domains, the critical gelation concentrations of acceptor dopants, the gel-to-sol transition temperatures, the microstructures formed in the xerogel state and their spectroscopic properties. In particular, titrations and variable-temperature UV-visible absorption spectroscopy demonstrated the key role of donor-acceptor interactions with a remarkable correlation between the phase transition temperatures and the disappearance of the characteristic charge transfer bands. The assignment of these electronic transitions was confirmed through time-dependent density functional theory (TD-DFT) calculations. Eventually, it was shown that the luminescent properties of these materials can be tuned with the temperature, either in intensity or emission wavelength.

The study of electronic transitions within a molecule connected to the absorption or emission of light is a common task in the process of the design of new materials. The transitions are complex quantum mechanical processes and a detailed analysis requires a breakdown of these processes into components that can be interpreted via characteristic chemical properties. We approach these tasks by providing a detailed analysis of the electron density field. This entails methods to quantify and visualize electron localization and transfer from molecular subgroups combining spatial and abstract representations. The core of our method uses geometric segmentation of the electronic density field coupled with a graph-theoretic formulation of charge transfer between molecular subgroups. The design of the methods has been guided by the goal of providing a generic and objective analysis following fundamental concepts. We illustrate the proposed approach using several case studies involving the study of electronic transitions in different molecular systems.

Conductive polymer PEDOT:Tos (3,4-ethylenedioxythiophene doped with molecular tosylate) gained considerable attention in various devices for bioelectronic applications, such as organic transistors and sensors. Many of these devices function upon oxidation/reduction processes in contact with aqueous electrolytes. So far, theoretical insight into morphological changes, ion injection, and water intake during these processes was rather limited. In the present work, we combined experiments and molecular dynamics simulations to study the water intake, swelling, and exchange of ions in the PEDOT:Tos film during cyclic voltammetry. We showed that the film underwent significant changes in morphology and mass during the redox processes. We observed both experimentally and in simulations that the film lost its mass during reduction, as tosylate and Na were expelled and gained mass during oxidation mainly due to the uptake of anions, i.e., tosylate and Cl. The results were in line with the UV-VIS-NIR absorption measurements and X-ray photoelectron spectroscopy (XPS) measurements, which revealed that during the redox process a portion of Tos was replaced by Cl- as the counterion for PEDOT. Also, the relative mass change between the most oxidized and reduced states was similar to 10 to 14% according to both experiments and simulations. We detected an overall material loss of the film during voltammetry cycles indicating that a portion of the material leaving the film during reduction did not return to the film during the consecutive oxidation. Our combined experimental/simulation study unraveled the underlying molecular processes in the PEDOT:Tos film upon the redox process, providing the essential understanding needed to improve and assess the performance of bioelectronic devices.

Self-assembly is ubiquitous in nature and underlies the formation of many complex systems from the molecular to the macroscopic scale. Kern-Frenkel-like patchy particles are powerful models to investigate this phenomenon by computational methods such as Monte Carlo or molecular dynamics simulations. However, in these models the interactions are mediated by circular patches at the particle surface, which can be hardly mapped to realistic systems, containing for instance faceted particles with rectangular surfaces. In this paper we extend the model to take into account such geometries, and we use it to build a supra coarse-grained model of the cellulose nanocrystal where the interactions are parametrized against all-atomistic molecular dynamics simulations. The formation of cholesteric ribbons and defects in cholesteric droplets of the cellulose nanocrystal are investigated and confirm experimental behavior reported in the literature. The flexibility of this new patchy particle model makes it a powerful tool to develop supra coarse-grained models of self-assembly for large space and time scales and should find a broad range of applications for self-assembly in chemical and biological systems.

The binding pocket proposed by Konig et al. [Chem. Commun. 2018, 54, 3030-3033] for the biomarker pentameric formyl thiophene acetic acid (p-FTAA) in the fibrillar structure of amyloid-beta(1-42) has been put to the test by the comparison of theoretical and experimental optical absorption and fluorescence spectra obtained in a water environment and inside the protein scaffold. The optical absorption/emission properties of this luminescent conjugated oligothiophene were studied by means of classical force field molecular dynamics simulations to account for the sampling of configuration space in conjunction with polarizable embedding time-dependent density functional theory calculations of spectra. The nuclear motions of residues in the beta-sheet were found to be modest, and the time dependence of embedding parameters was shown to be negligible so that a time-independent parameter set could be derived and used for all 300 snapshots considered in the spectrum averaging. In regard to linear absorption spectra, the calculated red shift due to protein binding for the dominant S-1 amp;lt;- S-0 transition in p-FTAA was found to be equal to 23 nm (0.17 eV), which is in excellent agreement with the corresponding experimental result of 18 nm and taken as corroborating evidence for having correctly identified the binding pocket of p-FTAA in the amyloid. The underlying mechanisms for the calculated red shift were disentangled, and it is shown that some 20 nm (0.15 eV) of the total 23 nm (0.17 eV) is associated with increased planarity of p-FTAA in the binding pocket, whereas a mere 3 nm (0.02 eV) is associated with changes in the environment. In regard to emission spectra, we demonstrate that intersystem crossing from the excited S-1 state to the triplet manifold of states is a less likely event for p-FTAA in the binding pocket as compared to in the aqueous solution, and we thereby partly explain the much higher quantum yield of fluorescence for the more rigid p-FTAA in the binding pocket. Two-photon absorption in p-FTAA is shown to predominantly occur to an overall symmetric excited state and be more than twice as strong for the biomarker in the binding pocket as compared to in water. The corresponding red shift, on the other hand, is very small. Earlier experimental two-photon fluorescence imaging using p-FTAA is shown not to target the dominant two-photon state, and ways to reach a higher image quality (lower signal-to-noise ratio) are proposed in terms of tuning the laser wavelength toward the region of 600 nm or the synthesis of asymmetric ligands with S-1 states that are both one- and two-photon allowed.

The hierarchical self-assembly of cellulose nanocrystals (CNCs) is an important phenomenon occurring naturally in plant cell walls. Utilization of this assembly for advanced applications requires a fundamental theoretical understanding of interactions between the CNCs, which is still incomplete. Hence, in this work, we used molecular dynamics simulations to study the effect of surface modification on the interactions between the CNCs and the resulting bundling process. We consider two types of common surface modifications of native CNCs, sulfated CNCs (SCNCs) and TEMPO-oxidized CNCs (TCNCs), in the presence of two types of counterions, Na+ and Ca2+, in solution. We used the umbrella sampling method to calculate the potential of the mean force (PMF), and we found that the strength of interaction between the modified CNCs decreases, compared with the native CNCs. The strength of interaction for TCNCs is almost similar to that for SCNCs at the same level of surface substitution, whereas the type of counterion has a strong effect on the PMF with a higher interaction energy between the CNCs in the presence of a divalent counterion as compared to a monovalent counterion. Finally, we studied the self-assembly of CNCs into a hexagonal bundle for the native CNCs and sulfated CNCs focusing on the twist of the bundle, bound water inside the bundle, inter-CNC gap, and interaction energy between the CNCs in the bundle, and the effect of the counterions on the morphology of the bundle. The equilibrium spacing of the CNCs within the bundle is found to be consistent with the results of PMF calculations for the minimum separation distance between the respective crystal surfaces.

Control over the photophysical properties and molecular organization of pi-conjugated oligothiophenes is essential to their use in organic electronics. Herein we synthesized and characterized a variety of anionic pentameric oligothiophenes with different substitution patterns of L- or D-tyrosine at distinct positions along the thiophene backbone. Spectroscopic, microscopic, and theoretical studies of L- or D-tyrosine substituted pentameric oligothiophene conjugates revealed the formation of optically active pi-stacked self-assembled aggregates under acid conditions. The distinct photophysical characteristics, as well as the supramolecular structures of the assemblies, were highly influenced by the positioning of the L- or D-tyrosine moieties along the thiophene backbone. Overall, the obtained results clearly demonstrate how fundamental changes in the position of the enantiomeric side-chain functionalities greatly affect the optical properties as well as the architecture of the self-assembled supramolecular structures.

Electronic coupling between adjacent molecules is one of the key parameters determining the charge transfer (CT) rates in bulk heterojunction (BHJ) polymer solar cells (PSCs). We calculate theoretically electronic couplings for exciton dissociation (ED) and charge recombination (CR) processes at local poly(thiophene-co-quinoxaline) (TQ)-PC71BM interfaces. We use eigenstate-based coupling schemes, i.e. the generalized Mulliken-Hush (GMH) and fragment charge difference (FCD) schemes, including 2 to multiple (3-11) states. Moreover, we study the effects of functionals, excited state methods, basis sets, surrounding media, and relative placements of TQ and PC71BM on the coupling values. Generally, both schemes provide consistent couplings with the global hybrid functionals, which yield more charge-localized diabatic states and constant coupling values regardless of the number of states, and so the 2-state schemes may be sufficient. The (non-tuned and optimally tuned) long-range corrected (LRC) functionals result in more notable mixing of the local components with the CT states. Employing multiple states reduces the mixing and thus improves the LRC results, although the method still affects the GMH CR couplings. As the FCD scheme is less sensitive, we recommend combining it with the multi-state treatment for polymer-fullerene systems when using the LRC functionals. Finally, we employ the 11-state FCD couplings to calculate the ED and CR rates, which are consistent with the experimental rates of the polymer-fullerene systems. Our results provide more insight into choosing a suitable eigenstate-based coupling scheme for predicting the electronic couplings and CT rates in photoactive systems.

Charge carrier traps are generally highly detrimental for the performance of semiconductor devices. Unlike the situation for inorganic semiconductors, detailed knowledge about the characteristics and causes of traps in organic semiconductors is still very limited. Here, we accurately determine hole and electron trap energies for a wide range of organic semiconductors in thin-film form. We find that electron and hole trap energies follow a similar empirical rule and lie similar to 0.3-0.4 eV above the highest occupied molecular orbital and below the lowest unoccupied molecular orbital, respectively. Combining experimental and theoretical methods, the origin of the traps is shown to be a dielectric effect of water penetrating nanovoids in the organic semiconductor thin film. We also propose a solvent-annealing method to remove water-related traps from the materials investigated, irrespective of their energy levels. These findings represent a step towards the realization of trap-free organic semiconductor thin films.

Weak noncovalent interactions between large disclike molecules in poorly solvating media generally lead to the formation of fibers where the molecules stack atop one another. Here, we show that a particular chiral spacing group between large aromatic moieties, which usually lead to columnar stacks, in this case gives rise to an intramolecularly folded structure in relatively polar solvents, but in very apolar solvents forms finite aggregates. The molecule that displays this behavior has a C-3 symmetric benzene-1,3,5-tris(3,3-diamido-2,2-bipyridine) (BTAB) core with three metalloporphyrin units appended to it through short chiral spacers. Quite well-defined chromophore arrangements are evident by circular dichroism (CD) spectroscopy of this compound in solution, where clear exciton coupled bands of porphyrins are observed. In more polar solvents where the molecules are dispersed, a relatively weak CD signal is observed as a result of intramolecular folding, a feature confirmed by molecular modeling. The intramolecular folding was confirmed by measuring the CD of a C-2 symmetric analogue. The C-3 symmetric BTAB cores that would normally be expected to stack in a chiral arrangement in apolar solvents show no indication of CD, suggesting that there is no transfer of chirality through it (although the expected planar conformation of the 2,2-bipyridine unit is confirmed by NMR spectroscopy). The incorporation of the porphyrins on the 3,3-diamino-2,2-bipyridine moiety spaced by a chiral unit leaves the latter incapable of assembling through supramolecular pi-pi stacking. Rather, modeling indicates that the three metalloporphyrin units interact, thanks to van der Waals interactions, favoring their close interactions over that of the BTAB units. Atomic force microscopy shows that, in contrast to other examples of molecules with the same core, disclike aggregates (rather than fibrillar one dimensional aggregates) are favored by the C-3 symmetric molecule. The closed structures are formed through nondirectional interlocking of porphyrin rings. The chiral spacer between the rigid core and the porphyrin moieties is undoubtedly important in determining the outcome in polar or less polar solvents, as modeling shows that this joint in the molecule has two favored conformations that render the molecule relatively flat or convex.

Selecting components and observing changes ofproperties and configurations over time is an important step in the analysis of molecular dynamics (MD) data. In this paper, we present a selection tool combining text-based queries with spatial selection and filtering. Morphological operations facilitate refinement of the selection by growth operators, e.g. across covalent bonds. The combination of different selection paradigms enables flexible and intuitive analysis on different levels of detail and visual depiction of molecular events. Immediate visual feedback during interactions ensures a smooth exploration of the data. We demonstrate the utility of our selection framework by analyzing temporal changes in the secondary structure of poly-alanineand the binding ofaspirin to phospholipase A2.

The vast majority of ferroelectric materials demonstrate a positive piezoelectric effect. Theoretically, the negative piezoelectric coefficient d₃₃ could be found in certain classes of ferroelectrics, yet in practice, the number of materials showing linear longitudinal contraction with increasing applied field (d₃₃ < 0) is limited to few ferroelectric polymers. Here, we measure a pronounced negative piezoelectric effect in the family of organic ferroelectric small-molecular BTAs (trialkylbenzene-1,3,5-tricarboxamides), which can be tuned by mesogenic tail substitution and structural disorder. While the large- and small-signal strain in highly-ordered thin-film BTA capacitor devices are dominated by intrinsic contributions and originates from piezostriction, rising disorder introduces additional extrinsic factors that boost the large-signal d33 up to −20 pm V^-ˆ’1 in short-tailed molecules. Interestingly, homologues with longer mesogenic tails show a large-signal electromechanical response that is dominated by the quadratic Maxwell strain with significant mechanical softening upon polarization switching, whereas the small-signal strain remains piezostrictive. Molecular dynamics and DFT calculations both predict a positive d₃₃ for defect-free BTA stacks. Hence, the measured negative macroscopic d₃₃ is attributed to the presence of structural defects that enable the dimensional effect to dominate the piezoelectric response of BTA thin films.

In the field of organic electronics, understanding complex material morphologies and their role in efficient charge transport in solar cells is extremely important. Related processes are studied using the Ising model and Kinetic Monte Carlo simulations resulting in large ensembles of stochastic trajectories. Naive visualization of these trajectories, individually or as a whole, does not lead to new knowledge discovery through exploration. In this paper, we present novel visualization and exploration methods to analyze this complex dynamic data, which provide succinct and meaningful abstractions leading to scientific insights. We propose a morphology abstraction yielding a network composed of material pockets and the interfaces, which serves as backbone for the visualization of the charge diffusion. The trajectory network is created using a novel way of implicitly attracting the trajectories to the skeleton of the morphology relying on a relaxation process. Each individual trajectory is then represented as a connected sequence of nodes in the skeleton. The final network summarizes all of these sequences in a single aggregated network. We apply our method to three different morphologies and demonstrate its suitability for exploring this kind of data.

We present a visual exploration environment tailored for large-scale spatio-temporal molecular dynamics simulation data. The environment is referred to as VIA-MD (visual interactive analysis of molecular dynamics) and has been developed in a participatory design process with domain experts on molecular dynamics simulations of complex molecular systems. A key feature of our approach is the support for linked interactive 3D exploration of geometry and statistical analysis using dynamic temporal windowing and animation. Based on semantic level descriptions and hierarchical aggregation of molecular properties we enable interactive filtering, which enables the user to effectively find spatial, temporal and statistical patterns. The VIA-MD environment provides an unprecedented tool for analysis of complex microscopic interactions hidden in large data volumes. We demonstrate the utility of the VIA-MD environment with four use cases. The first two deal with simulation of amyloid plaque associated with development of Alzheimer's, and we study an aqueous solution of 100 probes and an amyloid fibril. The identification of interaction "hotspots" is achieved with the use of combined filter parameters connected with probe molecular planarity and probe-fibril interaction energetics. The third and fourth examples show the wide applicability of the environment by applying it to analysis of molecular properties in material design.

A study of electron mobility in a PCBM system is performed by means of analytical considerations and Kinetic Monte Carlo simulations. Orbital energies are calculated at the ZINDO level of theory and successively corrected considering contributions from permanent charges and polarization interactions. The relative importance of these environmental effects is analyzed in details, furthermore the predicted mobilities are compared with experimental results and similar simulations performed in C60. (C) 2017 Elsevier B.V. All rights reserved.

We have performed a multiscale approach to study the influence of peripheral substitution in the semiconducting properties of discotic liquid-crystalline triindoles. Charge carrier mobility as high as 1.4 cm(2) V-1 s(-1) was experimentally reported for triindoles substituted with alkynyl chains on the periphery (Gomez-Lor et al. Angew. Chem., Int. Ed., 2011, 50, 7399-7402). In this work, our goal is to get a deeper understanding of both the molecular electronic structure and microscopic factors affecting the charge transport properties in triindoles as a function of the spacer group connecting the central cores with the external alkyl chains (i.e., alkyne or phenyl spacers groups). To this end, we first perform Quantum Mechanical (QM) calculations to assess how the peripheral substitution affects the electronic structure and the internal reorganization energy. Secondly, boxes of stacked molecules were built and relaxed through molecular dynamics to obtain realistic structures. Conformational analysis and calculations of transfer integrals for closed neighbours were performed. Our results show that the insertion of ethynyl spacers between the central aromatic core and the flexible peripheral chains results in lower reorganization energies and enhanced intermolecular order within the stacks with a preferred cofacial 60 degrees staggered conformation, which would result in high charge-carrier mobilities in good agreement with the experimental data. This work allows a deeper understanding of charge carrier mobility in columnar phases, linking the structural order at the molecular level to the property of interest, i.e. the charge carrier mobility. We hope that this understanding will improve the design of systems at the supramolecular level aiming at obtaining a more defined conducting channel, higher mobility and smaller fluctuations within the column.

Charge transfer (CT) state separation is one of the most critical processes in the functioning of an organic solar cell. In this article, we study a bilayer of TQ1 and PC71BM molecules presenting disorder at the interface, obtained by means of Molecular Dynamics. The study of the CT state splitting can be first analyzed through the CT state splitting diagram, introduced in a previous work. Through this analysis, we identify the possibility of CT state splitting within Marcus Theory in function of the electric field. Once the right range of electric fields has been identified, we perform Kinetic Monte Carlo simulations to estimate percentages and times for the CT state splitting and the free charge carriers collection. Statistical information extracted from these simulations allows us to highlight the importance of polarization and to test the limits of the predictions given by the CT state splitting diagram. (c) 2017 Wiley Periodicals, Inc.

Artificial light-harvesting systems have until now not been able to self-assemble into structures with a large photon capture cross-section that upon a stimulus reversibly can switch into an inactive state. Here we describe a simple and robust FLFL-dipeptide construct to which a meso-tetraphenylporphyrin has been appended and which self-assembles to fibrils, platelets or nanospheres depending on the solvent composition. The fibrils, functioning as quenched antennas, give intense excitonic couplets in the electronic circular dichroism spectra which are mirror imaged if the unnatural FDFD-analogue is used. By slightly increasing the solvent polarity, these light-harvesting fibres disassemble to spherical structures with silent electronic circular dichroism spectra but which fluoresce. Upon further dilution with the nonpolar solvent, the intense Cotton effects are recovered, thus proving a reversible switching. A single crystal X-ray structure shows a head-to-head arrangement of porphyrins that explains both their excitonic coupling and quenched fluorescence.

We report the synthesis and self-assembly of chiral, conformationally flexible C-3-symmetrical trisamides. A strong Cotton effect is observed for the supramolecular polymers in linear alkanes but not in cyclic alkanes. MD simulations suggest 2:1 conformations of the amides within the aggregates in both types of solvents, but a chiral bias in only linear alkanes.

This study presents the influence of various substituents on the photophysical features of heteroleptic copper(I) complexes bearing both N-heterocyclic carbene (NHC) and dipyridylamine (dpa = dipyridylamine skeleton corresponding to ligand L1) ligands. The luminescent properties have been compared to our recently reported archetypal blue emitting [Cu(IPr)(dpa)][PF6] complex. The choice of the substituents on both ligands has been guided to explore the effect of the electron donor/acceptor and "push-pull" on the emission wavelengths and photoluminescence quantum yields. A selection of the best candidates in terms of their photophysical features were applied for developing the first blue light emitting electrochemical cells (LECs) based on copper(I) complexes. The device analysis suggests that the main concern is the moderate redox stability of the complexes under high applied driving currents, leading to devices with moderate stabilities pointing to a proof-of-concept for further development. Nevertheless, under low applied driving currents the blue emission is stable, showing performance levels competitive to those reported for blue LECs baged on iridium(III) complexes. Overall, this work provides valuable guidelines to tackle the design of enhanced NHC copper complexes for lighting applications in the near future.

We present a study of mobility field and temperature dependence for C60 with Kinetic Monte-Carlo simulations. We propose a new scheme to take into account polarization effects in organic materials through atomic induced dipoles on nearby molecules. This leads to an energy correction for the single site energies and to an external reorganization happening after each hopping. The inclusion of polarization allows us to obtain a good agreement with experiments for both mobility field and temperature dependence.

We introduce a hybrid complex polarization propagator/molecular mechanics method for the calculation of near-resonant and resonant response properties of molecules in heterogeneous environments, which consist of a metallic surface, or nanoparticle, and a solvent. The applicability and performance of the method is demonstrated by computations of linear absorption spectra of p-nitroaniline physisorbed at a gold/dimethyl sulfoxide interface in the UV/vis and near carbon-K-edge regions of the spectrum. It is shown that the shift of absorption cross-section induced by the heterogeneous environment varies significantly depending on the nature,of the excited states encountered in the targeted frequency region as well as on the actual size of the resonant frequencies, and that the solvent component of the heterogeneous environment is responsible for the major part of the environmental shift, especially in the higher frequency range of the carbon K-edge region.

We report a multiscale modeling of electronic structure of a conducting polymer poly(3,4-ethylenedioxythiopehene) (PEDOT) based on a realistic model of its morphology. We show that when the charge carrier concentration increases, the character of the density of states (DOS) gradually evolves from the insulating to the semimetallic, exhibiting a collapse of the gap between the bipolaron and valence bands with the drastic increase of the DOS between the bands. The origin of the observed behavior is attributed to the effect of randomly located counterions giving rise to the states in the gap. These results are discussed in light of recent experiments. The method developed in this work is general and can be applied to study the electronic structure of other conducting polymers.

We study, within Marcus theory, the possibility of the charge-transfer (CT) state splitting at organic interfaces and a subsequent transport of the free charge carriers to the electrodes. As a case study we analyze model anthracene-C-60 interfaces. Kinetic Monte Carlo (KMC) simulations on the cold CT state were performed at a range of applied electric fields, and with the fields applied at a range of angles to the interface to simulate the action of the electric field in a bulk heterojunction (BHJ) interface. The results show that the inclusion of polarization in our model increases CT state dissociation and charge collection. The effect of the electric field on CT state splitting and free charge carrier conduction is analyzed in detail with and without polarization. Also, depending on the relative orientation of the anthracene and C-60 molecules at the interface, CT state splitting shows different behavior with respect to both applied field strength and applied field angle. The importance of the hot CT in helping the charge carrier dissociation is also analyzed in our scheme.

By replacing the central thiophene unit of an anionic pentameric oligothiophene with other heterocyclic moities, a palette of pentameric thiophene-based ligands with distinct fluorescent properties were synthesized. All ligands displayed superior selectivity towards recombinant amyloid fibrils as well as disease-associated protein aggregates in tissue sections.

The molecular recognition of human telomeric G-quadruplexes by a novel cationic pi-extended Ni-II-porphyrin (Ni-II-TImidP4) is studied in aqueous solutions via (chir) optical spectroscopy, Fluorescence Resonance Energy Transfer (FRET) melting assay, and computational molecular modeling. The results are systematically compared with the recognition by a conventional meso-substituted Ni-II-porphyrin (Ni-II-TMPyP4), which allows us to pinpoint the differences in binding modes depending on the G-quadruplex topology. Importantly, FRET melting assays show the higher selectivity of Ni-II-TImidP4 towards human telomeric G4 than that of Ni-II-TMPyP4.

A series of chiral synthetic compounds is reported that shows intricate but specific hierarchical assembly because of varying positions of coordination and hydrogen bonds. The evolution of the aggregates (followed by absorption spectroscopy and temperature-dependent circular dichroism studies in solution) reveal the influence of the proportion of stereogenic centers in the side groups connected to the chromophore ring in their optical activity and the important role of pyridyl groups in the self-assembly of these chiral macrocycles. The optical activity spans 2 orders of magnitude depending on composition and constitution. Two of the aggregates show very high optical activity even though the isolated chromophores barely give a circular dichroism signal. Molecular modeling of the aggregates, starting from the pyridine zinc(II) porphyrin interaction and working up, and calculation of the circular dichroism signal confirm the origin of this optical activity as the chiral supramolecular organization of the molecules. The aggregates show a broad absorption range, between approximately 390 and 475 rim for the transitions associated with the Soret region alone, that spans wavelengths far more than the isolated chromophore. The supramolecular assemblies of the metalloporphyrins in solution were deposited onto highly oriented pyrolitic graphite in order to study their hierarchy in assembly by atomic force microscopy. Zero and one-dimensional aggregates were observed, and a clear dependence on deposition temperature was shown, indicating that the hierarchical assembly took place largely in solution. Moreover, scanning electron microscopy images of porphyrins and metalloporphyrins precipitated under out-of-equilibrium conditions showed the dependence of the number and position of chiral amide groups in the formation of a fibrillar nanomaterial. The combination of coordination and hydrogen bonding in the complicated assembly of these molecules where there is a clear hierarchy for zinc(II)-pyridyl interaction followed by hydrogen-bonding between amide groups, and then van der Waals interactions paves the way for the preparation of molecular materials with multiple chromophore environments.

The morphology of organic interfaces plays an important role in charge-transfer (CT) state splitting, and therefore has a significant impact on the efficiency of organic solar cells. In this article, we use our kinetic Monte Carlo (KMC) method on molecular dynamics-simulated anthracene-C60 interfaces to study the relation between interface morphology and CT state splitting. These KMC simulations were performed at a range of applied electric fields, and with the fields applied at a range of angles to the interface. The results show that depending on the relative orientation of the anthracene and C60 molecules, CT state splitting shows different behavior with respect to both applied field strength and applied field angle. Different orientations may be better suited for different applications. The inclusion of polarization in our model is shown to  increase CT state splitting for both orientations studied.