Total absorption spectrum of benzene aggregates obtained from two different approaches

CONTEXT

The study of molecular aggregation effects on the electronic spectrum is essential for the development of optoelectronic devices. However, investigating the entire valence absorption spectrum of aggregates using quantum mechanical methods is a challenging task. In this work, we perform systematic simulations of the absorption spectrum of benzene molecular clusters up to 35 eV applying two approaches based on time-dependent density functional theory. The results show that depending on the dimer packing, different energy shifts occur for the symmetry allowed [Formula: see text] transition, in comparison to the monomer. The transition intensity increases for the band around 6 eV for larger aggregates from the monomer to dimers and tetramer, indicating the occurrence of the symmetry forbidden (in [Formula: see text] point group) [Formula: see text] [Formula: see text] transition. The benzene crystal exhibits a large redshift following the experimental spectrum. Also, the continuum regions of all spectra show a good agreement with the experiments both in gas and solid phases.

METHODS

Geometry optimization of the monomer was carried out with Gaussian 09 software using the PBE0/def2-TZVP level of theory. We used dimers and tetramer molecular geometries extracted from the experimental crystal structure. The absorption spectra were directly obtained by the Liouville-Lanczos TDDFT approach with plane waves basis set or indirectly by TDDFT pseudo-spectra calculated in a [Formula: see text] basis followed by analytic continuation procedure to obtain complex polarizability. The former is available at Quantum ESPRESSO, and the latter was calculated using Gaussian 09 with the post-processing performed with a code previously developed in our group.

Gas-phase C60Hn+q (n = 0-4, q = 0,1) fullerenes and fulleranes: spectroscopic simulations shed light on cosmic molecular structures

The discovery of C60, C60+, and C70 in the interstellar medium has ignited a profound interest in the astrochemistry of fullerene and related systems. In particular, the presence of diffuse interstellar bands and their association with C60+ has led to the hypothesis that hydrogenated derivatives, known as fulleranes, may also exist in the interstellar medium and contribute to these bands. In this study, we systematically investigated the structural and spectroscopic properties of C60Hn+q (n = 0-4, q = 0,1) using an automated global minimum search and density functional theory calculations. Our results revealed novel global minimum structures for C60H2 and C60H4, distinct from previous reports. Notably, all hydrogenated fullerenes exhibited lower ionization potentials and higher proton affinities compared to C60. From an astrochemical perspective, our results exposed the challenges in establishing definitive spectroscopic criteria for detecting fulleranes using mid-infrared and UV-Vis spectroscopies. However, we successfully identified distinct electronic transitions in the near-infrared range that serve as distinctive signatures of cationic fulleranes. We strongly advocate for further high-resolution experimental studies to fully explore the potential of these transitions for the interstellar detection of fulleranes.

Revisiting the Spectrum of Co(CN)63-: The Role of Correlation, Solvation, and Vibronic and Spin-Orbit Couplings

In the present work, we revisit the spectrum of the hexacyanocobaltate(III) ion, [Co(CN)₆]^3-, which has been considered a prototype complex in the coordination chemistry, with modern quantum chemistry methods. The main features have been describing by revealing the role of different effects, such as vibronic coupling, solvation and spin-orbit coupling. The UV-vis spectrum is composed by two bands (¹A_1g → ¹T_1g and ¹A_1g → ¹T_2g), characterized by singlet-singlet metal-centered transitions, and a more intense third one, characterized by charge transfer transition. There is also a small band shoulder. The first two are symmetry-forbidden transitions in the O_h group. Their intensity can only be explained by a vibronic coupling mechanism. For the band shoulder, additional to vibronic coupling, spin-orbit coupling is also necessary, since the transition is characterized as singlet to triplet, ¹A_1g → ³T_1g.

Electron-molecule collisions with explicit rovibrational resolution at MRCI level and using even tempered basis sets

A method for calculating the generalized oscillator strengths (GOSs) and differential cross section (DCS) with vibration and rotation resolution is presented. The importance of accounting for the rotational contribution is to be emphasized since it has not previously been considered in GOS calculations. Although largely neglected due to its small effect on various properties, the rotational resolution proved to be fundamental in the study of certain phenomena, such as the interference between rotational states in a molecule. As the general goal of this work is to obtain theoretical values comparable to high resolution experiments, special care was taken on the calculation of the electronic part of the scattering amplitude, particularly in what concerns the choice of the atomic basis set. Accordingly, even-tempered basis sets have proved to lead to good results. The helium atom was taken as a model system for this aspect of the problem. Then, GOS and DCS, for explicit vibrational and rotational transitions, were calculated for hydrogen and nitrogen molecules. For higher accuracy, a non-Franck-Condon approach was used to obtain transitions involving vibrational states. The resultant values have shown good agreement with the available experimental data.

Structure, Stability, and Spectroscopic Properties of Small Acetonitrile Cation Clusters

Ionization and fragmentation pathways induced by ionizing agents are key to understanding the formation of complex molecules in astrophysical environments. Acetonitrile (CH₃CN), the simplest organic nitrile, is an important molecule present in the interstellar medium. In this work, DFT and MP2 calculations were performed in order to obtain the low energy structures of the most relevant cations formed from electron-stimulated ion desorption of CH₃CN ices. Selected reaction pathways and spectroscopic properties were also calculated. Our results indicate that the most stable acetonitrile cation structure is CH₂CNH⁺ and that hydrogenation can occur successively without isomerization steps until its complete saturation. Moreover, the stability of distinct cluster families formed from the interaction of acetonitrile with small fragments, such as CH_n⁺, C₂H_n⁺, and CH_nCNH⁺, is discussed in terms of their respective binding energies. Some of these molecular clusters are stabilized by hydrogen bonds, leading to species whose infrared features are characterized by a strong redshift of the N-H stretching mode. Finally, the rotational spectra of CH₃CN and protonated acetonitrile, CH₃CNH⁺, were simulated using distinct computational protocols based on DFT, MP2, and CCSD(T) considering centrifugal distortion, vibrational-rotational coupling, and vibrational anharmonicity corrections. By adopting an empirical scaling procedure for calculating spectroscopic parameters, we were able to estimate the rotational frequencies of CH₃CNH⁺ with an expected average error below 1 MHz for J values up to 10.

Fragment and cluster ions from gaseous and condensed pyridine produced under electron impact

The ion-distribution from condensed pyridine due to 2 keV electron impact shows hydrogenated fragments and clusters with m/z ≤ 320 u and shifts towards higher masses compared to the gas-phase fragmentation. The formation of a bond between the pyridine and a carbenium ion is crucial for the stability of the selected cluster ions.

Spin-orbit splitting for inner-shell 2p states

A strategy to calculate spin-orbit splitting for inner-shell transitions at an ab initio level is presented. The initial wave function is calculated for a spinless Hamiltonian at a multiconfigurational level, with just a few configurations, followed by multireference configuration interaction in order to establish a set of singlet and triplet states at 2p excitation edge. Then, the full Breit-Pauli Hamiltonian is formed and diagonalized on this state basis. The spin-orbit splitting is determined by a graphical procedure depending on the intensity of the transition from ground state. The specific states studied are those originating from 2p transitions in argon, HCl, H2S, and PH3.

Yellow Stunt, a Tobacco Disease Caused by Pythium dissotocum, in Southern Parts of Brazil

Yellow stunt, an emerging disease of tobacco (Nicotiana tabacum), has become increasingly prevalent in tobacco-growing regions in southern Brazil. Major symptoms are moderate to severe stunting, yellowing of leaves, severe wilting, darkened roots, necrosis of stem tissue directly above the soil line, and plant death. Phytophthora glovera was first proposed in 1999 as the primary causal agent of yellow stunt (1), but since then, there has been no data or completion of Koch's postulates to support this. Fifty-six isolates of fungi and fungus-like organisms were obtained from stem and root samples of tobacco plants with typical symptoms of yellow stunt in the Brazilian States of Rio Grande do Sul, Santa Catarina, and Paraná during the growing seasons of 2004/05 to 2006/07. They were identified to species level by analysis of the morphological characteristics (2) and sequence of rDNA internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) (3). The isolates were identified as Pythium dissotocum (29), Fusarium oxysporum (10), P. graminicola (5), Rhizoctonia solani (4), F. solani (3), P. ultimum (3), P. deliense (1), and P. inflatum (1). The ITS sequences of the 29 isolates identified as P. dissotocum were identical. The nucleotide sequence of one isolate, LFM27/2005, has been deposited in GenBank (GQ495982). Analysis of ITS sequences alone was not sufficient to differentiate this isolate from other species in the Pythium subclade B2, such as P. coloratum, P. lutarium, P. marinum, or P. diclinum. However, the combination of morphological and cultural characteristics (2) and sequence data support our identification of LFM27/2005 and similar isolates as P. dissotocum. Colonies of LFM27/2005 on cornmeal agar had filamentous sporangia and formed slightly inflated, dendroid structures. Zoospores formed at 5°C. Daily growth rate on potato carrot agar was 13 mm at 25°C. The oogonia (22 μm in diameter) were nonornamented and either intercalary or terminal. Antheridia, commonly 1 to 2 per oogonium, were sessile, born on unbranched stalks, and either monoclinous or diclinous. Aplerotic or nearly plerotic oospores measured 20 μm in diameter with a smooth wall 2.5 μm thick. Pathogenicity tests for each pathogen were performed in a greenhouse at ~24°C in pots filled with pine bark substrate infested with inoculum at the time Burley tobacco plants showed five expanded leaves. Each test consisted of five plants and was repeated three times. Inoculum for one to three isolates representative of each pathogen was prepared by growing 2-month-old cultures at 28°C in the dark for 7 days on potato dextrose agar medium overlaid with three sterile oat kernels. Noninfested oat kernels were used for control plants. Forty days after inoculation, only plants inoculated with isolates of P. dissotocum exhibited all symptoms associated with yellow stunt. P. inflatum and R. solani did not induce yellow stunt symptoms and the others induced only wilting and root rot. P. dissotocum was recovered from an inoculated, symptomatic plant, fulfilling Koch's postulates. Its morphology was identical to isolates obtained from original field samples. The results demonstrate the association of isolates of P. dissotocum with tobacco yellow stunt in Brazil. References: (1) H. D. Shew et al. Phytopathology (Abstr.) 89(suppl):S72, 1999. (2) A. J. van der Plaats-Niterink. Stud. Mycol. 21:1, 1981. (3) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA, 1990.

Theoretical investigation on the stability of negatively charged formic acid clusters

Recent experimental results on negatively charged formic acid clusters generated by the impact of (252)Cf fission fragments on icy formic acid target are compared to quantum mechanical calculations. Structures for the clusters series, (HCOOH)nOH(-), where 2 < or = n < or = 4, are proposed based on ab initio electronic structure methods. The results show that cluster growth does not have a regular pattern of nucleation. A stability analysis was performed considering the commonly defined stability function. Temporal behavior of the clusters was evaluated by Born-Oppenheimer molecular dynamics to check the mechanism that provides cluster stability. The evaluated temporal profiles indicate the importance of hydrogen atom migration between the formic acid moieties in maintaining the stability of the structures and the water formation due to hydrogen abstraction by the hydroxyl approach.

Screening for cytotoxic activity of extracts and isolated alkaloids from bulbs of Hippeastrum vittatum

The dichloromethane and n-butanol extracts obtained from fresh bulbs of Hippeastrum vittatum (Amaryllidaceae), collected in Southern Brazil, were evaluated for their cytotoxic activity in vitro against five human cell lines (HT29 colon adenocarcinoma, H460 non-small cell lung carcinoma, RXF393 renal cell carcinoma, MCF7 breast cancer, and OVCAR3 epithelial ovarian cancer), using the sulphorhodamine B assay. Both extracts showed potential antiproliferative activity. From CH(2)Cl(2) fraction, three alkaloids were isolated: lycorine, vittatine and montanine. The two last compounds were submitted to the antiproliferative assay and the highest level of cytotoxicity was found for the alkaloid montanine.

Intensity of d−d Symmetry-Forbidden Electronic Transition in Cr(CO)6

Absolute absorption intensities (oscillator strengths) are calculated for the d-d symmetry-forbidden transition in hexacarbonyl chromium. The vibronic coupling mechanism is taken into account in a way that represents an alternative to the traditional perturbative approach of Herzberg and Teller. In the so-called direct method, the electronic transition moment is directly expanded in a power series of the vibrational normal coordinates of suitable symmetry. In the present case, i.e., d-d ligand field transitions, or more specifically (1)A(1g) --> (1)T(1g) and (1)A(1g) --> (1)T(2g) transitions, the dipole selection rule is broken by vibronic interaction induced by normal modes that transform like T(1u) and T(2u) representations of the O(h) group. An analysis of the relative importance of normal modes in promoting electronic transitions is carried out.

Characterization by 27Al NMR, X-ray Absorption Spectroscopy, and Density Functional Theory Techniques of the Species Responsible for Benzene Hydrogenation in Y Zeolite-Supported Carburized Molybdenum Catalysts

Carburized molybdenum catalysts supported on a dealuminated NaH-Y zeolite were prepared by carburization under a 20% methane in hydrogen flow of two precursors obtained by adsorption of molybdenum hexacarbonyl, one containing 5 wt % and the other 10 wt % Mo, and a third one was prepared by impregnation with aqueous ammonium heptamolybdate, containing 5 wt % Mo. The three catalysts displayed very distinct behaviors in the benzene hydrogenation reaction at atmospheric pressure and 363 K. By using XANES spectroscopy at the molybdenum L edge, EXAFS and XANES spectroscopy at the molybdenum K edge, and 27Al solid-state NMR spectroscopy, it was shown that different carburized molybdenum species exist in each sample. In the catalyst containing 10 wt % Mo, formation of molybdenum carbide nanoparticles was observed, with an estimated diameter of 1.8 nm. In the catalyst containing 5 wt % Mo and prepared by carburization of adsorbed molybdenum hexacarbonyl, formation of molybdenum oxycarbide dimers is proposed. In the latter case, density functional theory calculations have led to a dimer structure which is compatible with EXAFS results. In the catalyst prepared by impregnation with ammonium heptamolybdate solution followed by carburization, the molybdenum seems to interact with extraframework alumina to produce highly disordered mixed molybdenum-aluminum oxycarbides.

On the Conformational Memory in the Photodissociation of Formic Acid

The photodissociation of formic acid at 248 and 193 nm was investigated by classical trajectory and RRKM calculations using an interpolated potential energy surface, iteratively constructed using the B3LYP/aug-cc-pVDZ level of calculation. Several sampling schemes in the ground electronic state were employed to explore the possibility of conformational memory in formic acid. The CO/CO2 branching ratios obtained from trajectories initiated at the cis and at the trans conformers are almost identical to each other and in very good accordance with the RRKM results. In addition, when a specific initial excitation that simulates more rigorously the internal conversion process is used, the calculated branching ratio does not vary with respect to those obtained from cis and trans initializations. This result is at odds with the idea of conformational memory in the ground state proposed recently for the interpretation of the experimental results. It was also found that the calculated CO vibrational distributions after dissociation of the parent molecule at 248 nm are in agreement with the experimental available data.

Retinol-induced changes in the phosphorylation levels of histones and high mobility group proteins from Sertoli cells

Chromatin proteins play a role in the organization and functions of DNA. Covalent modifications of nuclear proteins modulate their interactions with DNA sequences and are probably one of the multiple factors involved in the process of switch on/off transcriptionally active regions of DNA. Histones and high mobility group proteins (HMG) are subject to many covalent modifications that may modulate their capacity to bind to DNA. We investigated the changes induced in the phosphorylation pattern of cultured Wistar rat Sertoli cell histones and high mobility group protein subfamilies exposed to 7 microM retinol for up to 48 h. In each experiment, 6 h before the end of the retinol treatment each culture flask received 370 KBq/ml [32P]-phosphate. The histone and HMGs were isolated as previously described [Moreira et al. Medical Science Research (1994) 22: 783-784]. The total protein obtained by either method was quantified and electrophoresed as described by Spiker [Analytical Biochemistry (1980) 108: 263-265]. The gels were stained with Coomassie brilliant blue R-250 and the stained bands were cut and dissolved in 0.5 ml 30% H2O2 at 60oC for 12 h. The vials were chilled and 5.0 ml scintillation liquid was added. The radioactivity in each vial was determined with a liquid scintillation counter. Retinol treatment significantly changed the pattern of each subfamily of histone and high mobility group proteins.

Influence of the biomatrix on the response of Sertoli cells to FSH

Sertoli cell preparations isolated from 15-day-old Wistar rats were cultured on two different substrates, i.e., plastic and a biomatrix isolated from seminiferous tubules of rat testis. Sertoli cells cultured on a biomatrix acquired a phenotype and morphology more characteristic of in vivo differentiated cells. In order to determine the influence of a biomatrix on the response of Sertoli cells to FSH, on the 7th day of culture, untreated cells, or cells pretreated for 12 h with FSH (1 microgram/ml), were incubated with [U-14C] leucine or [2-3H] mannose. Cells cultured on the biomatrix showed higher [U-14C] leucine and [2-3H] mannose incorporation into proteins and glycoproteins. FSH increased these activities in cells cultured on both substrates, although its stimulating effect was higher on cells cultured on the biomatrix. These results demonstrate that the biomatrix increases protein and glycoprotein synthesis and secretion, and also influences the response of Sertoli cells to FSH.

Biomatrix effect on Sertoli cells phospholipids

In order to investigate the influence of biomatrix on Sertoli cell morphology and on the phospholipids content, these cells were isolated from testes of 15-day old Wistar rats and plated onto plastic coated with extracellular matrix extracted from seminiferous tubules, here denoted biomatrix. When the Sertoli cells were cultured on biomatrix they did not form a monolayer until day 7 of culture, while cells plated onto plastic did so 48 h after plating. On day 5 of culture, Sertoli cells were incubated for 48 h with 5 microCi/ml 32P. There was no difference in 32P incorporation into lipids of cells plated onto biomatrix or plastic. However, there was a larger amount of phospholipid phosphate in cells plated onto biomatrix than onto plastic. When the phospholipids were analyzed by bidimensional thin-layer chromatography, no differences were detected in their distribution; however, there was a significant decrease in the percentage of sphingomyelin in cells plated onto biomatrix when compared to plastic. These results showed that the cells cultured on biomatrix change their phospholipids content, but not their distribution. The importance of a small reduction in sphingomyelin content remains to be investigated.