The role of electronic triplets and high-lying singlet states in the deactivation mechanism of the parent BODIPY: An ADC(2) and CASPT2 study

The potential tunability of the spectroscopic properties of the BODIPY parent dye by suitable functionalization makes it attractive for a number of applications. Unfortunately, its strong fluorescence against minor intersystem crossing to the triplet states prevents its application in photodynamic therapy. With the perspective of designing BODIPY derivatives with enhanced intersystem crossing, the goal of this work is two-fold: (i) investigate the main deactivation channels of the parent BODIPY following irradiation, paying particular attention to the accessibility of the triplet state potential energy surfaces, as well as the non-radiative pathways involving the second brightest more stable singlet electronic state, S2, and (ii) evaluate the performance of the computationally efficient second order algebraic-diagrammatic construction scheme for the polarization propagator, (ADC(2)) against the complete active space second-order perturbation theory (CASPT2) method. Three singlet/triplet crossings were found, all of them with small spin-orbit couplings, being the S1/T2 crossing the most plausible for the observed intersystem crossing yield. Methodologically, it is found that the ADC(2) method qualitatively reproduces the landscape of the potential energy profiles for the photophysical processes investigated; however, it systematically underestimates the energies of the stationary points and crossings of the same and different multiplicity, with the largest discrepancies found at S1/S0 crossing points. Our CASPT2 results provide a comprehensive picture of the landscape of the excited state potential energy surfaces of the parent BODIPY that might serve as a basis for the rational design of photosensitizers with a particular photophysical profileThis work has been supported by the Project CTQ2015-63997- C2 of the Ministerio de Economía y Competitividad of Spain. I.C. gratefully acknowledges the “Ramón y Cajal” program of the Ministerio de Economía y Competitividad of Spain. M.D.V. thanks the Marie Curie Actions, within the Innovative Training Network-European Join Doctorate in Theoretical Chemistry and Computational Modelling TCCM-ITN-EJD-642294, for financial suppor

A study on waste-derived NiZn soft ferrites as EMI suppressor

Nickel-zinc soft ferrites with spinel structure are important electronic components popularly used as EMI suppressor, electromagnet core and transformer core. It contains nickel, zinc or manganese, and the raw material is mainly hematite. The most commonly use soft ferrites are NiZn ferrites and MnZn ferrites. NiZn ferrites exhibit higher resistivity than MnZn ferrites and are therefore more suitable for frequencies above 1 MHz. In this work, iron oxide waste generated from a local cold-rolling steel mill was purified and converted into hematite. The waste-derived hematite was used as the raw material in the synthesis of NiZn ferrites. The magnetic properties such as permeability, saturation magnetization and coercivity of the waste-derived NiZn ferrites was analyzed and compared to the industrial grade NiZn ferrites. Our results show that the waste-derived ferrite possesses excellent magnetic properties. The microstructure of the waste-derived NiZn ferrite is also discussed

Predictive response-relevant clustering of expression data provides insights into disease processes

This article describes and illustrates a novel method of microarray data analysis that couples model-based clustering and binary classification to form clusters of ;response-relevant' genes; that is, genes that are informative when discriminating between the different values of the response. Predictions are subsequently made using an appropriate statistical summary of each gene cluster, which we call the ;meta-covariate' representation of the cluster, in a probit regression model. We first illustrate this method by analysing a leukaemia expression dataset, before focusing closely on the meta-covariate analysis of a renal gene expression dataset in a rat model of salt-sensitive hypertension. We explore the biological insights provided by our analysis of these data. In particular, we identify a highly influential cluster of 13 genes-including three transcription factors (Arntl, Bhlhe41 and Npas2)-that is implicated as being protective against hypertension in response to increased dietary sodium. Functional and canonical pathway analysis of this cluster using Ingenuity Pathway Analysis implicated transcriptional activation and circadian rhythm signalling, respectively. Although we illustrate our method using only expression data, the method is applicable to any high-dimensional datasets

Carbon chemistry in Galactic Bulge Planetary Nebulae

Galactic Bulge Planetary Nebulae show evidence of mixed chemistry with emission from both silicate dust and PAHs. This mixed chemistry is unlikely to be related to carbon dredge up, as third dredge-up is not expected to occur in the low mass Bulge stars. We show that the phenomenon is widespread, and is seen in 30 nebulae out of 40 of our sample, selected on the basis of their infrared flux. HST images and UVES spectra show that the mixed chemistry is not related to the presence of emission-line stars, as it is in the Galactic disk population. We also rule out interaction with the ISM as origin of the PAHs. Instead, a strong correlation is found with morphology, and the presence of a dense torus. A chemical model is presented which shows that hydrocarbon chains can form within oxygen-rich gas through gas-phase chemical reactions. The model predicts two layers, one at $A_V\sim 1.5$ where small hydrocarbons form from reactions with C$^+$, and one at $A_V\sim 4$, where larger chains (and by implication, PAHs) form from reactions with neutral, atomic carbon. These reactions take place in a mini-PDR. We conclude that the mixed chemistry phenomenon occurring in the Galactic Bulge Planetary Nebulae is best explained through hydrocarbon chemistry in an UV-irradiated, dense torus.Comment: 13 pages, 10 figue

The control parameterization method for nonlinear optimal control: A survey

The control parameterization method is a popular numerical technique for solving optimal control problems. The main idea of control parameterization is to discretize the control space by approximating the control function by a linear combination of basis functions. Under this approximation scheme, the optimal control problem is reduced to an approximate nonlinear optimization problem with a finite number of decision variables. This approximate problem can then be solved using nonlinear programming techniques. The aim of this paper is to introduce the fundamentals of the control parameterization method and survey its various applications to non-standard optimal control problems. Topics discussed include gradient computation, numerical convergence, variable switching times, and methods for handling state constraints. We conclude the paper with some suggestions for future research

Electron affinities of the first- and second- row atoms: benchmark ab initio and density functional calculations

A benchmark ab initio and density functional (DFT) study has been carried out on the electron affinities of the first- and second-row atoms. The ab initio study involves basis sets of $spdfgh$ and $spdfghi$ quality, extrapolations to the 1-particle basis set limit, and a combination of the CCSD(T), CCSDT, and full CI electron correlation methods. Scalar relativistic and spin-orbit coupling effects were taken into account. On average, the best ab initio results agree to better than 0.001 eV with the most recent experimental results. Correcting for imperfections in the CCSD(T) method improves the mean absolute error by an order of magnitude, while for accurate results on the second-row atoms inclusion of relativistic corrections is essential. The latter are significantly overestimated at the SCF level; for accurate spin-orbit splitting constants of second-row atoms inclusion of (2s,2p) correlation is essential. In the DFT calculations it is found that results for the 1st-row atoms are very sensitive to the exchange functional, while those for second-row atoms are rather more sensitive to the correlation functional. While the LYP correlation functional works best for first-row atoms, its PW91 counterpart appears to be preferable for second-row atoms. Among ``pure DFT'' (nonhybrid) functionals, G96PW91 (Gill 1996 exchange combined with Perdew-Wang 1991 correlation) puts in the best overall performance. The best results overall are obtained with the 1-parameter hybrid modified Perdew-Wang (mPW1) exchange functionals of Adamo and Barone [J. Chem. Phys. {\bf 108}, 664 (1998)], with mPW1LYP yielding the best results for first-row, and mPW1PW91 for second-row atoms. Indications exist that a hybrid of the type $a$ mPW1LYP + $(1-a)$ mPW1PW91 yields better results than either of the constituent functionals.Comment: Phys. Rev. A, in press (revised version, review of issues concerning DFT and electron affinities added

Disease progression in Plasmodium knowlesi malaria is linked to variation in invasion gene family members.

Emerging pathogens undermine initiatives to control the global health impact of infectious diseases. Zoonotic malaria is no exception. Plasmodium knowlesi, a malaria parasite of Southeast Asian macaques, has entered the human population. P. knowlesi, like Plasmodium falciparum, can reach high parasitaemia in human infections, and the World Health Organization guidelines for severe malaria list hyperparasitaemia among the measures of severe malaria in both infections. Not all patients with P. knowlesi infections develop hyperparasitaemia, and it is important to determine why. Between isolate variability in erythrocyte invasion, efficiency seems key. Here we investigate the idea that particular alleles of two P. knowlesi erythrocyte invasion genes, P. knowlesi normocyte binding protein Pknbpxa and Pknbpxb, influence parasitaemia and human disease progression. Pknbpxa and Pknbpxb reference DNA sequences were generated from five geographically and temporally distinct P. knowlesi patient isolates. Polymorphic regions of each gene (approximately 800 bp) were identified by haplotyping 147 patient isolates at each locus. Parasitaemia in the study cohort was associated with markers of disease severity including liver and renal dysfunction, haemoglobin, platelets and lactate, (r = ≥ 0.34, p =  <0.0001 for all). Seventy-five and 51 Pknbpxa and Pknbpxb haplotypes were resolved in 138 (94%) and 134 (92%) patient isolates respectively. The haplotypes formed twelve Pknbpxa and two Pknbpxb allelic groups. Patients infected with parasites with particular Pknbpxa and Pknbpxb alleles within the groups had significantly higher parasitaemia and other markers of disease severity. Our study strongly suggests that P. knowlesi invasion gene variants contribute to parasite virulence. We focused on two invasion genes, and we anticipate that additional virulent loci will be identified in pathogen genome-wide studies. The multiple sustained entries of this diverse pathogen into the human population must give cause for concern to malaria elimination strategists in the Southeast Asian region

Photochemistry of Furyl- and Thienyldiazomethanes: Spectroscopic Characterization of Triplet 3-Thienylcarbene

Photolysis (λ \u3e 543 nm) of 3-thienyldiazomethane (1), matrix isolated in Ar or N2 at 10 K, yields triplet 3-thienylcarbene (13) and α-thial-methylenecyclopropene (9). Carbene 13 was characterized by IR, UV/vis, and EPR spectroscopy. The conformational isomers of 3-thienylcarbene (s-E and s-Z) exhibit an unusually large difference in zero-field splitting parameters in the triplet EPR spectrum (|D/hc| = 0.508 cm–1, |E/hc| = 0.0554 cm–1; |D/hc| = 0.579 cm–1, |E/hc| = 0.0315 cm–1). Natural Bond Orbital (NBO) calculations reveal substantially differing spin densities in the 3-thienyl ring at the positions adjacent to the carbene center, which is one factor contributing to the large difference in D values. NBO calculations also reveal a stabilizing interaction between the sp orbital of the carbene carbon in the s-Z rotamer of 13 and the antibonding σ orbital between sulfur and the neighboring carbon—an interaction that is not observed in the s-E rotamer of 13. In contrast to the EPR spectra, the electronic absorption spectra of the rotamers of triplet 3-thienylcarbene (13) are indistinguishable under our experimental conditions. The carbene exhibits a weak electronic absorption in the visible spectrum (λmax = 467 nm) that is characteristic of triplet arylcarbenes. Although studies of 2-thienyldiazomethane (2), 3-furyldiazomethane (3), or 2-furyldiazomethane (4) provided further insight into the photochemical interconversions among C5H4S or C5H4O isomers, these studies did not lead to the spectroscopic detection of the corresponding triplet carbenes (2-thienylcarbene (11), 3-furylcarbene (23), or 2-furylcarbene (22), respectively)

Ribosomal oxygenases are structurally conserved from prokaryotes to humans

2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components1,2 and in the hydroxylation of transcription factors3 and splicing factor proteins4. Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA5,6,7 and ribosomal proteins8 have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy9,10,11,12. The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans8 raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses arginine hydroxylation in the ribosomal protein L16; in humans, MYC-induced nuclear antigen (MINA53; also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone Nε-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases catalysing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate-oxidizing species reacts. This coordination flexibility has probably contributed to the evolution of the wide range of reactions catalysed by oxygenases

Molecular excitation in the Interstellar Medium: recent advances in collisional, radiative and chemical processes

We review the different excitation processes in the interstellar mediumComment: Accepted in Chem. Re