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The unfolding dynamics of ubiquitin were studied using a combination of x-ray solution scattering (XSS) and molecular dynamics (MD) simulations. The kinetic analysis of the XSS ubiquitin signals showed that the protein unfolds through a two-state process, independent of the presence of destabilizing salts. In order to characterize the ensemble of unfolded states in atomic detail, the experimental XSS results were used as a constraint in the MD simulations through the incorporation of x-ray scattering derived potential to drive the folded ubiquitin structure toward sampling unfolded states consistent with the XSS signals. We detail how biased MD simulations provide insight into unfolded states that are otherwise difficult to resolve and underscore how experimental XSS data can be combined with MD to efficiently sample structures away from the native state. Our results indicate that ubiquitin samples unfolded in states with a high degree of loss in secondary structure yet without a collapse to a molten globule or fully solvated extended chain. Finally, we propose how using biased-MD can significantly decrease the computational time and resources required to sample experimentally relevant nonequilibrium states. [ABSTRACT FROM AUTHOR]

Organic solar cells (OSCs) using non-fullerene acceptors (NFAs) afford exceptional photovoltaic performance metrics, however, their stability remains a significant challenge. Existing OSC stability studies focus on understanding degradation rate-performance relationships, improving interfacial layers, and suppressing degradative chemical reaction pathways. Nevertheless, there is a knowledge gap concerning how such degradation affects crystal structure, electronic states, and recombination dynamics that ultimately impact NFA performance. Here we seek a quantitative relationship between OSC metrics and blend morphology, trap density of states, charge carrier mobility, and recombination processes during the UV-light-induced degradation of PBDB-TF:Y6 inverted solar cells as the PCE (power conversion efficiency) falls from 17.3 to 5.0%. Temperature-dependent electrical and impedance measurements reveal deep traps at 0.48 eV below the conduction band that are unaffected by Y6 degradation, and shallow traps at 0.15 eV below the conduction band that undergo a three-fold density of states increase at the PCE degradation onset. Computational analysis correlates vinyl oxidation with a new trap state at 0.25 eV below the conduction band, likely involving charge transfer from the UV-absorbing ZnO electron transport layer. In situ integrated photocurrent analysis and transient absorption spectroscopy reveal that these traps lower electron mobility and increase recombination rates during degradation. Grazing-incidence wide-angle X-ray scattering and computational analysis reveal that the degraded Y6 crystallite morphology is largely preserved but that <1% of degraded Y6 molecules cause OSC PCE performance degradation by ≈50%. Together the detailed electrical, impedance, morphological, ultrafast spectroscopic, matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) spectroscopy, and computational data reveal that the trap state energies and densities accompanying Y6 vinyl oxidation are primarily responsible for the PCE degradation in these operating NFA-OSCs. [ABSTRACT FROM AUTHOR]

Organic semiconductors (OSCs) are making great progress as active components in alternative energy and flexible electronics technologies that are of interest to many undergraduates. However, in materials governed by the confluence of multiple length scales (molecular (Angstrom), intermolecular (nm), domain (100s nm)), providing a pedagogically accessible pathway to incorporating OSCs into undergraduate education can be difficult. Here, we provide a multiscale description of OSCs that relies only on concepts covered in typical undergraduate chemistry and chemical engineering curricula: a tight-binding description of molecular orbitals using Hückel theory, the miscibility of intermolecular domains using thermodynamic principles based on the Ising spin model, the incorporation of thermal disorder of both the electronic and molecular states using the Boltzmann distribution, and a simple description of charge percolation using low-level graph theory. We illustrate these topics on a small organic molecule, 1,3,5-hexatriene, simple enough to be utilized in an undergraduate course without resorting to opaque metrics.

[Figurre: see text]. Protein aggregation can be defined as the sacrifice of stabilizing intrachain contacts of the functional state that are replaced with interchain contacts to form non-functional states. The resulting aggregate morphologies range from amorphous structures without long-range order typical of nondisease proteins involved in inclusion bodies to highly structured fibril assemblies typical of amyloid disease proteins. In this Account, we describe the development and application of computational models for the investigation of nondisease and disease protein aggregation as illustrated for the proteins L and G and the Alzheimer's Abeta systems. In each case, we validate the models against relevant experimental observables and then expand on the experimental window to better elucidate the link between molecular properties and aggregation outcomes. Our studies show that each class of protein exhibits distinct aggregation mechanisms that are dependent on protein sequence, protein concentration, and solution conditions. Nondisease proteins can have native structural elements in the denatured state ensemble or rapidly form early folding intermediates, which offers avenues of protection against aggregation even at relatively high concentrations. The possibility that early folding intermediates may be evolutionarily selected for their protective role against unwanted aggregation could be a useful strategy for reengineering sequences to slow aggregation and increase folding yield in industrial protein production. The observed oligomeric aggregates that we see for nondisease proteins L and G may represent the nuclei for larger aggregates, not just for large amorphous inclusion bodies, but potentially as the seeds of ordered fibrillar aggregates, since most nondisease proteins can form amyloid fibrils under conditions that destabilize the native state. By contrast, amyloidogenic protein sequences such as Abeta 1-40,42 and the familial Alzheimer's disease (FAD) mutants favor aggregation into ordered fibrils once the free-energy barrier for forming a critical nucleus is crossed. However, the structural characteristics and oligomer size of the soluble nucleation species have yet to be determined experimentally for any disease peptide sequence, and the molecular mechanism of polymerization that eventually delineates a mature fibril is unknown. This is in part due to the limited experimental access to very low peptide concentrations that are required to characterize these early aggregation events, providing an opportunity for theoretical studies to bridge the gap between the monomer and fibril end points and to develop testable hypotheses. Our model shows that Abeta 1-40 requires as few as 6-10 monomer chains (depending on sequence) to begin manifesting the cross-beta order that is a signature of formation of amyloid filaments or fibrils assessed in dye-binding kinetic assays. The richness of the oligomeric structures and viable filament and fibril polymorphs that we observe may offer structural clues to disease virulence variations that are seen for the WT and hereditary mutants.

Using a coarse-grained model of the Abeta peptide, we analyze the Arctic (E22G), Dutch (E22Q), and Flemish (A21G) familial Alzheimer's disease (FAD) mutants for any changes in the stability of amyloid assemblies with respect to the wild-type (WT) sequence. Based on a structural reference state of two protofilaments aligned to create the "agitated" protofibril as determined by solid-state NMR, we determine free energy trends for Abeta assemblies for the WT and FAD familial sequences. We find that the structural characteristics and oligomer size of the critical nucleus vary dramatically among the hereditary mutants. The Arctic mutant's disorder in the turn region introduces new stabilizing interactions that better align the two protofilaments, yielding a well-defined protofibril axis at relatively small oligomer sizes with respect to WT. By contrast, the critical nucleus for the Flemish mutant is beyond the 20 chains characterized in this study, thereby showing a strong shift in the equilibrium toward monomers with respect to larger protofibril assemblies. The Dutch mutant forms more ordered protofilaments than WT, but exhibits greater disorder in protofibril structure that includes an alternative polymorph of the WT fibril. An important conclusion of this work is that the Dutch mutant does not support the agitated protofibril assembly. We discuss the implications of the structural ensembles and free energy profiles for the FAD mutants in regards to interpretation of the kinetics of fibril assembly using chromatography and dye-binding experiments.

The protein folding process often proceeds through partially folded transient states. Therefore, a structural understanding of these disordered states is crucial for developing mechanistic models of the folding process. Characterization of unfolded states remains challenging due to their disordered nature, and incorporating multiple methods is necessary. Combining the time-resolved x-ray solution scattering (TRXSS) signal with molecular dynamics (MD), we are able to characterize transient partially folded states of bovine α-lactalbumin, a model system widely used for investigation of molten globule states, during its unfolding triggered by a temperature jump. We track the unfolding process between 20 µs and 70 ms and demonstrate that it passes through three distinct kinetic states. The scattering signals associated with these transient species are then analyzed with TRXSS constrained MD simulations to produce protein structures that are compatible with the input signals. Without utilizing any experimentally extracted kinetic information, the constrained MD simulation successfully drove the protein to an intermediate molten globule state; signals for two later disordered states are refined to terminal unfolded states. From our examination of the structural characteristics of these disordered states, we discuss the implications disordered states have on the folding process, especially on the folding pathway. Finally, we discuss the potential applications and limitations of this method. [ABSTRACT FROM AUTHOR]

In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association. [ABSTRACT FROM AUTHOR]

We develop a lattice model utilizing coarse-grained molecular sites to study charge transport in molecular semiconducting materials. The model bridges atomistic descriptions and structureless lattice models by mapping molecular structure onto sets of spatial vectors isomorphic with spin vectors in a classical n-vector Heisenberg model. Specifically, this model incorporates molecular topologydependent orientational and intermolecular coupling preferences, including the direct inclusion of spatially correlated transfer integrals and site energy disorder. This model contains the essential physics required to explicitly simulate the interplay of molecular topology and correlated structural disorder, and their effect on charge transport. As a demonstration of its utility, we apply this model to analyze the effects of long-range orientational correlations, molecular topology, and intermolecular interaction strength on charge motion in bulk molecular semiconductors. [ABSTRACT FROM AUTHOR]

The synthesis and characterization of new semiconducting materials is essential for developing high‐efficiency organic solar cells. Here, the synthesis, physiochemical properties, thin film morphology, and photovoltaic response of ITN‐F4 and ITzN‐F4, the first indacenodithienothiophene nonfullerene acceptors that combine π‐extension and fluorination, are reported. The neat acceptors and bulk‐heterojunction blend films with fluorinated donor polymer poly{[4,8‐bis[5‐(2‐ethylhexyl)‐4‐fluoro‐2‐thienyl]benzo[1,2‐b:4,5‐b′]‐dithiophene‐2,6‐diyl]‐alt‐[2,5‐thiophenediyl[5,7‐bis(2‐ethylhexyl)‐4,8‐dioxo‐4H,8H‐benzo[1,2‐c:4,5‐c′]dithiophene‐1,3‐diyl]]} (PBDB‐TF, also known as PM6) are investigated using a battery of techniques, including single crystal X‐ray diffraction, fs transient absorption spectroscopy (fsTA), photovoltaic response, space‐charge‐limited current transport, impedance spectroscopy, grazing incidence wide angle X‐ray scattering, and density functional theory level computation. ITN‐F4 and ITzN‐F4 are found to provide power conversion efficiencies greater and internal reorganization energies less than their non‐π‐extended and nonfluorinated counterparts when paired with PBDB‐TF. Additionally, ITN‐F4 and ITzN‐F4 exhibit favorable bulk‐heterojunction relevant single crystal packing architectures. fsTA reveals that both ITN‐F4 and ITzN‐F4 undergo ultrafast hole transfer (<300 fs) in films with PBDB‐TF, despite excimer state formation in both the neat and blend films. Taken together and in comparison to related structures, these results demonstrate that combined fluorination and π‐extension synergistically promote crystallographic π‐face‐to‐face packing, increase crystallinity, reduce internal reorganization energies, increase interplanar π–π electronic coupling, and increase power conversion efficiency. [ABSTRACT FROM AUTHOR]

Photonic crystals have been widely studied due to their broad technological applications in lasers, sensors, optical telecommunications, and display devices. Typically, photonic crystals are periodic structures of touching dielectric materials with alternating high and low refractive indices, and to date, the variables of interest have focused primarily on crystal symmetry and the refractive indices of the constituent materials, primarily polymers and semiconductors. In contrast, finite difference time domain (FDTD) simulations suggest that plasmonic nanoparticle superlattices with spacer groups offer an alternative route to photonic crystals due to the controllable spacing of the nanoparticles and the high refractive index of the lattices, even far away from the plasmon frequency where losses are low. Herein, the stopband features of 13 Bravais lattices are characterized and compared, resulting in paradigm-shifting design principles for photonic crystals. Based on these design rules, a simple cubic structure with an ~130-nm lattice parameter is predicted to have a broad photonic stopband, a property confirmed by synthesizing the structure via DNA programmable assembly and characterizing it by reflectance measurements. We show through simulation that a maximum reflectance of more than 0.99 can be achieved in these plasmonic photonic crystals by optimizing the nanoparticle composition and structural parameters. [ABSTRACT FROM AUTHOR]

The physical properties of matter rely fundamentally on the symmetry of constituent building blocks. This is particularly true for structures that interact with light via the collective motion of their conduction electrons (i.e., plasmonic materials), where the observation of exotic optical effects, such as negative refraction and electromagnetically induced transparency, require the coupling of modes that are only present in systems with nontrivial broken symmetries. Lithography has been the predominant fabrication technique for constructing plasmonic metamaterials, as it can be used to form patterns of arbitrary complexity, including those with broken symmetry. Here, we show that low-symmetry, one-dimensional plasmonic structures that would be challenging to make using traditional lithographic techniques can be assembled using DNA as a programmable surface ligand. We investigate the optical properties that arise as a result of systematic symmetry breaking and demonstrate the appearance of π-type coupled modes formed from both dipole and quadrupole nanoparticle sources. These results demonstrate the power of DNA assembly for generating unusual structures that exhibit both fundamentally insightful and technologically important optical properties. [ABSTRACT FROM AUTHOR]

With the abundant variety and increasing chemical complexity of conjugated polymers proliferating the field of organic semiconductors, it has become increasingly important to correlate the polymer molecular structure with its mesoscale conformational and morphological attributes. For instance, it is unknown which combinations of chemical moieties and periodicities predictably produce mesoscale ordering. Interestingly, not all ordered morphologies result in efficient devices. In this work we have parametrized accurate classical force-fields and used these to compute the conformational and aggregation characteristics of single strands of common conjugated polymers. Molecular dynamics trajectories are shown to reproduce experimentally observed polymeric ordering, concluding that efficient organic photovoltaic devices span a range of polymer conformational classes, and suggesting that the solution-phase morphologies have far-reaching effects. Encouragingly, these simulations indicate that despite the wide-range of conformational classes present in successful devices, local molecular ordering, and not long-range crystallinity, appears to be the necessary requirement for efficient devices. Finally, we examine what makes a "good" solvent for conjugated polymers, concluding that dispersive π-electron solvent-polymer interactions, and not the electrostatic potential of the backbone interacting with the solvent, are what primarily determine a polymer's solubility in a particular solvent, and consequently its morphological characteristics. [ABSTRACT FROM AUTHOR]

We investigate the self-assembly of crystals from reconfigurable colloidal building blocks. The building blocks possess the unique ability, inspired by recent experiments, to continuously alter their shape before, during, and after assembly. Using molecular simulations, we report the assembly of a reconfigurable degenerate crystal containing a fractionally filled kagome sublattice. We show that this degenerate crystal differs from, and assembles more easily than, its counterpart known for rigid dimers. We further report that the reconfigurable crystal has unique mechanical properties under shear strain compared to a crystal comprised of rigid building blocks. We find that even a small amount of reconfigurability in an assembly of otherwise rigid building blocks can greatly affect mechanical properties. [ABSTRACT FROM AUTHOR]

Two-dimensional covalent organic frameworks (COFs) are an emerging class of photocatalytic materials for solar energy conversion. In this work, we report a pair of structurally isomeric COFs with reversed imine bond directions, which leads to drastic differences in their physical properties, photophysical behaviors, and photocatalytic CO 2 reduction performance after incorporating a Re(bpy)(CO) 3 Cl molecular catalyst through bipyridyl units on the COF backbone (Re-COF). Using the combination of ultrafast spectroscopy and theory, we attributed these differences to the polarized nature of the imine bond that imparts a preferential direction to intramolecular charge transfer (ICT) upon photoexcitation, where the bipyridyl unit acts as an electron acceptor in the forward imine case (f-COF) and as an electron donor in the reverse imine case (r-COF). These interactions ultimately lead the Re-f-COF isomer to function as an efficient CO 2 reduction photocatalyst, while the Re-r-COF isomer shows minimal photocatalytic activity. These findings not only reveal the essential role linker chemistry plays in COF photophysical and photocatalytic properties but also offer a unique opportunity to design photosensitizers that can selectively direct charges.

The end-capping group (EG) is the essential electron-withdrawing component of nonfullerene acceptors (NFAs) in bulk heterojunction (BHJ) organic solar cells (OSCs). To systematically probe the impact of two frequent EG functionalization strategies, π-extension and halogenation, in A-DAD-A type NFAs, we synthesized and characterized four such NFAs: BT-BIC , LIC , L4F , and BO-L4F . To assess the relative importance of these strategies, we contrast these NFAs with the baseline acceptors, Y5 and Y6 . Up to 16.6% power conversion efficiency (PCE) in binary inverted OSCs with BT-BO - L4F combining π-extension and halogenation was achieved. When these two factors are combined, the effect on optical absorption is cumulative. Single-crystal π-π stacking distances are similar for the EG strategies of π-extension. Increasing the alkyl substituent length from BT-L4F to BT-BO-L4F significantly alters the packing motif and eliminates the EG core interactions of BT-L4F . Electronic structure computations reveal some of the largest NFA π-π electronic couplings observed to date, 103.8 meV in BT-L4F and 47.5 meV in BT-BO-L4F . Computed electronic reorganization energies, 132 and 133 meV for BT-L4F and BT-BO-L4F , respectively, are also lower than Y6 (150 meV). BHJ blends show preferential π-face-on orientation, and both fluorination and π-extension increase NFA crystallinity. Femto/nanosecond transient absorption spectroscopy (fs/nsTA) and integrated photocurrent device analysis (IPDA) indicate that π-extension modifies the phase separation to enhance film ordering and carrier mobility, while fluorination suppresses unimolecular recombination. This systematic study highlights the synergistic effects of NFA π-extension and fluorination in affording efficient OSCs and provides insights into designing next-generation materials.

The nanoassembly behavior of trivalent small molecule-DNA hybrids (SMDH 3 s) was investigated as a function of core geometry and supramolecular flexibility through a synergistic experimental-modeling study. While complementary SMDH 3 s possessing a highly flexible tetrahedral trivalent core primarily assemble into nanoscale caged dimers, the nanoassemblies of SMDH 3 comonomers with rigid pyramidal and trigonal cores yield fewer caged dimers and more large-oligomer networks. Specifically, the rigid pyramidal SMDH 3 comonomers tend to form smaller nanosized aggregates (dimers, tetramers, and hexamers) upon assembly, attributable to the small (<109°) branch-core-branch angle of the pyramidal core. In contrast, the more-rigid trigonal planar SMDH 3 comonomers have a larger (∼120°) branch-core-branch angle, which spaces their DNA arms farther apart, facilitating the formation of larger nanoassemblies (≥nonamers). The population distributions of these nanoassemblies were successfully captured by coarse-grained molecular dynamics (CGMD) simulations over a broad range of DNA concentrations. CGMD simulations can also forecast the effect of incorporating T n spacer units between the hydridizing DNA arms and the rigid organic cores to increase the overall flexibility of the SMDH 3 comonomers. Such "decoupling" of the DNA arms from the organic core was found to result in preferential formation of nanoscale dimers up to an optimal spacer length, beyond which network formation takes over due to entropic factors. This excellent agreement between the simulation and experimental results confirms the versatility of the CGMD model as a useful and reliable tool for elucidating the nanoassembly of SMDH-based building blocks.

The design of materials needed for the storage, delivery, and conversion of (re)useable energy is still hindered by the lack of new, hierarchical molecular screening methodologies that encode information on more than one length scale. Using a molecular network theory as a foundation, we show that to describe charge transport in disordered materials the network methodology must be scaled-up. We detail the scale-up through the use of adjacency lists and depth first search algorithms for during operations on the adjacency matrix. We consider two types of electronic acceptors, perylenediimide (PDI) and the fullerene derivative phenyl-C61-butyric acid methyl ester (PCBM), and we demonstrate that the method is scalable to length scales relevant to grain boundary and trap formations. Such boundaries lead to a decrease in the percolation ratio of PDI with system size, while the ratio for PCBM remains constant, further quantifying the stable, diverse transport pathways of PCBM and its success as a charge-accepting material.

The hybridization of free oligonucleotides to densely packed, oriented arrays of DNA modifying the surfaces of spherical nucleic acid (SNA)-gold nanoparticle conjugates occurs with negative cooperativity; i.e., each binding event destabilizes subsequent binding events. DNA hybridization is thus an ever-changing function of the number of strands already hybridized to the particle. Thermodynamic quantification of this behavior reveals a 3 orders of magnitude decrease in the binding constant for the capture of a free oligonucleotide by an SNA conjugate as the fraction of pre-hybridized strands increases from 0 to ∼30%. Increasing the number of pre-hybridized strands imparts an increasing enthalpic penalty to hybridization that makes binding more difficult, while simultaneously decreasing the entropic penalty to hybridization, which makes binding more favorable. Hybridization of free DNA to an SNA is thus governed by both an electrostatic barrier as the SNA accumulates charge with additional binding events and an effect consistent with allostery, where hybridization at certain sites on an SNA modify the binding affinity at a distal site through conformational changes to the remaining single strands. Leveraging these insights allows for the design of conjugates that hybridize free strands with significantly higher efficiencies, some of which approach 100%.

Herein, we report the synthesis of structurally uniform gold circular disks as two-dimensional plasmonic nanostructures that complement the well-established one-dimensional rod and three-dimensional shell structures. We show that a Au conproportionation reaction can be used to etch a collection of nonuniform triangular prisms into a uniform circular disk product with thickness and diameter varying <10%. These new particles have broadly tunable plasmon resonances (650-1000 nm) with narrow bandwidths (0.23-0.28 eV) and can be described as "effectively two-dimensional" plasmonic structures, as they do not support a significant transverse mode.

Spherical nucleic acid (SNA) nanostructures assemble into a large variety of well-defined crystalline superlattices via DNA-directed hybridization. Crystallities of SNA with various shapes emerge during the assembly process, which coalesce during coarsening, leading to polycrystalline materials. Here, we investigate the growth dynamics of SNAs into body-centered cubic superlattices and the coalescence of SNA aggregates using a colloidal model formulated from the competition of electrostatic core repulsions and localized DNA hybridization attractions. We find that the growth law of isolated SNA crystallities is well-described by the power law t(1/2), in agreement with experimental observations. At later times, coalescence slows the growth dynamics considerably and is dependent on the orientational mismatch (misorientation angle) of the coalescing crystallites. Molecular dynamics simulations show that the misorientation angle decreases continually during the coalescence, which is a signature of the grain rotation induced coalescence mechanism. This mechanism is followed by the coarsening of a "neck" that develops at the boundary between the coalescing crystallites. Remarkably, we find faster coalescence dynamics for larger SNAs compared to smaller SNAs due to their enhanced surface diffusion, which more effectively reduces curvature at the boundary of two superlattices. These findings provide fundamental insight into the relationship between nanoparticle surface chemistry and its crystallite growth and coalescence.