Unlocking the unfolded structure of ubiquitin: Combining time-resolved x-ray solution scattering and molecular dynamics to generate unfolded ensembles.

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.

Control over Charge Separation by Imine Structural Isomerization in Covalent Organic Frameworks with Implications on CO2 Photoreduction.

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 CO2 reduction performance after incorporating a Re(bpy)(CO)3Cl 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 CO2 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 Role of Transient Intermediate Structures in the Unfolding of the Trp-Cage Fast-Folding Protein: Generating Ensembles from Time-Resolved X-ray Solution Scattering with Genetic Algorithms.

The Trp-cage miniprotein is one of the smallest systems to exhibit a stable secondary structure and fast-folding dynamics, serving as an apt model system to study transient intermediates with both experimental and computational analyses. Previous spectroscopic characterizations that have been done on Trp-cage have inferred a single stable intermediate on a pathway from folded to unfolded basins. We aim to bridge the understanding of Trp-cage structural folding dynamics on microsecond-time scales, by utilizing time-resolved X-ray solution scattering to probe the temperature-induced unfolding pathway. Our results indicate the formation of a conformationally extended intermediate on the time scale of 1 µs, which undergoes complete unfolding within 5 µs. We further investigated the atomistic structural details of the unfolding pathway using a genetic algorithm to generate ensemble model fits to the scattering profiles. This analysis paves the way for direct benchmarking of theoretical models of protein folding ensembles produced with molecular dynamics simulations.

Controlling Aggregation-Induced Two-Photon Absorption Enhancement via Intermolecular Interactions.

Historically, two-photon absorption (2PA) cross sections reported in the literature have been derived from solution-phase measurements. However, such techniques fail to grasp the implications of how these cross sections can be impacted by varying degrees of aggregation or in the condensed phase as bulk solids or thin films. For a precise determination of how aggregation impacts 2PA at a molecular level, computational methods present themselves as ideal. Herein, a series of quadrupolar π-conjugated dyes were simulated by molecular dynamics (MD) in the gas phase and condensed phase. In the condensed phase, their intermolecular interactions and electronic coupling behavior were fully characterized, both quantitatively and qualitatively. Using quadratic-response time-dependent density functional theory, 2PA cross sections of structures derived from MD trajectories were calculated. Comparisons are made between gas-phase and condensed-phase results, and enhancement factors are defined to show how certain dyes may experience changes in their respective 2PA cross sections as a function of aggregation. It was found that these cross sections depend heavily on conformational locking in the condensed phase and relative stacking arrangements. J-aggregates were associated with enhanced 2PA and H-aggregates with quenched 2PA activity. However, in a highly disordered aggregate, the effects of these stacking arrangements are averaged out of the bulk result, and the effects of conformational locking dominate.

Impact of π-Conjugation Length on the Excited-State Dynamics of Star-Shaped Carbazole-π-Triazine Organic Chromophores.

Correlating star-shaped donor-bridge-acceptor (DBA) molecular structures with intramolecular charge transfer (ICT) and intersystem crossing (ISC) is essential to their application in photocatalysis, photovoltaics, and organic light-emitting diodes (OLEDs). In this work, we report a systematic photophysical study on a series of star-shaped triazine-phenylene-carbazole DBA molecules with 0, 1, and 2 bridging phenylene units (pTCT-0P, pTCT-1P, pTCT-2P). Using a combination of steady-state and time-resolved spectroscopy with time-dependent density functional theory (TDDFT), we find that the bridge length can strongly impact the structural conformation, ICT, and ISC. Global target analysis of the time-resolved spectroscopy reveals that pTCT-0P has the most favorable ISC rate of 1.96 × 10-4 ps-1, which is competitive with a singlet relaxation rate of 1.92 × 10-4 ps-1. TDDFT aligns with spectroscopic results within an order of magnitude, predicting an ISC rate of 2.1 × 10-5 ps-1 and revealing that the donor/acceptor orthogonalization concomitantly suppresses singlet exciton recombination and lowers the singlet-triplet energy gap. The new fundamental insights gained from this work will help design the next generation of star-shaped DBA-type molecules for photocatalytic and photoelectronic applications.

Regiospecific N-alkyl substitution tunes the molecular packing of high-performance non-fullerene acceptors.

The rapid development of non-fullerene acceptors (NFAs) with strong near-infrared absorption has led to remarkably enhanced short-circuit current density (Jsc) values in organic solar cells (OSCs). NFAs based on the benzotriazole (Bz) fused-ring π-core have great potential in delivering both high Jsc and decent open-circuit voltage values due to their strong intramolecular charge transfer with reasonably low energy loss. In this work, we have designed and synthesized a series of Bz-based NFAs, PN6SBO-4F, AN6SBO-4F and EHN6SEH-4F, via regiospecific N-alkyl engineering based on the high-performance NFA mBzS-4F that was reported previously. The molecular packing of mBzS-4F, AN6SBO-4F, and EHN6SEH-4F single crystals was analyzed using X-ray crystallography in order to provide a comprehensive understanding of the correlation between the molecular structure, the charge-transporting properties, and the solar cell performance. Compared with the typical honeycomb single-crystal structure of Y6 derivatives, these NFAs exhibit distinctly different molecular packing patterns. The strong interactions of terminal indanone groups in mBzS-4F and the J-aggregate-like packing in EHN6SEH-4F lead to the formation of ordered 3D networks in single-crystals with channels for efficient charge transport. Consequently, OSCs based on mBzS-4F and EHN6SEH-4F show efficient photon-to-current conversions, achieving the highest power conversion efficiency of 17.48% with a Jsc of 28.83 mA cm-2.

Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.

Proteins have been found to inhabit a diverse set of three-dimensional structures. The dynamics that govern protein interconversion between structures happen over a wide range of time scales─picoseconds to seconds. Our understanding of protein functions and dynamics is largely reliant upon our ability to elucidate physically populated structures. From an experimental structural characterization perspective, we are often limited to measuring the ensemble-averaged structure both in the steady-state and time-resolved regimes. Generating kinetic models and understanding protein structure-function relationships require atomistic knowledge of the populated states in the ensemble. In this Perspective, we present ensemble refinement methodologies that integrate time-resolved experimental signals with molecular dynamics models. We first discuss integration of experimental structural restraints to molecular models in disordered protein systems that adhere to the principle of maximum entropy for creating a complete set of ensemble structures. We then propose strategies to find kinetic pathways between the refined structures, using time-resolved inputs to guide molecular dynamics trajectories and the use of inference to generate tailored stimuli to prepare a desired ensemble of protein states.

Systematic Merging of Nonfullerene Acceptor π-Extension and Tetrafluorination Strategies Affords Polymer Solar Cells with >16% Efficiency.

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.

Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations.

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.

Crystallography, Morphology, Electronic Structure, and Transport in Non-Fullerene/Non-Indacenodithienothiophene Polymer:Y6 Solar Cells.

Emerging nonfullerene acceptors (NFAs) with crystalline domains enable high-performance bulk heterojunction (BHJ) solar cells. Thermal annealing is known to enhance the BHJ photoactive layer morphology and performance. However, the microscopic mechanism of annealing-induced performance enhancement is poorly understood in emerging NFAs, especially regarding competing factors. Here, optimized thermal annealing of model system PBDB-TF:Y6 (Y6 = 2,2'-((2Z,2'Z)-((12,13-bis(2-ethylhexyl)-3,9-diundecyl-12,13-dihydro-[1,2,5]thiadiazolo[3,4-e]thieno[2″,3'':4',5']thieno[2',3':4,5]pyrrolo[3,2-g]thieno[2',3':4,5]-thieno[3,2-b]indole-2,10-diyl)bis(methanylylidene))bis(5,6-difluoro-3-oxo-2,3-dihydro-1H-indene-2,1-diylidene))dimalononitrile) decreases the open circuit voltage (VOC) but increases the short circuit current (JSC) and fill factor (FF) such that the resulting power conversion efficiency (PCE) increases from 14 to 15% in the ambient environment. Here we systematically investigate these thermal annealing effects through in-depth characterizations of carrier mobility, film morphology, charge photogeneration, and recombination using SCLC, GIXRD, AFM, XPS, NEXAFS, R-SoXS, TEM, STEM, fs/ns TA spectroscopy, 2DES, and impedance spectroscopy. Surprisingly, thermal annealing does not alter the film crystallinity, R-SoXS characteristic size scale, relative average phase purity, or TEM-imaged phase separation but rather facilitates Y6 migration to the BHJ film top surface, changes the PBDB-TF/Y6 vertical phase separation and intermixing, and reduces the bottom surface roughness. While these morphology changes increase bimolecular recombination (BR) and lower the free charge (FC) yield, they also increase the average electron and hole mobility by at least 2-fold. Importantly, the increased µh dominates and underlies the increased FF and PCE. Single-crystal X-ray diffraction reveals that Y6 molecules cofacially pack via their end groups/cores, with the shortest π-π distance as close as 3.34 Å, clarifying out-of-plane π-face-on molecular orientation in the nanocrystalline BHJ domains. DFT analysis of Y6 crystals reveals hole/electron reorganization energies of as low as 160/150 meV, large intermolecular electronic coupling integrals of 12.1-37.9 meV rationalizing the 3D electron transport, and relatively high µe of 10-4 cm2 V-1 s-1. Taken together, this work clarifies the richness of thermal annealing effects in high-efficiency NFA solar cells and tasks for future materials design.

Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data.

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.

Building Blocks for High-Efficiency Organic Photovoltaics: Interplay of Molecular, Crystal, and Electronic Properties in Post-Fullerene ITIC Ensembles.

Accurate single-crystal X-ray diffraction data offer a unique opportunity to compare and contrast the atomistic details of bulk heterojunction photovoltaic small-molecule acceptor structure and packing, as well as provide an essential starting point for computational electronic structure and charge transport analysis. Herein, we report diffraction-derived crystal structures and computational analyses on the n-type semiconductors which enable some of the highest efficiency organic solar cells produced to date, 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone))-5,5,11,11-tetrakis(4-hexylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (ITIC) and seven derivatives (including three new crystal structures: 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone))-5,5,11,11-tetrakis(4-propylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (ITIC-C3), 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone))-5,5,11,11-tetrakis(3-hexylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (m-ITIC-C6), and 3,9-bis(2-methylene-((3-(1,1-dicyanomethylene)-6,7-difluoro)-indanone))-5,5,11,11-tetrakis(4-butylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (ITIC-C4-4F). IDTT acceptors typically pack in a face-to-face fashion with π-π distances ranging from 3.28-3.95 Å. Additionally, edge-to-face packing is observed with S⋯π interactions as short as 3.21-3.24 Å. Moreover, ITIC end group identities and side chain substituents influence the nature and strength of noncovalent interactions (e. g. H-bonding, π-π) and thus correlate with the observed packing motif, electronic structure, and charge transport properties of the crystals. Density functional theory (DFT) calculations reveal relatively large nearest-neighbor intermolecular π-π electronic couplings (5.85-56.8 meV) and correlate the nature of the band structure with the dispersion interactions in the single crystals and core-end group polarization effects. Overall, this combined experimental and theoretical work reveals key insights into crystal engineering strategies for indacenodithienothiophene (IDTT) acceptors, as well as general design rules for high-efficiency post-fullerene small molecule acceptors.

Photovoltaic Blend Microstructure for High Efficiency Post-Fullerene Solar Cells. To Tilt or Not To Tilt?

Achieving efficient polymer solar cells (PSCs) requires a structurally optimal donor-acceptor heterojunction morphology. Here we report the combined experimental and theoretical characterization of a benzodithiophene-benzothiadiazole donor polymer series (PBTZF4-R; R = alkyl substituent) blended with the non-fullerene acceptor ITIC-Th and analyze the effects of substituent dimensions on blend morphology, charge transport, carrier dynamics, and PSC metrics. Varying substituent dimensions has a pronounced effect on the blend morphology with a direct link between domain purity, to some extent domain dimensions, and charge generation and collection. The polymer with the smallest alkyl substituent yields the highest PSC power conversion efficiency (PCE, 11%), reflecting relatively small, high-purity domains and possibly benefiting from "matched" donor polymer-small molecule acceptor orientations. The distinctive morphologies arising from the substituents are investigated using molecular dynamics (MD) simulations which reveal that substituent dimensions dictate a well-defined set of polymer conformations, in turn driving chain aggregation and, ultimately, the various film morphologies and mixing with acceptor small molecules. A straightforward energetic parameter explains the experimental polymer domain morphological trends, hence PCE, and suggests strategies for substituent selection to optimize PSC materials morphologies.

Closely packed, low reorganization energy π-extended postfullerene acceptors for efficient polymer solar cells.

New organic semiconductors are essential for developing inexpensive, high-efficiency, solution-processable polymer solar cells (PSCs). PSC photoactive layers are typically fabricated by film-casting a donor polymer and a fullerene acceptor blend, with ensuing solvent evaporation and phase separation creating discrete conduits for photogenerated holes and electrons. Until recently, n-type fullerene acceptors dominated the PSC literature; however, indacenodithienothiophene (IDTT)-based acceptors have recently enabled remarkable PSC performance metrics, for reasons that are not entirely obvious. We report two isomeric IDTT-based acceptors 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-benz-(5, 6)indanone))-5,5,11,11-tetrakis(4-nonylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']di-thiophene (ITN-C9) and 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-benz(6,7)indanone))-5,5,11,11-tetrakis(4-nonylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (ITzN-C9) that shed light on the exceptional IDTT properties vis-à-vis fullerenes. The neat acceptors and blends with fluoropolymer donor poly{[4,8-bis[5-(2- ethylhexyl)-4-fluoro-2-thienyl]benzo[1,2-b:4,5-b']dithiophene2,6-diyl]-alt-[2,5-thiophenediyl[5,7-bis(2-ethylhexyl)-4,8-dioxo4H,8H-benzo[1,2-c:4,5-c']dithiophene-1,3-diyl]]} (PBDB-TF) are investigated by optical spectroscopy, cyclic voltammetry, thermogravimetric analysis, differential scanning calorimetry, single-crystal X-ray diffraction, photovoltaic response, space-charge-limited current transport, atomic force microscopy, grazing incidence wide-angle X-ray scattering, and density functional theory-level quantum chemical analysis. The data reveal that ITN-C9 and ITzN-C9 organize such that the lowest unoccupied molecular orbital-rich end groups have intermolecular π-π distances as close as 3.31(1) Å, with electronic coupling integrals as large as 38 meV, and internal reorganization energies as small as 0.133 eV, comparable to or superior to those in fullerenes. ITN-C9 and ITzN-C9 have broad solar-relevant optical absorption, and, when blended with PBDB-TF, afford devices with power conversion efficiencies near 10%. Performance differences between ITN-C9 and ITzN-C9 are understandable in terms of molecular and electronic structure distinctions via the influences on molecular packing and orientation with respect to the electrode.

Design principles for photonic crystals based on plasmonic nanoparticle superlattices.

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.

The competing effects of core rigidity and linker flexibility in the nanoassembly of trivalent small molecule-DNA hybrids (SMDH3s)-a synergistic experimental-modeling study.

The nanoassembly behavior of trivalent small molecule-DNA hybrids (SMDH3s) was investigated as a function of core geometry and supramolecular flexibility through a synergistic experimental-modeling study. While complementary SMDH3s possessing a highly flexible tetrahedral trivalent core primarily assemble into nanoscale caged dimers, the nanoassemblies of SMDH3 comonomers with rigid pyramidal and trigonal cores yield fewer caged dimers and more large-oligomer networks. Specifically, the rigid pyramidal SMDH3 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 SMDH3 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 Tn spacer units between the hydridizing DNA arms and the rigid organic cores to increase the overall flexibility of the SMDH3 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.

Deterministic Symmetry Breaking of Plasmonic Nanostructures Enabled by DNA-Programmable Assembly.

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.

Improved Scaling of Molecular Network Calculations: The Emergence of Molecular Domains.

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.

A n-vector model for charge transport in molecular semiconductors.

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 topology-dependent 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.

Design Considerations for RNA Spherical Nucleic Acids (SNAs).

Ribonucleic acids (RNAs) are key components in many cellular processes such as cell division, differentiation, growth, aging, and death. RNA spherical nucleic acids (RNA-SNAs), which consist of dense shells of double-stranded RNA on nanoparticle surfaces, are powerful and promising therapeutic modalities because they confer advantages over linear RNA such as high cellular uptake and enhanced stability. Due to their three-dimensional shell of oligonucleotides, SNAs, in comparison to linear nucleic acids, interact with the biological environment in unique ways. Herein, the modularity of the RNA-SNA is used to systematically study structure-function relationships in order to understand how the oligonucleotide shell affects interactions with a specific type of biological environment, namely, one that contains serum nucleases. We use a combination of experiment and theory to determine the key architectural properties (i.e., sequence, density, spacer moiety, and backfill molecule) that affect how RNA-SNAs interact with serum nucleases. These data establish a set of design parameters for SNA architectures that are optimized in terms of stability.