Emergence of a Low-Energy Peak in the Smoothed Absolute Value Circular Dichroism Spectra of Small Helical Gold Nanorods.

We calculate, using time-dependent density functional theory, absorption and circular dichroism (CD) spectra for a series of small helical gold nanorod structures with a width of 0.6 nm and length increasing from 0.7 nm for Au24 to 1.9 nm for Au56. For a low-energy window, ranging from 1.7 to 4.1 eV, broadening the lines in the absorption spectra results in a low energy peak which previous studies have identified as the (localized) plasmon resonance. As expected, the absorption peak position of the plasmon resonance systematically redshifts as the length of the nanorod increases. However, trends in the CD and straightforwardly broadened CD spectra are more difficult to discern. We introduce the idea of an absolute value CD spectrum and show that broadening the lines results in a low energy peak that has not previously been reported. The peak position systematically redshifts as the length of the nanorod increases but over a significantly smaller range than that for the absorption spectrum.

Cavity Quantum Electrodynamics Complete Active Space Configuration Interaction Theory.

Polariton chemistry has attracted great attention as a potential route to modify chemical structure, properties, and reactivity through strong interactions among molecular electronic, vibrational, or rovibrational degrees of freedom. A rigorous theoretical treatment of molecular polaritons requires the treatment of matter and photon degrees of freedom on equal quantum mechanical footing. In the limit of molecular electronic strong or ultrastrong coupling to one or a few molecules, it is desirable to treat the molecular electronic degrees of freedom using the tools of ab initio quantum chemistry, yielding an approach we refer to as ab initio cavity quantum electrodynamics, where the photon degrees of freedom are treated at the level of cavity quantum electrodynamics. Here, we present an approach called Cavity Quantum Electrodynamics Complete Active Space Configuration Interaction theory to provide ground- and excited-state polaritonic surfaces with a balanced description of strong correlation effects among electronic and photonic degrees of freedom. This method provides a platform for ab initio cavity quantum electrodynamics when both strong electron correlation and strong light-matter coupling are important and is an important step toward computational approaches that yield multiple polaritonic potential energy surfaces and couplings that can be leveraged for ab initio molecular dynamics simulations of polariton chemistry.

Correlating structure and photophysical properties in thiazolo[5,4-d]thiazole crystal derivatives for use in solid-state photonic and fluorescence-based optical devices.

There is a growing demand for new fluorescent small molecule dyes for solid state applications in the photonics and optoelectronics industry. Thiazolo[5,4-d]thiazole (TTz) is an organic heterocycle moiety which has previously shown remarkable properties as a conjugated polymer and in solution-based studies. For TTz-based small molecules to be incorporated in solid-state fluorescence-based optical devices, a thorough elucidation of their structure-photophysical properties needs to be established. Herein, we have studied four TTz-based materials functionalized with alkyl appendages of varying carbon chain lengths. We report the single crystal structures of the TTz derivatives, three of which were previously unknown. The packing modes of the crystals reveal that molecular arrangements are largely governed by a chorus of synergistic intermolecular non-covalent interactions. Three crystals packed in herringbone mode and one crystal packed in slipped stacks proving that alkyl appendages modulate structural organization in TTz-based materials. Steady state and time-resolved photophysical properties of these crystals were studied via diffuse-reflectance, micro-Raman, and photoluminescence spectroscopy. The crystals fluoresce from orange-red to blue spanning through the whole gamut of the visible spectrum. We have established that photophysical properties are a function of crystal packing in symmetrically substituted TTz-based materials. This correlation was then utilized to fabricate crystalline blends. We demonstrate, for the first time, that symmetrically substituted donor-acceptor-donor TTz-based materials can be used for phosphor-converted color-tuning and white-light emission. Given the cost effectiveness, ease of synthesis and now a structure-photophysics correlation, we present a compelling case for the adoption of TTz-based materials in solid-state photonic and fluorescence-based optical devices.

Non-Hermitian cavity quantum electrodynamics-configuration interaction singles approach for polaritonic structure with ab initio molecular Hamiltonians.

We combine ab initio molecular electronic Hamiltonians with a cavity quantum electrodynamics model for dissipative photonic modes and apply mean-field theories to the ground- and excited-states of resulting polaritonic systems. In particular, we develop a non-Hermitian configuration interaction singles theory for mean-field ground- and excited-states of the molecular system strongly interacting with a photonic mode and apply these methods to elucidating the phenomenology of paradigmatic polaritonic systems. We leverage the Psi4Numpy framework to yield open-source and accessible reference implementations of these methods.

Dielectric Screening Modulates Semiconductor Nanoplatelet Excitons.

The influence of external dielectric environments is well understood for 2D semiconductor materials but overlooked for colloidally grown II-VI nanoplatelets (NPLs). In this work, we synthesize MX (M = Cd, Hg; X = Se, Te) NPLs of varying thicknesses and apply the Elliott model to extract exciton binding energies-reporting values in good agreement with prior methods and extending to less studied cadmium telluride and mercury chalcogenide NPLs. We find that the exciton binding energy is modulated both by the relative effect of internal vs external dielectric and by the thickness of the semiconductor material. An analytical model shows dielectric screening increases the exciton binding energy relative to the bulk by distorting the Coulombic potential across the NPL surface. We further confirm this effect by decreasing and recovering the exciton binding energy of HgTe NPLs through washing in polarizable solvents. Our results illustrate NPLs are colloidal analogues of van der Waals 2D semiconductors and point to surface modification as an approach to control photophysics and device properties.

Role of Cavity Losses on Nonadiabatic Couplings and Dynamics in Polaritonic Chemistry.

We present a non-Hermitian formulation of the polaritonic structure of azobenzene strongly coupled to a photonic mode that explicitly accounts for the fleeting nature of the photon-molecule interaction. This formalism reveals that the polaritonic nonadiabatic couplings that facilitate cis-trans isomerization can be dramatically modified by photonic dissipation. We perform Fewest-Switches Surface Hopping dynamics on the surfaces that derive from our non-Hermitian formalism and find that the polaritonic isomerization yields are strongly suppressed for moderate dissipation rates and that cavity-free isomerization dynamics are recovered under large dissipation rates. These findings highlight the important role that the finite lifetime of photonic degrees of freedom play in polaritonic chemistry.

High-Temperature Selective Emitter Design and Materials: Titanium Aluminum Nitride Alloys for Thermophotovoltaics.

The efficiency of a thermophotovoltaic (TPV) system depends critically upon the spectral selectivity and stability of an emitter, which may operate most effectively at temperatures in excess of 1000 °C. We computationally design and experimentally demonstrate a novel selective emitter design based on multilayer nanostructures, robust to off-normal emission angles. A computational search of the material and temperature compatibility space of simple emitter designs motivates new material classes and identifies several promising multilayer nanostructure designs for both TPV absorber and emitter applications. One such structure, comprising a thin (<100 nm) tunable TixAl1-xN (TiAlN) absorber and refractory oxide Bragg reflector is grown on W metal foil. In agreement with simulations, the emitter achieves record spectral efficiency (43.4%) and power density (3.6 W/cm2) for an emitter with at least 1 h of high temperature (>800 °C) operation.

Functionally Related Genes Cluster into Genomic Regions That Coordinate Transcription at a Distance in Saccharomyces cerevisiae.

Balancing gene expression is a fundamental challenge of all cell types. To properly regulate transcription on a genome-wide level, there are myriad mechanisms employed by the cell. One layer to this regulation is through spatial positioning, with particular chromosomal loci exerting an influence on transcription throughout a region. Many coregulated gene families utilize spatial positioning to coordinate transcription, with functionally related genes clustering together which can allow coordinated expression via adjacent gene coregulation. The mechanisms underlying this process have not been elucidated, though there are many coregulated gene families that exhibit this genomic distribution. In the present study, we tested for a role for the enhancer-promoter (EP) hypothesis, which demonstrates that regulatory elements can exert transcriptional effects over a broad distance, in coordinating transcriptional coregulation using budding yeast, Saccharomyces cerevisiae We empirically validated the EP model, finding that the genomic distance a promoter can affect varies by locus, which can profoundly affect levels of transcription, phenotype, and the extent of transcriptional disruption throughout a genomic region. Using the nitrogen metabolism, ribosomal protein, toxin response, and heat shock gene families as our test case, we report functionally clustered genes localize to genomic loci that are more conducive to transcriptional regulation at a distance compared to the unpaired members of the same families. Furthermore, we report that the coregulation of functional clusters is dependent, in part, on chromatin maintenance and remodeling, providing one mechanism underlying adjacent gene coregulation.IMPORTANCE The two-dimensional, physical positioning of genes along a chromosome can impact proper transcriptional regulation throughout a genomic region. The transcription of neighboring genes is correlated in a genome-wide manner, which is a characteristic of eukaryotes. Many coregulated gene families can be found clustered with another member of the same set-which can result in adjacent gene coregulation of the pair. Due to the myriad gene families that exhibit a nonrandom genomic distribution, there are likely multiple mechanisms working in concert to properly regulate transcriptional coordination of functionally clustered genes. In this study, we utilized budding yeast in an attempt to elucidate mechanisms that underlie this coregulation: testing and empirically validating the enhancer-promoter hypothesis in this species and reporting that functionally related genes cluster to genomic regions that are more conducive to transcriptional regulation at a distance. These clusters rely, in part, on chromatin maintenance and remodelers to maintain proper transcriptional coordination. Our work provides insight into the mechanisms underlying adjacent gene coregulation.

Systematic Identification, Characterization, and Conservation of Adjacent-Gene Coregulation in the Budding Yeast Saccharomyces cerevisiae.

It is essential that cells orchestrate gene expression for the specific niche that they occupy, and this often requires coordination of the expression of large sets of genes. There are multiple regulatory systems that exist for modulation of gene expression, including the adjacent-gene coregulation of the rRNA and ribosome biogenesis and ribosomal protein families. Both gene families exhibit a nonrandom genomic distribution, often clustered directly adjacent to another member of the same family, which results in a tighter transcriptional coordination among adjacent paired genes than that of the unpaired genes within each regulon and can result in a shared promoter that coordinates expression of the pairs. This nonrandom genomic distribution has been seen in a few functionally related gene families, and many of these functional pairings are conserved across divergent fungal lineages. To date, the significance of these observations has not been extended in a systematic way to characterize how prevalent the role of adjacent-gene coregulation is in transcriptional regulation. In the present study, we systematically analyzed the transcriptional coherence of the functional pairs compared to the singletons within all gene families defined by the Gene Ontology Slim designation, using Saccharomyces cerevisiae as a model system, finding that clusters exhibit a tighter transcriptional correlation under specific contexts. We found that the longer a functional pairing is conserved the tighter its response to broad stress and nutritional responses, that roughly 25% of gene families exhibit a nonrandom genomic distribution, and that many of these clusters are conserved. This suggests that adjacent-gene coregulation is a widespread, yet underappreciated, transcriptional mechanism.IMPORTANCE The spatial positioning of genes throughout the genome arrangement can alter their expression in many eukaryotic organisms. Often this results in a genomic context-specific effect on transcription. One example of this is through the clustering of functionally related genes, which results in adjacent-gene coregulation in the budding yeast Saccharomyces cerevisiae In the present study, we set out to systematically characterize the prevalence of this phenomenon, finding the genomic organization of functionally related genes into clusters is a characteristic of myriad gene families. These arrangements are found in many evolutionarily divergent fungi and thus represent a widespread, yet underappreciated, layer of transcriptional regulation.

Design of emitter structures based on resonant perfect absorption for thermophotovoltaic applications.

We report a class of thermophotovoltaic emitter structures built upon planar films that support resonant modes, known as perfectly-absorbing modes, that facilitate an exceptional optical response for selective emission. These planar structures have several key advantages over previously-proposed designs for TPV applications: they are simple to fabricate, are stable across a range of temperatures and conditions, and are capable of achieving some of the highest spectral efficiencies reported of any class of emitter structure. Utilization of these emitters leads to exceptionally high device efficiencies under low operating temperature conditions, which should open new opportunities for waste heat management. We present a theoretical framework for understanding this performance, and show that this framework can be leveraged as a search algorithm for promising candidate structures. In addition to providing an efficient theoretical methodology for identifying high-performance emitter structures, our methodology provides new insight into underlying design principles and should pave way for future design of structures that are simple to fabricate, temperature stable, and possess exceptional optical properties.

Reversible Modulation of Surface Plasmons in Gold Nanoparticles Enabled by Surface Redox Chemistry.

Switchable surface redox chemistry is demonstrated in gold@iron/iron oxide core-shell nanoparticles with ambient oxidation and plasmon-mediated reduction to modulate the oxidation state of shell layers. The iron shell can be oxidized to iron oxide through ambient oxidation, leading to an enhancement and red-shift of the gold surface plasmon resonance (SPR). This enhanced gold SPR can drive reduction of the iron oxide shell under broadband illumination to reversibly blue-shift and significantly dampen gold SPR absorption. The observed phenomena provide a unique mechanism for controlling the plasmonic properties and surface chemistry of small metal nanoparticles.

Interfaced metal heterodimers in the quantum size regime.

Synthesis of nanoparticle dimers made of asymmetric compositions is very challenging because of the difficulty in manipulating the nanoparticles' surface chemistries in order to control the assembly and/or growth of different nanoparticles. In this Letter, we report a seed-mediated, surface-confined epitaxial overgrowth strategy that enables the synthesis of high-quality interfaced Au-Ag heterodimers in the quantum size regime (diameters <10 nm). Au and Ag share a common face-centered cubic lattice and have nearly identical lattice constants, which facilitates epitaxial overgrowth and allows direct contact between the Au and Ag domains. Quantum size effects, formation of the Au/Ag interfaces, and chemical interactions with surfactant molecules strongly influence the optical properties of the dimers and lead to the observation of unique surface plasmon resonances. In particular, we find an unusual enhancement of the characteristic Au surface plasmon resonance and the emergence of a charge transfer plasmon across the Au/Ag domains, which together lead to broad-band absorption spanning visible to near-infrared wavelengths. A model that captures the changes in optical behavior due to chemical interactions and quantum size effects is used to calculate the absorption spectra of the interfaced heterodimers, resulting in good agreement with experimental measurements.

Cage versus prism: electronic energies of the water hexamer.

Recent experiments show that the cage isomer of the water hexamer is lower in energy than the prism isomer near 0 K, and yet state-of-the-art electronic structure calculations predict the prism to be lower in energy than the cage at 0 K. Here, we study the relative energies of the water hexamers from the parametric two-electron reduced density matrix (2-RDM) method in which the 2-RDM rather than the wave function is the basic variable of the calculations. In agreement with experiment and in contrast with traditional wave function methods, the 2-RDM calculations predict the cage to be more stable than the prism after vibrational zero-point correction. Multiple configurations from the hydrogen bonding are captured by the method. More generally, the results are consistent with our previous 2-RDM applications in that they reveal how multireference correlation in molecular systems is important for resolving small energy differences from hydrogen bonding as well as other types of intermolecular forces, even in systems that are not conventionally considered strongly correlated.

Strongly correlated mechanisms of a photoexcited radical reaction from the anti-Hermitian contracted Schrödinger equation.

Photoexcited radical reactions are critical to processes in both nature and materials, and yet they can be challenging for electronic structure methods due to the presence of strong electron correlation. Reduced-density-matrix (RDM) methods, based on solving the anti-Hermitian contracted Schrödinger equation (ACSE) for the two-electron RDM (2-RDM), are examined for studying the strongly correlated mechanisms of these reactions with application to the electrocyclic interconversion of allyl and cyclopropyl radicals. We combine recent extensions of the ACSE to excited states [G. Gidofalvi and D. A. Mazziotti, Phys. Rev. A 80, 022507 (2009)] and arbitrary spin states [A. E. Rothman, J. J. Foley IV, and D. A. Mazziotti, Phys. Rev. A 80, 052508 (2009)]. The ACSE predicts that the ground-state ring closure of the allyl radical has a high 52.5 kcal/mol activation energy that is consistent with experimental data, while the closure of an excited allyl radical can occur by disrotatory and conrotatory pathways whose transition states are essentially barrierless. Comparisons are made with multireference second- and third-order perturbation theories and multireference configuration interaction. While predicted energy differences do not vary greatly between methods, the ACSE appears to improve these differences when they involve a strongly and a weakly correlated radical by capturing a greater share of single-reference correlation that increases the stability of the weakly correlated radicals. For example, the ACSE predicts a -39.6 kcal/mol conversion of the excited allyl radical to the ground-state cyclopropyl radical in comparison to the -32.6 to -37.3 kcal/mol conversions predicted by multireference methods. In addition, the ACSE reduces the computational scaling with the number of strongly correlated orbitals from exponential (traditional multireference methods) to quadratic. Computed ground- and excited-state 2-RDMs are nearly N-representable.

Conical intersections in triplet excited states of methylene from the anti-Hermitian contracted Schrödinger equation.

A conical intersection in triplet excited states of methylene is computed through the direct calculation of two-electron reduced density matrices (2-RDMs) from solutions of the anti-Hermitian contracted Schrodinger equation (ACSE). The study synthesizes recent extensions of the ACSE method for the treatment of excited states [G. Gidofalvi and D. A. Mazziotti, Phys. Rev. A 80, 022507 (2009)] and arbitrary-spin states [A. E. Rothman, J. J. Foley, and D. A. Mazziotti, Phys. Rev. A 80, 052508 (2009)]. We compute absolute energies of the 1 (3)B(1), 1 (3)A(2), and 2 (3)B(1) states of methylene (CH(2)) and the location of the conical intersection along the 1 (3)A(2)-2 (3)B(1) potential-energy surfaces. To treat multireference correlation, we seed the ACSE with an initial 2-RDM from a multiconfiguration self-consistent field (MCSCF) calculation. The ACSE produces energies that significantly improve upon those from MCSCF and second-order multireference many-body perturbation theory, and the 2-RDMs from the ACSE nearly satisfy necessary N-representability conditions. Comparison of the results from augmented double-zeta and triple-zeta basis sets demonstrates the importance of augmented (or diffuse) functions for determining the location of the conical intersection.

Activation energies of sigmatropic shifts in propene and acetone enolate from the anti-Hermitian contracted Schrödinger equation.

The hydrogen [1,3]-sigmatropic shift in propene is predicted by the Woodward-Hoffman rules to occur by an antarafacial pathway, yet the lack of experimental evidence suggests that this pathway is not favorable. Two natural questions arise: (i) can the [1,3]-shift be made more favorable by a symmetry-forbidden multistep pathway, and (ii) can the energetics be influenced by a substituent on propene? As in many chemical reactions, describing the energetics of these reactions requires a balanced treatment of both single-reference and multireference electron correlations, and yet traditional wave function methods often excel in treating only one kind of correlation. An equitable description of correlation effects, however, can be achieved, at a cost similar to efficient single-reference methods, by computing the two-electron reduced density matrix (2-RDM) from the anti-Hermitian part of the contracted Schrödinger equation (ACSE) [D. A. Mazziotti, Phys. Rev. Lett. 97, 143002 (2006)]. As with the contracted Schrödinger equation, the indeterminacy of the ACSE is removed without the many-electron wave function by reconstructing the 3-RDM from the 2-RDM via cumulant theory [D. A. Mazziotti, Chem. Phys. Lett. 289, 419 (1998)]. In this paper we apply the ACSE to study sigmatropic shifts in both propene and acetone enolate while extending its formalism to treat doublet spin states. In the 6-311G(**) basis set the ACSE predicts the activation energy of the trimethylene-to-propene rearrangement to be 8.8 kcal/mol while multireference perturbation theory yields a smaller barrier of 2.2 kcal/mol and coupled cluster singles-doubles predicts a negative barrier. We further find that the [1,3]-shift in acetone enolate is more favorable by approximately 30 kcal/mol than the [1,3]-shift in propene, which is consistent with a prior theoretical investigation as well as experimental observations of these shifts in 2-butanone enolate.