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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.

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]

Several molecular simulations of different computational models are conducted to explain the mechanisms involved in the disease and nondisease protein aggregation. The aggregation mechanisms of different proteins are shown to be dependent on the protein sequence, concentration and solution conditions of the system.

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]