In situ assessment of the initial phase of wastewater biofilm formation: Effect of the presence of algae in an aerobic bacterial biofilm system.

The initial start-up attachment stage that dominates biofilm formation is an unstable process and is time-consuming. In the present study, Chlorella sp. was introduced into a general aerobic biofilm system to explore whether the addition of algae improved the initial attachment phase of biofilm. Compared with those of the bacterial biofilms, the initial algal-bacterial biofilms were more stable and had a thicker, denser, and rougher surface. Further investigation suggested that the concentration of extracellular polymeric substances (EPSs) in the algal-bacterial biofilm was 31.33 % greater than that in the bacterial biofilm. Additionally, the algal-bacterial flocs had greater free energies of absolute cohesion (ΔGcoh) and adhesion energy (∆Gadh) than did the bacterial flocs. These phenomena contribute to the speediness and stabilization of initial algal-bacterial start-up biofilms. Specifically, algae inoculation increased microbial community diversity and promoted the growth of bacterial members related to biofilm development. In conclusion, both physicochemical interactions and biological processes strongly influence microbial attachment during the initial biofilm formation process and further promote strengthening.

Improving the Efficiency and Stability of MAPbI3 Perovskite Solar Cells by Dipeptide Molecules.

Passivating the electronic defects of metal halide perovskite is regarded as an effective way to improve the power conversion efficiency (PCE) of perovskite solar cells (PVSCs). Here, a series of dipeptide molecules with abundant ─C═O, ─O─ and ─NH functional groups as defects passivators for perovskite films are employed. These dipeptide molecules are utilized to treat the surface of prototype methyl ammonium lead iodide (MAPbI3 ) films and the corresponding PVSCs exhibit enhanced photovoltaic performance and ambient stability, which can be ascribed to: 1) the ─C═O and ─O─ can interact with the undercoordinated Pb2+ ions and the ─NH groups can form hydrogen bonds with the I- ions, passivating the defects in perovskite film and reducing charge recombination in PVSCs; 2) the long alkyl chain of dipeptide molecules increases the hydrophobicity of the perovskite surface and thus enhance the stability of PVSCs. The passivated MAPbI3 -based PVSCs exhibit a champion PCE of 20.3% and retain 60% of the initial PCE after 1000 h. It is believed that the defects passivation engineering using polypeptide moleculars can be applied in other perovskite compositions for high device efficiency and stability.

Small secreted effector protein from Fusarium sacchari suppresses host immune response by inhibiting ScPi21-induced cell death.

Fusarium sacchari is one of the primary pathogens causing pokkah boeng disease, which impairs the yield and quality of sugarcane around the world. Understanding the molecular mechanisms of the F. sacchari effectors that regulate plant immunity is of great importance for the development of novel strategies for the persistent control of pokkah boeng disease. In a previous study, Fs00367 was identified to inhibit BAX-induced cell death. In this study, Fs00367nsp (without signal peptide) was found to suppress BAX-induced cell death, reactive oxygen species bursts and callose accumulation. The amino acid region 113-142 of Fs00367nsp is the functional region. Gene mutagenesis indicated that Fs00367 is important for the full virulence of F. sacchari. A yeast two-hybrid assay revealed an interaction between Fs00367nsp and sugarcane ScPi21 in yeast that was further confirmed using bimolecular fluorescence complementation, pull-down assay and co-immunoprecipitation. ScPi21 can induce plant immunity, but this effect could be blunted by Fs00367nsp. These results suggest that Fs00367 is a core pathogenicity factor that suppresses plant immunity through inhibiting ScPi21-induced cell death. The findings of this study provide new insights into the molecular mechanisms of effectors in regulating plant immunity.

Unraveling biological behavior and influence of magnetic iron-based nanoparticles in algal-bacterial systems: A comprehensive review.

Magnetic iron-based nanoparticles have been found to stimulate algae growth and harvest, repair disintegrated particles and improve stability, and facilitate operation in extreme environments, which help improve the wide application of algal-bacterial technology. Nevertheless, up to now, no literature collected to systematically review the research progress of on the employment of magnetic iron-based nanoparticles in the algal-bacterial system. This review summarizes the special effects (e.g., size effect, surface effect and biological effect) and corresponding properties of magnetic iron-based nanoparticles (e.g., magnetism, adsorption, electricity, etc.), which is closely related to biological effects and algal-bacterial behaviors. Additionally, it was found that magnetic iron-based nanoparticles offer remarkable impacts on improving the growth and metabolism of algal-bacterial consortia and the mechanisms mainly include its possible iron uptake pathways in bacteria and/or algae cells, as well as the magnetic biological effect of magnetic iron-based nanoparticles on algae-bacteria growth. Furthermore, in terms of the mechanism for establishing the algae-bacteria symbiotic relationship, the most recent works reveal that the charge effect, material transfer and signal transmission of magnetic iron-based nanoparticles possess a large array of potential mechanisms by which it can affect the establishment of algal-bacterial symbiosis. This discussion is expected to promote the progress of magnetic iron-based nanoparticles, as an eco-friendly, convenient and cost-effective technology that can be applied in algal-bacterial wastewater treatment fields.

Iodinated Electron Acceptor with Significantly Extended Exciton Diffusion Length for Efficient Organic Photovoltaic Cells.

Iodination has unlocked new potentials in organic photovoltaics (OPVs). A newly designed and synthesized iodinated non-fullerene acceptor, BO-4I, showcases exceptional excitation delocalization property with the exciton diffusion length increased to 80 nm. The enhanced electron delocalization property is attributed to the larger atomic radius and electron orbit of the iodine atom, which facilitates the formation of intra-moiety excitations in the acceptor phase. This effectively circumvents the charge transfer state-related recombination mechanisms, leading to a substantial reduction in non-radiative energy loss (ΔEnr ). As a result, OPV cell based on PBDB-TF : BO-4I achieves an impressive efficiency of 18.9 % with a notable ΔEnr of 0.189 eV, markedly surpassing their fluorinated counterparts. This contribution highlights the pivotal role of iodination in reducing energy loss, thereby affirming its potential as a key strategy in the development of advanced next-generation OPV cells.

Identification of common fungal extracellular membrane (CFEM) proteins in Fusarium sacchari that inhibit plant immunity and contribute to virulence.

IMPORTANCE: Common fungal extracellular membrane (CFEM) domain-containing protein has long been considered an essential effector, playing a crucial role in the interaction of pathogens and plant. Strategies aimed at understanding the pathogenicity mechanism of F. sacchari are eagerly anticipated to ultimately end the spread of pokkah boeng disease. Twenty FsCFEM proteins in the genome of F. sacchari have been identified, and four FsCFEM effector proteins have been found to suppress BCL2-associated X protein-triggered programmed cell death in N. benthamiana. These four effector proteins have the ability to enter plant cells and inhibit plant immunity. Furthermore, the expression of these four FsCFEM effector proteins significantly increases during the infection stage, with the three of them playing an essential role in achieving full virulence. These study findings provide a direction toward further exploration of the immune response in sugarcane. By applying these discoveries, we can potentially control the spread of disease through techniques such as host-induced gene silencing.

Understanding H-aggregates crystallization induced emissive behavior: insights from theory.

We conducted a theoretical investigation into how the molecular stacking effect impacts the photophysical properties in solid phases. Our findings indicated that in the aggregated state, the out-of-plane distorted vibration and imidazole ring stretching vibration of triimidazo-[1,3,5] triazinethe are significantly suppressed, which decreased the Huang-Rhys factor and the corresponding reorganization energy of the photophysical process, as a result, this restricted intramolecular motions and dissipation pathways of excess energy in the excited state, therefore, aggregation induced enhancement emission (AIEE) was found for the title compound from dichloromethane solution to solid state. Analysis of the emission spectrum through discrete spectral lines revealed that the main peak was affected by the vibrational modes with lower frequencies, while the middle-frequency modes influenced the shoulder peak. Furthermore, the predicted intersystem crossing rate (kiosk) and reverse intersystem crossing rate (krisc) using Marcus theory confirmed that an electron can successfully shift from its S1 state to the T1 state, however, the reverse T1 → S1 process can not come into being due to very small krisc (10-6-10-9 s-1), therefore the phosphorescence can be observed. At last, we explored the influence of charge transfer process of the title compound, our theoretical data declared this process can be ignored due to its low transfer rate.

Fluorescent Mechanism of a Highly Selective Probe for Copper(II) Detection: A Theoretical Study.

A highly selective probe for copper(II) detection based on the dansyl group was theoretically studied by means of (time-dependent) density functional theory. The calculated results indicated that the oscillator strength of the fluorescent process for the probe molecule is considerably large, but the counterpart of its copper(II) complex is nearly zero; therefore, the predicted radiative rate kr of the probe is several orders of magnitude larger than that of its complex; however, the predicted internal conversion rate kic of both the probe and its complex is of the same order of magnitude. In addition, the simulated intersystem crossing rate kisc of the complex is much greater than that of the probe due to the effect of heavy atom from the copper atom in the complex. Based on the above information, the calculated fluorescence quantum yield of the probe is 0.16% and that of the complex becomes 10-6%, which implies that the first excited state of the probe is bright state and that of the complex is dark state. For the complex, the hole-electron pair analysis indicates that the process of S0 → S1 belongs to metal-to-ligand charge transfer; its density-of-state diagram visually illustrates that the highest occupied molecular orbital (HOMO) contains the ingredient of the s orbital from the copper atom, which decreases the frontier orbital energy level and the overlap integral of HOMO and LUMO.

The luminescent and reaction mechanisms of a fluorescent probe for the detection of hypochlorous acid: Insights from theory.

We have designed and synthesized a novel fluorescent probe BMH for detection of hypochlorous acid (HClO), which can increase dramatically the fluorescence intensity and had ultrafast response, a low detection limit and a wide pH range of application. In this paper, we further studied its fluorescence quantum yield and photoluminescence mechanism theoretically. The calculated results indicated the first excited states of BMH and BM (it was the oxidized product by HClO) were bright states with large oscillator strengths, however, due to more larger reorganization energy of BMH, the predicted internal conversion rate kIC of BMH was four orders of magnitude larger than that of BM; moreover, owing to the effect of heavy atom from sulfur atom in BMH, the predicted intersystem crossing rate kisc of BMH was five orders of magnitude larger than that of BM; meanwhile there was no significant difference found between both the predicted radiative rates kr, thus the calculated fluorescence quantum yield of BMH was nearly zero and that of BM was more than 90%, the data showed the BMH had no fluorescence but its oxidated produce BM possessed strong fluorescence. In addition, the reaction mechanism of BMH transforming into BM has been investigated too, according to the potential energy profile, we found that the course of BMH converting into BM consisted of three elementary reactions. The research results revealed the solvent effect can decreased the activation energy, which was more favorable for these elementary reactions.

Defects-Abundant Ga2 O3 Nanobricks Enabled Multifunctional Solid Polymer Electrolyte for Superior Lithium-Metal Batteries.

Polyethylene oxide (PEO)-based polymer electrolytes with good flexibility and viscoelasticity, low interfacial resistance, and fabricating cost have caught worldwide attention, but their practical application is still hampered by the instability at high voltages and the low ionic conductivity (10-8 to 10-6  S cm-1 ). Herein, we rationally designed defects-abundant Ga2 O3 nanobricks as multifunctional fillers and constructed a PEO-based organic-inorganic electrolyte for lithium metal batteries. Due to the abundant O-defects feature of Ga2 O3 filler, this PEO-based composite electrolyte not only broadens electrochemical stability window (over 5.3 V versus Li/Li+ ) but also in situ forms a Li-Ga alloy and solid electrolyte interphase (SEI) film during the cycling process causing a rapid diffusion of Li+ ions. The as-prepared electrolyte has good interface compatibility with Li metal (without short-circuiting over 500 h at 0.2 mA cm-2 ) and possesses superior high ionic conductivity. The assembled all-solid-state LiFePO4 //Li cells attained an excellent cycling performance of 146 mAh g-1 over 100 cycles at 0.5 C. The XPS analysis reveals that Ga2 O3 nanobricks can form in situ a Li-Ga alloy layer at the polymer/anode interface. This work shed a light on designing high ionic conductivity lithium alloys in the composite electrolyte, which can improve the electrochemical properties of PEO-based polymer electrolytes.

A benzocoumarin-based fluorescent probe for ultra-sensitive and fast detection of endogenous/exogenous hypochlorous acid and its applications.

Hypochlorous acid (HOCl) is widely used in daily production and life because of its green and strongly oxidizing properties. Additionally, as a vital reactive oxygen species (ROS), it is an innate immune system weapon and performs a critical function in many pathophysiology processes. In this paper, a novel water-soluble fluorescent probe, BMH, with excellent performance is designed and synthesized by simple condensation of benzocoumarin and 2-mercaptoethanol. BMH has specific selectivity, excellent sensitivity, ultra-fast response (<3 s), and a wide pH detection range. The fluorescence intensity of BMH has an excellent linear correlation with the concentration of HOCl in the scope of 0-10 µM, and the calculated detection limit (DL) is 2.45 nM. The intramolecular charge transfer (ICT) sensing mechanism of BL has been verified by fluorescence, UV, and MS studies as well as density functional theory (DFT) calculations. Furthermore, BMH can be incorporated into a solid-state visual sensor to detect HOCl conveniently. BMH was applied to detect HOCl-spiked actual water samples and achieved satisfying recovery rates. Also, the low-toxicity BMH can be successfully used to track changes in endogenous/exogenous HOCl in living cells. In short, BL provides a robust and reliable monitoring tool to reveal the biological functions of HOCl and ensure its safe use.

Theoretical Studies on the Photophysical Properties of the Ag(I) Complex for Thermally Activated Delayed Fluorescence Based on TD-DFT and Path Integral Dynamic Approaches.

Theoretical calculation not only is a powerful tool to deeply explore photophysical processes of the emitters but also provides a theoretical basis for material renewal and design strategy in the future. In this work, the interconversion and decay rates of the thermally activated delayed fluorescence (TADF) process of the rigid Ag(dbp)(P2-nCB) complex are quantitatively calculated by employing the optimally tuned range-separated hybrid functional (ω*B97X-D3) method combined with the path integral approach to dynamics considering the Herzberg-Teller and the Duschinsky rotation effects within a multimode harmonic oscillator model. The calculated results show that the small energy splitting ΔE(S1-T1) = 742 cm-1 (experimental value of 650 cm-1) of the lowest singlet S1 and triplet T1 state and proper vibrational spin-orbit coupling interactions facilitate the reverse intersystem crossing (RISC) processes from the T1 to S1 states. The k RISC rate is estimated to be 1.72 × 108 s-1 that is far more than the intersystem crossing rate k ISC of 7.28 × 107 s-1, which will greatly accelerate the RISC process. In addition, the multiple coupling routes of zero-field splitting (ZFS) interaction can provide energetically nearby lying states, to speed up the RISC pathway, and restrict the phosphorescence decay rate. A smaller ZFS D-tensor of 0.143 cm-1, E/D ≈ 0.094 ≪ 1/3, and Δg > 0 are obtained, indicating that the excited singlet states are hardly mixed into the T1 state; thus, a lower phosphorescence decay rate (k p = 9.29 × 101 s-1) is expected to occur, and the T1 state has a long lifetime, which is helpful for the occurrence of the RISC process. These works are in excellent agreement with the experimental observation and are useful for improving and designing efficient TADF materials.

Predication of the Effector Proteins Secreted by Fusarium sacchari Using Genomic Analysis and Heterogenous Expression.

One of the causative agents of pokkah boeng disease (PBD), which affects sugarcane crops globally, is the fungus Fusarium sacchari. These fungal infections reduce sugar quality and yield, resulting in severe economic losses. Effector proteins play important roles in the interactions between pathogenic fungi and plants. Here, we used bioinformatic prediction approaches to identify 316 candidate secreted effector proteins (CSEPs) in the complete genome of F. sacchari. In total, 95 CSEPs contained known conserved structures, representing 40 superfamilies and 18 domains, while an additional 91 CSEPs contained seven known motifs. Of the 130 CSEPs containing no known domains or motifs, 14 contained one of four novel motifs. A heterogeneous expression system in Nicotiana benthamiana was used to investigate the functions of 163 CSEPs. Seven CSEPs suppressed BAX-triggered programmed cell death in N. benthamiana, while four caused cell death in N. benthamiana. The expression profiles of these eleven CSEPs during F. sacchari infection suggested that they may be involved in sugarcane-F. sacchari interaction. Our results establish a basis for further studies of the role of effector molecules in pathogen-sugarcane interactions, and provide a framework for future predictions of pathogen effector molecules.

Insights from QM/MM-ONIOM calculations: the TADF phenomenon of phenanthro[9,10-d]imidazole-anthraquinone in the solid state.

In this paper, we employed first-principles methods and the QM/MM technique to study the thermally activated delayed fluorescence (TADF) phenomenon of a near-infrared molecule (PIPAQ) in vacuum, solution, and the aggregation state. Our calculated results show that (1) the cluster can decrease the energy gap between the first singlet excited state (S1) and the first triplet state (T1) compared with the monomer, furthermore, the T1 state and S1 state in the cluster are energetically closer to each other, which implies that the energy gap is smaller in comparison with that in solution and can promote the intersystem crossing (ISC) process due to the surrounding effect; (2) the optimally tuned range-separated functional is applicable to simulation of excited states and the outcomes are in good agreement with experimental values; (3) the reorganization energies associated with ISC and the reverse intersystem crossing (RISC) processes between the S1 and T1 states are sensitive to the calculated methods and the environments, and thus the following calculated ISC and RISC rates vary dramatically according to different reorganization energies; (4) all radiative and nonradiative rates are insensitive to temperature, but sensitive to environments, all the radiative rates increase in the cluster while the nonradiative rates decrease, which enhances the fluorescence quantum efficiency and agrees with the observed value. The above results demonstrate that the surrounding effects are very important for modulating the photophysical properties of the PIPAQ compound. Finally, this studied conclusion can give a helpful insight into the TADF mechanism for the title compounds, by which novel TADF materials with excellent performance could be rationally designed.

Innovative Organic Electroluminescent Materials with a Doublet Ground State: A Theoretical Investigation.

The displaced and distorted harmonic oscillator model, which has been proven to be appropriate in calculating vibronic spectra, is employed to treat the emission spectrum of title molecules in combination with a thermal vibration correlation function. The calculated results indicate that the main peak of the emission spectrum is visibly impacted by the normal modes with lower frequencies and that the shoulder peak is originated from the middle-frequency modes. On the level of time-dependent density functional theory (TDDFT), the calculated fluorescence lifetimes of TTM-3NCz and TTM-3PCz are 22.1 and 26.0 ns, respectively, which happen to coincide with the observed values of TTM-3NCz (17.2 ns) and TTM-3PCz (21.2 ns). The above data indicate that both the calculated radiative decay rates are reasonable at room temperature. Furthermore, we investigate the influence of the Duschinsky effect on the fluorescence quantum efficiency (FQE). When it is considered, the predicted FQE of the TTM-3NCz molecule is only 0.11%, and the observed value (49% in toluene) deviates significantly. If we ignore the Duschinsky effect, the FQE of TTM-3NCz increases dramatically to 41.8%. For the TTM-3PCz molecule (the FQE is 46% in toluene), the calculated FQE is 0.042% with the Duschinsky effect and increases to 45.2% without the Duschinsky effect. This phenomenon might be related to external factors and the nature of the TDDFT only considering a single configuration. In addition, the fluorescent properties of the fluorinated TTM-3NCz molecules are studied predictably. The obtained results show that the perfluorinated TTM-3NCz shows better luminous performance due to larger oscillator strength. Finally, the dimers, which are composed of both single title molecules, are explored theoretically to determine how they impact the fluorescent property; however, the effect can be nearly eliminated because of the small binding energies.

Phosphorescent Modulation of Metallophilic Clusters and Recognition of Solvents through a Flexible Host-Guest Assembly: A Theoretical Investigation.

MP2 (Second order approximation of Møller⁻Plesset perturbation theory) and DFT/TD-DFT (Density functional theory/Time-dependent_density_functional_theory) investigations have been performed on metallophilic nanomaterials of host clusters [Au(NHC)2]⁺⋅⋅⋅[M(CN)2]-⋅⋅⋅[Au(NHC)2]⁺ (NHC = N-heterocyclic carbene, M = Au, Ag) with high phosphorescence. The phosphorescence quantum yield order of clusters in the experiments was evidenced by their order of µS1/ΔES1-T1 values ( µ S 1 : S0 → S1 transition dipole, ∆ E S 1 - T 1 : splitting energy between the lowest-lying singlet S1 and the triplet excited state T1 states). The systematic variation of the guest solvents (S1: CH3OH, S2: CH3CH2OH, S3: H2O) are employed not only to illuminate their effect on the metallophilic interaction and phosphorescence but also as the probes to investigate the recognized capacity of the hosts. The simulations revealed that the metallophilic interactions are mainly electrostatic and the guests can subtly modulate the geometries, especially metallophilic Au⋅⋅⋅M distances of the hosts through mutual hydrogen bond interactions. The phosphorescence spectra of hosts are predicted to be blue-shifted under polar solvent and the excitation from HOMO (highest occupied molecular orbital) to LUMO (lowest unoccupied molecular orbital) was found to be responsible for the ³MLCT (triplet metal-to-ligand charge transfer) characters in the hosts and host-guest complexes. The results of investigation can be introduced as the clues for the design of promising blue-emitting phosphorescent and functional materials.

Molecular mechanism of Hoxd13-mediated congenital malformations in rat embryos.

OBJECTIVE: To investigate the molecular mechanism of Hoxd13-mediated congenital malformations in rat embryos. METHODS: SD female rats were mated with male rats in a 1:1 mating scheme. Thirty pregnant female rats were randomly divided into three groups: the control group receiving a normal diet, the model group receiving a vitamin A-deficient diet, and the treatment group receiving a vitamin A-deficient diet supplemented with pcDNA-Hoxd13. The expression of Hoxd13 mRNA and protein in normal embryonic tissue and congenital malformations was determined by RT-PCR and Western blot analysis. At day 20, rats were dissected, and the fetal weight, body and tail length, and the number of live births, absorbed fetus, and stillbirth in each group were recorded. Wnt and Slim1 expression was detected by RT-PCR and Western blot analysis. ß-catenin and c-myc expression was also quantified by Western blot analysis. RESULTS: The expression of Hoxd13 mRNA and protein in congenital malformations was significantly lower compared with normal embryonic tissue (P<0.01). The administration of exogenous Hoxd13 in the treatment group markedly increased the fetal weight, body and tail length (P<0.05), improved the embryonic survival rate, and reduced the embryonic resorption rate and stillbirth rate (P<0.05). Exogenous Hoxd13 markedly promoted the expression of Wnt2, Wnt5a, Wnt7b and Slim1 protein and mRNA (P<0.01), and the expression of ß-catenin and c-myc protein in congenital malformations (P<0.01). CONCLUSION: Hoxd13 expression was decreased in rat embryos with congenital malformations. The administration of exogenous Hoxd13 alleviated fetal malformation probably through stimulation of Slim1 expression and Wnt/ß-catenin signaling pathway.

The mutual interactions based on amphipathic tetraoxacalix[2]arene[2]triazine: recognition cases of anion and cation investigated by a computational study.

The nature of anion···π (anion X1-4(-) = SCN(-), PF6(-), BF4(-) and NO3(-), respectively) interactions with electron-deficient and cavity self-tunable macrocyclic host tetraoxacalix[2]arene[2]triazine 1 as electron-acceptor (J. Am. Chem. Soc., 2013, 135, 892) have been theoretically investigated with the density functional theory (B3LYP, M06-2X, M06-L, M06, M05-2X, M05, DFT-D3) and the second-order Møller-Plesset perturbation theory (MP2) using a series of basis sets. The binding energies calculated are in good quantitative agreement with the experiments. The LMO-EDA (local molecular orbital energy decomposition analysis) results show that the major contributors of anion···π are electrostatic. The alkali metal cations M(+) (Na(+), K(+)) and alkaline earth metal cations M(2+) (Mg(2+), Ca(2+)) can also interact with 1 and, the cation···π binding of M(2+)···1 is stronger than that of M(+)···1, as well as their strength is gradually decreased along with an increase in the radius of M(+,2+). The investigation of interplay between the anion···π and the cation···π shows that the interactions among three-body, X(-), 1 and M(+) is varied with different phases. The polar solvent can strongly reduce the strength of the interaction, and the more increased the solvent polarity, the more reduced is the binding energy.

Theoretical study of the electronic-vibrational coupling in the Q(y) states of the photosynthetic reaction center in purple bacteria.

Inspired by the recent observation of correlated excitation energy fluctuations of neighboring chromophores (Lee et al. Science 2007, 316, 1462), quantum chemistry calculations and molecular dynamics simulations were employed to calculate the electronic-vibrational coupling in the excited states of the photosynthetic reaction center of purple bacteria Rhodobacter (Rb.) sphaeroides. The ground states and lowest excited (Q(y)) states of isolated bacteriochlorophyll a (BChl a) and bacteriopheophytin (BPhe) molecules were first optimized using density functional theory (DFT) and time-dependent density functional theory (TDDFT). Normal mode analyses were then performed to calculate the Huang-Rhys factors of the intramolecular vibrational modes. To account for intermolecular electronic-vibrational coupling, molecular dynamics simulations were first performed. The ZINDO/S method and partial charge coupling method were then used to calculate the excitation energy fluctuations caused by the protein environment and obtain the spectral density. No obvious correlations in transition energy fluctuations between BChl a and BPhe pigments were observed in the time scale of our MD simulation. Finally, by comparing the calculated absorption spectra with experimental ones, magnitudes of inhomogeneous broadening due to the static disorder were estimated. The large amplitude of the static disorder indicates that a large portion of the spectral density and their correlations may still be hidden in the inhomogeneous broadening due to the finite MD simulation time.

Theoretical study on charge carrier mobilities of tetrathiafulvalene derivatives.

We calculated the hole and electron mobilities of tetrathiafulvalene (TTF) derivative crystals using first-principles calculations and the Marcus theory of electron transfer. The hole and electron reorganization energies were found to decrease with the extension of π-conjugated orbitals. The calculated hole mobilities of TTF, dibenzo-tetrathiafulvalene (DB-TTF), and dinaphtho-tetrathiafulvalene (DN-TTF) agree well with the experimental results. In addition, with the increase of the number of benzene rings attached to the TTF skeleton, the hole mobilities decrease and the electron mobilities increase. The calculated electron mobility of dianthro-tetrathiafulvalene (DA-TTF) based on a virtual crystal structure is much larger than the hole one due to the small electron reorganization energy and large electron coupling. This suggests that the charge transfer properties of the TTF derivatives can be modified when the number of aromatic rings on TTF skeleton increases.