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 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.

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.

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.

Machine learning the frontier orbital energies of SubPc based triads.

Organic photovoltaic devices are promising candidates for efficient energy harvesting from sunlight. Designing new dye molecules suitable for such devices is a challenging task restricted by the rapid increase of computational cost with system size. Solar cell material properties are closely related to the electronic structure of the dye, and an effective molecular orbital energy screening method for a family of dyes is therefore desired. In this work, a machine learning approach is used to sort through the chemical space of peripheral double-substituted boron-Subphthalocyanine dyes. A database of 12,102 PM6 optimized structures was built and for each of the structures time-dependent density functional theory (LC-[Formula: see text]HPBE/6-31+G(d)) calculations were performed. We investigated the changes of the molecular orbital energies of the molecular orbitals related to reduction and oxidation of the compounds. With the Electrotopological-state index moleculear representation all the tested algorithms, Support Vector Machine, Random Forest Regression, Neural Network, and Simple Linear Regression, captured the calculated frontier orbital energies with a prediction root-mean-square-error in the order of 0.05 eV. Finally, frontier orbital energies were predicted for more than 40,000 new structures by the trained Support Vector Machine algorithm. Compared to the parent boron-Subphthalocyanine structure, 237 and 132 functionalized dyes were predicted to have upshifted molecular orbital energies using the Electrotopological-state index and OneHot encoding feature vector, respectively. Out of 27 investigated donor and acceptor ligands, the acetamide and hydroxyl ligands gave rise to the desired increase in frontier molecular orbital energy.

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.

Coingestion of protein and carbohydrate in the early recovery phase, compared with carbohydrate only, improves endurance performance despite similar glycogen degradation and AMPK phosphorylation.

The present study compared the effects of postexercise carbohydrate plus protein (CHO+PROT) and carbohydrate (CHO)-only supplementation on muscle glycogen metabolism, anabolic cell signaling, and subsequent exercise performance. Nine endurance-trained males cycled twice to exhaustion (muscle glycogen decreased from ~495 to ~125 mmol/kg dry wt) and received either CHO only (1.2 g·kg-1·h-1) or CHO+PROT (0.8/0.4 g·kg-1·h-1) during the first 90 min of recovery. Glycogen content was similar before the performance test after 5 h of recovery. Glycogen synthase (GS) fractional activity increased after exhaustive exercise and remained activated 5 h after, despite substantial glycogen synthesis (176.1 ± 19.1 and 204.6 ± 27.0 mmol/kg dry wt in CHO and CHO+PROT, respectively; P = 0.15). Phosphorylation of GS at site 3 and site 2+2a remained low during recovery. After the 5-h recovery, cycling time to exhaustion was improved by CHO+PROT supplementation compared with CHO supplementation (54.6 ± 11.0 vs. 46.1 ± 9.8 min; P = 0.009). After the performance test, muscle glycogen was equally reduced in CHO+PROT and CHO. Akt Ser473 and p70s6k Thr389 phosphorylation was elevated after 5 h of recovery. There were no differences in Akt Ser473, p70s6k Thr389, or TSC2 Thr1462 phosphorylation between treatments. Nitrogen balance was positive in CHO+PROT (19.6 ± 7.6 mg nitrogen/kg; P = 0.04) and higher than CHO (-10.7 ± 6.3 mg nitrogen/kg; P = 0.009). CHO+PROT supplementation during exercise recovery improved subsequent endurance performance relative to consuming CHO only. This improved performance after CHO+PROT supplementation could not be accounted for by differences in glycogen metabolism or anabolic cell signaling, but may have been related to differences in nitrogen balance.NEW & NOTEWORTHY Endurance athletes competing consecutive days need optimal dietary intake during the recovery period. We report that coingestion of protein and carbohydrate soon after exhaustive exercise, compared with carbohydrate only, resulted in better performance the following day. The better performance after coingestion of protein and carbohydrate was not associated with a higher rate of glycogen synthesis or activation of anabolic signaling compared with carbohydrate only. Importantly, nitrogen balance was positive after coingestion of protein and carbohydrate, which was not the case after intake of carbohydrate only, suggesting that protein synthesis contributes to the better performance the following day.

Hole Hopping through Cytochrome P450.

High-potential iron-oxo species are intermediates in the catalytic cycles of oxygenase enzymes. They can cause heme degradation and irreversible oxidation of nearby amino acids. We have proposed that there are protective mechanisms in which hole hopping from oxidized hemes through tryptophan/tyrosine chains generates a surface-exposed amino-acid oxidant that could be rapidly disarmed by reaction with cellular reductants. In investigations of cytochrome P450BM3, we identified Trp96 as a critical residue that could play such a protective role. This Trp is cation-π paired with Arg398 in 81% of mammalian P450s. Here we report on the effect of the Trp/Arg cation-π interaction on Trp96 formal potentials as well as on electronic coupling strengths between Trp96 and the heme both for wild type cytochrome P450 and selected mutants. Mutation of Arg398 to His, which decreases the Trp96 formal potential, increases Trp-heme electronic coupling; however, surprisingly, the rate of phototriggered electron transfer from a Ru-sensitizer (through Trp96) to the P450BM3 heme was unaffected by the Arg398His mutation. We conclude that Trp96 has moved away from Arg398, suggesting that the protective mechanism for P450s with this Trp-Arg pair is conformationally gated.

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.

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.

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.

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.

Subphthalocyanine-radiaannulene scaffold - a multi-electron acceptor and strong chromophore.

Two subphthalocyanine (SubPc) units and a perethynylated, alkyne-expanded radiaannulene (RA) were fused together by a four-fold Sonogashira reaction to give a compound exhibiting: (i) four reversible one-electron reductions, the first signalling good acceptor strength of the RA core itself, while the following three are a consequence of the entire scaffold, and (ii) intense light absorption that spans a remarkably broad region.

Glucose metabolism and metabolic flexibility in cultured skeletal muscle cells is related to exercise status in young male subjects.

We hypothesised that skeletal muscles of healthy young people have a large variation in oxidative capacity and fibre-type composition, and aimed therefore to investigate glucose metabolism in biopsies and myotubes isolated from musculus vastus lateralis from healthy males with varying degrees of maximal oxygen uptake. Trained and intermediary trained subjects showed higher carbohydrate oxidation in vivo. Fibre-type distribution in biopsies and myotubes did not differ between groups. There was no correlation between fibre-type I expression in biopsies and myotubes. Myotubes from trained had higher deoxyglucose accumulation and fractional glucose oxidation (glucose oxidation relative to glucose uptake), and were also more sensitive to the suppressive action of acutely added oleic acid to the cells. Despite lack of correlation of fibre types between skeletal muscle biopsies and cultured cells, myotubes from trained subjects retained some of their phenotypes in vitro with respect to enhanced glucose metabolism and metabolic flexibility.

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.

Drastic difference between hole and electron injection through the gradient shell of CdxSeyZn1-xS1-y quantum dots.

Ultrafast fluorescence spectroscopy was used to investigate the hole injection in CdxSeyZn1-xS1-y gradient core-shell quantum dot (CSQD) sensitized p-type NiO photocathodes. A series of CSQDs with a wide range of shell thicknesses was studied. Complementary photoelectrochemical cell measurements were carried out to confirm that the hole injection from the active core through the gradient shell to NiO takes place. The hole injection from the valence band of the QDs to NiO depends much less on the shell thickness when compared to the corresponding electron injection to n-type semiconductor (ZnO). We simulate the charge carrier tunneling through the potential barrier due to the gradient shell by numerically solving the Schrödinger equation. The details of the band alignment determining the potential barrier are obtained from X-ray spectroscopy measurements. The observed drastic differences between the hole and electron injection are consistent with a model where the hole effective mass decreases, while the gradient shell thickness increases.

Intermolecular Modes between LH2 Bacteriochlorophylls and Protein Residues: The Effect on the Excitation Energies.

Light-harvesting system 2 (LH2) executes the primary processes of photosynthesis in purple bacteria; photon absorption, and energy transportation to the reaction center. A detailed mechanistic insight into these operations is obscured by the complexity of the light-harvesting systems, particularly by the chromophore-environment interaction. In this work, we focus on the effects of the protein residues that are ligated to the bacteriochlorophylls (BChls) and construct potential energy surfaces of the ground and first optically excited state for the various BChl-residue systems where we in each case consider two degrees of freedom in the intermolecular region. We find that the excitation energies are only slightly affected by the considered modes. In addition, we see that axial ligands and hydrogen-bonded residues have opposite effects on both excitation energies and oscillator strengths by comparing to the isolated BChls. Our results indicate that only a small part of the chromophore-environment interaction can be associated with the intermolecular region between a BChl and an adjacent residue, but that it may be possible to selectively raise or lower the excitation energy at the axial and planar residue positions, respectively.

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.