The effect of ruthenium on the performance of porphyrin dye and porphyrin–fullerene dyad solar cells predicted by DFT and TD-DFT calculations

The effect of ruthenium on the performance of porphyrin dye and porphyrin–fullerene (PF) dyad solar cells is investigated by using density functional theory and time-dependant density functional theory calculations. The results reveal that ruthenium facilitates rapid electron injection from porphyrin to fullerene, narrows the band gaps of porphyrin dye and PF dyad and alters the density of states near the corresponding Fermi levels. The HOMOs are localised on the donor moieties and the LUMOs on the acceptor moieties. The donor and acceptor dyads form good donor–acceptor pairs for photo-to-current conversion under the effect of ruthenium. HOMOs of porphyrin and ruthenium metalloporphyrin dyes fall within the (TiO₂)₆₀ and Ti₃₈O₇₆ gaps, and support the issue of typical interfacial electron transfer reaction. The calculated transition energies of porphyrin are almost insensitive to ethanol solvent effects. The introduction of ruthenium to the porphyrin ring leads to more active nonlinear optical performance, stronger response to the external electric field and induces higher photo-to-current conversion efficiency. Moreover, ruthenium shifts the absorption bands of porphyrin and makes it a potential candidate for harvesting light for photovoltaic applications.     

A model for the effects of primary substrates on the kinetics of reductive dehalogenation

A kinetic model that describes substrate interactions during reductive dehalogenation reactions is developed. This model describes how the concentrations of primary electron-donor and -acceptor substrates affect the rates of reductive dehalogenation reactions. A basic model, which considers only exogenous electron-donor and -acceptor substrates, illustrates the fundamental interactions that affect reductive dehalogenation reaction kinetics. Because this basic model cannot accurately describe important phenomena, such as reductive dehalogenation that occurs in the absence of exogenous electron donors, it is expanded to include an endogenous electron donor and additional electron acceptor reactions. This general model more accurately reflects the behavior that has been observed for reductive dehalogenation reactions. Under most conditions, primary electron-donor substrates stimulate the reductive dehalogenation rate, while primary electron acceptors reduce the reaction rate. The effects of primary substrates are incorporated into the kinetic parameters for a Monod-like rate expression. The apparent maximum rate of reductive dehalogenation (q _{m, ap} ) and the apparent half-saturation concentration (K _ap ) increase as the electron donor concentration increases. The electron-acceptor concentration does not affect q _{m, ap} , but K _ap is directly proportional to its concentration.Definitions for model parameters RX halogenated aliphatic substrate - E-M ⁿ reduced dehalogenase - E-M ⁿ⁺² oxidized dehalogenase - [E-M ⁿ ] steady-state concentration of the reduced dehalogenase (moles of reduced dehalogenase per unit volume) - [E-M ⁿ⁺²] steady-state concentration of the oxidized dehalogenase (moles of reduced dehalogenase per unit volume) - DH₂ primary exogenous electron-donor substrate - A primary exogenous electron-acceptor substrate - A2 second primary exogenous electron-acceptor substrate - X biomass concentration (biomass per unit volume) - f fraction of biomass that is comprised of the dehalogenase (moles of dehalogenase per unit biomass) - stoichiometric coefficient for the reductive dehalogenation reaction (moles of dehalogenase oxidized per mole of halogenated substrate reduced) - stoichiometric coefficient for oxidation of the primary electron donor (moles of dehalogenase reduced per mole of donor oxidized) - stoichiometric coefficient for oxidation of the endogenous electron donor (moles of dehalogenase reduced per unit biomass oxidized) - stoichiometric coefficient for reduction of the primary electron acceptor (moles of dehalogenase oxidized per mole of acceptor reduced) - stoichiometric coefficient for reduction of the second electron acceptor (moles of dehalogenase oxidized per mole of acceptor reduced) - r _RX rate of the reductive dehalogenation reaction (moles of halogenated substrate reduced per unit volume per unit time) - r _d1 rate of oxidation of the primary exogenous electron donor (moles of donor oxidized per unit volume per unit time) - r _d2 rate of oxidation of the endogenous electron donor (biomass oxidized per unit volume per unit time) - r _a1 rate of reduction of the primary exogenous electron acceptor (moles of acceptor reduced per unit volume per unit time) - r _a2 rate of reduction of the second primary electron acceptor (moles of acceptor reduced per unit volume per unit time) - k _RX mixed second-order rate coefficient for the reductive dehalogenation reaction (volume per mole dehalogenase per unit time) - k _d1 mixed-second-order rate coefficient for oxidation of the primary electron donor (volume per mole dehalogenase per unit time) - k _d2 mixed-second-order rate coefficient for oxidation of the endogenous electron donor (volume per mole dehalogenase per unit time) - b first-order biomass decay coefficient (biomass oxidized per unit biomass per unit time) - k _a1 mixed-second-order rate coefficient for reduction of the primary electron acceptor (volume per mole dehalogenase per unit time) - k _a2 mixed-second-order rate coefficient for reduction of the second primary electron acceptor (volume per mole dehalogenase per unit time) - q _m,ap apparent maximum specific rate of reductive dehalogenation (moles of RX per unit biomass per unit time) - K _ap apparent half-saturation concentration for the halogenated aliphatic substrate (moles of RX per unit volume) - k _ap apparent pseudo-first-order rate coefficient for reductive dehalogenation (volume per unit biomass per unit time)     

The Synthesis of New Porphyrin–Quinone Dyad Systems

New porphyrin–quinone dyad systems containing spacer groups of various lengths and structures and sterically hindered 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)porphyrin as an electron donor were synthesized. These compounds seem to be promising models for studying the photoinduced electron transfer.     

Synthesis of novel porphyrin-quinone compounds

New porphyrin-quinone dyad systems containing spacer groups of various lengths and structures and sterically hindered 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)porphyrin as an electron donor were synthesized. These compounds seem to be promising models for studying the photoinduced electron transfer.     

Enhanced Photovoltaic Performance of Amorphous Donor–Acceptor Copolymers Based on Fluorine‐Substituted Benzodioxocyclohexene‐Annelated Thiophene

Donor–acceptor (D‐A) type π‐conjugated copolymers with crystalline behavior have been extensively investigated as donor semiconductors in organic photovoltaics (OPVs). On the other hand, the development of high‐performance amorphous donor materials is still behind. The amorphous donor copolymer DTS‐C₀(F₂) consisting of dithieno[3,2‐b:2′,3′‐d]silole ( DTS ) donor unit and the recently developed fluorine‐substituted naphtho[2,3‐c]thiophene‐4,9‐dione ( C₀(F₂) ) acceptor unit shows moderate photovoltaic performance upon blending with PC₇₁BM. In this work, to enhance the hole‐transporting characteristics, a 3‐hexylthiophene ( HT ) spacer unit is integrated into the conjugated backbone, resulting in a new amorphous copolymer DTS‐HT‐C₀(F₂) . The strong electron‐accepting nature of C₀(F₂) allows the introduction of the HT spacer without affecting the frontier orbital energies and thus the D‐A character. Without using solvent additives and thermal annealing, OPVs based on DTS‐HT‐C₀(F₂) and [6,6]‐phenyl‐C71‐butyric acid methyl ester PC₇₁BM show an improved power conversion efficiency of 9.12%. Investigation of the device physics unambiguously reveals that the hole mobility of the copolymer in the blend is increased by an order of magnitude by the introduction of HT , while keeping an amorphous film nature, leading to higher short‐circuit current density and fill factor. These results demonstrate the realization of high‐performance OPVs based on amorphous active layers.     

Role of bicarbonate in photosystem II, the water-plastoquinone oxido-reductase of plant photosynthesis

Depletion of bicarbonate (carbon dioxide) from oxygenic cells or organelles not only causes cessation of carbon dioxide fixation, but also a strong decrease in the activity of photosystem II; the photosystem II activity can be restored by readdition of bicarbonate. Effects of bicarbonate exist on both the acceptor as well as on the donor side of photosystem II. The influence on the acceptor side is located between the primary and secondary quinone electron acceptor of photosystem II, and can be demonstrated in intact cells or leaves as well as in isolated thylakoids and reaction center preparations. At physiological pH, bicarbonate ions are suggested to form hydrogen bonds to several amino acids on both D1 and D2 proteins, the reaction center subunits of photosystem II, as well as to form ligands to the non-heme iron between the D1 and D2 proteins. Bicarbonate, at physiological pH, has an important role in the water-plastoquinone oxido-reductase: on the one hand it may stabilize, by conformational means, the reaction center protein of photosystem II that allows efficient electron flow and protonation of certain amino acids near the secondary quinone electron acceptor of photosystem II; and, on the other hand, it akppears to play a significant role in the assembly or functioning of the manganese complex at the donor side. Functional roles of bicarbonate in vivo, including protection against photoinhibition, are also discussed.     

The effects of spacer length on the fluorescence quantum yields of the benzofurazan compounds bearing a donor–acceptor system

We studied the effects of spacer length on the fluorescence quantum yields (Φ) of photoinduced electron transfer (PET) reagents, using nitrobenzoxadiazole (NBD) derivatives that have the –NMe₂ moiety and NBD–NH– fluorophore as electron donor (D) and electron acceptor (A), respectively. The Φ values were reduced as the spacer length became shorter (n ≤ 4; n is the number of methylene units of the spacer) and the fluorescence recovered by suppression of the PET process. It is necessary for the useful PET reagents to link D and A with a short spacer to obtain a difference in the Φ values between fluorescent ‘off‐state’ and ‘on‐state’. Copyright © 2002 John Wiley & Sons, Ltd.     

Pigment-protein interactions in the photosynthetic reaction centre from Rhodopseudomonas viridis

An X-ray structure analysis of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis provides structural details of the pigment-binding sites. The photosynthetic pigments are found in rather hydrophobic environments provided by the subunits L and M. In addition to apolar interactions, the bacteriochlorophylls of the primary electron donor (`special pair') and the bacteriopheophytins, but not the accessory bacteriochlorophylls, form hydrogen bonds with amino acid side chains of these protein subunits. The two branches of pigments which originate at the primary electron donor, and which mark possible electron pathways across the photosynthetic membrane, are in different environments and show different hydrogen bonding with the protein: this may help to understand why only one branch of pigments is active in the light-driven electron transfer. The primary electron acceptor, a menaquinone (Q_A), is in a pocket formed by the M subunit and interacts with it by hydrophobic contacts and hydrogen bonds. Competitive inhibitors of the secondary quinone Q_B (o-phenanthroline, the herbicide terbutryn) are bound into a pocket provided by the L subunit. Apart from numerous van der Waals interactions they also form hydrogen bonds to the protein.     

Relationship between the oxidation potential of the bacteriochlorophyll dimer and electron transfer in photosynthetic reaction centers

The primary electron donor in the photosynthetic reaction center from purple bacteria is a bacteriochlorophyll dimer containing four conjugated carbonyl groups that may form hydrogen bonds with amino acid residues. Spectroscopic analyses of a set of mutant reaction centers confirm that hydrogen bonds can be formed between each of these carbonyl groups and histidine residues in the reaction center subunits. The addition of each hydrogen bond is correlated with an increase in the oxidation potential of the dimer, resulting in a 355-mV range in the midpoint potential. The resulting changes in the free-energy differences for several reactions involving the dimer are related to the electron transfer rates using the Marcus theory. These reactions include electron transfer from cytochrome c₂ to the oxidized dimer, charge recombination from the primary electron acceptor quinone, and the initial forward electron transfer.     

Light Dependent Reduction of Pertechnetate (TcO(4)) by Broken Chloroplasts

Arguments are given for a ferredoxin-mediated reduction of TcO₄⁻, preponderantly into extractable Tc(V) complexes, by illuminated, broken chloroplasts. Photosynthetic O₂- and NADP-reduction competitively inhibit Tc incorporation. As for O₂, the reaction can be stimulated by the auto-oxidizable electron acceptor methyl viologen. Furthermore TcO₄⁻ can function as terminal acceptor in the diaphorase reaction, with NADPH as electron donor.     

Three-dimensional structure at 5 Å resolution of cytosolic aspartate transaminase from chicken heart

An X-ray study of orthorhombic crystals of cytosolic aspartate transaminase from chicken heart has been carried out at 5 Å resolution. The crystals belong to space group P2₁2₁2₁, with unit cell dimensions $\text{a = 62.7}\text{A}\text{?}\text{, b = 118.1}\text{A}\text{?}\text{, c = 124.5}\text{A}\text{?}$. The electron density map has been calculated on the basis of five heavy-atom derivatives. The model of the molecule derived from this map revealed clearly two subunits of similar structure related by a non-crystallographic dyad. The secondary structure of the protein comprises nine helical segments per subunit.The enzyme has been shown to be catalytically active in the crystal form. Removal of the coenzyme from the crystals made it possible to derive from the difference Fourier map the position of the active site in the enzyme molecule.Significant conformational changes have been observed which accompany the interconversion of intermediates of the enzymic reaction.     

A Large-Scale Allosteric Transition in Cytochrome P450 3A4 Revealed by Luminescence Resonance Energy Transfer (LRET)

Effector-induced allosteric transitions in cytochrome P450 3A4 (CYP3A4) were investigated by luminescence resonance energy transfer (LRET) between two SH-reactive probes attached to various pairs of distantly located cysteine residues, namely the double-cysteine mutants CYP3A4(C64/C468), CYP3A4(C377/C468) and CYP3A4(C64/C121). Successive equimolar labeling of these proteins with the phosphorescent probe erythrosine iodoacetamide (donor) and the near-infrared fluorophore DY-731 maleimide (acceptor) allowed us to establish donor/acceptor pairs sensitive to conformational motions. The interactions of all three double-labeled mutants with the allosteric activators α-naphthoflavone and testosterone resulted in an increase in the distance between the probes. A similar effect was elicited by cholesterol. These changes in distance vary from 1.3 to 8.5 Å, depending on the position of the donor/acceptor pair and the nature of the effector. In contrast, the changes in the interprobe distance caused by such substrates as bromocriptine or 1-pyrenebutanol were only marginal. Our results provide a decisive support to the paradigm of allosteric modulation of CYP3A4 and indicate that the conformational transition caused by allosteric effectors increases the spatial separation between the beta-domain of the enzyme (bearing residues Cys₆₄ and Cys₃₇₇) and the alpha-domain, where Cys₁₂₁ and Cys₄₆₈ are located.     

Combined effects of girdling and leaf removal on fluorescence characteristic of Alhagi sparsifolia leaf senescence

Plant senescence is largely influenced by carbohydrate content. In order to investigate the impact of carbohydrate content on leaf senescence and photosystem II (PSII) during the senescence process, phloem girdling (PG), leaf removal (LR) and a combination of phloem girdling and leaf removal (GR) were performed on Alhagi sparsifolia (Fabaceae) at the end of the growing season. The results showed that during senescence, leaf soluble sugar content, starch content, the energy absorbed by the unit reaction centre (ABS/RC) increased; whereas, leaf photosynthetic rate, photosynthetic pigment content, maximum photochemical efficiency (φ_Po) and energy used by the acceptor site in electron transfer (ET_o/RC) decreased. The degree of change was PG> GR> CK (control)> LR. The results of the present work implied that phloem girdling (PG) significantly accelerated leaf senescence, and that single leaf removal (LR) slightly delayed leaf senescence; although leaf removal significantly delayed the senescence process on the girdled leaf (GR). Natural or delayed senescence only slightly inhibited the acceptor site of PSII and did not damage the donor site of PSII. On the other hand, induced senescence not only damaged the donor site of PSII (e.g. oxygen‐evolving complex), but also significantly inhibited the acceptor site of PSII. In addition, leaf senescence led to an increase in the energy absorbed by the unit reaction centre (ABS/RC), which subsequently resulted in increasing excitation pressure in the reaction centre (DI_o/RC), as well as additional saved Car for absorbing residual light energy and quenching reactive oxygen species during senescence.     

The Chlorophyll <Emphasis Type="Italic">a</Emphasis> Fluorescence Characteristic in Different Types of Leaf Senescence in <Emphasis Type="Italic">Alhagi sparsifolia</Emphasis>

Senescence is both a highly controlled and a strictly regulated process that is gene dependent. To study the PSII reaction in different types of leaf senescence processes, stem girdling was performed on Alhagi sparsifolia to investigate the leaf status in the control, natural senescence, and girdling-induced senescence leaves. The results showed that during senescence, leaf soluble sugar content, starch content, and the energy absorbed by the unit reaction center (ABS/RC) increased; whereas leaf photosynthetic rate, photosynthetic pigment content, maximum photochemical efficiency (φ _Po), and energy used by the acceptor site in electron transfer (ET_o/RC) decreased. The result of the present research implied that stem girdling significantly accelerated leaf senescence, which was due to the accumulation of carbohydrate. Natural senescence is a highly controlled process, which is an ordered process played by genes, whereas girdling-induced senescence is a disordered one. In addition, natural senescence slightly inhibits the acceptor site of PSII but did not damage the donor site of PSII. Conversely, girdling-induced senescence not only damaged the donor site of PSII (for example, oxygen-evolving complex), but also significantly inhibited the acceptor site of PSII. Moreover, both types of senescence led to an increase in the energy absorbed by the unit reaction center (ABS/RC), which subsequently resulted in an increasing excitation pressure in the reaction center (DI_o/RC), as well as additional saved carotenoid for absorbing residual light energy and quenching reactive oxygen species during senescence.     

Influence of Cooperativity on Hydrogen Bond Networks

Abstract

Cooperative effects are known to strongly affect the geometrical, energetic and vibrational properties of hydrogen bonded systems. In particular, such effects strongly favor molecular arrangements where each molecule is simultaneously a donor and an acceptor of hydrogen bonds (HBs), regardless of the chemical nature of the monomer subunits. In the particular case of water systems, it has been shown that the more a molecule is a proton donor in HBs, the more the HBs where it is a proton acceptor are reinforced. Such a property could be at the origin of the equilibrium between the two species of hydrogen bonded water molecules in liquid water (one with a strong hydrogen bonding character, and one with a weaker one), as experimentally evidenced and as a molecular dynamic study of the small (H₂O)₂₄ cluster clearly suggests.     

A Supramolecular “Double‐Cable” Structure with a 12944 Helix in a Columnar Porphyrin‐C60 Dyad and its Application in Polymer Solar Cells

A novel porphyrin‐C₆₀ dyad (PCD1) is designed and synthesized to investigate and manipulate the supramolecular structure where geometrically isotropic [such as [60]fullerene (C₆₀)] and anisotropic [such as porphyrin (Por)] units coexist. It is observed that PCD1 possesses an enantiomeric phase behavior. The melting temperature of the stable PCD1 thermotropic phase is 160 °C with a latent heat (ΔH) of 18.5 kJ mol^?1. The phase formation is majorly driven by the cooperative intermolecular Por–Por and C₆₀–C₆₀ interactions. Structural analysis reveals that this stable phase possesses a supramolecular “double‐cable” structure with one p‐type Por core columnar channel and three helical n‐type C₆₀ peripheral channels. These “double‐cable” columns further pack into a hexagonal lattice with a = b = 4.65 nm, c = 41.3 nm, α = β = 90°, and γ = 120°. The column repeat unit is determined to possess a 129₄₄ helix. With both donor (D; Pro) and acceptor (A; C₆₀) units having their own connecting channels as well as the large D/A interface within the supramolecular “double‐cable” structure, PCD1 has photogenerated carriers with longer lifetimes compared to the conventional electron acceptor [6,6]‐phenyl‐C₆₁‐butyric acid methyl ester. A phase‐separated columnar morphology is observed in a bulk‐heterojunction (BHJ) material made by the physical blend of a low band‐gap conjugated polymer, [poly[2,6‐(4,4‐bis‐(2‐ethylhexyl)‐4H‐cyclopenta [2,1‐b;3,4‐b′]‐dithiophene)‐alt‐4,7‐(2,1,3‐benzothia‐diazole)] (PCPDTBT), and PCD1. With a specific phase structure in the solid state and in the blend, PCD1 is shown to be a promising candidate as a new electron acceptor in high performance BHJ polymer solar cells.     

Role of bicarbonate at the acceptor side of Photosystem II

Besides being the substrate for the carboxylation reaction of photosynthesis, CO₂ (bicarbonate) is required for the activity of Photosystem II (water plastoquinone oxido-reductase). It plays a role on the electron donor side as well as the electron acceptor side. In this contribution, attention will mostly be focused on the history of research into the effects of bicarbonate on electron flow reactions on the acceptor side. Donor side reactions are discussed in this issue by Alan Stemler. This revised version was published online in June 2006 with corrections to the Cover Date.     

Application of the standard theory of electronic transitions to the description of oscillations in the kinetics of electron transfer in reaction centers of purple bacteria

The standard theory of electron transfer between donor and acceptor molecules was used to describe oscillations in the reduction kinetics of the intermediate electron acceptor B_A and the primary electron acceptor H_A. The kinetics of B_A and H_A reduction were simulated on the basis of the model with one and two accepting modes. A crucial experiment is offered for choosing the version of theory that would adequately describe oscillations in the kinetics of electron transfer in the reaction centers of purple bacteria.     

Resonance energy transfer between the active sites of rabbit muscle creatine kinase: analysis by steady-state and time-resolved fluorescence

Resonance energy transfer between the reactive thiols of rabbit muscle creatine kinase was evaluated. The reactive thiols are located at the active site, one occurring on each subunit of the dimeric protein that is known to be a constituent of the M-line structure of the myofibril. Transfer efficiency was evaluated from energy donor quenching of fluorescence by steady-state and phase-modulation lifetime measurements and determination of sensitized emission of the acceptor. Several sulfhydryl-specific donor fluorophores were used including 5-[[[(iodoacetyl)amino]ethyl]amino]naphthalene-1-sulfonic acid, 7-(dimethylamino)-3-(4-maleimidylphenyl)-4-methylcoumarin, and 2-[4-(iodoacetamido)anilino]naphthalene-6-sulfonic acid (IAANS). Energy transfer acceptors included 5-(iodoacetamido)fluorescein and the nonfluorescent dye [4-[[4-(dimethylamino)phenyl]azo]phenyl]iodoacetamide. In order to prepare the necessary homodimer labeled with both donor and acceptor, advantage was taken of the biphasic reaction between creatine kinase and IAANS. In some instances, donor/acceptor hybrids were prepared by denaturation/renaturation procedures, and possible deviations from expected hybridization stoichiometry were considered. Disproportionation of singly labeled dimers (to unlabeled and doubly labeled dimers) was not observed when the brain isozyme of creatine kinase was used to trap dissociated dye-conjugated or unlabeled muscle-type subunits of creatine kinase. From studies of five different donor/acceptor combinations, the efficiency of energy transfer was found to occur over a range of 5-14%, indicating that the reactive thiols are well separated. Overlap integrals and quantum yields were evaluated, and estimates of the range of orientation factor were obtained to determine a range for the distance between the active sites of creatine kinase. When the ranges are overlapped, a limited distance of 48.6-60.4 A is obtained.(ABSTRACT TRUNCATED AT 250 WORDS)