The color of fruits in photographs and still life paintings.

Still life paintings comprise a wealth of data on visual perception. Prior work has shown that the color statistics of objects show a marked bias for warm colors. Here, we ask about the relative chromatic contrast of these object-associated colors compared with background colors in still life paintings. We reasoned that, owing to the memory color effect, where the color of familiar objects is perceived more saturated, warm colors will be relatively more saturated than cool colors in still life paintings as compared with photographs. We analyzed color in 108 slides of still life paintings of fruit from the teaching slide collection of the Fogg University Art Museum and 41 color-calibrated photographs of fruit from the McGill data set. The results show that the relatively higher chromatic contrast of warm colors was greater for paintings compared with photographs, consistent with the hypothesis.

A Green's Function Approach for Determining Surface Induced Broadening and Shifting of Molecular Energy Levels.

Upon adsorption of a molecule onto a surface, the molecular energy levels (MELs) broaden and change their alignment. This phenomenon directly affects electron transfer across the interface and is, therefore, a fundamental observable that influences electrochemical device performance. Here, we propose a rigorous parameter-free framework, built upon the theoretical construct of Green's functions, for studying the interface between a molecule and a bulk surface and its effect on MELs. The method extends beyond the usual wide-band limit approximation, and its generality allows its use with any level of electronic structure theory. We demonstrate its ability to predict the broadening and shifting of MELs as a function of intramolecular coupling, molecule/surface coupling, and the surface density of states for a molecule with two MELs adsorbed on a one-dimensional model metal surface. The new approach could help provide guidelines for the design and experimental characterization of electrochemical devices with optimal electron transport.

Macrocycle ring deformation as the secondary design principle for light-harvesting complexes.

Natural light-harvesting is performed by pigment-protein complexes, which collect and funnel the solar energy at the start of photosynthesis. The identity and arrangement of pigments largely define the absorption spectrum of the antenna complex, which is further regulated by a palette of structural factors. Small alterations are induced by pigment-protein interactions. In light-harvesting systems 2 and 3 from Rhodoblastus acidophilus, the pigments are arranged identically, yet the former has an absorption peak at 850 nm that is blue-shifted to 820 nm in the latter. While the shift has previously been attributed to the removal of hydrogen bonds, which brings changes in the acetyl moiety of the bacteriochlorophyll, recent work has shown that other mechanisms are also present. Using computational and modeling tools on the corresponding crystal structures, we reach a different conclusion: The most critical factor for the shift is the curvature of the macrocycle ring. The bending of the planar part of the pigment is identified as the second-most important design principle for the function of pigment-protein complexes-a finding that can inspire the design of novel artificial systems.

Spectral shifts of BODIPY derivatives: a simple continuous model.

The BODIPY dyes are a versatile family of chromophores that have found use in fluorescence based bioimaging and other applications. The BODIPY core can be substituted in a vast number of ways, but the photophysical changes, such as shifts in absorption spectra, are not always immediately obvious from the molecular structure. We introduce a simple model that let you vary the electron withdrawing or electron donating character of each substituent continuously to get an overview of the landscape of possible spectral shifts. The features of substituted BODIPY cores are compared to the corresponding linear system, giving a new perspective on BODIPY photophysics. Using the model, we are able to rationalize the trend seen in a family of BODIPY, with chalcogen-containing substituents, as being due to a change in electronegativity.

Computational construction of the electronic Hamiltonian for photoinduced electron transfer and Redfield propagation.

The construction of open-system diabatic Hamiltonians relevant for investigation of electron transfer processes is a computational challenge. In this paper, we present how the full system Hamiltonian, as well as relevant system-bath coupling parameters can be computed from a purely computational starting point. We have investigated two methods for calculating electronic couplings, Generalized Mulliken Hush (GMH) and Fock Matrix Reconstruction (FMR). We apply these methods to calculate the couplings in a model molecular triad, thus constructing the system-Hamiltonian in a diabatic basis. The triad is constructed with a donor-antenna-acceptor type architecture, and a two-step photoinduced electron transfer is expected in this system. With the calculated electronic couplings in combination with Huang-Rhys type electron-phonon couplings, we are able to construct two open-system Hamiltonians from a computational bottom-up approach, where the phonon-reservoir is approximated as harmonic oscillators. Based on these Hamiltonians, two separate propagations of populations are performed using the Redfield formalism. Based on the dynamics, we observe small differences between the results from the GMH and FMR simulations. The overall picture is similar for the two methods. Thereby, we conclude that the FMR approach is suitable as an initial screening tool for identifying long-lived photoinduced charge separated states and that a GMH based Hamiltonian can then be constructed to scrutinize promising candidate molecules. Furthermore, either method can be used to construct all relevant operators needed for the Redfield tensor, without prior knowlegde from experimental data.

Q y and Q x Absorption Bands for Bacteriochlorophyll a Molecules from LH2 and LH3.

Light-harvesting systems 2 and 3 (LH2 and LH3) act as antennas for the initial light capture by photosynthetic purple bacteria, thus initiating the conversion of solar energy into chemical energy. The main absorbers are carotenoids and bacteriochlorophylls (BChls), which harvest different parts of the solar spectrum. The first two optical transitions in BChl produce the Q y and Q x absorption bands. The large size of BChl molecules has prevented accurate computational determination of the electronic structures for the relevant states, until we recently succeeded in obtaining the excitation energies and transition dipole moments of the first (Q y) transition for all BChls in LH2 and LH3 using multi-state multiconfigurational second-order perturbation theory calculations. In this work, we go one step further, compute the corresponding values for the Q x transition, in line with previous work [ J. Am. Chem. Soc . 2017 , 139 , 7558 - 7567 ], and compare and assess our data against excitation energies obtained through time-dependent density functional theory methods. Interestingly, we find that the two transitions respond differently to BChls' geometrical factors, such as the macrocycle ring curvature and the dihedral torsion of the acetyl moiety. These findings will aid the unraveling of structure-function relationships for absorption and energy transfer processes in purple bacteria, and once again this demonstrates the viability of multireference quantum chemical methods as computational tools for the photophysics of biomolecules.

Two-dimensional electronic spectroscopy of anharmonic molecular potentials.

Two-dimensional electronic spectroscopy (2DES) is a powerful tool in the study of coupled electron-phonon dynamics, yet very little is known about how nonlinearities in the electron-phonon coupling, arising from anharmonicities in the nuclear potentials, affect the spectra. These become especially relevant when the coupling is strong. From the linear spectroscopies, anharmonicities are known to give structure to the zero-phonon line and to break mirror-symmetry between absorption and emission, but the 2D analogues of these effects have not been identified. Using a simple two-level model where the electronic states are described by (displaced) harmonic oscillators with differing curvatures or displaced Morse oscillators, we find that the zero-phonon line shape is essentially transferred to the diagonal in 2DES spectra, and that anharmonicities break a horizontal mirror-symmetry in the infinite waiting time limit. We also identify anharmonic effects that are only present in 2DES spectra: twisting of cross-peaks stemming from stimulated emission signals; and oscillation period mismatch between ground state bleach and stimulated emission (for harmonic oscillators with differing curvatures), or inherently chaotic oscillations (for Morse oscillators). Our findings will facilitate an improved understanding of 2DES spectra and aid the interpretation of signals that are more realistic than those arising from simple models.

Conformationally controlled ultrafast intersystem crossing in bithiophene systems.

Bithiophenes serve as model systems for larger polythiophenes used in solar cell applications and molecular electronics. We report a study of ultrafast dynamics of two bithiophene systems measured with femtosecond time-resolved photoelectron spectroscopy, and show that their intersystem crossing takes place within the first few picoseconds after excitation, in line with previous studies. We show that the intersystem crossing rate can be explained in terms of arguments based on symmetry of the S1 minimum energy geometry, which depends on the specific conformation of bithiophene. Furthermore, this work shows that the minor cis-conformer contributes to an even higher intersystem crossing rate than the major trans conformer. The work presented here can provide guiding principles towards the design of solar cell components with even faster formation of long-lived excited states for solar energy harvesting.

Two-dimensional Fano lineshapes: Excited-state absorption contributions.

Fano interferences in nanostructures are influenced by dissipation effects as well as many-body interactions. Two-dimensional coherent spectroscopies have just begun to be applied to these systems where the spectroscopic signatures of a discrete-continuum structure are not known. In this article, we calculate the excited-state absorption contribution for different models of higher lying excited states. We find that the characteristic asymmetry of one-dimensional spectroscopies is recovered from the many-body contributions and that the higher lying excited manifolds have distorted lineshapes that are not anticipated from discrete-level Hamiltonians. We show that the Stimulated Emission cannot have contributions from a flat continuum of states. This work completes the Ground-State Bleach and Stimulated Emission signals that were calculated previously [D. Finkelstein-Shapiro et al., Phys. Rev. B 94, 205137 (2016)]. The model reproduces the observations reported for molecules on surfaces probed by 2DIR.

A Study of Electrocyclic Reactions in a Molecular Junction: Mechanistic and Energetic Requirements for Switching in the Coulomb Blockade Regime.

Molecular photoswitches incorporated in molecular junctions yield the possibility of light-controlled switching of conductance due to the electronic difference of the photoisomers. Another isomerization mechanism, dark photoswitching, promoted by a voltage stimulus rather than by light, can be operative in the Coulomb blockade regime for a specific charge state of the molecule. Here we elucidate theoretically the mechanistic and thermodynamic restrictions for this dark photoswitching for donor-acceptor substituted 4n and 4n+2 π-electron open-chain oligoenes (1,3-butadiene and 1,3,5-hexatriene) by considering the molecular energies and orbitals of the molecules placed in a junction. For an electrocyclic ring closure reaction to occur for these compounds, we put forward two requirements: a) the closed stereoisomer (cis or trans form) must be of lower energy than the open form, and b) the reaction pathway must be in accordance to the orbital symmetry rules expressed by the Woodward-Hoffmann rules (when the electrodes do not significantly alter the molecular orbital appearances). We find these two requirements to be valid for the dianion of (1E,3Z,5E)-hexa-1,3,5-triene-1,6-diamine, and the Coulomb blockade diamonds were therefore modeled for this compound to elucidate how a dark photoswitching event would manifest itself in the stability plot. From this modeling of conductance as a function of gate and bias potentials, we predict a collapse in Coulomb diamond size, that is, a decrease in the height of the island of zero conductance.

Predicting transport regime and local electrostatic environment from Coulomb blockade diamond sizes.

Electron transport through a molecule is often described in one of the two regimes: the coherent tunnelling regime or the Coulomb blockade regime. The twilight zone of the two regimes still possesses many unsolved questions. A theoretical analysis of the oligophenylenevinylene OPV3 experiments by Bjørnholm and co-workers is performed. The experiments showed how two OPV3 derivatives performed very differently despite the strong similarity of the molecular structure, hence the experimental data showed two different transport mechanisms. The different transport mechanisms of the two OPV3 derivatives are explained from quantum mechanical calculations of the molecular redox energies and from the experimentally accessible window size.

Color contributes to object-contour perception in natural scenes.

The magnitudes of chromatic and achromatic edge contrast are statistically independent and thus provide independent information, which can be used for object-contour perception. However, it is unclear if and how much object-contour perception benefits from chromatic edge contrast. To address this question, we investigated how well human-marked object contours can be predicted from achromatic and chromatic edge contrast. We used four data sets of human-marked object contours with a total of 824 images. We converted the images to the Derrington-Krauskopf-Lennie color space to separate chromatic from achromatic information in a physiologically meaningful way. Edges were detected in the three dimensions of the color space (one achromatic and two chromatic) and compared to human-marked object contours using receiver operating-characteristic (ROC) analysis for a threshold-independent evaluation. Performance was quantified by the difference of the area under the ROC curves (ΔAUC). Results were consistent across different data sets and edge-detection methods. If chromatic edges were used in addition to achromatic edges, predictions were better for 83% of the images, with a prediction advantage of 3.5% ΔAUC, averaged across all data sets and edge detectors. For some images the prediction advantage was considerably higher, up to 52% ΔAUC. Interestingly, if achromatic edges were used in addition to chromatic edges, the average prediction advantage was smaller (2.4% ΔAUC). We interpret our results such that chromatic information is important for object-contour perception.

Boron Subphthalocyanine Based Molecular Triad Systems for the Capture of Solar Energy.

In this study a number of chromophores based on boron subphthalocyanines are investigated for use in the future design of organic photovoltaic devices based on molecular triad systems. The computational study is performed at the TD-DFT CAM-B3LYP/6-311G(d) level of theory. The absorption spectra of these chromophores are simulated using TD-DFT and compared to experimental results. All investigated chromophores absorb light in the visible range and thus are suitable for absorption of sunlight in solar cell applications. On the basis of energy-level alignments, suitable combinations of moieties for a molecular triad system are proposed. The molecular triads will be used in future work as the functional part of organic photovoltaic devices, where the chromophore will be used both to absorb the incoming solar radiation and to increase the distance between the separated charges on donor and acceptor units to increase the lifetime of the charge-separated state.

Controlling two-step multimode switching of dihydroazulene photoswitches.

We present the synthesis and switching studies of systems with two photochromic dihydroazulene (DHA) units connected by a phenylene bridge at either para or meta positions, which correspond to a linear or cross-conjugated pathway between the photochromes. According to UV/Vis absorption and NMR spectroscopic measurements, the meta-phenylene-bridged DHA-DHA exhibited sequential light-induced ring openings of the two DHA units to their corresponding vinylheptafulvenes (VHFs). Initially, the VHF-DHA species was generated, and, ultimately, after continued irradiation, the VHF-VHF species. Studies in different solvents and quantum chemical calculations indicate that the excitation of DHA-VHF is no longer a local DHA excitation but a charge-transfer transition that involves the neighboring VHF unit. For the linearly conjugated para-phenylene-bridged dimer, electronic communication between the two units is so efficient that the photoactivity is reduced for both the DHA-DHA and DHA-VHF species, and DHA-DHA, DHA-VHF, and VHF-VHF were all present during irradiation. In all, by changing the bridging unit, we can control the degree of stepwise photoswitching.

Computational assignment of redox states to Coulomb blockade diamonds.

With the advent of molecular transistors, electrochemistry can now be studied at the single-molecule level. Experimentally, the redox chemistry of the molecule manifests itself as features in the observed Coulomb blockade diamonds. We present a simple theoretical method for explicit construction of the Coulomb blockade diamonds of a molecule. A combined quantum mechanical/molecular mechanical method is invoked to calculate redox energies and polarizabilities of the molecules, including the screening effect of the metal leads. This direct approach circumvents the need for explicit modelling of the gate electrode. From the calculated parameters the Coulomb blockade diamonds are constructed using simple theory. We offer a theoretical tool for assignment of Coulomb blockade diamonds to specific redox states in particular, and a study of chemical details in the diamonds in general. With the ongoing experimental developments in molecular transistor experiments, our tool could find use in molecular electronics, electrochemistry, and electrocatalysis.

Communication: Finding destructive interference features in molecular transport junctions.

Associating molecular structure with quantum interference features in electrode-molecule-electrode transport junctions has been difficult because existing guidelines for understanding interferences only apply to conjugated hydrocarbons. Herein we use linear algebra and the Landauer-Büttiker theory for electron transport to derive a general rule for predicting the existence and locations of interference features. Our analysis illustrates that interferences can be directly determined from the molecular Hamiltonian and the molecule-electrode couplings, and we demonstrate its utility with several examples.

A Multireference View of Photosynthesis: Uncovering Significant Site Energy Variations among Isolated Photosystem II Reaction Center Chlorophylls.

Oxygenic photosynthesis begins in the reaction center (RC) of the protein complex photosystem II (PSII). PSII has an intriguing, nearly symmetrical arrangement of cofactors within its RC. Despite this symmetry, evolution has favored only one of the two branches of PSII for efficient electron transfer. Current spectroscopic experiments explore the electronic dynamics during the picoseconds after energy has entered the RC and until the electron transfers to the pheophytin of the first branch. We present state-of-the-art multiconfigurational multireference calculations of the excitation energies or site energies of the four chlorophyll pigments of the RC without protein environment considerations. We see a significant variation that breaks the apparent symmetry of the RC. The inner chlorophyll of the productive RC branch possessed the lowest excitation energy of the four central chlorophylls. Our computational method used here is expensive; thus, geometry optimization of the crystal structure is currently not possible. In future work, charge and energy dynamics within the RC will be included as well as a dynamic description of the protein environment and its coupling to the RC. Other state-of-the-art studies of the RC, at lower levels of electronic structure, include a static treatment of the protein environment. These almost unanimously report that the outer chlorophyll of the active branch had the lowest excitation energy. Future work is needed to reconcile this discrepancy.

Higher order color mechanisms: evidence from noise-masking experiments in cone contrast space.

This study addresses a fundamental question concerning the number of cortical, i.e., higher order mechanisms in color vision. The initial subcortical stages in color vision can be described by three cone mechanisms, S, M, L, and three pairs of second-stage mechanisms (achromatic L + M and -L - M, chromatic S - (L + M) and -S + (L + M), and chromatic L - M and M - L). The further mechanistic description of cortical color vision is controversial. On the one hand, numerous studies that defined their stimuli in a color-opponent Derrington-Krauskopf-Lennie (DKL) color space found evidence for higher order mechanisms. On the other hand, some studies that defined their stimuli in cone contrast (CC) space failed to find such evidence. Here we show that this failure was due to a restricted choice of stimuli. We used a noise-masking paradigm to measure discrimination thresholds for textured patterns modulated along chromatic directions in CC space. Unlike previous studies we defined noise directions in DKL space and converted them to CC space. When the noise contrast was sufficiently high we found selective masking, but this did not occur when the noise contrast was low. Selective masking indicates higher order mechanisms, since so far no alternative model has been proposed. Previous studies in CC space failed to find selective masking due to the low contrast of the noise and due to the restricted choice of perceptually highly similar noise directions that mainly stimulated the second-stage mechanisms. We conclude that cortical color vision is governed by higher order mechanisms.

Host Plant Species Influences the Composition of Milkweed and Monarch Microbiomes.

Plants produce defensive chemicals for protection against insect herbivores that may also alter plant and insect associated microbial communities. However, it is unclear how expression of plant defenses impacts the assembly of insect and plant microbiomes, for example by enhancing communities for microbes that can metabolize defensive chemicals. Monarch butterflies (Danaus plexippus) feed on milkweed species (Asclepias spp.) that vary in production of toxic cardiac glycosides, which could alter associated microbiomes. We therefore sought to understand how different milkweed species, with varying defensive chemical profiles, influence the diversity and composition of monarch and milkweed (root and leaf) bacterial communities. Using a metabarcoding approach, we compared rhizosphere, phyllosphere and monarch microbiomes across two milkweed species (Asclepias curassavica, Asclepias syriaca) and investigated top-down effects of monarch feeding on milkweed microbiomes. Overall, monarch feeding had little effect on host plant microbial communities, but each milkweed species harbored distinct rhizosphere and phyllosphere microbiomes, as did the monarchs feeding on them. There was no difference in diversity between plants species for any of the microbial communities. Taxonomic composition significantly varied between plant species for rhizospheres, phyllospheres, and monarch microbiomes and no dispersion were detected between samples. Interestingly, phyllosphere and monarch microbiomes shared a high proportion of bacterial taxa with the rhizosphere (88.78 and 95.63%, respectively), while phyllosphere and monarch microbiomes had fewer taxa in common. Overall, our results suggest milkweed species select for unique sets of microbial taxa, but to what extent differences in expression of defensive chemicals directly influences microbiome assembly remains to be tested. Host plant species also appears to drive differences in monarch caterpillar microbiomes. Further work is needed to understand how monarchs acquire microbes, for example through horizontal transfer during feeding on leaves or encountering soil when moving on or between host plants.

Aphid species specializing on milkweed harbor taxonomically similar bacterial communities that differ in richness and relative abundance of core symbionts.

Host plant range is arguably one of the most important factors shaping microbial communities associated with insect herbivores. However, it is unclear whether host plant specialization limits microbial community diversity or to what extent herbivores sharing a common host plant evolve similar microbiomes. To investigate whether variation in host plant range influences the assembly of core herbivore symbiont populations we compared bacterial diversity across three milkweed aphid species (Aphis nerii, Aphis asclepiadis, Myzocallis asclepiadis) feeding on a common host plant (Asclepias syriaca) using 16S rRNA metabarcoding. Overall, although there was significant overlap in taxa detected across all three aphid species (i.e. similar composition), some structural differences were identified within communities. Each aphid species harbored bacterial communities that varied in terms of richness and relative abundance of key symbionts. However, bacterial community diversity did not vary with degree of aphid host plant specialization. Interestingly, the narrow specialist A. asclepiadis harbored significantly higher relative abundances of the facultative symbiont Arsenophonus compared to the other two aphid species. Although many low abundance microbes were shared across all milkweed aphids, key differences in symbiotic partnerships were observed that could influence host physiology or additional ecological variation in traits that are microbially-mediated. Overall, this study suggests overlap in host plant range can select for taxonomically similar microbiomes across herbivore species, but variation in core aphid symbionts within these communities may still occur.