High-Multiplicity Natural Orbitals in Multireference Configuration Interaction for Excited States

Multireference configuration interaction (MRCI) is a very useful tool in studying excited states, dissociation of molecules, and chemical systems with multireference character. In many cases however, poor computational scaling limits its use to small systems. In the past, several different approaches have been taken in order to make MRCI and other multireference methods more accessible when dealing with larger systems. Here we propose the use of high-multiplicity natural orbitals (HMNO) in order to improve several aspects of the MRCI calculation. Natural orbitals, derived from a configuration interaction with single and double excitations calculation on a high-multiplicity reference state, were used in lieu of the standard complete active space self-consistent field (CASSCF) canonical molecular orbitals. This work examines the ability of the MRCI/HMNO approach to reliably reproduce vertical excitation energies for singlet states as well as energies for conical intersections. It is found that the MRCI/HMNO approach reliably reproduces vertical excitation energies obtained from a standard MRCI using CASSCF orbitals, with an average deviation of 0.12 and 0.15 eV for the uncorrected and Davidson corrected energies, respectively. We also explore some of the computational savings that the new method affords via systematic truncation of the virtual space. Overall, it is found that the HMNO approach is a reliable method for computing MRCI excited-state energies in a fraction of the time it would take to run a standard MRCI calculation

Excited State Relaxation of Neutral and Basic 8‑Oxoguanine

8-Oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dGuo) is one of the most common forms of DNA oxidative damage. Recent studies have shown that 8-oxo-dGuo can repair cyclobutane pyrimidine dimers in double-stranded DNA when photoexcited, making its excited state dynamics of particular interest. The excited state lifetimes of 8-oxo-dGuo and its anion have been previously probed using transient absorption spectroscopy; however, more information is required to understand the decay mechanisms. In this work, excited state potential energy surfaces for the neutral and deprotonated forms of the free base, 8-oxoguanine (8-oxo-G), are explored theoretically using multireference methods while the nucleoside is experimentally studied using steady-state fluorescence spectroscopy. It is determined that the neutral species exhibits ultrafast radiationless decay via easy access to conical intersections. The relatively long lifetime for the anion can be explained by the existence of sizable barriers between the Franck–Condon region and two S₁/S₀ minimum energy conical intersections. A Strickler–Berg analysis of the experimentally measured fluorescence quantum yields and lifetimes is consistent with emission from <i>ππ</i>* excited states in line with theoretical predictions

DataSheet_1_Proteomic and metabolomic analysis on cadmium-induced mitochondrial toxicity in liver tissues of juvenile olive flounder Paralichthys olivaceus.pdf

IntroductionCadmium (Cd) is one of the most dominant heavy metals in the Bohai Sea. Our previous study proved that Cd could induce gill mitochondrial toxicity in marine animals. Herein, we aimed to elucidate the toxicity mechanism of Cd on liver mitochondria, as liver is the main metabolic and detoxification organ and generally rich in mitochondria.MethodsThe mitochondrial responses induced by Cd (5 and 50 μg/L) were characterized by observing mitochondrial morphology, measuring mitochondrial membrane potential (MMP), and proteomic and metabolomic analysis in juvenile olive flounder Paralichthys olivaceus livers.ResultsAfter water-bonre exposure for 14 days, two Cd treatments decreased MMPs significantly and caused ultrastructural-damaged mitochondria in flounder livers. NMR-based metabolomics revealed that Cd exposure mainly altered the abundances of metabolites (ATP, AMP, phosphocholine, lactate and succinate) related to energy metabolism in flounder livers. iTRAQ-based mitochondrial proteomics indicated that 27 differentially expressed proteins (DEPs) were screened out from liver mitochondria after Cd treatments. These proteins were mainly associated with energy metabolism (oxidative phosphorylation (OXPHOS) and tricarboxylic acid (TCA) cycle) and apoptosis.DiscussionThese results indicated that Cd disrupted mitochondrial morphology, energy homeostasis and apoptosis in liver mitochondria in flounder P. olivaceus. This work revealed a comprehensive view on Cd-induced mitochondrial responses in the liver tissues of flounder using an integrated proteomic and metabolomic approach.</p

High-Level Production of l‑Fucose by Plasmid-Free or Antibiotic-Independent Metabolically Engineered Escherichia coli Strains

l-Fucose is an important monosaccharide unit that exists in various biomasses, especially in microalgae. Microbial l-fucose using metabolically engineered strains has attracted attention due to its high yield and industrial feasibility. Previously, we engineered Escherichia coli MG1655 to efficiently produce 2′-fucosyllactose by genomic integration. Herein, this plasmid-free strain was further engineered to produce l-fucose by integrating a specific α-l-fucosidase gene and deleting the l-fucose degradation pathway. Its effectiveness of l-fucose biosynthesis by plasmid-free and inducer-free fermentation was demonstrated by both shake-flask and fed-batch cultivation with titers of 2.74 and 21.15 g/L, respectively. The precursor GDP-l-fucose supply was strengthened to obviously enhance l-fucose biosynthesis by introducing a single plasmid expressing four pathway genes. The hok/sok system was introduced to promote the plasmid stabilization without antibiotic. The final engineered strain efficiently could produce l-fucose without antibiotics, with titers of 6.83 and 35.68 g/L by shake-flask and fed-cultivation cultivation, respectively

DataSheet_2_Proteomic and metabolomic analysis on cadmium-induced mitochondrial toxicity in liver tissues of juvenile olive flounder Paralichthys olivaceus.doc

IntroductionCadmium (Cd) is one of the most dominant heavy metals in the Bohai Sea. Our previous study proved that Cd could induce gill mitochondrial toxicity in marine animals. Herein, we aimed to elucidate the toxicity mechanism of Cd on liver mitochondria, as liver is the main metabolic and detoxification organ and generally rich in mitochondria.MethodsThe mitochondrial responses induced by Cd (5 and 50 μg/L) were characterized by observing mitochondrial morphology, measuring mitochondrial membrane potential (MMP), and proteomic and metabolomic analysis in juvenile olive flounder Paralichthys olivaceus livers.ResultsAfter water-bonre exposure for 14 days, two Cd treatments decreased MMPs significantly and caused ultrastructural-damaged mitochondria in flounder livers. NMR-based metabolomics revealed that Cd exposure mainly altered the abundances of metabolites (ATP, AMP, phosphocholine, lactate and succinate) related to energy metabolism in flounder livers. iTRAQ-based mitochondrial proteomics indicated that 27 differentially expressed proteins (DEPs) were screened out from liver mitochondria after Cd treatments. These proteins were mainly associated with energy metabolism (oxidative phosphorylation (OXPHOS) and tricarboxylic acid (TCA) cycle) and apoptosis.DiscussionThese results indicated that Cd disrupted mitochondrial morphology, energy homeostasis and apoptosis in liver mitochondria in flounder P. olivaceus. This work revealed a comprehensive view on Cd-induced mitochondrial responses in the liver tissues of flounder using an integrated proteomic and metabolomic approach.</p

Additional File 5:

KEGG enrichment results (XLSX 46 kb

Additional File 2:

Thirty-six scatterplot diagrams of gene pairwise correlation (RAR 1443 kb

Recognition of “Oxygen-/Water-Fueled” PET-RAFT Protocol Matched to Covalent Organic Frameworks

The reactive oxygen species (ROS)-mediated photoinduced electron transfer reversible addition-fragmentation chain transfer (PET-RAFT) process is an attractive tool to enhance the oxygen tolerance of radical polymerization systems. In this paper, we investigate the relationship between the covalent organic framework (COF) structure and polymerization performance based on the O2•–/H2O system by modulating the COF at atomic and molecular levels. We combine density functional theory (DFT) calculations and experiments to clarify the “oxygen-/water-fueled” PET-RAFT polymerization mechanism and identify the key steps of the protocol. Based on the modulation of the TD-1 COF template structure, the relatively efficient charge–hole separation efficiency allows the matching of TD-2 COF and TD-3 COF with the O2•–/H2O system to achieve high-quality RAFT polymerization, providing insights into the rational design and development of catalytic systems with better performance

Additional file 1 of 3-dimensional analysis of hard- and soft-tissue symmetry in a Chinese population

Additional file 1: Supplementary Table 1. Descriptive data of different menton deviation in males. Supplementary Table 2. Mann-Whitney U test of RMS of different menton deviation in males. Supplementary Table 3. Descriptive data of different menton deviation in females. Supplementary Table 4. Mann-Whitney U test of RMS of different menton deviation in females. Supplementary Table 5. Descriptive data of different skeletal classes in males. Supplementary Table 6. Mann-Whitney U test of RMS of different skeletal classes in males. Supplementary Table 7. Descriptive data of different skeletal classes in females. Supplementary Table 8. Mann-Whitney U test of RMS of different skeletal classes in females. Supplementary Table 9. Correlation coefficient values of hard- and soft-tissue in males. Supplementary Table 10. Correlation coefficient values of hard- and soft-tissue in females

Additional File 3:

All DEGs list (XLSX 1713 kb