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At least 703 records · Page 39

Understanding Gas Solubility of Pure Component and Binary Mixtures within Multivalent Ionic Liquids from Molecular Simulations

Understanding the molecular-level solubility of CO 2 and its mixtures is essential to the progress of gas treating technologies. Herein, we use grand canonical Monte Carlo simulations to study the single component gas absorption of SO 2 , N 2 , CH 4 , and H 2 , and binary mixtures of CO 2 /SO 2 , CO 2 /N 2 , CO 2 /CH 4 , and CO 2 /H 2 of varying mole fractions within multivalent ionic liquids (ILs). Our results highlight the importance of the free volume effect and the anion effect when interpreting the absorption behavior of these mixtures, similar to the behavior of CO 2 found in our previous study. The deviation of the gas solubility between the pure component absorption versus the binary absorption, as well as the solubility selectivity, highlight the importance of the relative affinity of gas species within a mixture to the different anions. Further, the absorption selectivity within a specific IL system can be predicted based on the relative gas affinity to the anion.

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Understanding Relationships between Free Volume and Oxygen Absorption in Ionic Liquids

In this report understanding the factors that govern gas absorption in ionic liquids is critical to the development of high-capacity solvents for catalysis, electrochemistry, and gas separations. Here, we report experimental probes of liquid structure that provide insights into how free volume impacts the O 2 absorption properties of ionic liquids. Specifically, we establish that isothermal compressibility - measured rapidly and accurately through small-angle X-ray scattering - reports on the size distribution of transient voids within a representative series of ionic liquids and is correlated with O 2 absorption capacity. Additionally, O 2 absorption capacities are correlated with thermal expansion coefficients, reflecting the beneficial effect of weak intermolecular interactions in ionic liquids on free volume and gas absorption capacity. Molecular dynamics simulations show that the void size distribution - in particular, the probability of forming larger voids within an ionic liquid - has a greater impact on O 2 absorption than the total free volume. These results establish relationships between the ionic liquid structure and gas absorption properties that offer design strategies for ionic liquids with high gas solubilities.

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Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments

Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.

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Toward an Understanding of the Excitonic Structure of the CP47 Antenna Protein Complex of Photosystem II Revealed via Circularly Polarized Luminescence

Identification of the lowest energy pigments in the photosynthetic CP47 antenna protein complex of Photosystem II (PSII) is essential for understanding its excitonic structure, as well as excitation energy pathways in the PSII core complex. Unfortunately, there is no consensus concerning the nature of the low-energy state(s) nor chlorophyll (Chl) site energies in this important photosynthetic antenna. Although, we raised concerns regarding the estimations of Chl site energies obtained from modeling studies of various types of CP47 optical spectra [Reinot, T; et al., Anal. Chem. Insights 2016, 11, 35–48] recent new assignments imposed by the shape of the circularly polarized luminescence (CPL) spectrum [Hall, J.; et al., Biochim. Biophys. Acta 2016, 1857, 1580–1593] necessitate our comments. We demonstrate that other combinations of lowenergy Chls provide equally good or improved simultaneous fits of various optical spectra (absorption, emission, CPL, circular dichroism, and nonresonant hole-burned spectra), but more importantly, we expose the heterogeneous nature of the recently studied complexes and argue that the published composite nature of the CPL (contributed to by CPL 685 , CPL 691 , and CPL 695 ) does not represent an intact CP47 protein. A positive CPL 695 is extracted for the intact protein, which when simultaneously fitted with multiple other optical spectra, provides new information on the excitonic structure of intact and destabilized CP47 complexes and their lowest energy state(s).

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Understanding the Twisted Structure of Amyloid Fibrils via Molecular Simulations

According to the article, accumulation and aggregation of amyloid are associated with the pathogenesis of many human diseases, such as Alzheimer’s disease and Type 2 diabetes mellitus. Therefore, a quantitative understanding of the molecular mechanisms causing different aggregated structures and biomechanical properties of amyloid fibrils could shed some light into the progression of these diseases. In this work, we develop coarse-grained molecular dynamics (CGMD) models to simulate the dynamic self-assembly of two types of amyloids (amylin and amyloid β (Aβ)). We investigate the structural and mechanical properties of different types of aggregated amyloid fibrils. Our simulations demonstrate that amyloid fibrils could result from longitudinal growth of protofilament bundles, confirming one of the hypotheses on the fibril formation. In addition, we find that the persistence length of amylin fibrils increases concurrently with their pitch length, suggesting that the bending stiffness of amylin fibrils becomes larger when the amylin fibrils are less twisted. Similar results are observed for Aβ fibrils. These findings quantify the connection between the structural and the biomechanical properties of the fibrils. The CGMD models developed in this work can be potentially used to examine efficacy of anti-aggregation drugs, which could help in developing new treatments.

Chemistry↗

Understanding Binder–Silicon Interactions during Slurry Processing

The conformation of poly(acrylic acid) (PAA) as a function of shear during slurry processing to construct silicon-based anodes is elucidated via rheology-coupled ultra-small-angle neutron scattering (rheo-USANS). Rheo-USANS shows that PAA with encapsulated silicon exists as discrete aggregates that do not interact with one another. As a result, a well-connected matrix of silicon and carbon black dispersed in PAA does not exist; thus, the electrode is inhomogeneous. Raman mapping and X-ray photoelectron spectroscopy were used to confirm the electrode heterogeneity and further understand the cycling properties. These results are correlated to silicon surface chemistry to provide a pathway to making better electrodes.

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Understanding the Surface Structure and Catalytic Activity of SnO x /Au(111) Inverse Catalysts for CO 2 and H 2 Activation

Carbon dioxide hydrogenation is a promising approach for the reduction of greenhouse gas pollution via the production of fuels and high-value chemicals utilizing C1 chemistry. In this process, the activation of nonpolar molecules, CO 2 and H 2 , at mild conditions is challenging. In this study, we report a well-defined inverse SnO x /Au(111) catalyst that shows the ability to activate both CO 2 and H 2 at room temperature. Scanning tunneling microscopy (STM) and ambient pressure X-ray photoemission spectroscopy (AP-XPS) are combined to understand the surface structure, growth mode, chemical state, and activity of SnO x /Au(111) surfaces. Nanostructures of SnO x at the sub-monolayer level were prepared by depositing Sn on Au(111) followed by O 2 oxidation. For the as-prepared SnO x /Au(111), two-dimensionally formed SnO x thin films on a Au(111) substrate were observed with STM of two different moieties, discernible based on their height: clusters (~0.4 Å) and nanoparticles (NPs, 1–2.5 Å), which are assigned to Sn–Au alloys and SnO x , respectively, in corroboration with XPS analysis. Furthermore, SnO x /Au(111) was annealed under UHV to test its thermal stability. Upon annealing at 400–600 K, a disappearance of SnO x NPs and reappearance of highly dispersed Sn clusters were clearly noticeable from the STM and XPS results, identifying the thermal decomposition of SnO x and subsequent formation of Sn–Au alloys on the surface due to the recombination of Sn clusters with Au. We investigated the reactivity of the SnO x /Au(111) surfaces toward CH 4 , CO 2 , and H 2 . The SnO x /Au(111) surfaces have excellent CO 2 and H 2 activation abilities even at room temperature with negligible reactivity for methane activation. Our AP-XPS results show that H 2 can be activated on the SnO x NPs by the reduction to Sn. For CO 2 , the activation and further dissociation are identified by a reoxidation of Sn with newly formed Sn–O bonds and the formation of surface carbon. Therefore, we propose that SnO x is a potential catalyst or additive to achieve CO 2 hydrogenation under mild conditions.

36 MATERIALS SCIENCE↗

Understanding the Mechanism of Secondary Cation Release from the (001) Surface of Li(Ni 1/3 Mn 1/3 Co 1/3 )O 2 : Insights from First-Principles

The transformations of complex metal oxides in aqueous settings must be studied to form a chemical understanding of how technologically relevant nanomaterials impact the environment upon disposal. Owing to the inherent heterogeneity and structural complexity of the ternary intercalation material Li(Ni x Mn y Co 1-x-y )O 2 (NMC), the mechanisms of chemical processes at the solid–water interfac e are challenging to model. Here, density functional theory (DFT) + solvent ion methodology is used to study the energetics of stepwise release of two surface metals following unique pathways. Further, the study spans different combinations of metal removal and also considers unique patterns of defects formed by modeling the NMC surface in supercells. The approach here also considers the equilibration of the surface with the surroundings between successive metal removals. A key finding is that a second metal removal prefers to proceed at a metal lattice site adjacent to the initial defect, and this is attributed in part to how the resulting slab with two metal vacancies maintains the most antiferromagnetic couplings between the remaining Ni/Mn.

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Atomic-Scale Understanding of Catalyst Activation: Carboxylic Acid Solutions, but Not the Acid Itself, Increase the Reactivity of Anatase (001) Faceted Nanocatalysts

Our ability to predict nanocatalyst reactivity has been hindered by our lack of atomic-scale understanding of nanocatalyst surface structure. Do nanocatalyst surfaces adopt a bulk-terminated structure or do they reconstruct to minimize their free energy, thereby lowering their reactivity as often observed in vacuum? Similarly, do nanocatalysts processed at high temperatures maintain their low reactivity, reconstructed surfaces when used at low temperatures? Using a new technique for the preparation of anatase nanocatalysts suitable for atomic-scale imaging and surface spectroscopy, we show that solution-prepared anatase is terminated by a monolayer of fluorine, which acts as an atomic-scale oleophobic coating, preventing the accumulation of adventitious carbon. We further show that the most common TiO 2 functionalization chemistry, a carboxylic acid solution, causes the spontaneous reorganization of a reconstructed anatase nanocatalyst, leading to a five-fold increase in reactive sites. This reorganization is not observed when carboxylic acids are deposited from the gas phase, suggesting that model experiments in vacuum environments can lead to a nonequilibrium, kinetically trapped state that may not be catalytically relevant. Aqueous carboxylic acid solutions produce densely packed carboxylate monolayers with richer adsorption geometries than previously predicted. Ab initio simulations show that although the carboxylate termination is somewhat less effective at removing surface stress than the reconstruction, it is more effective in lowering the surface energy. This observation suggests that bulk-terminated metal-oxide nanocrystals may be common in reactive environments, even if high temperatures are used to process the nanocatalyst or if the reactant is later rinsed off. As such, the assumption of a bulk-terminated surface may be a reasonable starting point for “materials-by-design” approaches to computationally engineered nanocatalysts.

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Understanding Chemical Bonding in Alloys and the Representation in Atomistic Simulations

Alloys are widely used in catalysts and structural materials. The nature of chemical bonding and the origin of alloy formation energies, defect energies, and interfacial properties have not been well understood to date but are critical to material performance. In this contribution, we explain the polar nature of chemical bonding and an implementation in classical and reactive atomistic simulations to understand such properties more quantitatively. Electronegativity differences between metal atoms lead to polar bonding, and exothermic alloy formation energies are related to charge transfer between the different elements. These differences can be quantified by atomic charges using pairwise charge increments, determined by matching the computed alloy formation energy to experimentally measured alloy formation energies using pair potentials for the pure metals. The polar character of alloys is comparable to organic molecules and partially ionic minerals, for example, AlNi and AlNi3 alloys assume significant atomic charges of ±0.40e and +0.60e/–0.20e, respectively. The subsequent analysis of defect sites and defect energies using force-field-based calculations shows excellent agreement with calculations using density functional theory and embedded atom models (EAM). The formation of vacancy and antisite defects is characterized by a redistribution of charge in the first shell of neighbor atoms in the classical models whereby electroneutrality is maintained and charge increments correlate with differences in electronegativity. The proposed atomic charges represent internal dipole and multipole moments, consistent with existing definitions for organic and inorganic compounds and with the extended Born model (Heinz, H.; Suter, U. W. J. Phys. Chem. B2004,108 (47), 18341–18352). The method can be applied to any alloy and has a reproducibility of ±10%. In contrast, quantum mechanical charge schemes remain associated with deviations exceeding ±100%. The atomic charges for alloys provide a simple initial measure for the internal electronic structure, surface adsorption of molecules, and reactivity in catalysis and corrosion. The models are compatible with the Interface force field (IFF), CHARMM, AMBER, OPLS-AA, PCFF, CVFF, and GROMOS for reliable atomistic simulations of alloys and their interfaces with minerals and electrolytes from the nanometer scale to the micrometer scale.

Chemistry↗

Understanding Surface Reactivity of Amorphous Transition-Metal-Incorporated Aluminum Oxide Thin Films

The electronic structure of multi-metal, amorphous oxides, can be varied across a wide range of elemental compositions. Bulk properties such as conductivity, work function, and absorption can thus be tailored to suit a range of applications spanning from carrier-selective contacts to catalysis. Missing, however, is an understanding of how the surface reactivity is impacted in mixed metal-oxide amorphous films. Here we investigate the propensity of Al(1-x)M(x)Oy (M = Fe, Mn) amorphous oxide films to dissociate water into hydroxyl groups in a humid environment, and find comparable hydroxylation at the low relative humidity (~0.3% RH) probed by ambient pressure X-ray photoelectron spectroscopy. In contrast, films with both Al and Fe show an increased formation of methoxy groups upon methanol exposure compared to pure Al- and Fe-oxide end members, indicating the coordination environment of the amorphous oxide network impacts the acidity and redox character of surface metal and oxygen sites. These results provide guidance for the rational design of amorphous oxide layers with tailored chemical reactivity or passivity for a given application.

Stoerzinger, Kelsey A.↗

Understanding Fragmentation of Organic Small Molecules in Atom Probe Tomography

In atom probe tomography of molecular organic materials, field ionization of either entire molecules or molecular fragments can occur, but the mechanism governing this behavior was not previously understood. This work explains when a doubly ionized small molecule organic material is expected to undergo fragmentation. Here, we find that multiple detection events arising from post-ionization fragmentation of a parent molecular dication into two daughter ions is well explained by the free energy and geometries of the molecules computed using density functional theory. Of the systems studied, exergonic free energies for formation of the daughter ions, smaller activation energies for dissociation, and increases in bond length are all found to be quantitative predictors for ion fragmentation. This work expands the applicability of atom probe tomography to organic materials by increasing the fundamental understanding of processes occurring during this analysis technique.

36 MATERIALS SCIENCE↗

Understanding the Surprising Ionic Conductivity Maximum in Zn(TFSI) 2 Water/Acetonitrile Mixture Electrolytes

Aqueous electrolytes composed of 0.1 M zinc bis-(trifluoromethyl-sulfonyl)-imide (Zn-(TFSI) 2 ) and acetonitrile (ACN) were studied using combined experimental and simulation techniques. The electrolyte was found to be electrochemically stable when the ACN V% is higher than 74.4. In addition, it was found that the ionic conductivity of the mixed solvent electrolytes changes as a function of ACN composition, and a maximum was observed at 91.7 V% of ACN although the salt concentration is the same. This behavior was qualitatively reproduced by molecular dynamics (MD) simulations. Detailed analyses based on experiments and MD simulations show that at high ACN composition the water network existing in the high water composition solutions breaks. As a result, the screening effect of the solvent weakens and the correlation among ions increases, which causes a decrease in ionic conductivity at high ACN V%. Furthermore, this study provides a fundamental understanding of this complex mixed solvent electrolyte system.

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Understanding Electrochemical Sulfur-Based Phase Evolution via Complementary Insight from Operando Spatially Resolved X-ray Diffraction and X-ray Absorption Spectroscopy

Lithium/sulfur batteries are emerging as promising candidates for use in large-scale energy storage, but practical challenges, including insufficient power density and polysulfide shuttling, remain. Here, this work presents the first use of operando energy dispersive X-ray diffraction (EDXRD) to monitor Li/S electrochemistry within a liquid electrolyte. Complementary operando synchrotron-based EDXRD, X-ray absorption spectroscopy (XAS), X-ray powder diffraction (XPD), and ex situ laboratory Raman analysis provide evidence for α-S 8 conversion upon discharge into Li 2 S x polysulfide phases and conversion into β-S 8 during charge. Understanding the underlying mechanisms of sulfur reduction and oxidation within thick electrodes will enable advances in next-generation Li/S batteries and material design.

36 MATERIALS SCIENCE↗

Understanding anisotropic growth of Au penta-twinned nanorods by liquid cell transmission electron microscopy

Morphology control of anisotropic metal nanocrystals plays an important role in tuning shape-dependent physicochemical properties for various applications, but underlying understanding of their anisotropic growth mechanism remains a great challenge. Here, we investigate the formation of Au penta-twinned nanorod by in situ liquid cell transmission electron microscopy (LC-TEM). It is found that a truncated-decahedron forms in the absence of cetyl-trimethyl ammonium bromide (CTAB), whereas in the presence of CTAB a reentrant groove appears in decahedron to relieve strain during the nanorod formation, which induces the formation of {100} facets. The growth dynamics of penta-twinned nanorod implies that CTAB molecules can promote the nanorod growth by selectively inhibiting atom addition to {100} facets. Density functional theory (DFT) simulations confirm that the partial relieve of strain energy of decahedron nanoparticle is caused by the adsorption of Br- ions. Moreover, the selective adsorption of CTAB lowers the surface energy of {100} facets, resulting in the nanorod growth along the [110] direction. Based on the appearance of reentrant groove and growth dynamics unraveled by LC-TEM, the synergy of strain and surface energy tuning by additives is discovered. The study provides an in-depth insight into the anisotropic growth of nanorods and lays foundations for controlled synthesis of nano-materials.

Jin, Biao↗

Understanding Pore Filling Processes and Adsorption/Desorption Hysteresis in Nanoporous Metal–Organic Frameworks: Insights from Grand Canonical Monte Carlo Simulations and Free Energy Calculations

Grand canonical Monte Carlo (GCMC) simulations were used to investigate pore filling and hysteresis in nanoporous metal-organic frameworks (MOFs). Adsorption and desorption isotherms were calculated for argon at 87 K in 1866 MOFs from the CoRE MOF database and for short n-alkanes in selected MOFs, keeping the adsorbent structure rigid. Analysis of the molecular configurations showed two different mechanisms and origins of hysteresis: one involving a transition of the adsorbate arrangement in the pores similar to a gas-to-liquid transition associated with a large change in the loading and one more similar to a liquid-to-solid transition associated with a relatively small change in the loading. Our GCMC simulations in MOFs with diverse pore topologies indicate exceptions to an empirical relationship for the minimum diameter of a cylindical pore required for hysteresis as a function of the adsorbate diameter and reduced temperature. The simulations reveal some structures where isotherms exhibit two steps in the adsorption branch and only one step in the desorption branch. Hysteresis loops with a different number of adsorption and desorption steps are not common. Here, to better understand why hysteresis is observed in the GCMC simulations, the concept of the transition probability for observing a step in the adsorption isotherm at a given pressure in a GCMC simulation is introduced. We used two different methods to calculate the transition probabilities and find that these yield comparable results. Furthermore, the transition probability provides a measure for the length of GCMC simulations to yield reliable results.

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Understanding the Nature of Amino Acid Interactions with Pd(111) or Pd–Au Bimetallic Catalysts in the Aqueous Phase

In this study, the interaction of methionine (Met) with different bimetallic-segregated surfaces comprising a uniform distribution of strips and islands of Au on the Pd(111) surface was examined using molecular dynamics (MD) simulations. Out of all the segregated and uniformly doped surfaces studied, the design of Pd–Au islands showed some reduction in the interaction energy (E int = -43.7 kJ/mol) as compared to that of the pure Pd(111) surface (E int = -50 kJ/mol) for a single Met molecule. However, at a higher coverage of 9 Met molecules/simulation cell, none of the Pd–Au alloy surfaces showed any improvement as compared to the Pd(111) surface. In order to develop a comprehensive understanding of the nature of the nonbonded interaction of aqueous biogenic impurities with the Pd catalyst surface, the MD study was extended to include a variety of aliphatic, S-containing, aromatic, and polar amino acids. The potential of mean force (PMF) profiles were observed to be distinct for each class of amino acids with substantial differences among amino acids with acidic and basic side chains. The side chains of all the polar and aromatic amino acids showed direct contact with the surface while aliphatic amino acids had their hydrophobic side chain aligned away from the surface. Interestingly, lysine (Lys) and tyrosine (Tyr) were the only two amino acids which interacted preferentially via the distant backbone nitrogen and backbone oxygen, respectively, despite their side chains being in direct contact with the metal surface. The strength of interaction was correlated with the size of the amino acid; the interaction energies were observed to be the maximum for large molecules such as arginine (Arg, E int = -87.7 kJ/mol) and tryptophan (Trp, E int = -73.4 kJ/mol), while it was a minimum for aliphatic amino acids such as alanine (Ala, E int = -10.9 kJ/mol). Lastly, the study is focused on examining the sensitivity of the choice of the preferential interaction site, conformational preferences, and interaction energies to the side-chain specificity.

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Understanding Solution State Conformation and Aggregate Structure of Conjugated Polymers via Small Angle X-ray Scattering

Donor-acceptor (D-A) conjugated polymers are high-performance organic electronic materials that exhibit complex aggregation behavior. Understanding the solution state conformation and aggregation of conjugated polymers is crucial for controlling morphology during thin-film deposition and the subsequent electronic performance. However, a precise multiscale structure of solution state aggregates is lacking. Here, we present an in-depth small-angle X-ray scattering (SAXS) analysis of the solution state structure of an isoindigo-bithiophene-based D-A polymer (PII-2T) in chlorobenzene and decane as our primary system. Modeling the system as a combination of hierarchical fibrillar aggregates mixed with dispersed polymers, we extract information about conformation and multiscale aggregation and also clarify the physical origin of features often observed but unaddressed or misinterpreted in small-angle scattering patterns of conjugated polymers. The persistence length of the D-A polymer extracted from SAXS agrees well with a theoretical model based on the dihedral potentials. Additionally, we show that the broad high q structure factor peak seen in scattering profiles can be attributed to lamellar stacking occurring within the fibril aggregates and that the low q aggregate scattering is strongly influenced by the polymer molecular weight. Overall, the SAXS profiles of D-A polymers in general exhibit a sensitive dependence on the co-existence of fibrillar aggregate and dispersed polymer chain populations. We corroborate our findings from SAXS with electron microscopy of freeze-dried samples for direct imaging of fibrillar aggregates. Finally, we demonstrate the generality of our approach by fitting the scattering profiles of a variety of D-A polymers based on thieno-isoindigo (PTII-2T), diketopyrrolopyrrole (DPP2T-TT, DPP-BTZ, PDPP2FT-C- 16 ), naphthalenediimide (P(NDI2OD-T2)), and a conjugated block copolymer P3HT-b-DPPT-T. The results presented here establish a picture of the D-A polymer solution state structure and provide a general method of interpreting and analyzing their scattering profiles.

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