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Sample records for brasiliense camb caryocaraceae

  1. In vitro and in vivo efficacy of aqueous extract of Caryocar brasiliense Camb. to control gastrointestinal nematodes in sheep.

    PubMed

    Nogueira, Flávia A; Fonseca, Leydiana D; da Silva, Rayana B; de Paiva Ferreira, Adriano V; Nery, Patrícia S; Geraseev, Luciana C; Duarte, Eduardo R

    2012-07-01

    A major problem faced in sheep rearing has been the rapid acquisition of anthelminthic-resistant populations of gastrointestinal nematodes. In the search for alternatives, aqueous extract of the peel of Caryocar brasiliense was evaluated for larval development inhibition, egg-hatching inhibition, and fecal nematode egg count reduction in sheep. For in vivo analysis, the doses were calculated according to a 10% lethal dose derived from acute toxicity tests in mice, and the efficacy was evaluated for two periods following oral administration of the extract. Egg-hatching inhibition at concentrations of 15 and 7.5 mg/ml was significantly higher than observed in negative controls with distilled water. For larval development inhibition, all concentrations showed anthelminthic activity significantly higher than controls and were not significantly different from ivermectin treatment. The LC(90) of larval development inhibition was 53.19 mg/ml. In vivo analysis for first and second weeks after treatment found 32.2% and 33% anthelminthic efficacy, respectively.

  2. Storage of Calophyllum brasiliense Cambess. seeds.

    PubMed

    Nery, F C; Prudente, D O; Alvarenga, A A; Paiva, R; Nery, M C

    2016-09-26

    Calophyllum brasiliense is a species native to Brazil and has potential for use in the timber industry, in the reforestation of degraded areas, besides having medicinal properties. Its propagation is mainly by seeds which, depending on their recalcitrant characteristics, leads to difficulty in conservation, due to changes in its physiological potential during storage. Aiming to contribute to the expansion of its cultivation, rational use and conservation, the objective of this study was to investigate the behavior of C. brasiliense seeds during storage. Different packings (paper, aluminum and polyethylene) and environmental conditions (room temperature and cold chamber) were quarterly tested over 12 months, by evaluating germination viability and vigor. Based on the results, it was concluded that packaging in polyethylene and freezer storage provided the best conditions for the conservation of seeds, keeping them viable for a period of nine months.

  3. Apoptosis inducing activity of 4-substituted coumarins from Calophyllum brasiliense in human leukaemia HL-60 cells.

    PubMed

    Ito, Chihiro; Murata, Tomiyasu; Itoigawa, Masataka; Nakao, Keisuke; Kaneda, Norio; Furukawa, Hiroshi

    2006-07-01

    With the objective of identifying anti-tumour-promoting agents, we carried out a primary screening of ten 4-substituted coumarins isolated from Calophyllum brasiliense Camb. (Guttiferae), to determine the ability of these compounds to inhibit proliferation of the human leukaemia cell line HL-60. Among the 4-substituted coumarins isolated, calophyllolide (2) and mammea B/BB (3) showed significant cytotoxicity against HL-60 cells. Fluorescence microscopy with Hoechst 33342 staining revealed that the percentage of apoptotic cells with fragmented nuclei and condensed chromatin increased in a time-dependent manner after treatment with calophyllolide (2) or mammea B/BB (3). In addition, the activity of caspase-9 and caspase-3 was also enhanced in a time-dependent manner upon treatment with the 4-substituted coumarins 2 and 3. Caspase-9 and caspase-3 inhibitors suppressed apoptosis induced by 4-substituted coumarins 2 and 3. These results suggest that calophyllolide (2) and mammea B/ BB (3) induced apoptosis in HL-60 cells through activation of the caspase-9/caspase-3 pathway, which is triggered by mitochondrial dysfunction.

  4. Draft Genome Sequences for Canadian Isolates of Pectobacterium carotovorum subsp. brasiliense with Weak Virulence on Potato

    PubMed Central

    Yuan, Kat (Xiaoli); Cullis, Jeff; Lévesque, C. André; Chen, Wen; Lewis, Christopher T.; De Boer, Solke H.

    2015-01-01

    Pectobacterium carotovurum subsp. brasiliense causes soft rot and blackleg diseases on potato. Here, we report the draft genome sequences of three weakly virulent P. carotovurum subsp. brasiliense strains isolated in Canada. Analysis of these genome sequences will help to pinpoint differences in virulence among P. carotovurum subsp. brasiliense strains from tropical/subtropical and temperate regions, such as Canada and United States. A small number of key factors for adaptation to this bacterium's specific environmental niche were also evaluated. PMID:25858837

  5. Antileishmanial Activity of a Calophyllum brasiliense Leaf Extract.

    PubMed

    Cardoso, Bruna Muller; De Mello, Tatiane Franca Perles; Lera, Daniele Stefani Lopes; Brenzan, Mislaine Adriana; Cortez, Diógenes Aparecido Garcia; Donatti, Lucélia; Silveira, Thais Gomes Verzignassi; Lonardoni, Maria Valdrinez Campana

    2017-01-01

    Calophyllum brasiliense (Clusiaceae) is a tree that grows mainly in the Atlantic Forest in Brazil. Its leaves possess antibacterial activity, cytotoxic activity against certain tumor cell lines, and antimicrobial activity in BALB/c mice infected with Leishmania (Leishmania) amazonensis.Aiming to identify ultrastructural changes and DNA fragmentation in Leishmania (Viannia) braziliensis, promastigotes were treated with a concentration of the dichloromethane extract and coumarin (-) mammea A/BB from C. brasiliense leaves that inhibited 50 % of the parasites (IC50), and were evaluated by transmission and scanning electron microscopy. Ultrastructural changes showed different levels of mitochondrial alterations, including mitochondrial swelling and a reduction in the density of the mitochondrial matrix. Induced DNA fragmentation, as observed by TUNEL, suggested that the extract and coumarin (-) mammea A/BB induced apoptosis-like cell death. These results suggest that the combination of C. brasiliense extract and coumarin (-) mammea A/BB can be considered a promising candidate for the development of new antiprotozoal agents, because of its significant leishmanicidal activity.

  6. Pequi (Caryocar brasiliense Camb.) almond oil attenuates carbon tetrachloride-induced acute hepatic injury in rats: Antioxidant and anti-inflammatory effects.

    PubMed

    Torres, Lucillia R de O; Santana, Fernanda C de; Torres-Leal, Francisco L; Melo, Illana L P de; Yoshime, Luciana T; Matos-Neto, Emidio M; Seelaender, Marília C L; Araújo, Cintia M M; Cogliati, Bruno; Mancini-Filho, Jorge

    2016-11-01

    Carbon tetrachloride (CCl4) is a potent hepatotoxin, capable of generating free radicals that lead to oxidative stress and the inflammation process. Pequi almond oil (PAO) has been reported to possess unsaturated fatty acid and antioxidant compounds related to beneficial effects on oxidation and inflammatory conditions. The present study was undertaken to evaluate the hepatoprotective effects of handmade and coldpressed PAO on CCl4-induced acute liver injury. The possible mechanisms underlying the effect on liver injury enzymes, histopathological parameters, lipid profile, lipid peroxidation, and antioxidant and detoxification defense systems, as well as inflammatory parameters, were determined. Rats treated with PAO (3 or 6 mL/kg) for 21 days before CCl4 induction (3 mL/kg, 70%) showed significantly decreased levels of alanine aminotransferase and aspartate aminotransferase, milder hepatic lesions and higher levels of serum high-density lipoprotein compared to CCl4 group. Moreover, PAO enhanced antioxidant capacity by increasing hepatic glutathione peroxidase and glutathione reductase enzyme activities, as well as reducing circulating concentrations of leptin and inflammatory mediators such as interleukin-6, leukotrienes -4 and -5 and the tumor necrosis factor receptor. In summary, PAO, especially cold-pressed oil, attenuated the CCl4-induced alterations in serum and hepatic tissue in rats due to its antioxidant and anti-inflammatory properties.

  7. Chemical composition and analgesic activity of Calophyllum brasiliense leaves.

    PubMed

    da Silva, K L; dos Santos, A R; Mattos, P E; Yunes, R A; Delle-Monache, F; Cechinel-Filho, V

    2001-01-01

    This paper describes a phytochemical and pharmacological study with Calophyllum brasiliense leaves, a medicinal plant employed in folk medicine for the treatment of several ailments. Based on spectroscopic evidence, five phenolic compounds were identified as hyperin (hyperoside), amentoflavone, quercetin, gallic acid, and protocatechuic acid. The fractions and some phenolic compounds exhibited significant analgesic activity against the writhing test and in relation to the second phase (inflammatory pain) of the formalin test in mice, suggesting that this plant can be useful for the treatment of dolorous processes.

  8. Toxicogenomic analysis of pharmacological active coumarins isolated from Calophyllum brasiliense

    PubMed Central

    Gomez-Verjan, J.C.; Estrella-Parra, E.A.; Gonzalez-Sanchez, I.; Rivero-Segura, N.A.; Vazquez-Martinez, R.; Magos-Guerrero, G.; Mendoza-Villanueva, D.; Cerbón-Cervantes, M.A.; Reyes-Chilpa, R.

    2015-01-01

    Calophyllum brasiliense (Calophyllaceae) is a tropical rain forest tree, mainly distributed in South and Central America. It is an important source of bioactive natural products like, for instance soulatrolide, and mammea type coumarins. Soulatrolide is a tetracyclic dipyranocoumarins and a potent inhibitor of HIV-1 reverse transcriptase and Mycobacterium tuberculosis. Mammea A/BA and A/BB coumarins, pure or as a mixture, are highly active against several leukemia cell lines, Trypanosoma cruzi and Leishmania amazonensis. In the present work, a toxicogenomic analysis of Soulatrolide and Mammea A/BA + A/BB (3:1) mixture was performed in order to validate the toxicological potential of this type of compounds. Soulatrolide or mixture of mammea A/BA + A/BB (3:1) was administered orally to male mice (CD-1) at dose of 100 mg/kg/daily, for 1 week. After this time, mice were sacrificed, and RNA extracted from the liver of treated animals. Transcriptomic analysis was performed using Affymetrix Mouse Gene 1.0 ST Array. Robust microarray analysis (RMA) and two way ANOVA test revealed for mammea mixture treatment 46 genes upregulated and 72 downregulated genes; meanwhile, for soulatrolide 665 were upregulated and 1077 downregulated genes. Enrichment analysis for such genes revealed that in both type of treatments genetic expression were mainly involved in drug metabolism. Overall results indicate a safety profile. The microarray data complies with MIAME guidelines and are deposited in GEO under accession number GSE72755. PMID:26697389

  9. Toxicogenomic analysis of pharmacological active coumarins isolated from Calophyllum brasiliense.

    PubMed

    Gomez-Verjan, J C; Estrella-Parra, E A; Gonzalez-Sanchez, I; Rivero-Segura, N A; Vazquez-Martinez, R; Magos-Guerrero, G; Mendoza-Villanueva, D; Cerbón-Cervantes, M A; Reyes-Chilpa, R

    2015-12-01

    Calophyllum brasiliense (Calophyllaceae) is a tropical rain forest tree, mainly distributed in South and Central America. It is an important source of bioactive natural products like, for instance soulatrolide, and mammea type coumarins. Soulatrolide is a tetracyclic dipyranocoumarins and a potent inhibitor of HIV-1 reverse transcriptase and Mycobacterium tuberculosis. Mammea A/BA and A/BB coumarins, pure or as a mixture, are highly active against several leukemia cell lines, Trypanosoma cruzi and Leishmania amazonensis. In the present work, a toxicogenomic analysis of Soulatrolide and Mammea A/BA + A/BB (3:1) mixture was performed in order to validate the toxicological potential of this type of compounds. Soulatrolide or mixture of mammea A/BA + A/BB (3:1) was administered orally to male mice (CD-1) at dose of 100 mg/kg/daily, for 1 week. After this time, mice were sacrificed, and RNA extracted from the liver of treated animals. Transcriptomic analysis was performed using Affymetrix Mouse Gene 1.0 ST Array. Robust microarray analysis (RMA) and two way ANOVA test revealed for mammea mixture treatment 46 genes upregulated and 72 downregulated genes; meanwhile, for soulatrolide 665 were upregulated and 1077 downregulated genes. Enrichment analysis for such genes revealed that in both type of treatments genetic expression were mainly involved in drug metabolism. Overall results indicate a safety profile. The microarray data complies with MIAME guidelines and are deposited in GEO under accession number GSE72755.

  10. Cytotoxic effects of mammea type coumarins from Calophyllum brasiliense.

    PubMed

    Reyes-Chilpa, Ricardo; Estrada-Muñiz, Elizabet; Apan, Teresa Ramírez; Amekraz, Badia; Aumelas, Andre; Jankowski, Christopher K; Vázquez-Torres, Mario

    2004-08-13

    Calophyllum brasiliense (Clusiaceae) is a big tree from the Tropical Rain Forests of the American continent. The organic extracts from the leaves yielded coumarins of the mammea type: mammea A/BA, A/BB, B/BA, B/BB, C/OA, C/OB, B/BA cyclo F, B/BB cyclo F, and isomammeigin. The triterpenoids friedelin and canophyllol, as well as the biflavonoid amentoflavone, protocatechuic and shikimic acids, were also obtained. Most of the isolated compounds were tested in vitro against K562, U251, and PC3 human tumor cell lines. The coumarins were cytotoxic against the three cell lines, the highest activity was shown by mammea A/BA (IC50 = 0.04 to 0.59 microM). The mixtures of mammea A/BA + A/BB, mammea B/BA + B/BB and mammea C/OA + C/OB were also highly active (IC50 < 4.05 microM). Friedelin was cytotoxic only against PC3, and U251 lines. Inhibition of HIV-1 reverse transcriptase was also assayed in vitro; however, none of the tested compounds (250 microM) prevented the activity of this enzyme. Most of the isolated compounds were also inactive against fourteen bacterial strains; however mammea A/BA + A/BB, and mammea C/OA + C/OB inhibited the growth of Staphylococcus aureus, S. epidermidis and Bacillus subtilis.

  11. Caryocar brasiliense supercritical CO2 extract possesses antimicrobial and antioxidant properties useful for personal care products

    PubMed Central

    2014-01-01

    Background The cosmetic and pharmaceutical industries have an increasing interest in replacing synthetic antimicrobials in dermatological products due to increased microbial resistance to conventional antimicrobial agents. Pequi (Caryocar brasiliense) is a native fruit tree of the Brazilian Cerrado, specifically used in cosmetics, in the food industry, and for medicinal purposes. Leishmanicidal and antifungal activities have been reported previously. This study was designed to evaluate the antimicrobial and antioxidant activities of a C. brasiliense extract obtained by supercritical CO2 extraction. Methods The minimum inhibitory concentrations (MICs) against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus were determined by the classical microdilution method. Antiseptic activity against these organisms was evaluated by the plate diffusion method. The antioxidant potential of the extract was evaluated using a method based on the oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS). The extract’s chemical profile was analyzed for the presence of alkaloids, saponins, anthraquinones, steroids, tannins, flavonoids, and phenolic compounds according to standard colorimetric methods. Results The C. brasiliense supercritical CO2 extract exhibits antimicrobial activity against all bacteria tested. It also possesses antioxidant activity, when compared to a vitamin E standard. Conclusions The C. brasiliense supercritical CO2 extract may be useful for the development of personal care products, primarily for antiseptic skin products that inactivate, reduce, prevent, or arrest the growth of microorganisms with the inherent intent to mitigate or prevent disease as well as products that minimize damage caused by free radicals. PMID:24565304

  12. Association between interleukin 6 -174 G/C promoter gene polymorphism and runners' responses to the dietary ingestion of antioxidant supplementation based on pequi (Caryocar brasiliense Camb.) oil: a before-after study

    PubMed Central

    Miranda-Vilela, Ana Luisa; Ribeiro, Ieler Ferreira; Grisolia, Cesar Koppe

    2016-01-01

    Abstract Exercise is a double-edged sword: when practiced in moderation, it increases the expression of antioxidant enzymes, but when practiced strenuously it causes oxidative stress and cell damage. In this context, polymorphisms in the interleukin (IL)-6 gene should be investigated better because they can influence performance, at least in exercise that generates oxidative stress and leads to muscular injuries with consequent inflammation. In this work, we investigated the influence of IL-6 –174 G/C polymorphism on tissue damage and inflammation markers, lipid peroxidation, hemogram and lipid profile of runners before and after ingestion of 400 mg of pequi oil in capsules supplied daily for 14 consecutive days. The IL-6 genotypes were associated with significant differences in lipid peroxidation, with the CC mutant having lower values. There were also significant differences among these genotypes in the response to supplementation with pequi oil, exercise-induced damage and C-reactive protein (CRP) levels. The best protection against damage was observed with the heterozygous genotype. Although the CC genotype showed an increase in CRP levels after supplementation, the lack of a positive correlation between triglycerides and high-sensitivity CRP in this mutant genotype after supplementation indicated a protective effect of pequi. These findings deserve further investigation, particularly with regard to the quantification of circulating IL-6 concentrations. PMID:27727360

  13. In Vitro Antiophidian Mechanisms of Hypericum brasiliense Choisy Standardized Extract: Quercetin-Dependent Neuroprotection

    PubMed Central

    Lucho, Ana Paula de Bairros; Vinadé, Lúcia; Seibert França, Hildegardo; Marangoni, Sérgio; Rodrigues-Simioni, Léa

    2013-01-01

    The neuroprotection induced by Hypericum brasiliense Choisy extract (HBE) and its main active polyphenol compound quercetin, against Crotalus durissus terrificus (Cdt) venom and crotoxin and crotamine, was enquired at both central and peripheral mammal nervous system. Cdt venom (10 μg/mL) or crotoxin (1 μg/mL) incubated at mouse phrenic nerve-diaphragm preparation (PND) induced an irreversible and complete neuromuscular blockade, respectively. Crotamine (1 μg/mL) only induced an increase of muscle strength at PND preparations. At mouse brain slices, Cdt venom (1, 5, and 10 μg/mL) decreased cell viability. HBE (100 μg/mL) inhibited significantly the facilitatory action of crotamine (1 μg/mL) and was partially active against the neuromuscular blockade of crotoxin (1 μg/mL) (data not shown). Quercetin (10 μg/mL) mimicked the neuromuscular protection of HBE (100 μg/mL), by inhibiting almost completely the neurotoxic effect induced by crotoxin (1 μg/mL) and crotamine (1 μg/mL). HBE (100 μg/mL) and quercetin (10 μg/mL) also increased cell viability in mice brain slices. Quercetin (10 μg/mL) was more effective than HBE (100 μg/mL) in counteracting the cell lysis induced by Cdt venom (1 and 10 μg/mL, resp.). These results and a further phytochemical and toxicological investigations could open new perspectives towards therapeutic use of Hypericum brasiliense standardized extract and quercetin, especially to counteract the neurotoxic effect induced by snake neurotoxic venoms. PMID:24490174

  14. Anti-Mycobacterium tuberculosis activity and cytotoxicity of Calophyllum brasiliense Cambess (Clusiaceae)

    PubMed Central

    Pires, Claudia Terencio Agostinho; Brenzan, Mislaine Adriana; Scodro, Regiane Bertin de Lima; Cortez, Diógenes Aparício Garcia; Lopes, Luciana Dias Ghiraldi; Siqueira, Vera Lucia Dias; Cardoso, Rosilene Fressatti

    2014-01-01

    We evaluated the in vitro anti-Mycobacterium tuberculosis activity and the cytotoxicity of dichloromethane extract and pure compounds from the leaves of Calophyllum brasiliense. Purification of the dichloromethane extract yielded the pure compounds (-) mammea A/BB (1), (-) mammea B/BB (2) and amentoflavone (3). The compound structures were elucidated on the basis of spectroscopic and spectrometric data. The contents of bioactive compounds in the extracts were quantified using high performance liquid chromatography coupled to an ultraviolet detector. The anti-M. tuberculosis activity of the extracts and the pure compounds was evaluated using a resazurin microtitre assay plate. The cytotoxicity assay was performed in J774G.8 macrophages using the 3-(4,5-dimethyl thiazol-2-yl)-2,5-diphenyl tetrazolium bromide colourimetric method. The quantification of the dichloromethane extract showed (1) and (2) at concentrations of 31.86 ± 2.6 and 8.24 ± 1.1 µg/mg of extract, respectively. The dichloromethane and aqueous extracts showed anti-M. tuberculosis H37Rv activity of 62.5 and 125 µg/mL, respectively. Coumarins (1) and (2) showed minimal inhibitory concentration ranges of 31.2 and 62.5 µg/mL against M. tuberculosis H37Rv and clinical isolates. Compound (3) showed no activity against M. tuberculosis H37Rv. The selectivity index ranged from 0.59-1.06. We report the activity of the extracts and coumarins from the leaves of C. brasiliense against M. tuberculosis. PMID:24676652

  15. Anti-Mycobacterium tuberculosis activity and cytotoxicity of Calophyllum brasiliense Cambess (Clusiaceae).

    PubMed

    Pires, Claudia Terencio Agostinho; Brenzan, Mislaine Adriana; Scodro, Regiane Bertin de Lima; Cortez, Diógenes Aparício Garcia; Lopes, Luciana Dias Ghiraldi; Siqueira, Vera Lucia Dias; Cardoso, Rosilene Fressatti

    2014-06-01

    We evaluated the in vitro anti-Mycobacterium tuberculosis activity and the cytotoxicity of dichloromethane extract and pure compounds from the leaves of Calophyllum brasiliense. Purification of the dichloromethane extract yielded the pure compounds (-) mammea A/BB (1), (-) mammea B/BB (2) and amentoflavone (3). The compound structures were elucidated on the basis of spectroscopic and spectrometric data. The contents of bioactive compounds in the extracts were quantified using high performance liquid chromatography coupled to an ultraviolet detector. The anti-M. tuberculosis activity of the extracts and the pure compounds was evaluated using a resazurin microtitre assay plate. The cytotoxicity assay was performed in J774G.8 macrophages using the 3-(4,5-dimethyl thiazol-2-yl)-2,5-diphenyl tetrazolium bromide colourimetric method. The quantification of the dichloromethane extract showed (1) and (2) at concentrations of 31.86 ± 2.6 and 8.24 ± 1.1 µg/mg of extract, respectively. The dichloromethane and aqueous extracts showed anti-M. tuberculosis H37Rv activity of 62.5 and 125 µg/mL, respectively. Coumarins (1) and (2) showed minimal inhibitory concentration ranges of 31.2 and 62.5 µg/mL against M. tuberculosis H37Rv and clinical isolates. Compound (3) showed no activity against M. tuberculosis H37Rv. The selectivity index ranged from 0.59-1.06. We report the activity of the extracts and coumarins from the leaves of C. brasiliense against M. tuberculosis.

  16. Comparing conventional and supercritical extraction of (-)-mammea A/BB and the antioxidant activity of Calophyllum brasiliense extracts.

    PubMed

    Gonçalves, Renata Menoci; Lemos, Caroline Ortega Terra; Leal, Ivana Correa Ramos; Nakamura, Celso Vataru; Cortez, Diógenes Aparício Garcia; da Silva, Edson Antonio; Cabral, Vladimir Ferreira; Cardozo-Filho, Lúcio

    2013-05-24

    Calophyllum brasiliense is a rich source of bioactive coumarins, xanthones and biflavonoids. The aim of the study was to compare the phenol contents and the antioxidant activity of C. brasiliense extracts obtained by conventional and supercritical fluid extraction (SFE) methods, as well as the quantification of crude extracts and (-)-mammea A/BB yields. Dichloromethane and hexane were used as solvents for the conventional extractions and SFE was developed using supercritical CO₂; the kinetic curves were modeled using a second-order empirical model. The dichloromethane extract presented the best total yield, although it showed the lowest content of (-)-mammea A/BB. The concentration of the coumarin was considerably higher in extracts obtained by the supercritical fluid method and a higher antioxidant activity was assigned to extracts obtained by this technique. Concerning the total phenolic contents, both the dichloro-methane and the supercritical extractions produced satisfactory amounts. The SFE method proved to be more promising than conventional methods.

  17. RNA-seq Profiling Reveals Defense Responses in a Tolerant Potato Cultivar to Stem Infection by Pectobacterium carotovorum ssp. brasiliense.

    PubMed

    Kwenda, Stanford; Motlolometsi, Tshepiso V; Birch, Paul R J; Moleleki, Lucy N

    2016-01-01

    Pectobacterium carotovorum subsp. brasiliense is a member of the soft rot Enterobacteriaceae (SRE) family that causes tuber soft rot and blackleg diseases of stems in potato plants. Currently, there are no effective chemical strategies for the control of members of the SRE. Thus, an understanding of the inducible defense responses in stems of potato plants is important, particularly during colonization of the vascular system. Here, time-course RNA-sequencing analysis was used to compare expressed genes between a susceptible potato cultivar (Solanum tuberosum cv Valor) and a tolerant cultivar (S. tuberosum cv BP1) at 0, 6, 12, 24, and 72 h post-inoculation with P. c. brasiliense. In total, we identified 6139 and 8214 differentially expressed genes (DEGs) in the tolerant and susceptible cultivars, compared to mock-inoculated controls, respectively. Key DEGs distinguishing between tolerance and susceptibility were associated with negative regulation of cell death and plant-type cell wall organization/biogenesis biological processes in the tolerant and susceptible cultivars, respectively. Among these were DEGs involved in signaling (mainly MAPK cascade and ethylene pathway), defense-related transcription regulation including WRKY transcription factors, and downstream secondary cell biosynthesis. Together, our results suggest that S. tuberosum cv BP1 likely employs quantitative defense response against P. c. brasiliense. Overall, our study provides the first transcriptome-wide insight into the molecular basis of tolerance and/or resistance of potato stems to SRE infection.

  18. RNA-seq Profiling Reveals Defense Responses in a Tolerant Potato Cultivar to Stem Infection by Pectobacterium carotovorum ssp. brasiliense

    PubMed Central

    Kwenda, Stanford; Motlolometsi, Tshepiso V.; Birch, Paul R. J.; Moleleki, Lucy N.

    2016-01-01

    Pectobacterium carotovorum subsp. brasiliense is a member of the soft rot Enterobacteriaceae (SRE) family that causes tuber soft rot and blackleg diseases of stems in potato plants. Currently, there are no effective chemical strategies for the control of members of the SRE. Thus, an understanding of the inducible defense responses in stems of potato plants is important, particularly during colonization of the vascular system. Here, time-course RNA-sequencing analysis was used to compare expressed genes between a susceptible potato cultivar (Solanum tuberosum cv Valor) and a tolerant cultivar (S. tuberosum cv BP1) at 0, 6, 12, 24, and 72 h post-inoculation with P. c. brasiliense. In total, we identified 6139 and 8214 differentially expressed genes (DEGs) in the tolerant and susceptible cultivars, compared to mock-inoculated controls, respectively. Key DEGs distinguishing between tolerance and susceptibility were associated with negative regulation of cell death and plant-type cell wall organization/biogenesis biological processes in the tolerant and susceptible cultivars, respectively. Among these were DEGs involved in signaling (mainly MAPK cascade and ethylene pathway), defense-related transcription regulation including WRKY transcription factors, and downstream secondary cell biosynthesis. Together, our results suggest that S. tuberosum cv BP1 likely employs quantitative defense response against P. c. brasiliense. Overall, our study provides the first transcriptome-wide insight into the molecular basis of tolerance and/or resistance of potato stems to SRE infection. PMID:28066465

  19. Growth, morphology, ammonium uptake and nutrient allocation of Myriophyllum brasiliense Cambess. under high NH₄⁺ concentrations.

    PubMed

    Saunkaew, Piyanart; Wangpakapattanawong, Prasit; Jampeetong, Arunothai

    2011-11-01

    The effects of high NH(4)(+) concentration on growth, morphology, NH(4) (+) uptake and nutrient allocation of Myriophyllum brasiliense were investigated in hydroponic culture. The plants were grown under greenhouse conditions for 4 weeks using four levels of NH(4)(+) concentration: 1, 5, 10 and 15 mM. M. brasiliense grew well with a relative growth rate of c.0.03 day(-1) at NH(4)(+) concentration up to 5 mM. At the higher NH(4)(+) concentrations the growth of the plants was stunted and the plants had short roots and few new buds, especially when grown in 15 mM NH(4)(+) where the submerged leaves were lost and there were rotten roots and submerged stems. To avoid NH(4)(+) toxicity, the plants may have a mechanism to prevent cytoplasmic NH(4)(+) accumulation in plant cells. The net uptake of NH(4)(+) significantly decreased and the total N significantly increased in the plants treated with 10 and 15 mM NH(4)(+), respectively. The plant may employ NH(4)(+) assimilation and extrusion as a mechanism to compensate for the high NH(4)(+) concentrations. However, the plants may show nutrient deficiency symptoms, especially K deficiency symptoms, after they were exposed to NH(4)(+) concentration higher than 10 mM. The present study provides a basic ecophysiology of M. brasiliense that it can grow in NH(4)(+) enriched water up to concentrations as high as 5 mM.

  20. 'Candidatus Phytoplasma brasiliense', a new phytoplasma taxon associated with hibiscus witches' broom disease.

    PubMed

    Montano, H G; Davis, R E; Dally, E L; Hogenhout, S; Pimentel, J P; Brioso, P S

    2001-05-01

    Hibiscus rosa-sinensis is a valuable ornamental species widely planted in Brazil. Many plants are affected by witches' broom disease, which is characterized by excessive axillary branching, abnormally small leaves, and deformed flowers, symptoms that are characteristic of diseases attributed to phytoplasmas. A phytoplasma was detected in diseased Hibiscus by amplification of rRNA operon sequences by PCRs, and was characterized by RFLP and nucleotide sequence analyses of 16S rDNA. The collective RFLP patterns of amplified 16S rDNA differed from the patterns described previously for other phytoplasmas. On the basis of the RFLP patterns, the hibiscus witches' broom phytoplasma was classified in a new 16S rRNA RFLP group, designated group 16SrXV. A phylogenetic analysis of 16S rDNA sequences from this and other phytoplasmas identified the hibiscus witches' broom phytoplasma as a member of a distinct subclade (designated subclade xiv) of the class Mollicutes. A phylogenetic tree constructed on the basis of 16S rRNA gene sequences was consistent with the hypothesis that there was divergent evolution of hibiscus witches' broom phytoplasma and its closest relatives (members of 16S rRNA RFLP group 16SrII) from a common ancestor. On the basis of unique properties of the DNA from hibiscus witches' broom phytoplasma, it is proposed that it represents a new taxon, namely 'Candidatus Phytoplasma brasiliense'.

  1. Antileishmanial activity of crude extract and coumarin from Calophyllum brasiliense leaves against Leishmania amazonensis.

    PubMed

    Brenzan, Mislaine Adriana; Nakamura, Celso Vataru; Prado Dias Filho, Benedito; Ueda-Nakamura, Tânia; Young, Maria Claudia M; Aparício Garcia Cortez, Diógenes

    2007-08-01

    Infections by protozoans of the genus Leishmania are a major worldwide health problem, with high endemicity in developing countries. The drugs of choice for the treatment of leishmaniasis are the pentavalent antimonials, which show renal and cardiac toxicity. As part of a search for new drugs against leishmaniasis, we evaluated the in vitro leishmanicidal activity of the (-) mammea A/BB. The compound (-) mammea A/BB is a coumarin-type mammea purified from a dichloromethane crude extract of leaves of Calophyllum brasiliense Cambess (Clusiaceae). The isolated compound was characterized using spectral analyses by UV, infrared, nuclear magnetic resonance of (1)H, (13)C, distortionless enhancement by polarization transfer, correlation spectroscopy, heteronuclear multiple bond correlation, and heteronuclear multiple quantum coherence. The compound (-) mammea A/BB showed significant activity against promastigote and amastigote forms of L. amazonensis, with IC(50) (50% inhibition concentration of cell growth) at a concentration of 3.0 and 0.88 mug/ml and IC(90) (90% inhibition concentration of cell growth) of 5.0 and 2.3 microg/ml, respectively. The coumarin (-) mammea A/BB showed no cytotoxicity against J774G8 macrophages in culture, when it was tested at high concentrations that inhibited promastigote forms. Electron microscopy studies revealed considerable ultrastructural changes when promastigote forms of L. amazonensis were treated with 3.0 microg/ml of the coumarin (-) mammea A/BB for 72 h. We observed significant changes such as mitochondrial swelling with concentric membranes in the mitochondrial matrix and intense exocytic activity in the region of the flagellar pocket. Other alterations included the appearance of binucleate cells and multiple cytoplasmic vacuolization. These results showed that (-) mammea A/BB is a potent growth inhibitor of L. amazonensis and caused important changes in the parasite's ultrastructure. This study provided new perspectives on the

  2. Immunostimulatory acivity of Calophyllum brasiliense, Ipomoea pes-caprae and Matayba elaeagnoides demonstrated by human peripheral blood mononuclear cells proliferation.

    PubMed

    Philippi, Marina Elisa; Duarte, Bruna Momm; Da Silva, Carolina Vieira; De Souza, Michel Thomaz; Niero, Rivaldo; Cechinel Filho, Valdir; Bueno, Edneia Casagranda

    2010-01-01

    This study evaluates the effect of methanol extracts of three Brazilian medicinal plants on in vitro proliferation of human mononuclear cells. Lymphoproliferation assay was carried out by incubating human peripheral blood mononuclear cells from healthy donors (1 x 10(6) cells/mL) with extracts of Calophyllum brasiliense (roots), Ipomoea pes-caprae (whole plant) and Matayba elaeagnoides (bark), both at 10, 50, 100 and 200 microg/mL, alone or with phytohemagglutinin (PHA, 5 microg/mL), in 96-well microplates at 37 degrees C with 5% CO2, for 72 h. The quantification of cell proliferation assay was performed by blue tetrazolium (MTT) reduction with reading at 540 nm. Cells incubated with only the culture medium were used as negative control for cell proliferation, while the positive control consisted of cells and PHA. The results suggest that the extracts of all three studied plants induce T lymphocyte proliferation. I. pes-caprae showed immunostimulatory activity three times higher than the C. brasiliense extract, while that of the M. elaeagnoides extract was 1.5 times higher. The results demonstrate immunostimulatory effects of these three plants, therefore the continuity of these studies is recommended, in order to determine the active principles.

  3. Soulamarin Isolated from Calophyllum brasiliense (Clusiaceae) Induces Plasma Membrane Permeabilization of Trypanosoma cruzi and Mytochondrial Dysfunction

    PubMed Central

    Rea, Alexandre; Tempone, Andre G.; Pinto, Erika G.; Mesquita, Juliana T.; Rodrigues, Eliana; Silva, Luciana Grus M.; Sartorelli, Patricia; Lago, João Henrique G.

    2013-01-01

    Chagas disease is caused by the parasitic protozoan Trypanosoma cruzi. It has high mortality as well as morbidity rates and usually affects the poorer sections of the population. The development of new, less harmful and more effective drugs is a promising research target, since current standard treatments are highly toxic and administered for long periods. Fractioning of methanol (MeOH) extract of the stem bark of Calophyllum brasiliense (Clusiaceae) resulted in the isolation of the coumarin soulamarin, which was characterized by one- and two-dimensional 1H- and 13C NMR spectroscopy as well as ESI mass spectrometry. All data obtained were consistent with a structure of 6-hydroxy-4-propyl-5-(3-hydroxy-2-methyl-1-oxobutyl)-6″,6″-dimethylpyrane-[2″,3″:8,7]-benzopyran-2-one for soulamarin. Colorimetric MTT assays showed that soulamarin induces trypanocidal effects, and is also active against trypomastigotes. Hemolytic activity tests showed that soulamarin is unable to induce any observable damage to erythrocytes (cmax. = 1,300 µM). The lethal action of soulamarin against T. cruzi was investigated by using amino(4-(6-(amino(iminio)methyl)-1H-indol-2-yl)phenyl)methaniminium chloride (SYTOX Green and 1H,5H,11H,15H-Xantheno[2,3,4-ij:5,6,7-i′j′]diquinolizin-18-ium, 9-[4-(chloromethyl)phenyl]-2,3,6,7,12,13,16,17-octahydro-chloride (MitoTracker Red) as fluorimetric probes. With the former, soulamarin showed dose-dependent permeability of the plasma membrane, relative to fully permeable Triton X-100-treated parasites. Spectrofluorimetric and fluorescence microscopy with the latter revealed that soulamarin also induced a strong depolarization (ca. 97%) of the mitochondrial membrane potential. These data demonstrate that the lethal action of soulamarin towards T. cruzi involves damages to the plasma membrane of the parasite and mitochondrial dysfunction without the additional generation of reactive oxygen species, which may have also contributed to the death of

  4. Inhibition of HIV-1 reverse transcriptase, toxicological and chemical profile of Calophyllum brasiliense extracts from Chiapas, Mexico.

    PubMed

    César, García-Zebadúa Julio; Alfonso, Magos-Guerrero Gil; Marius, Mumbrú-Massip; Elizabeth, Estrada-Muñoz; Angel, Contreras-Barrios Miguel; Maira, Huerta-Reyes; Guadalupe, Campos-Lara María; Manuel, Jiménez-Estrada; Ricardo, Reyes-Chilpa

    2011-10-01

    Calophyllum species are sources of calanolides, which inhibit human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). The hexane extract of the leaves from C. brasiliense collected in Soconusco, State of Chiapas, Mexico, analyzed by HPLC showed to contain apetalic acid, calanolides B, and C. It showed potent anti-HIV-1 RT inhibition (IC(50)=20.2 μg/ml), but was not toxic in mice (LD(50)=1.99 g/kg). The histological study of the mice treated at the highest dose revealed no alteration on hepatocytes, and an increase in the number of spleen megakaryocytes. These results suggest this extract is suitable to continue studies for developing a phytodrug against HIV-1.

  5. The validation of Calophyllum brasiliense ("guanandi") uses in Brazilian traditional medicine as analgesic by in vivo antinociceptive evaluation and its chemical analysis.

    PubMed

    Klein-Júnior, Luiz Carlos; Zambiasi, Daniele; Salgado, Giovana Rocha; Delle Monache, Franco; Filho, Valdir Cechinel; de Campos Buzzi, Fátima

    2017-04-08

    Calophyllum brasiliense is used as anti-inflammatory and analgesic in Brazilian traditional medicine. Thus, the main purpose of this study is to evaluate the antinociceptive effect of the chloroform fraction of C. brasiliense (CFCB) roots and to investigate its main mechanism of action. The antinociceptive effect of CFCB was evaluated in mice using acetic acid-induced writhing, formalin-induced paw licking, and hot-plate tests and capsaicin- and glutamate-induced nociception. Brasiliensic acid and 1,2-dimethoxyxanthone were isolated and evaluated in writhing test. The amount of 1,2-dimethoxyxanthone was determined in the fraction by UPLC-DAD. CFCB inhibited abdominal constrictions induced by acetic acid up to 97%, with an ID50 of 9.4 mg/kg (i.p.) and 131.8 mg/kg (p.o.). In the formalin test, CFCB impaired paw licking with an ID50 of 26.3 mg/kg for the first phase and 27.5 mg/kg for the second phase (i.p.). The painful response evoked by capsaicin and glutamate was significantly reduced (ID50 26.7 and 47.9 mg/kg, i.p.). The latency time was increased up to 76% at 60 mg/kg (i.p.) in the hot-plate test. 1,2-Dimethoxyxanthone was almost three times more potent (ID50 27.6 μmol/kg, i.p.) than brasiliensic acid (72.0 μmol/kg) in acetic acid-induced writhing test. The amount of the xanthone was estimated as 92.5 mg/g in the extract. CFCB inhibited the nociceptive response associated to several agents. TRPV1 channels play an important role in the mechanism of action of the fraction. In addition, 1,2-dimethoxyxanthone largely contributes to the antinociceptive effect of CFCB.

  6. Hexane Extracts of Calophyllum brasiliense Inhibit the Development of Gastric Preneoplasia in Helicobacter felis Infected INS-Gas Mice.

    PubMed

    Lemos, Larissa M S; Miyajima, Fabio; Castilho, Geovane R C; Martins, Domingos Tabajara O; Pritchard, D Mark; Burkitt, Michael D

    2017-01-01

    Objectives: Indigenous Latin American populations have used extracts from Calophyllum brasiliense, a native hardwood, to treat gastrointestinal symptoms for generations. The hexane extract of Calophyllum brasiliense stem bark (HECb) protects against ethanol-mediated gastric ulceration in Swiss-Webster mice. We investigated whether HECb inhibits the development of gastric epithelial pathology following Helicobacter felis infection of INS-Gas mice. Materials and Methods: Groups of five male, 6-week-old INS-Gas mice were colonized with H. felis by gavage. From 2 weeks after colonization their drinking water was supplemented with 2% Tween20 (vehicle), low dose HECb (33 mg/L, lHECb) or high dose HECb (133 mg/L, hHECb). Equivalent uninfected groups were studied. Animals were culled 6 weeks after H. felis colonization. Preneoplastic pathology was quantified using established histological criteria. Gastric epithelial cell turnover was quantified by immunohistochemistry for Ki67 and active-caspase 3. Cytokines were quantified using an electrochemiluminescence assay. Results: Vehicle-treated H. felis infected mice exhibited higher gastric atrophy scores than similarly treated uninfected mice (mean atrophy score 5.6 ± 0.87 SEM vs. 2.2 ± 0.58, p < 0.01). The same pattern was observed following lHECb. Following hHECb treatment, H. felis status did not significantly alter atrophy scores. Gastric epithelial apoptosis was not altered by H. felis or HECb administration. Amongst vehicle-treated mice, gastric epithelial cell proliferation was increased 2.8-fold in infected compared to uninfected animals (p < 0.01). Administration of either lHECb or hHECb reduced proliferation in infected mice to levels similar to uninfected mice. A Th17 polarized response to H. felis infection was observed in all infected groups. hHECb attenuated IFN-γ, IL-6, and TNF production following H. felis infection [70% (p < 0.01), 67% (p < 0.01), and 41% (p < 0.05) reduction vs. vehicle, respectively

  7. Hexane Extracts of Calophyllum brasiliense Inhibit the Development of Gastric Preneoplasia in Helicobacter felis Infected INS-Gas Mice

    PubMed Central

    Lemos, Larissa M. S.; Miyajima, Fabio; Castilho, Geovane R. C.; Martins, Domingos Tabajara O.; Pritchard, D. Mark; Burkitt, Michael D.

    2017-01-01

    Objectives: Indigenous Latin American populations have used extracts from Calophyllum brasiliense, a native hardwood, to treat gastrointestinal symptoms for generations. The hexane extract of Calophyllum brasiliense stem bark (HECb) protects against ethanol-mediated gastric ulceration in Swiss–Webster mice. We investigated whether HECb inhibits the development of gastric epithelial pathology following Helicobacter felis infection of INS-Gas mice. Materials and Methods: Groups of five male, 6-week-old INS-Gas mice were colonized with H. felis by gavage. From 2 weeks after colonization their drinking water was supplemented with 2% Tween20 (vehicle), low dose HECb (33 mg/L, lHECb) or high dose HECb (133 mg/L, hHECb). Equivalent uninfected groups were studied. Animals were culled 6 weeks after H. felis colonization. Preneoplastic pathology was quantified using established histological criteria. Gastric epithelial cell turnover was quantified by immunohistochemistry for Ki67 and active-caspase 3. Cytokines were quantified using an electrochemiluminescence assay. Results: Vehicle-treated H. felis infected mice exhibited higher gastric atrophy scores than similarly treated uninfected mice (mean atrophy score 5.6 ± 0.87 SEM vs. 2.2 ± 0.58, p < 0.01). The same pattern was observed following lHECb. Following hHECb treatment, H. felis status did not significantly alter atrophy scores. Gastric epithelial apoptosis was not altered by H. felis or HECb administration. Amongst vehicle-treated mice, gastric epithelial cell proliferation was increased 2.8-fold in infected compared to uninfected animals (p < 0.01). Administration of either lHECb or hHECb reduced proliferation in infected mice to levels similar to uninfected mice. A Th17 polarized response to H. felis infection was observed in all infected groups. hHECb attenuated IFN-γ, IL-6, and TNF production following H. felis infection [70% (p < 0.01), 67% (p < 0.01), and 41% (p < 0.05) reduction vs. vehicle, respectively

  8. Effects of (-) mammea A/BB isolated from Calophyllum brasiliense leaves and derivatives on mitochondrial membrane of Leishmania amazonensis.

    PubMed

    Brenzan, M A; Santos, A O; Nakamura, C V; Filho, B P Dias; Ueda-Nakamura, T; Young, M C M; Côrrea, A G; Júnior, J Alvim; Morgado-Díaz, J A; Cortez, D A G

    2012-02-15

    We have previously demonstrated antileishmanial activity on Leishmania amazonensis of the natural (1-2), synthetic (7) and derivatives of coumarin (-) mammea A/BB (3-6) isolated from the dichloromethane extract of Calophyllum brasiliense leaves. The aim of the present study was to evaluate morphological and ultrastructural alterations in Leishmania amazonensis induced by these compounds. In promastigote forms, all seven compounds produced significant morphological and ultrastructural alterations, as revealed by scanning and transmission electron microscopy. The compound 5,7-dihydroxy-8-(2-methylbutanoyl)-6-(3-methylbutyl)-4-phenyl-chroman-2-one (3), the most active antileishmanial with LD₅₀ of 0.9 μM), induced cell shrinkage and a rounded appearance of the cells. Parasites incubated in the presence of compound (3) showed ultrastructural changes, such as the appearance of mitochondrial swelling with a reduction in the density of the mitochondrial matrix and the presence of vesicles inside the mitochondrion, indicating damage and significant change in this organelle; abnormal chromatin condensation, alterations in the nuclear envelope, intense atypical cytoplasmic vacuolization, and the appearance of autophagic vacuoles were also observed. In addition, the compound (3) may be acting to depolarize the mitochondrial membrane potential of the cells, leading to death of the parasite.

  9. Crenosoma brasiliense sp. n. (Nematoda: Metastrongyloidea) parasitic in lesser grison, Galictis cuja (Molina, 1782) (Carnivora, Mustelidae) from Brazil, with a key to species of Crenosoma Molin, 1861.

    PubMed

    Vieira, Fabiano M; Muniz-Pereira, Luis C; de Souza, Lima Sueli; Neto, Antonio H A Moraes; Gonçalves, Pamela R; Luque, José L

    2012-09-01

    This study describes Crenosoma brasiliense (Nematoda, Metastrongyloidea), a new species parasitic in bronchi and bronchioles of Galictis cuja (Molina) (Carnivora, Mustelidae) from Brazil. This species differs from other 11 species of Crenosoma by having a cuticular projection at the distal end of the spicules, forming a prominent blade at the tip of the spicule, a vulval cuticular appendage with a triangular shape and prominent vulval lips. There are no previous records of species of Metastrongyloidea in G. cuja or species of Crenosoma in South America. Therefore, the new species represents the first host record and first geographical record of species of Crenosoma in South America.

  10. Antioxidant properties of xanthones from Calophyllum brasiliense: prevention of oxidative damage induced by FeSO4

    PubMed Central

    2013-01-01

    Background Reactive oxygen species (ROS) are important mediators in a number of degenerative diseases. Oxidative stress refers to the imbalance between the production of ROS and the ability to scavenge these species through endogenous antioxidant systems. Since antioxidants can inhibit oxidative processes, it becomes relevant to describe natural compounds with antioxidant properties which may be designed as therapies to decrease oxidative damage and stimulate endogenous cytoprotective systems. The present study tested the protective effect of two xanthones isolated from the heartwood of Calophyllum brasilienses against FeSO4-induced toxicity. Methods Through combinatory chemistry assays, we evaluated the superoxide (O2●—), hydroxyl radical (OH●), hydrogen peroxide (H2O2) and peroxynitrite (ONOO—) scavenging capacity of jacareubin (xanthone III) and 2-(3,3-dimethylallyl)-1,3,5,6-tetrahydroxyxanthone (xanthone V). The effect of these xanthones on murine DNA and bovine serum albumin degradation induced by an OH• generator system was also evaluated. Additionally, we investigated the effect of these xanthones on ROS production, lipid peroxidation and glutathione reductase (GR) activity in FeSO4-exposed brain, liver and lung rat homogenates. Results Xanthone V exhibited a better scavenging capacity for O2●—, ONOO- and OH● than xanthone III, although both xanthones were unable to trap H2O2. Additionally, xanthones III and V prevented the albumin and DNA degradation induced by the OH● generator system. Lipid peroxidation and ROS production evoked by FeSO4 were decreased by both xanthones in all tissues tested. Xanthones III and V also prevented the GR activity depletion induced by pro-oxidant activity only in the brain. Conclusions Altogether, the collected evidence suggests that xanthones can play a role as potential agents to attenuate the oxidative damage produced by different pro-oxidants. PMID:24119308

  11. Anti-Mycobacterium tuberculosis Activity of Calophyllum brasiliense Extracts Obtained by Supercritical Fluid Extraction and Conventional Techniques.

    PubMed

    Pires, Claudia T A; de L Scodro, Regiane B; Brenzan, Mislaine A; Cortez, Diógenes A G; Siqueira, Vera L D; Cardozo-Filho, Lúcio; Goncalves, Renata M; Caleffi-Ferracioli, Katiany R; Cardoso, Rosilene F

    2016-01-01

    The conventional techniques used to extract natural products have many disadvantages, and alternative methods have been used, such as supercritical fluid extraction (SFE-CO2). We compared the anti-Mycobacterium tuberculosis activity and cytotoxicity of extracts and major pure compounds were obtained from the leaves of Calophyllum brasiliense by SFE-CO2, maceration and Soxhlet. Anti-M tuberculosis activity was evaluated by resazurin microtiter assay plate and cytotoxicity assay was performed using 3-(4,5-dimethyl thiazol-2-yl)-2,5-diphenyl tetrazolium bromide. The (-) mammea A/BB, (-) mammea B/BB, mammea B/BB cyclo D, ponnalide, mammea A/BA cyclo D, and amentoflavone were identified as the majority compounds. SFE-CO2, especially at 313 K and 10.92 MPa showed better yield for (-) mammea A/BB. Anti-M. tuberculosis activity (62.5 μg/mL) and cytotoxicity (Selectivity Index = 0.320-0.576) were similar for the three extracts. Mammea B/BB cyclo D had a minimum inhibitory concentration (MIC) of 125 μg/mL, and ponnalide and mammea A/BA cyclo D had MICs > 250 μg/mL. The pure compounds isolated showed low Selectivity Index (< 0.09). SFE-CO2 may be more promising than conventional methods for the extraction of compound (-) mammea A/BB, which presented the best anti-M. tuberculosis activity in our previous study. This is important for current industrial requirements to obtain extracts from medicinal plants using clean technologies.

  12. Systematic study on the TD-DFT calculated electronic circular dichroism spectra of chiral aromatic nitro compounds: A comparison of B3LYP and CAM-B3LYP

    NASA Astrophysics Data System (ADS)

    Komjáti, Balázs; Urai, Ákos; Hosztafi, Sándor; Kökösi, József; Kováts, Benjámin; Nagy, József; Horváth, Péter

    2016-02-01

    B3LYP is one of the most widely used functional for the prediction of electronic circular dichroism spectra, however if the studied molecule contains aromatic nitro group computations may fail to produce reliable results. A test set of molecules of known stereochemistry were synthesized to study this phenomenon in detail. Spectra were computed by B3LYP and CAM-B3LYP functionals with 6-311 ++G(2d,2p) basis set. It was found that the range separated CAM-B3LYP gives better predictions than B3LYP for all test molecules. Fragment population analysis revealed that the nitro groups form highly localized molecule orbitals but the exact composition depends on the functional. CAM-B3LYP allows sufficient spatial overlap between the nitro group and distant parts of the molecule, which is necessary for the accurate description of excited states especially for charge transfer states. This phenomenon and the synthesized test molecules can be used to benchmark theoretical methods as well as to help the development of new functionals intended for spectroscopical studies.

  13. Systematic study on the TD-DFT calculated electronic circular dichroism spectra of chiral aromatic nitro compounds: A comparison of B3LYP and CAM-B3LYP.

    PubMed

    Komjáti, Balázs; Urai, Ákos; Hosztafi, Sándor; Kökösi, József; Kováts, Benjámin; Nagy, József; Horváth, Péter

    2016-02-15

    B3LYP is one of the most widely used functional for the prediction of electronic circular dichroism spectra, however if the studied molecule contains aromatic nitro group computations may fail to produce reliable results. A test set of molecules of known stereochemistry were synthesized to study this phenomenon in detail. Spectra were computed by B3LYP and CAM-B3LYP functionals with 6-311++G(2d,2p) basis set. It was found that the range separated CAM-B3LYP gives better predictions than B3LYP for all test molecules. Fragment population analysis revealed that the nitro groups form highly localized molecule orbitals but the exact composition depends on the functional. CAM-B3LYP allows sufficient spatial overlap between the nitro group and distant parts of the molecule, which is necessary for the accurate description of excited states especially for charge transfer states. This phenomenon and the synthesized test molecules can be used to benchmark theoretical methods as well as to help the development of new functionals intended for spectroscopical studies.

  14. Flavan-3-ols and proanthocyanidins from Limonium brasiliense inhibit the adhesion of Porphyromonas gingivalis to epithelial host cells by interaction with gingipains.

    PubMed

    de Oliveira Caleare, Angelo; Hensel, Andreas; Mello, João Carlos Palazzo; Pinha, Andressa Blainski; Panizzon, Gean Pier; Lechtenberg, Matthias; Petereit, Frank; Nakamura, Celso Vataru

    2017-03-11

    Porphyromonas gingivalis is a pathogen strongly involved in chronic and aggressive forms of periodontitis. Natural products, mainly polyphenols, have been described for advanced treatment of periodontitis by inhibition of the bacterial adhesion of P. gingivalis to the epithelial host cells. An acetone:water extract (LBE) from the rhizomes of Limonium brasiliense (Boiss.) Kuntze was tested under in vitro conditions for potential antiadhesive effects against P. gingivalis to human KB cells and for inhibition of the proteolytic activity of gingipains, the main virulence factor of P. gingivalis. LBE≤100μg/mL had no cytotoxicity against the bacteria and did not influence the cell physiology of human epithelial KB cells. At 100μg/mL LBE reduced the adhesion of P. gingivalis to KB cells significantly by about 80%. LBE at 20μg/mL reduced the proteolytic activity of the arginin-specific Rgp gingipain by about 75%. Chemical profiling of LBE indicated the presence of gallic acid, epigallocatechin-3-O-gallate and samarangenins A and B as lead compounds. UHPLC by using MS and UV detection displays a suitable method for quality control of the extract for identification and quantification of the lead compounds.

  15. Risk assessment of Soulatrolide and Mammea (A/BA+A/BB) coumarins from Calophyllum brasiliense by a toxicogenomic and toxicological approach.

    PubMed

    Gomez-Verjan, J C; Estrella-Parra, E; Vazquez-Martinez, E R; Gonzalez-Sanchez, I; Guerrero-Magos, G; Mendoza-Villanueva, D; Isus, L; Alfaro, A; Cerbón-Cervantes, M; Aloy, P; Reyes-Chilpa, R

    2016-05-01

    Calophyllum brasiliense (Calophyllaceae) is a tropical rain forest tree distributed in Central and South America. It is an important source of tetracyclic dipyrano coumarins (Soulatrolide) and Mammea type coumarins. Soulatrolide is a potent inhibitor of HIV-1 reverse transcriptase and displays activity against Mycobacterium tuberculosis. Meanwhile, Mammea A/BA and A/BB, pure or as a mixture, are highly active against several human leukemia cell lines, Trypanosoma cruzi and Leishmania amazonensis. Nevertheless, there are few studies evaluating their safety profile. In the present work we performed toxicogenomic and toxicological analysis for both type of compounds. Soulatrolide, and the Mammea A/BA + A/BB mixture (2.1) were slightly toxic accordingly to Lorke assay classification (DL50 > 3000 mg/kg). After a short-term administration (100 mg/kg/daily, orally, 1 week) liver toxicogenomic analysis revealed 46 up and 72 downregulated genes for Mammea coumarins, and 665 up and 1077 downregulated genes for Soulatrolide. Gene enrichment analysis identified transcripts involved in drug metabolism for both compounds. In addition, network analysis through protein-protein interactions, tissue evaluation by TUNEL assay, and histological examination revealed no tissue damage on liver, kidney and spleen after treatments. Our results indicate that both type of coumarins displayed a safety profile, supporting their use in further preclinical studies to determine its therapeutic potential.

  16. A quorum sensing-defective mutant of Pectobacterium carotovorum ssp. brasiliense 1692 is attenuated in virulence and unable to occlude xylem tissue of susceptible potato plant stems.

    PubMed

    Moleleki, Lucy Novungayo; Pretorius, Rudolph Gustav; Tanui, Collins Kipngetich; Mosina, Gabolwelwe; Theron, Jacques

    2017-01-01

    Pectobacterium carotovorum ssp. brasiliense 1692 (Pcb1692) is an important emerging pathogen of potatoes causing blackleg in the field and soft rot during post-harvest storage. Blackleg diseases involve the bacterial colonization of vascular tissue and the formation of aggregates, also known as biofilms. To understand the role of quorum sensing in vascular colonization by Pcb1692, we generated a Pcb1692ΔexpI mutant strain. Inactivation of expI led to the reduced production of plant cell wall-degrading enzymes (PCWDEs), the inability to produce acyl homoserine lactone (AHL) and reduced virulence in potato tubers and stems. Complementation of the mutant strain with the wild-type expI gene in trans successfully restored AHL and PCWDE production as well as virulence. Transmission electron microscopy and in vitro motility assays demonstrated hyperpiliation and loss of flagella and swimming motility in the mutant strain compared with the wild-type Pcb1692. Furthermore, we noted that, in the early stages of infection, Pcb1692 wild-type cells had intact flagella which were shed at the later stages of infection. Confocal laser microscopy of PcbΔexpI-inoculated plants showed that the mutant strain tended to aggregate in intercellular spaces, but was unable to transit to xylem tissue. On the contrary, the wild-type strain was often observed forming aggregates within xylem tissue of potato stems. Gene expression analyses confirmed that flagella are part of the quorum sensing regulon, whereas fimbriae and pili appear to be negatively regulated by quorum sensing. The relative expression levels of other important putative virulence genes, such as those encoding different groups of PCWDEs, were down-regulated in the mutant compared with the wild-type strain.

  17. Biology and occurrence of Inga Busk species (Lepidoptera: Oecophoridae) on Cerrado host plants.

    PubMed

    Diniz, Ivone R; Bernardes, Carolina; Rodovalho, Sheila; Morais, Helena C

    2007-01-01

    We sampled Inga Busk species caterpillars weekly in the cerrado on 15 plants of Diospyros burchellii Hern. (Ebenaceae) from January 2002 to December 2003, on 30 plants of Caryocar brasiliense (Caryocaraceae) from July 2003 to June 2004, and since 1991 on several other plant species. In total we found 15 species of Inga on cerrado host plants. Nine species were very rare, with only one to five adults reared. The other six species occurred throughout the year, with higher abundance during the dry season, from May to July, coinciding with overall peaks of caterpillar abundance in the cerrado. Caterpillars of the genus Inga build shelters by tying and lining two mature or old leaves with silk and frass, where they rest and develop (a common habit found in Oecophorinae). The final instar builds a special envelope inside the leaf shelter, where it will complete the larval stage and pupate. The species are very difficult to distinguish in the immature stages. External features were useful in identifying only four species: I. haemataula (Meyrick), I. phaecrossa (Meyrick), I. ancorata (Walsingham), and I. corystes (Meyrick). These four species are polyphagous and have wide geographical distributions. In this paper we provide information on the natural history and host plants of six Inga species common on cerrado host plants, for which there are no reports in the literature.

  18. Bioactive Compounds Found in Brazilian Cerrado Fruits

    PubMed Central

    Bailão, Elisa Flávia Luiz Cardoso; Devilla, Ivano Alessandro; da Conceição, Edemilson Cardoso; Borges, Leonardo Luiz

    2015-01-01

    Functional foods include any natural product that presents health-promoting effects, thereby reducing the risk of chronic diseases. Cerrado fruits are considered a source of bioactive substances, mainly phenolic compounds, making them important functional foods. Despite this, the losses of natural vegetation in the Cerrado are progressive. Hence, the knowledge propagation about the importance of the species found in Cerrado could contribute to the preservation of this biome. This review provides information about Cerrado fruits and highlights the structures and pharmacologic potential of functional compounds found in these fruits. Compounds detected in Caryocar brasiliense Camb. (pequi), Dipteryx alata Vog. (baru), Eugenia dysenterica DC. (cagaita), Eugenia uniflora L. (pitanga), Genipa americana L. (jenipapo), Hancornia speciosa Gomes (mangaba), Mauritia flexuosa L.f. (buriti), Myrciaria cauliflora (DC) Berg (jabuticaba), Psidium guajava L. (goiaba), Psidium spp. (araçá), Solanum lycocarpum St. Hill (lobeira), Spondias mombin L. (cajá), Annona crassiflora Mart. (araticum), among others are reported here. PMID:26473827

  19. Soybean SDS in South Africa is caused by Fusarium brasiliense and a novel undescribed Fusarium sp.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean sudden death syndrome (SDS) was detected in South Africa for the first time during pathogen surveys conducted in 2013-2014. The primary objective of this study was to characterize the 16 slow-growing Fusarium strains that were isolated from the roots of symptomatic plants. Molecular phylogen...

  20. Benchmarking two-photon absorption cross sections: performance of CC2 and CAM-B3LYP.

    PubMed

    Beerepoot, Maarten T P; Friese, Daniel H; List, Nanna H; Kongsted, Jacob; Ruud, Kenneth

    2015-07-15

    We investigate the performance of CC2 and TDDFT/CAM-B3LYP for the calculation of two-photon absorption (TPA) strengths and cross sections and contrast our results to a recent coupled cluster equation-of-motion (EOM-EE-CCSD) benchmark study [K. D. Nanda and A. I. Krylov, J. Chem. Phys., 2015, 142, 064118]. In particular, we investigate whether CC2 TPA strengths are significantly overestimated compared to higher-level coupled-cluster calculations for fluorescent protein chromophores. Our conclusion is that CC2 TPA strengths are only slightly overestimated compared to the reference EOM-EE-CCSD results and that previously published overestimated cross sections are a result of inconsistencies in the conversion of the TPA strengths to macroscopic units. TDDFT/CAM-B3LYP TPA strengths, on the other hand, are found to be 1.5 to 3 times smaller than the coupled-cluster reference for the molecular systems considered. The unsatisfactory performance of TDDFT/CAM-B3LYP can be linked to an underestimation of excited-state dipole moments predicted by TDDFT/CAM-B3LYP.

  1. Cognitive and Functional Decline among Individuals 50 Years of Age or Older in Cambé, Paraná, Brazil: A Population-Based Study

    PubMed Central

    Cabrera, Marcos Aparecido Sarria; Bortoletto, Maira Aira Sayuri Sakay; de Souza, Regina Kazue Tanno; Prina, Douglas Manuel Carrapeiro; Vieira, Maria Cristina Umpierrez; Silva, Ana Maria Rigo

    2016-01-01

    Aims To identify the frequency of cognitive and functional decline (CFD) among adults 50 years of age and older by a population-based study. Methods Cognitive function was analyzed by the Mini-Mental State Examination, and the functional conditions were based on instrumental activities of daily living (IADL). Cases of CFD included individuals with cognitive decline and 2 or more compromised IADL. Results A total of 693 individuals were studied. The frequency of CFD was 16.3%. A low socioeconomic profile was associated with greater CFD independent of gender, age, education, and presence of depression (OR = 2.46; 95% CI: 1.53-3.97). Conclusions These data show a high frequency of CFD among adults 50 years and older. Individuals with less education and a lower socioeconomic level exhibited poorer cognitive and functional conditions. PMID:27350779

  2. Physicochemical characterization, antioxidant capacity, total phenolic and proanthocyanidin content of flours prepared from pequi (Caryocar brasilense Camb.) fruit by-products.

    PubMed

    Leão, Daniela P; Franca, Adriana S; Oliveira, Leandro S; Bastos, Rita; Coimbra, Manuel A

    2017-06-15

    The potential of pequi by-products as substrates for the production of flours rich in antioxidant dietary fibers was evaluated. Dietary fiber contents ranged from 39.8 to 43.3g/100g with pectic polysaccharide fraction constituted of rhamnogalacturonans and hemicellulose fraction consisted of arabinogalactans, xylans and glucomannans. Total polyphenols, non-extractable proanthocyanidins (NEPA) and carotenoid contents of the flours were determined (respectively, 15.5-17.4g GAE/100g, 215.54-346.84mg/100g and 2116.52-3499.03μg/100g). The antioxidant capacities of pequi by-product flours (986.94-1154.42μM TE/g ABTS; 44.43-48.02g/g DPPH; and 3027.31-3216.27μmol Fe2SO4/g FRAP) were found to be exceptionally higher than those of fruits and fruits by-products reported in the literature. Exocarp removal promoted no significant changes in the technological properties of the flour, except for color. Results showed promising prospects for future exploitation of pequi peel as a potential source of dietary fiber and natural antioxidants.

  3. [Association of Constrictotermes cyphergaster Silvestri (Isoptera: Termitidae) with trees in the Brazilian Cerrado].

    PubMed

    Lima-Ribeiro, Matheus de S; Pinto, Míriam P; Costa, Shirley S; Nabout, João C; Rangel, Thiago F L V B; de Melo, Tatiana L; de Moura, Iona'i O

    2006-01-01

    Termites usually build nests differently shaped and characterized according to each species, to protect and keep society cohesion. Some species build nests in the ground, some prefer tree thunks or branches as support, whereas other dig galleries in the wood. The purpose of this study is to analyze the relationship between the occurrence of arboreal termites Constrictotermes cyphergaster Silvestri and tree species that support the nest of this species, in a Cerrado sensu strictu of the Serra de Caldas Novas, GO. Data suggest a association relationship between C. Cyphergaster and the tree species Qualea grandiflora Mart., Annona crassiflora Mart., Caryocar brasiliense Camb. and Plathymenia reticulata Benth., shown by high Qui-squared values (chi2 = 214.986, gl. = 20, P < 0.001). This relationship may be found among other termites and tree species, including Cerrado biome, and may be due to several factors, such as natural competitors and predators, toxin production by other tree species or benefits between associated species (facultative mutualism or facilitation).

  4. Discrimination of pulp oil and kernel oil from pequi (Caryocar brasiliense) by fatty acid methyl esters fingerprinting, using GC-FID and multivariate analysis.

    PubMed

    Faria-Machado, Adelia F; Tres, Alba; van Ruth, Saskia M; Antoniassi, Rosemar; Junqueira, Nilton T V; Lopes, Paulo Sergio N; Bizzo, Humberto R

    2015-11-18

    Pequi is an oleaginous fruit whose edible oil is composed mainly by saturated and monounsaturated fatty acids. The biological and nutritional properties of pequi oil are dependent on its composition, which can change according to the oil source (pulp or kernel). There is little data in the scientific literature concerning the differences between the compositions of pequi kernel and pulp oils. Therefore, in this study, different pequi genotypes were evaluated to determine the fatty acid composition of pulp and kernel oils. PCA and PLS-DA were applied to develop a model to distinguish these oils. For all evaluated genotypes, the major fatty acids of both pulp and kernel oils were oleic and palmitic acids. Despite the apparent similarity between the analyzed samples, it was possible to discriminate pulp and kernel oils by means of their fatty acid composition using chemometrics, as well as the unique pequi genotype without endocarp spines (CPAC-PQ-SE-06).

  5. Phytoaccumulation of trace elements by wetland plants: 3. Uptake and accumulation of ten trace elements by twelve plant species

    SciTech Connect

    Qian, J.H.; Zayed, A.; Zhu, Y.L.; Yu, M.; Terry, N.

    1999-10-01

    Interest is increasing in using wetland plants in constructed wetlands to remove toxic elements from polluted wastewater. To identify those wetland plants that hyperaccumulate trace elements, 12 plant species were tested for their efficiency to bioconcentrate 10 potentially toxic trace elements including As, b, Cd, Cr, Cu, Pb, Mn, Hg, Ni, and Se. Individual plants were grown under carefully controlled conditions and supplied with 1 mg L{sup {minus}1} of each trace element individually for 10 d. Except B, all elements accumulated to much higher concentrations in roots than in shoots. Highest shoot tissue concentrations (mg kg{sup {minus}1} DW) of the various trace elements were attained by the following species: umbrella plant (Cyperus alternifolius L.) for Mn (198) and Cr (44); water zinnia (Wedelia trilobata Hitchc.) for Cd (148) and Ni (80); smartweed (Polygonum hydropiperoides Michx.) for Cu (95) and Pb (64); water lettuce (Pistia stratiotes L.) for Hg (92), As (34), and Se (39); and mare's tail (hippuris vulgaris L.) for B (1132). Whereas, the following species attained the highest root tissue concentrations (mg kg{sup {minus}1} DW); stripped rush (Baumia rubiginosa) for Mn (1683); parrot's feather (Myriophyllum brasiliense Camb.) for Cd (1426) and Ni (1077); water lettuce for Cu (1038), Hg (1217), and As (177); smartweed for Cr (2980) and Pb (1882); mare's tail for B (1277); and monkey flower (Mimulus guttatus Fisch.) for Se (384). From a phytoremediation perspective, smartweed was probably the best plant species for trace element removal from wastewater due to its faster growth and higher plant density.

  6. Efficacy of orally delivered cochleates containing amphotericin B in a murine model of aspergillosis.

    PubMed

    Delmas, G; Park, S; Chen, Z W; Tan, F; Kashiwazaki, R; Zarif, L; Perlin, D S

    2002-08-01

    Cochleates containing amphotericin B (CAMB) were administered orally at doses ranging from 0 to 40 mg/kg of body weight/day for 14 days in a murine model of systemic aspergillosis. The administration of oral doses of CAMB (20 and 40 mg/kg/day) resulted in a survival rate of 70% and a reduction in colony counts of more than 2 logs in lungs, livers, and kidneys. Orally administered CAMB shows promise for the treatment of aspergillosis.

  7. Efficacy of Orally Delivered Cochleates Containing Amphotericin B in a Murine Model of Aspergillosis

    PubMed Central

    Delmas, G.; Park, S.; Chen, Z. W.; Tan, F.; Kashiwazaki, R.; Zarif, L.; Perlin, D. S.

    2002-01-01

    Cochleates containing amphotericin B (CAMB) were administered orally at doses ranging from 0 to 40 mg/kg of body weight/day for 14 days in a murine model of systemic aspergillosis. The administration of oral doses of CAMB (20 and 40 mg/kg/day) resulted in a survival rate of 70% and a reduction in colony counts of more than 2 logs in lungs, livers, and kidneys. Orally administered CAMB shows promise for the treatment of aspergillosis. PMID:12121962

  8. Antifungal Activity of Amphotericin B Cochleates against Candida albicans Infection in a Mouse Model

    PubMed Central

    Zarif, Leila; Graybill, John R.; Perlin, David; Najvar, Laura; Bocanegra, Rosie; Mannino, Raphael J.

    2000-01-01

    Cochleates are lipid-based supramolecular assemblies composed of natural products, negatively charged phospholipid, and a divalent cation. Cochleates can encapsulate amphotericin B (AmB), an important antifungal drug. AmB cochleates (CAMB) have a unique shape and the ability to target AmB to fungi. The minimal inhibitory concentration and the minimum lethal concentration against Candida albicans are similar to that for desoxycholate AmB (DAMB; Fungizone). In vitro, CAMB induced no hemolysis of human red blood cells at concentrations of as high as 500 μg of AmB/ml, and DAMB was highly hemolytic at 10 μg of AmB/ml. CAMB protect ICR mice infected with C. albicans when the agent is administered intraperitoneally at doses of as low as 0.1 mg/kg/day. In a tissue burden study, CAMB, DAMB, and AmBisome (liposomal AmB; LAMB) were effective in the kidneys, but in the spleen CAMB was more potent than DAMB at 1 mg/kg/day and was equivalent to LAMB at 10 mg/kg/day. In summary, CAMB are highly effective in treating murine candidiasis and compare well with AmBisome and AmB. PMID:10817694

  9. Antifungal activity of amphotericin B cochleates against Candida albicans infection in a mouse model.

    PubMed

    Zarif, L; Graybill, J R; Perlin, D; Najvar, L; Bocanegra, R; Mannino, R J

    2000-06-01

    Cochleates are lipid-based supramolecular assemblies composed of natural products, negatively charged phospholipid, and a divalent cation. Cochleates can encapsulate amphotericin B (AmB), an important antifungal drug. AmB cochleates (CAMB) have a unique shape and the ability to target AmB to fungi. The minimal inhibitory concentration and the minimum lethal concentration against Candida albicans are similar to that for desoxycholate AmB (DAMB; Fungizone). In vitro, CAMB induced no hemolysis of human red blood cells at concentrations of as high as 500 microg of AmB/ml, and DAMB was highly hemolytic at 10 microg of AmB/ml. CAMB protect ICR mice infected with C. albicans when the agent is administered intraperitoneally at doses of as low as 0.1 mg/kg/day. In a tissue burden study, CAMB, DAMB, and AmBisome (liposomal AmB; LAMB) were effective in the kidneys, but in the spleen CAMB was more potent than DAMB at 1 mg/kg/day and was equivalent to LAMB at 10 mg/kg/day. In summary, CAMB are highly effective in treating murine candidiasis and compare well with AmBisome and AmB.

  10. In vitro Antioxidant and Enzymatic Approaches to Evaluate Neuroprotector Potential of Blechnum Extracts without Cytotoxicity to Human Stem Cells

    PubMed Central

    Andrade, Juliana Maria de Mello; Biegelmeyer, Renata; Dresch, Roger Remy; Maurmann, Natasha; Pranke, Patrícia; Henriques, Amélia T.

    2016-01-01

    Background: Investigation of selected plant extracts on multi-targets related to neurodegeneration, such as monoamine oxidases (MAO), cholinesterase enzymes, and antioxidant activities (AOA) is a useful tool for identification of new scaffolds. Objective: This work investigated biological effects of three Blechnum methanol extracts from Brazil and chemical profile of the most active sample. Materials and Methods: AOA included scavenging of hydroxyl and nitric oxide radicals, also lipid peroxidation inhibition. Enzymatic modulation of Blechnum binervatum, Blechnum brasiliense, and Blechnum occidentale extracts on MAO and cholinesterases was conducted. Moreover, total phenol content was performed with all samples, and high-performance liquid chromatography-diode array detection mass spectrometry HPLC-DAD-MS analysis was carried out with B. brasiliense. Possible toxic effects were evaluated on Wistar rats polymorphonuclear cells (PMN) and human stem cells. Results: B. brasiliense extract presented the highest phenolic amount (9.25 g gallic acid equivalent/100 g extract) and lowest IC50 values (112.3 ± 2.61 and 176.1 ± 1.19 μg/mL) against hydroxyl radicals and on lipid peroxidation, respectively, showing strong AO effects. On nitric oxide assay and cholinesterase inhibition, all extracts were considered inactive. MAO-A selective action was evidenced, being B. brasiliense powerful against this enzyme (IC50: 72.7 μg/mL), followed by B. occidentale and B. binervatum (IC50: 130.85 and 165.2 μg/mL). No cytotoxic effects were observed on PMN and human stem cells treated with Blechnum extracts. HPLC-DAD-MS analysis of B. brasiliense allowed the identification of chlorogenic and rosmarinic acids. Conclusion: Our results especially highlight B. brasiliense, with pronounced phenols content and strong effects on selected targets related to neurodegeneration, being characterized as a natural safe source of bioactive hydroxycinnamic acids. SUMMARY Blechnum crude extracts

  11. Factors Promoting a Cool Cambrian Climate: Role of Land Surface Conditions and Atmospheric Greenhouse Gases

    NASA Astrophysics Data System (ADS)

    Shellito, L. J.

    2011-12-01

    In light of recent work suggesting episodic cooling during the Late Cambrian (~500 Ma), an Earth System Model of Intermediate Complexity is utilized to evaluate the roles of Late Cambrian continental configuration, mountain height, and atmospheric CO2 concentration on Earth's climate. The Planetary Simulator (PLASIM), developed at the Meteorological Institute of the University of Hamburg, is utilized at T21 spectral resolution (5.6° latitude x 5.6° longitude) with a 50 m deep slab ocean in four experiments. The first three experiments are run with a Late Cambrian continental configuration. Two experiments are run with an atmospheric CO2 concentration of 10 x pre-industrial (2800 ppm). This is in the range estimated for the Late Cambrian by carbon cycle modeling studies. One of these experiments utilizes a flat topography (CAMB_FLAT), and the other, includes mountains (CAMB_MTN). A third experiment is identical to CAMB_MTN, but CO2 is set to 280 ppm (CAMB_COLD). All Cambrian experiments are integrated without any vegetation, and with solar luminosity reduced by 6%. The Cambrian experiments also utilize a uniform land surface boundary condition consisting of sand with an albedo of 0.37. A fourth scenario was run with pre-industrial boundary conditions (modern geography and vegetation and 280 ppm CO2) as a control experiment (CONTROL). Despite the high level of CO2, global average temperatures in CAMB_FLAT and CAMB_MTN are cooler than that of CONTROL. In CAMB_COLD, the oceans freeze over completely and 'snowball Earth' conditions are present. These results highlight the importance of vegetation, land surface albedo, and continental position in maintaining an equable climate in modern times. They also suggest that a drop in greenhouse gases during the Cambrian, whether due to reduced natural emissions from biologic or volcanic sources, or an increase in biologic activity in the oceans, could have been responsible for the initiation of cooler climatic conditions.

  12. Metabolomic studies for the interaction Glycine max- Fusarium tucumaniae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sudden-death syndrome (SDS) of soybean can be caused in Argentina by 4 different Fusarium species: F. brasiliense, F. crassistipitatum, F. tucumaniae and F. virguliforme. Fusarium tucumaniae and F. virguliforme are the primary etiological agents of soybean SDS in Argentina and United States, respect...

  13. Clinical study on liposomal amphotericin B (Ambisome) in deep fungal infections in China.

    PubMed

    Wei, H; Hai, W; Wanqing, L

    2003-02-01

    Ambisome (L-Amb) was used to treat nine cases of meningitis or menigoencephalitis by Cryptococcus neoformans and 28 cases of other deep fungal infections. A retrospective study on conventional amphotericin B (C-Amb) was performed as the control. A series of indices was observed including curative effect, fungal clearance rate, course of treatment, daily dose, cumulative dose and adverse effects. Nine cases of cryptococcal meningitis or menigoencephalitis treated with Ambisome were clinically cured with an effective rate of 100%, within a mean course of 50 days, which was shorter than that of C-Amb, by a mean cumulative dose of 1807.2 mg, which was not statistically significant in comparison with C-Amb. Fungal clearance rate on the second month of treatment was 89% with Ambisome, which was higher than that of C-Amb. Twenty-eight cases of other deep fungal infections treated with Ambisome were clinically cured with an effective rate of 92%, within a mean course of 19.3 days, by a mean cumulative dose of 907.5 mg, and fungal clearance rate on the second and third month was 75 and 92%, respectively. The adverse effects by Ambisome decreased evidently compared with those by C-Amb.

  14. Rescheduling Behavioral Subunits of a Fixed Action Pattern by Genetic Manipulation of Peptidergic Signaling

    PubMed Central

    Kim, Do-Hyoung; Han, Mi-Ran; Lee, Gyunghee; Lee, Sang Soo; Kim, Young-Joon; Adams, Michael E.

    2015-01-01

    The ecdysis behavioral sequence in insects is a classic fixed action pattern (FAP) initiated by hormonal signaling. Ecdysis triggering hormones (ETHs) release the FAP through direct actions on the CNS. Here we present evidence implicating two groups of central ETH receptor (ETHR) neurons in scheduling the first two steps of the FAP: kinin (aka drosokinin, leucokinin) neurons regulate pre-ecdysis behavior and CAMB neurons (CCAP, AstCC, MIP, and Bursicon) initiate the switch to ecdysis behavior. Ablation of kinin neurons or altering levels of ETH receptor (ETHR) expression in these neurons modifies timing and intensity of pre-ecdysis behavior. Cell ablation or ETHR knockdown in CAMB neurons delays the switch to ecdysis, whereas overexpression of ETHR or expression of pertussis toxin in these neurons accelerates timing of the switch. Calcium dynamics in kinin neurons are temporally aligned with pre-ecdysis behavior, whereas activity of CAMB neurons coincides with the switch from pre-ecdysis to ecdysis behavior. Activation of CCAP or CAMB neurons through temperature-sensitive TRPM8 gating is sufficient to trigger ecdysis behavior. Our findings demonstrate that kinin and CAMB neurons are direct targets of ETH and play critical roles in scheduling successive behavioral steps in the ecdysis FAP. Moreover, temporal organization of the FAP is likely a function of ETH receptor density in target neurons. PMID:26401953

  15. The use of Coulomb-attenuated methods for the calculation of electronic circular dichroism spectra

    NASA Astrophysics Data System (ADS)

    Shcherbin, Dmitry; Ruud, Kenneth

    2008-06-01

    We explore different parametrizations of the Coulomb-attenuated method B3LYP functional (CAM-B3LYP) for the calculation of circular dichroism spectra. In order to assess the performance of the different parametrizations, the calculated results are compared with high-level coupled-cluster calculations at the CC2 and CCSD levels of theory. We demonstrate that it is not possible to directly obtain good results both for the excitation energies and the rotational strengths simultaneously for any of the parametrizations of the CAM-B3LYP functional that we have tested. However, using the lowest excited state as a reference instead of the ground state—that is, shifting uniformly all excitation energies—leads to one parametrization which performs better than the others and thus can be recommended for studies of circular dichroism using the CAM-B3LYP functional.

  16. Amphotericin B cochleates: a vehicle for oral delivery.

    PubMed

    Perlin, David S

    2004-02-01

    Cochleates are a novel lipid-based delivery vehicle consisting of crystalline phospholipid-cation structures that form spiral lipid sheets. They represent a new technology platform for oral delivery of clinically important drugs that possess poor oral bioavailability. Orally administered cochleates containing amphotericin B (CAMB) showed broad-spectrum activity in murine infection models of candidiasis, aspergillosis and cryptococcosis. Initial biodistribution studies of CAMB administered orally in mice demonstrated that cochleates delivered significant levels of AMB to target organs. The lipid particulate nature of cochleates also imparted reduced toxicity that mimics other lipid-amphotericin B complexes. Cochleates are a promising new vehicle for oral delivery of amphotericin B at therapeutic levels.

  17. "Escola Familia": A Proposal

    ERIC Educational Resources Information Center

    Carani, George; Carani, José; Strong-Wilson, Teresa

    2014-01-01

    "Alphabetização" (literacy) of young children involves a school exclusively devoted to the early years, parental participation, and teachers specialized in early literacy. This is the basis of José Carani's proposal for an "escola familia" in the municipality of Cambé (Brazil). This "Note from the Field," based on our…

  18. SPT Lensing Likelihood: South Pole Telescope CMB lensing likelihood code

    NASA Astrophysics Data System (ADS)

    Feeney, Stephen M.; Peiris, Hiranya V.; Verde, Licia

    2014-11-01

    The SPT lensing likelihood code, written in Fortran90, performs a Gaussian likelihood based upon the lensing potential power spectrum using a file from CAMB (ascl:1102.026) which contains the normalization required to get the power spectrum that the likelihood call is expecting.

  19. Applied Computational Electromagnetics Society Journal, Volume 9, Number 1, March 1994

    DTIC Science & Technology

    1994-03-01

    CULIIAM LAB Milton Road/Science Park Via Guglielmo Reiss Romoli 274 UK Atomic Energy Authority Cambridge. Cambs. UK CB5 4DW Turin. ITALY 10148 Abingdon...Chelsford St. San Carlos, CA 94404 Palo Alto. CA 94304 Lowell, MA01851 MARCONI DEFENCE SYSTEMS MARITELERADAR/BIBLUOTECA MISSISSIPPI STATE UNIV

  20. In vitro activity of amphotericin B cochleates against Leishmania chagasi.

    PubMed

    Sesana, Aretha Molina; Monti-Rocha, Renata; Vinhas, Solange Alves; Morais, Carlos Gustavo; Dietze, Reynaldo; Lemos, Elenice Moreira

    2011-03-01

    Cochleate delivery vehicles are a novel lipid-based system with potential for delivery of amphotericin B (AmB). In this study, the efficacy of cochleates was evaluated by examining the in vitro activity of AmB cochleates (CAMB) against Leishmania chagasi in a macrophage model of infection. We demonstrate that CAMB is nontoxic to macrophages at concentrations as high as 2.5 μg/mL, whereas the conventional formulation, AmB deoxycholate, showed high toxicity at this concentration. The in vitro activity of CAMB against L. chagasi was found to be similar to that of the reference drug AmB deoxycholate, with ED50s of 0.017 μg/mL and 0.021 μg/mL, respectively. Considering that L. chagasi affects organs amenable to cochleate-mediated delivery of AmB, we hypothesize that CAMB will be an effective lipid system for the treatment of visceral leishmaniasis.

  1. CosmoSlik: Cosmology sampler of likelihoods

    NASA Astrophysics Data System (ADS)

    Millea, Marius

    2017-01-01

    CosmoSlik quickly puts together, runs, and analyzes an MCMC chain for analysis of cosmological data. It is highly modular and comes with plugins for CAMB (ascl:1102.026), CLASS (ascl:1106.020), the Planck likelihood, the South Pole Telescope likelihood, other cosmological likelihoods, emcee (ascl:1303.002), and more. It offers ease-of-use, flexibility, and modularity.

  2. Trichomycetes (Zygomycota) in the digestive tract of arthropods in Amazonas, Brazil.

    PubMed

    Alencar, Yamile B; Ríos-Velásquez, Claudia M; Lichtwardt, Robert W; Hamada, Neusa

    2003-09-01

    Eight species of Harpellales and three species of Eccrinales (Zygomycota: Trichomycetes) were found associated with the digestive tract of arthropods from terrestrial and aquatic environments in the central Amazon region of Brazil. New species of Harpellales include: Harpella amazonica, Smittium brasiliense, Genistellospora tropicalis in Simuliidae larvae and Stachylina paucispora in Chironomidae larvae. Axenic cultures of S. brasiliense were obtained. Probable new species of Enterobryus (Eccrinales), Harpella, and Stachylina (Harpellales) are described but not named. Also reported are the previously known species of Eccrinales, Passalomyces compressus and Leidyomyces attenuatus in adult Coleoptera (Passalidae), and Smittium culisetae and Smittium aciculare (Harpellales) in Culicidae and Simuliidae larvae, respectively. Comments on the distribution of some of these fungi and their hosts in the Neotropics are provided.

  3. Phytotoxic Lipophilic Metabolites Produced by Grapevine Strains of Lasiodiplodia Species in Brazil.

    PubMed

    Cimmino, Alessio; Cinelli, Tamara; Masi, Marco; Reveglia, Pierluigi; da Silva, Marcondes Araujo; Mugnai, Laura; Michereff, Sami J; Surico, Giuseppe; Evidente, Antonio

    2017-02-15

    Phytotoxic metabolites produced in liquid culture by six species of Lasiodiplodia isolated in Brazil and causing Botryosphaeria dieback of grapevine were chemically identified. As ascertained by LC/MS, L. brasiliense, L. crassispora, L. jatrophicola, and L. pseudotheobromae produced jasmonic acid, and L. brasiliense synthesized, besides jasmonic acid, also (3R,4S)-4-hydroxymellein. L. euphorbicola and L. hormozganensis produced some low molecular weight lipophilic toxins. Specifically, L. euphorbicola produced (-)-mellein, (3R,4R)-(-)- and (3R,4S)-(-)-4-hydroxymellein, and tyrosol, and L. hormozganensis synthesized tyrosol and p-hydroxybenzoic acid. This is the first report on the production of the above cited metabolites from L. euphorbicola and L. hormozganensis. The phytotoxic activity of the metabolites produced is also discussed and related to the symptoms these pathogens cause in the grapevine host plants.

  4. Intra- and extracellular osmotic regulation in the hololimnetic Caridea and Anomura: a phylogenetic perspective on the conquest of fresh water by the decapod Crustacea.

    PubMed

    de Faria, Samuel Coelho; Augusto, Alessandra Silva; McNamara, John Campbell

    2011-02-01

    We investigate extra- and intracellular osmoregulatory capability in two species of hololimnetic Caridea and Anomura: Macrobrachium brasiliense, a palaemonid shrimp, and Aegla franca, an aeglid anomuran, both restricted to continental waters. We also appraise the sharing of physiological characteristics by the hololimnetic Decapoda, and their origins and role in the conquest of fresh water. Both species survive salinity exposure well. While overall hyperosmoregulatory capability is weak in A. franca and moderate in M. brasiliense, both species strongly hyporegulate hemolymph [Cl(-)] but not osmolality. Muscle total free amino acids (FAA) increase slowly but markedly in response to the rapid rise in hemolymph osmolality consequent to hyperosmotic challenge: 3.5-fold in A. franca and 1.9-fold in M. brasiliense. Glycine, taurine, arginine, alanine and proline constitute ≈85% of muscle FAA pools in fresh water; taurine, arginine, alanine each contribute ≈22% in A. franca, while glycine predominates (70%) in M. brasiliense. These FAA also show the greatest increases on salinity challenge. Muscle FAA titers correlate strongly (R = 0.82) with hemolymph osmolalities across the main decapod sub/infraorders, revealing that marine species with high hemolymph osmolalities achieve isosmoticity of the intra- and extracellular fluids partly through elevated intracellular FAA concentrations; freshwater species show low hemolymph osmolalities and exhibit reduced intracellular FAA titers, consistent with isosmoticity at a far lower external osmolality. Given the decapod phylogeny adopted here and their multiple, independent invasions of fresh water, particularly by the Caridea and Anomura, our findings suggest that homoplastic strategies underlie osmotic and ionic homeostasis in the extant freshwater Decapoda.

  5. Angiotensin-converting enzyme inhibition by Brazilian plants.

    PubMed

    Braga, Fernão C; Serra, Carla P; Viana, Nilton S; Oliveira, Alaíde B; Côrtes, Steyner F; Lombardi, Júlio A

    2007-07-01

    The potential antihypertensive activity of Brazilian plants was evaluated in vitro by its ability to inhibit the angiotensin-converting enzyme (ACE). Forty-four plants belonging to 30 families were investigated. Plants were selected based on their popular use as antihypertensive and/or diuretics. The following plants presented significant ACE inhibition rates: Calophyllum brasiliense, Combretum fruticosum, Leea rubra, Phoenix roebelinii and Terminalia catappa.

  6. Trypanocidal constituents in plants: 7. Mammea-type coumarins.

    PubMed

    Reyes-Chilpa, Ricardo; Estrada-Muñiz, Elizabeth; Vega-Avila, Elisa; Abe, Fumiko; Kinjo, Junei; Hernández-Ortega, Simón

    2008-08-01

    Calophyllum brasiliense and Mammea americana (Clusiaceae) are two trees from the tropical rain forests of the American continent. A previous screening showed high trypanocidal activity in the extracts of these species. Several mammea-type coumarins, triterpenoids and biflavonoids were isolated from the leaves of C. brasiliense. Mammea A/AA was obtained from the fruit peels of M. americana. These compounds were tested in vitro against epimastigotes and trypomastigotes of Trypanosoma cruzi, the etiologic agent of Chagas disease. The most potent compounds were mammea A/BA, A/BB, A/AA, A/BD and B/BA, with MC100 values in the range of 15 to 90 microg/ml. Coumarins with a cyclized gamma,gamma-dimethylallyl substituent on C-6, such as mammea B/BA, cyclo F + B/BB cyclo F, and isomammeigin, showed MC100 values > 200 microg/ml. Several active coumarins were also tested against normal human lymphocytes in vitro, which showed that mammea A/AA and A/BA were not toxic. Other compounds from C. brasiliense, such as the triterpenoids, friedelin, canophyllol, the biflavonoid amentoflavone, and protocatechuic and shikimic acids, were inactive against the epimastigotes. The isopropylidenedioxy derivative of shikimic acid was inactive, and its structure was confirmed by X-ray diffraction. Our results suggest that mammea-type coumarins could be a valuable source of trypanocidal compounds.

  7. Benchmark study of UV/Visible spectra of coumarin derivatives by computational approach

    NASA Astrophysics Data System (ADS)

    Irfan, Muhammad; Iqbal, Javed; Eliasson, Bertil; Ayub, Khurshid; Rana, Usman Ali; Ud-Din Khan, Salah

    2017-02-01

    A benchmark study of UV/Visible spectra of Simple coumarins and Furanocoumarins derivatives was conducted by employing the Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TD-DFT) approaches. In this study the geometries of ground and excited states, excitation energy and absorption spectra were estimated by using the DFT functional CAM-B3LYP, WB97XD, HSEH1PBE, MPW1PW91 and TD-B3LYP with 6-31 + G (d,p) basis set. CAM-B3LYP functional was found to have close agreement with the experimental values of Furranocoumarin class of coumarins while MPW1PW91 gave close results for simple coumarins. This study provided an insight about the electronic characteristics of the selected compounds and provided an effective tool for developing and designing the better UV absorber compounds.

  8. Isolation and characterization of nicotiflorin obtained by enzymatic hydrolysis of two precursors in tea seed extract.

    PubMed

    Lee, Hyang-Bok; Kim, Eun-Ki; Park, Sang-Jae; Bang, Sang-Gu; Kim, Tae Gil; Chung, Dae-Won

    2010-04-28

    Two flavonol triglycosides, camelliaside A (CamA) and camelliaside B (CamB), of tea seed extract (TSE) were subjected to enzymatic hydrolysis. Among five kinds of glycosidases investigated, beta-galactosidase (Gal) induced selective hydrolysis of CamA. On the other hand, pectinase (Pec) and cellulase (Cel) induced hydrolysis of CamB. For Gal and Pec, only kaempferol diglycoside (nicotiflorin, NF) was produced; on the other hand, significant amounts of kaempferol monoglycoside (astragalin, AS) and kaempferol (KR) were also detected for Cel. The combination of the use of Gal and Pec in the enzymatic hydrolysis of TSE afforded NF with high specificity. Crude NF with 22% purity was recovered from the enzymatic reaction mixture by extraction with organic solvent, and pure NF with >95% purity was obtained by crystallized in water. The chemical structure of NF was confirmed by (1)H and (13)C NMR analyses.

  9. Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.

    PubMed

    Martínez-Fernández, L; Pepino, A J; Segarra-Martí, J; Banyasz, A; Garavelli, M; Improta, R

    2016-09-13

    The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models.

  10. Predicting accurate fluorescent spectra for high molecular weight polycyclic aromatic hydrocarbons using density functional theory

    NASA Astrophysics Data System (ADS)

    Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.

    2016-10-01

    The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.

  11. Species Profiles: Life Histories and Environmental Requirements of Coastal Fishes and Invertebrates (South Florida). Reef-Building Corals.

    DTIC Science & Technology

    1987-08-01

    Stoddart, D.R. 1969. Ecology and Sammarco, P.W. 1985. The Great morphology of recent coral reefs . Barrier Reef vs. the Caribbean: Biol. Rev. Camb. Philos...Sambo Reef , Florida, involving cervicornis and M. annularis tolerated bleaching and loss of symbiotic oxygen tensions as low as 1.0 ppm for zooxanthellae...Montastraea (1.0-2.0 cm/yr), but both species of Montastraea are also important in reef development due to their massive form and great longevity

  12. On the linear and non-linear electronic spectroscopy of chlorophylls: a computational study.

    PubMed

    Graczyk, Alicja; Żurek, Justyna M; Paterson, Martin J

    2014-01-01

    A theoretical analysis of linear and non-linear (two-photon absorption) electronic spectroscopy of all known porphyrinic pigments has been performed using linear and quadratic density functional response theory, with the long-range corrected CAM-B3LYP functional. We found that higher Soret transitions often contain non-Gouterman contributions and that each chlorophyll has the possibility for resonance enhanced TPA in the Soret region, although there is also significant TPA in the Q region.

  13. Sediment-Submersed Macrophyte Relationships in Freshwater Systems.

    DTIC Science & Technology

    1982-06-01

    to decay-related processes. The species examined, being representative of three dis- tinctly different taxonomic groups, included Bacopa caroliniana...Walt.) Robins, Myriophyllum braziliense Camb., Potamogeton ilinoensis Morong, and Proserpinacc paZustris L. Among these species, Bacopa , Myriophylum...Means and Standard Errors are Based on Four Replications Sediment Species Nutrient Branched Oak Keystone Pawnee Bacopa N 27.5 + 0.2 24.7 + 0.2 26.4 + 0.1

  14. DFT study of linear and nonlinear optical properties of donor-acceptor substituted stilbenes, azobenzenes and benzilideneanilines.

    PubMed

    Krawczyk, Przemysław

    2010-04-01

    A theoretical analysis of the linear and nonlinear optical properties of six push-pull pi-conjugated molecules with stilbene, azobenzene and benzilideneaniline as a backbone is presented. The photophysical properties of the investigated systems were determined by using response functions combined with density functional theory (DFT). Several different exchange-correlation potentials were applied in order to determine parameters describing the one- and two-photon spectra of the studied molecules. In particular, the recently proposed Coulomb-attenuated model (CAM-B3LYP) was used to describe charge-transfer (CT) excited states. In order to compare theoretical predictions with available experimental data, calculations with inclusion of solvent effects were performed. The BLYP and the CAM-B3LYP functionals were found to yield values of two-photon absorption (TPA) probabilities closer to experimental values than the B3LYP functional or the HF wavefunction. Moreover, molecular static hyperpolarisabilities were determined using both DFT and second-order Møller-Plesset perturbation (MP2) theory. Likewise, the CAM-B3LYP functional was found to outperform other applied exchange-correlation potentials in determining first hyperpolarisability (beta). Moreover, it was confirmed on a purely theoretical basis that the presence of a -C=C- bridge between the phenyl rings leads to a much larger nonlinear optical response in comparison with a -N=N- bridge.

  15. Experimental and computational studies of 4-(Trifluoromethyl)pyridine-2-carboxylic acid

    NASA Astrophysics Data System (ADS)

    Vural, Hatice

    2016-05-01

    The vibrational spectrum of 4-(Trifluoromethyl)pyridine-2-carboxylic acid was recorded using Fourier transform infrared spectrometer in the range 4000-400 cm-1. The optimized geometric structure of 4-(Trifluoromethyl)pyridine-2-carboxylic acid was searched by B3LYP, CAMB3LYP, and PBEPBE levels of density functional theory (DFT). The vibrational wavenumbers of the title molecule in the ground state were computed by using B3LYP, CAMB3LYP, and PBEPBE methods with the 6-31G (d) basis set. NMR chemical shifts of the title compound were calculated using the gauge-independent atomic orbital (GIAO) method. The solvent effect on the UV-Vis absorption spectrum of the molecule was also examined using the B3LYP method by applying the integral equation formalism-polarized continuum model (IEF-PCM). The nonlinear optical (NLO) properties were measured by means of hyperpolarizability calculation. The electric dipole moment, the mean polarizability and the mean first hyperpolarizability were calculated by using the DFT method with B3LYP, CAMB3LYP, and PBEPBE levels.

  16. Molecular structure and vibrational properties of pyramidal MPc+ phthalocyanine cation in InPcI and LuPc(OAc) complexes

    NASA Astrophysics Data System (ADS)

    Hanuza, J.; Godlewska, P.; Kadłubański, P.; Ptak, M.; Mączka, M.; Gerasymchuk, Y. S.; Legendziewicz, J.

    2017-02-01

    Room temperature FT-IR spectra in the range 30-4000 cm-1 and FT-Raman spectra in the range 80-4000 cm-1 of indium and lutetium MPX-type phthalocyanines have been compared. The assignment of the observed bands has been accomplished on the basis of DFT chemical calculations using the B3LYP functional and its long range corrected version - CAM-B3LYP. The calculations were carried out for the indium derivative using the LANL2DZ, CC-PVDZ basis sets, i.e. the following approximations were used: B3LYP/CC-PVDZ, B3LYP/CC-PVTZ, B3LYP/LANL2DZ, CAM-B3LYP/CC-PVDZ and CAM-B3LYP/LANL2DZ. The molecular structures of these derivatives have been discussed in terms of group theory and geometry optimisation taking into account the shape and number of the bands corresponding to the stretching and bending vibrations of MN4 coordination polyhedron as well as the whole studied complex. The calculated structural parameters have been related to those from XRD studies. The usefulness of the proposed theoretical approaches in the prediction of the structural and vibrational data were analysed.

  17. Ticks infesting humans in Northern Misiones, Argentina.

    PubMed

    Lamattina, Daniela; Nava, Santiago

    2016-01-01

    This work presents records of ticks infesting humans in northern Misiones Province, Argentina. Also, notes on potential transmission of tick-borne pathogens are included. A total of 282 ticks attached to researchers were collected and identified by their morphological characters. Eight tick species were found: Amblyomma brasiliense, Amblyomma coelebs, Amblyomma dubitatum, Amblyomma incisum, Amblyomma ovale, Haemaphysalis juxtakochi, Rhipicephalus sanguineus and Rhipicephalus microplus. Some of these species as A. dubitatum, A. ovale and R. sanguineus have been found infected with spotted fever group rickettsiae pathogenic to humans in Brazil and Argentina. The potential role as vectors of humans pathogens of the ticks found attached to humans in this study is discussed.

  18. Biochemical remediation of a TNT contaminated soil. Doctoral thesis

    SciTech Connect

    Young, D.G.

    1995-06-01

    This research presents the first field evidence for the phytoremediation of a TNT contaminated soil by the emersed aquatic plant, Myriophyllum brasiliense. Commonly known as Parrotfeather, this plant features a nitroreductase enzyme capable of promoting the reduction of the nitro groups on TNT to the corresponding amino groups. The proposed reductive pathway takes the TNT through isomers of monoamino and diamino to the final triaminonitrotoluene (TNT) Once in the TAT form and in the presence of oxygen, the final oxidative step quickly yields ring opened products and complete phytoremediation of TNT.

  19. Inhibition of HIV-1 entry by the tricyclic coumarin GUT-70 through the modification of membrane fluidity

    SciTech Connect

    Matsuda, Kouki; Hattori, Shinichiro; Kariya, Ryusho; Komizu, Yuji; Kudo, Eriko; Goto, Hiroki; Taura, Manabu; Ueoka, Ryuichi; Kimura, Shinya; Okada, Seiji

    2015-02-13

    Membrane fusion between host cells and HIV-1 is the initial step in HIV-1 infection, and plasma membrane fluidity strongly influences infectivity. In the present study, we demonstrated that GUT-70, a natural product derived from Calophyllum brasiliense, stabilized plasma membrane fluidity, inhibited HIV-1 entry, and down-regulated the expression of CD4, CCR5, and CXCR4. Since GUT-70 also had an inhibitory effect on viral replication through the inhibition of NF-κB, it is expected to be used as a dual functional and viral mutation resistant reagent. Thus, these unique properties of GUT-70 enable the development of novel therapeutic agents against HIV-1 infection.

  20. Seed Dispersal Anachronisms: Rethinking the Fruits Extinct Megafauna Ate

    PubMed Central

    Guimarães, Paulo R.; Galetti, Mauro; Jordano, Pedro

    2008-01-01

    Background Some neotropical, fleshy-fruited plants have fruits structurally similar to paleotropical fruits dispersed by megafauna (mammals >103 kg), yet these dispersers were extinct in South America 10–15 Kyr BP. Anachronic dispersal systems are best explained by interactions with extinct animals and show impaired dispersal resulting in altered seed dispersal dynamics. Methodology/Principal Findings We introduce an operational definition of megafaunal fruits and perform a comparative analysis of 103 Neotropical fruit species fitting this dispersal mode. We define two megafaunal fruit types based on previous analyses of elephant fruits: fruits 4–10 cm in diameter with up to five large seeds, and fruits >10 cm diameter with numerous small seeds. Megafaunal fruits are well represented in unrelated families such as Sapotaceae, Fabaceae, Solanaceae, Apocynaceae, Malvaceae, Caryocaraceae, and Arecaceae and combine an overbuilt design (large fruit mass and size) with either a single or few (<3 seeds) extremely large seeds or many small seeds (usually >100 seeds). Within-family and within-genus contrasts between megafaunal and non-megafaunal groups of species indicate a marked difference in fruit diameter and fruit mass but less so for individual seed mass, with a significant trend for megafaunal fruits to have larger seeds and seediness. Conclusions/Significance Megafaunal fruits allow plants to circumvent the trade-off between seed size and dispersal by relying on frugivores able to disperse enormous seed loads over long-distances. Present-day seed dispersal by scatter-hoarding rodents, introduced livestock, runoff, flooding, gravity, and human-mediated dispersal allowed survival of megafauna-dependent fruit species after extinction of the major seed dispersers. Megafauna extinction had several potential consequences, such as a scale shift reducing the seed dispersal distances, increasingly clumped spatial patterns, reduced geographic ranges and limited genetic

  1. Lytopylus Förster (Hymenoptera, Braconidae, Agathidinae) species from Costa Rica, with an emphasis on specimens reared from caterpillars in Area de Conservación Guanacaste

    PubMed Central

    Sharkey, Michael J.; Clutts, Stephanie; Tucker, Erika M.; Janzen, Daniel; Hallwachs, Winnie; Dapkey, Tanya; Smith, M. Alex

    2011-01-01

    Abstract Twelve species of Costa Rican Lytopylus are treated; these include all species reared from Lepidoptera caterpillars in Area de Conservación Guanacaste, Costa Rica, over 32 years of caterpillar inventory, as well as two species recorded in the literature as occurring in Costa Rica. Ten new species are described, i.e., Lytopylus bradzlotnicki, Lytopylus colleenhitchcockae, Lytopylus gregburtoni, Lytopylus jessicadimauroae, Lytopylus jessiehillae, Lytopylus mingfangi, Lytopylus rebeccashapleyae, Lytopylus robpringlei, Lytopylus sandraberriosae, Lytopylus vaughntani. The following species are transferred to Lytopylus: Metriosoma flavicalcar Enderlein 1920 to Lytopylus flavicalcar comb. n.; Bassus macadamiae Briceño and Sharkey 2000 to Lytopylus macadamiae comb. n.; Metriosoma bicarinatum Enderlein 1920 to Lytopylus bicarinatum comb. n.; Metriosoma brasiliense Enderlein 1920 to Lytopylus brasiliense comb. n.; Bassus tayrona Campos 2007 to Lytopylus tayrona comb. n.; Microdus femoratus Cameron 1887 to Lytopylus femoratus comb. n.; Microdus melanocephalus Cameron 1887 to Lytopylus melanocephalus comb. n.; Bassus pastranai Blanchard 1952 to Lytopylus pastranai comb. n.; Agathis nigrobalteata Cameron 1911 to Lytopylus nigrobalteatus comb. n. Two keys to species of Lytopylus are presented, one interactive and the other static. PMID:22259290

  2. Intramuscular and topical treatment of cutaneous leishmaniasis lesions in mice infected with Leishmania amazonensis using coumarin (-) mammea A/BB.

    PubMed

    Tiuman, Tatiana Shioji; Brenzan, Mislaine Adriana; Ueda-Nakamura, Tânia; Filho, Benedito Prado Dias; Cortez, Diógenes Aparicio Garcia; Nakamura, Celso Vataru

    2012-10-15

    Treatment of cutaneous leishmaniasis remains limited to a few available options. Recent studies showed in vitro antileishmanial activity of (-) mammea A/BB, a coumarin isolated from leaves of Calophyllum brasiliense. Moreover, the dichloromethane crude extract and hexane fraction from this plant demonstrated in vivo activity in mice infected with Leishmania amazonensis. We evaluated the antileishmanial activity of (-) mammea A/BB in the L. amazonensis BALB/c mice model. The animals were given intramuscular and topical treatment with (-) mammea A/BB for 30 consecutive days. The results demonstrated that 18mg/kg/d intramuscularly or 0.2% topically of (-) mammea A/BB significantly reduced the size of skin lesions in footpads of mice compared with those in the control group (p<0.05). The activity of Glucantime(®) (corresponding to 27mg/kg/d of pentavalent antimony) administered intramuscularly was similar to that of (-) mammea A/BB (p<0.05) by both routes of administration. The histopathological evaluation showed no changes in the organs analyzed. These results indicate that the coumarin obtained from C. brasiliense is the antileishmanially active compound and can be used to control the development of cutaneous leishmaniasis lesions caused by L. amazonensis.

  3. Empirical antifungal therapy in patients with neutropenia and persistent or recurrent fever of unknown origin.

    PubMed

    Martino, Rodrigo; Viscoli, Claudio

    2006-01-01

    Persistent or recurrent fever of unexplained origin (PFUO) in neutropenic patients receiving antibiotic therapy is commonly treated with empirical antifungal therapy (EAFT). EAFT was established as an adequate management of PFUO around 20 years ago with conventional amphotericin B deoxycholate (c-AmB), despite its high rate of infusional and systemic toxicities. In recent years, EAFT trials for PFUO have used less toxic agents, such as the lipid formulations of AmB, the new azoles, and the echinocandin, caspofungin. In clinical trials, the lipid formulations of AmB [especially liposomal AmB (L-AmB)] provided similar efficacy with lower toxicity but at a much higher cost. Although rarely used in clinical practice, fluconazole is equivalent to c-AmB, provided patients at high risk of Aspergillus infections are excluded. Intravenous itraconazole was shown to be equivalent to c-AmB, with a lower toxicity. Voriconazole did not meet non-inferiority criteria when compared with L-AmB. Caspofungin was shown to be non-inferior to L-AmB and more effective in treating baseline invasive fungal infections. To date, alternatives to AmB have shown less toxicity, but improved efficacy is less clear. This is probably because of the weakness of the indication and to the consequent difficulty in establishing objective and reproducible endpoints for comparisons. The new challenge for physicians in this field is probably presumptive antifungal therapy, an approach based on patient risk-group stratification for developing invasive candidiasis or aspergillosis and/or the use of new diagnostic techniques to identify patients at a very early stage of infection.

  4. Raman and infrared spectroscopy, DFT calculations, and vibrational assignment of the anticancer agent picoplatin: performance of long-range corrected/hybrid functionals for a platinum(II) complex.

    PubMed

    Malik, Magdalena; Wysokiński, Rafał; Zierkiewicz, Wiktor; Helios, Katarzyna; Michalska, Danuta

    2014-08-28

    Picoplatin, cis-[PtCl2(NH3)(2-picoline)], is a new promising anticancer agent undergoing clinical trials, which reveals high efficacy against many tumors and greatly reduced toxicity, in comparison to cisplatin. In this work, we present for the first time the Fourier-transform Raman and infrared spectra of picoplatin, in the region of 3500-50 cm(-1). The comprehensive theoretical studies on the molecular structure, the nature of Pt-ligand bonding, vibrational frequencies, and intensities were performed by employing different DFT methods, including hybrid (PBE0, mPW1PW, and B3LYP) and long-range-corrected hybrid density functionals (LC-ωPBE, CAM-B3LYP). Various effective core potentials (ECP) and basis sets have been used. In the prediction of the molecular structure of picoplatin, the best results have been obtained by LC-ωPBE, followed by PBE0, mPW1PW, and CAM-B3LYP density functionals, while the least accurate is B3LYP. The use of the LanL2TZ(f) ECP/basis set for Pt, in conjunction with all tested DFT methods, improves the calculated geometry of the title complex. The PBE0, mPW1PW, and CAM-B3LYP methods have shown the best performance in the calculations of the frequencies of Pt-ligand vibrations. A clear-cut assignment of all the bands in the IR and Raman spectra have been made on the basis of the calculated potential energy distribution (PED). The nature of the "vibrational signatures" of picoplatin have been determined. These results are indispensable for further investigation on drug-target interactions using vibrational spectroscopy.

  5. Efficacy of Oral Cochleate-Amphotericin B in a Mouse Model of Systemic Candidiasis

    PubMed Central

    Santangelo, Rosaria; Paderu, Padmaja; Delmas, Guillaume; Chen, Zi-Wei; Mannino, Raphael; Zarif, Leila; Perlin, David S.

    2000-01-01

    Amphotericin B (AMB) remains the principal therapeutic choice for deep mycoses. However, its application is limited by toxicity and a route of administration requiring slow intravenous injection. An oral formulation of this drug is desirable to treat acute infections and provide prophylactic therapy for high-risk patients. Cochleates are a novel lipid-based delivery system that have the potential for oral administration of hydrophobic drugs. They are stable phospholipid-cation crystalline structures consisting of a spiral lipid bilayer sheet with no internal aqueous space. Cochleates containing AMB (CAMB) inhibit the growth of Candida albicans, and the in vivo therapeutic efficacy of CAMB administered orally was evaluated in a mouse model of systemic candidiasis. The results indicate that 100% of the mice treated at all CAMB doses, including a low dosage of 0.5 mg/kg of body weight/day, survived the experimental period (16 days). In contrast, 100% mortality was observed with untreated mice by day 12. The fungal tissue burden in kidneys and lungs was assessed in parallel, and a dose-dependent reduction in C. albicans from the kidneys was observed, with a maximum 3.5-log reduction in total cell counts at 2.5 mg/kg/day. However, complete clearance of the organism from the lungs, resulting in more than a 4-log reduction, was observed at the same dose. These results were comparable to a deoxycholate AMB formulation administered intraperitoneally at 2 mg/kg/day (P < 0.05). Overall, these data demonstrate that cochleates are an effective oral delivery system for AMB in a model of systemic candidiasis. PMID:10952579

  6. Efficacy of oral cochleate-amphotericin B in a mouse model of systemic candidiasis.

    PubMed

    Santangelo, R; Paderu, P; Delmas, G; Chen, Z W; Mannino, R; Zarif, L; Perlin, D S

    2000-09-01

    Amphotericin B (AMB) remains the principal therapeutic choice for deep mycoses. However, its application is limited by toxicity and a route of administration requiring slow intravenous injection. An oral formulation of this drug is desirable to treat acute infections and provide prophylactic therapy for high-risk patients. Cochleates are a novel lipid-based delivery system that have the potential for oral administration of hydrophobic drugs. They are stable phospholipid-cation crystalline structures consisting of a spiral lipid bilayer sheet with no internal aqueous space. Cochleates containing AMB (CAMB) inhibit the growth of Candida albicans, and the in vivo therapeutic efficacy of CAMB administered orally was evaluated in a mouse model of systemic candidiasis. The results indicate that 100% of the mice treated at all CAMB doses, including a low dosage of 0.5 mg/kg of body weight/day, survived the experimental period (16 days). In contrast, 100% mortality was observed with untreated mice by day 12. The fungal tissue burden in kidneys and lungs was assessed in parallel, and a dose-dependent reduction in C. albicans from the kidneys was observed, with a maximum 3.5-log reduction in total cell counts at 2.5 mg/kg/day. However, complete clearance of the organism from the lungs, resulting in more than a 4-log reduction, was observed at the same dose. These results were comparable to a deoxycholate AMB formulation administered intraperitoneally at 2 mg/kg/day (P < 0.05). Overall, these data demonstrate that cochleates are an effective oral delivery system for AMB in a model of systemic candidiasis.

  7. Dark matter velocity dispersion effects on CMB and matter power spectra

    SciTech Connect

    Piattella, O.F.; Casarini, L.; Fabris, J.C.; Pacheco, J.A. de Freitas E-mail: luciano.casarini@cosmo-ufes.org E-mail: pacheco@oca.eu

    2016-02-01

    Effects of velocity dispersion of dark matter particles on the CMB TT power spectrum and on the matter linear power spectrum are investigated using a modified CAMB code. Cold dark matter originated from thermal equilibrium processes does not produce appreciable effects but this is not the case if particles have a non-thermal origin. A cut-off in the matter power spectrum at small scales, similar to that produced by warm dark matter or that produced in the late forming dark matter scenario, appears as a consequence of velocity dispersion effects, which act as a pressure perturbation.

  8. A Portable Parallel Implementation of the U.S. Navy Layered Ocean Model

    DTIC Science & Technology

    1995-01-01

    Wallcraft, PhD (I.C. 1981) Planning Systems Inc. & P. R. Moore, PhD (Camb. 1971) IC Dept. Math. DR Moore 1° Encontro de Metodos Numericos ...Kendall Square, Hypercube, D R Moore 1 ° Encontro de Metodos Numericos para Equacöes de Derivadas Parciais A. J. Wallcraft IC Mathematics...chips: Chips Machine DEC Alpha CrayT3D/E SUN Sparc Fujitsu AP1000 Intel 860 Paragon D R Moore 1° Encontro de Metodos Numericos para Equacöes

  9. Theoretical tuning of the firefly bioluminescence spectra by the modification of oxyluciferin

    NASA Astrophysics Data System (ADS)

    Cheng, Yuan-Yuan; Zhu, Jia; Liu, Ya-Jun

    2014-01-01

    Extending the firefly bioluminescence is of practical significance for the improved visualization of living cells and the development of a multicolor reporter. Tuning the color of bioluminescence in fireflies mainly involves the modification of luciferase and luciferin. In this Letter, we theoretically studied the emission spectra of 9 firefly oxyluciferin analogs in the gas phase and in solutions. Three density functionals, including B3LYP, CAM-B3LYP and M06-2X, were employed to theoretically predict the efficiently luminescent analogs. The reliable functionals for calculating the targeted systems were suggested. The luminescence efficiency, solvent effects, and substituent effects are discussed based on the calculated results.

  10. Numerical Modeling of Penetration Into a Compressible Viscoplastic Media

    DTIC Science & Technology

    2004-07-22

    u). (17) for all v ∈ V. Thus, the problem of the flow of compressible visco- plastic Bingham -type fluid becomes: Find the velocity field u and the...and Services Center. (1990) [22] J.G. Oldroyd, A rational formulation of the equations of plastic flow for a Bingham solid, Proc. Camb. Philos. Soc... Bingham fluid (see [3, 22, 8]), can sustain a shear stress even at rest and it starts to flow only if the applied forces exceed an yield limit κ. To

  11. Spectroscopic properties of chlorophyll f.

    PubMed

    Li, Yaqiong; Cai, Zheng-Li; Chen, Min

    2013-09-26

    The absorption and fluorescence spectra of chlorophyll f (newly discovered in 2010) have been measured in acetone and methanol at different temperatures. The spectral analysis and assignment are compared with the spectra of chlorophyll a and d under the same experimental conditions. The spectroscopic properties of these chlorophylls have further been studied by the aid of density functional CAM-B3LYP and high-level symmetric adapted coupled-cluster configuration interaction calculations. The main Q and Soret bands and possible sidebands of chlorophylls have been determined. The photophysical properties of chlorophyll f are discussed.

  12. First principal studies of spectroscopic (IR and Raman, UV-visible), molecular structure, linear and nonlinear optical properties of L-arginine p-nitrobenzoate monohydrate (LANB): A new non-centrosymmetric material.

    PubMed

    Shkir, Mohd; AlFaify, S; Abbas, Haider; Muhammad, Shabbir

    2015-08-05

    In current work, the authors have been applied the density functional theory (DFT) using B3LYP and CAM-B3LYP exchange-correlation functional with 6-31G(∗) basis set on l-arginine p-nitrobenzoate monohydrate (LANB) molecule for the first time to optimize its geometry and study the spectroscopic, electronic structure, nonlinear optical properties. Vibrational modes were found in good agreement with experimental reports. The calculated UV spectra by B3LYP/6-31G(∗) and CAM-B3LYP/6-31G(∗) level of theory shows an electronic transition at ∼268 nm (4.63 eV) and 264 nm (4.70 eV) respectively. To explain the charge interaction taking place within the molecule highest occupied molecular orbital and lowest unoccupied molecular orbital were analyzed and their calculated energy gap was found to be 4.3eV with an oscillatory strength 0.3796 at B3LYP/6-31G(∗) level of theory. The dipole moment (μtot), average and anisotropy of polarizability (αtot, Δα) and static and total first hyperpolarizability (β0, βtot) values were calculated. The value of μtot and βtot are found to be 4.124D and 1.630 × 10(-30) esu and 4.127D and 1.133 × 10(-30) esu using B3LYP/6-31G(∗) and CAM-B3LYP/6-31G(∗) functional respectively. The value of βtot is >4 and >3 times higher than prototype urea molecule calculated at both level of theory, respectively. The molecular electrostatic potential (MEP), frontier molecular orbital's (FMOs), global reactivity descriptors and thermodynamic properties are also calculated and discussed. The properties of LANB calculated at B3LYP are in good correlation with experimental than the CAM-B3LYP level of theory. The obtained results show that LANB molecule can be treated as a good candidate for nonlinear optical devices.

  13. On the Classification of Fractal Squares

    NASA Astrophysics Data System (ADS)

    Luo, Jun Jason; Liu, Jing-Cheng

    2016-01-01

    In the previous paper [K. S. Lau, J. J. Luo and H. Rao, Topological structure of fractal squares, Math. Proc. Camb. Phil. Soc. 155 (2013) 73-86], Lau, Luo and Rao completely classified the topological structure of so called fractal square F defined by F = (F + 𝒟)/n, where 𝒟 ⊊ {0, 1,…,n - 1}2,n ≥ 2. In this paper, we further provide simple criteria for the F to be totally disconnected, then we discuss the Lipschitz classification of F in the case n = 3, which is an attempt to consider non-totally disconnected sets.

  14. Experimental and theoretical study on the structure-property relationship of novel 1-aryl-3-methylsuccinimides

    NASA Astrophysics Data System (ADS)

    Banjac, Nebojša R.; Božić, Bojan Đ.; Mirković, Jelena M.; Vitnik, Vesna D.; Vitnik, Željko J.; Valentić, Nataša V.; Ušćumlić, Gordana S.

    2017-02-01

    A series of ten 1-aryl-3-methylsuccinimides was synthesized and their solvatochromic properties were studied in a set of fifteen binary solvent mixtures. The solute-solvent interactions were analyzed on the basis of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. The electronic effect of the substituents on the UV-Vis absorption and NMR spectra was analyzed using the simple Hammett equation. Moreover, the B3LYP, CAM-B3LYP, and M06-2X functionals using the 6-311G(d,p) basic set have been assessed in light of the position of experimental absorption maxima obtained for these compounds. The integration grid effects have also been evaluated. An interpretation of the substituent-effect transmission through the molecular skeleton and the nature of the HOMO and LUMO orbitals based on quantum-chemical calculations is given. The values of partial atomic charges from the atomic polar tenzors (APT), natural population analysis (NBO), and charges fit to the electrostatic potential using the B3LYP, CAM-B3LYP, and M06-2X methods are produced and correlated with different experimental properties. In order to estimate the chemical activity of the molecule, the molecular electrostatic potential (MEP) surface map is calculated for the optimized geometry of 1-phenyl-3-methylsuccinimide.

  15. Theoretical investigation of the borazine-melamine polymer as a novel candidate for hydrogen storage applications.

    PubMed

    Dabbagh, Hossein A; Shahraki, Maryam; Farrokhpour, Hossein

    2014-06-14

    Ab initio calculations and molecular dynamic simulation were employed to study the interaction of molecular hydrogen with the borazine-melamine polymer (BMP) in order to explore its potential for hydrogen storage applications. The calculations were performed using the long range corrected version of density functional theory, the Coulomb-attenuating method (CAM-B3LYP) and the second order Møller-Plesset perturbation theory (MP2). The results showed that the average adsorption energy per hydrogen is about -0.7 and -0.3 kcal mol(-1) at the MP2/6-311+G(d,p) and CAMB3LYP/6-311+G(d,p) levels of theory, respectively. The adsorption energies were corrected for the basis set superposition error (BSSE) by the counterpoise method. It was found that the hydrogen storage capacity of the BMP is about 6.49 wt%, which is close to the values reported for the other selected materials for the hydrogen storage in the literature. The maximum number of hydrogen molecules, which were adsorbed by the BMP building block, is about ten. Molecular dynamic simulation was performed to assess the potential of BMP for hydrogen storage.

  16. Reply to Comment on 'Excited states of DNA base pairs using long-range corrected time-dependent density functional theory

    SciTech Connect

    Jensen, Lasse; Govind, Niranjan

    2009-09-18

    In this work we present a study of the excitation energies of adenine, cytosine, guanine, thymine and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC-functionals, BNL, CAM-B3LYP and LC-PBE0 with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement a smaller attenuation parameter was needed which leads to non-optimum performance for ground state properties. B3LYP, on the other hand, severely underestimates the charge transfer (CT) transitions in the base pairs. Surprisingly we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair, but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance was obtained with the LC-PBE0 functional which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange.

  17. Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory

    SciTech Connect

    Jensen, Lasse; Govind, Niranjan

    2009-09-10

    In this work we present a study of the excitation energies of adenine, cytosine, guanine, thymine and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC-functionals, BNL, CAM-B3LYP and LC-PBE0 with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement a smaller attenuation parameter was needed which leads to non-optimum performance for ground state properties. B3LYP, on the other hand, severely underestimates the charge transfer (CT) transitions in the base pairs. Surprisingly we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair, but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance was obtained with the LC-PBE0 functional which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange.

  18. Modeling solvatochromism of a quinolinium betaine dye in water solvent using sequential hybrid QM/MM and semicontinuum approach.

    PubMed

    Murugan, N Arul

    2011-02-10

    We have investigated the ambient temperature structure of 1-methyl-8-oxyquinolinium betaine (MOQB) in water solvent and compared to its gas-phase structure. We have employed Car-Parrinello molecular dynamics (CPMD) simulations within hybrid quantum mechanics-molecular mechanics (QM/MM) framework to study MOQB in water while CPMD technique has been used for the gas phase. We report significant solvent-induced geometrical changes in MOQB. The dipole moment of MOQB in water is 2 times larger than the gas-phase value. The average absorption spectra calculated from gas-phase configurations using Coulomb attenuated-B3LYP (CAMB3LYP) level of theory is comparable with experimental spectra reported in benzene (λ(max) = 590 nm), a nonpolar solvent. We have also computed the absorption spectra of MOQB in water solvent using continuum and semicontinuum solvent models. Based on this, we have calculated contributions from solvent-induced geometrical changes, hydrogen bonding, and intermolecular charge transfer to the solvatochromic shift and absorption spectra of MOQB in water. Absorption spectra calculations for MOQB in water with a semicontinuum approach for solvents using CAMB3LYP level of theory excellently reproduce the experimental spectra in water, where the theoretical λ(max) is 433 nm and the experimental λ(max) is around 440 nm.

  19. On the interaction between supercritical CO2 and epoxides combining infrared absorption spectroscopy and quantum chemistry calculations.

    PubMed

    Foltran, Stéphanie; Méreau, Raphaël; Tassaing, Thierry

    2011-05-28

    The nature and strength of the interactions occurring between epoxides and CO(2) have been investigated by combining infrared spectroscopy with quantum chemistry calculations. A series of infrared absorption experiments on four model epoxide molecules highly diluted in supercritical CO(2) have been performed at constant temperature T = 40 °C for various CO(2) pressures varying from 1 to 30 MPa. Then, we carried out a theoretical analysis based on quantum chemistry calculations using Density Functional Theory (B3PW91 and CAM-B3LYP) and ab initio (MP2) computational methods. A very good agreement between experimental and calculated vibrational frequency shifts of the epoxide ring vibrations group was obtained using the CAM-B3LYP functional, hence validating the calculated optimized geometries of the epoxide-CO(2) complexes. Whatever the epoxide considered, CO(2) is found to be on average above the oxygen atom of the epoxy ring and interacts with the carbon atom of CO(2) through a Lewis acid-Lewis base type of interaction. The substituents on the epoxide ring are found to influence the stability of the epoxide-CO(2) complexes mainly because of the partial charge on the oxygen atom that is sensitive to the nature of the substituent.

  20. Land planarian assemblages in protected areas of the interior atlantic forest: implications for conservation.

    PubMed

    Negrete, Lisandro; Colpo, Karine D; Brusa, Francisco

    2014-01-01

    Land planarians are an interesting group of free-living flatworms that can be useful as bioindicators because of their high sensitivity to environmental changes and low dispersal capacity. In this study, we describe and compare assemblages of land planarians from areas with different conservation degrees of the Interior Atlantic Forest (Misiones, Argentina), and assess factors that could be related to their abundance and richness. Eight sites were tracked in search of land planarians in Reserva de Vida Silvestre Urugua-í (RVSU) and Campo Anexo Manuel Belgrano (CAMB). Diurnal and nocturnal surveys were performed in each site along nine sampling campaigns. We collected 237 individuals belonging to 18 species of the subfamily Geoplaninae. All sites were dominated by Geoplana sp. 1 and Pasipha hauseri. The richness estimators showed that there would be more species in RVSU than in CAMB. The abundance and richness of land planarians was high during the night and after rainfalls, suggesting an increased activity of flatworms under such conditions. The abundance and richness of land planarians were also related to the conservation condition of the sites. Disturbed sites showed less abundance and richness, and were segregated from non-disturbed ones by nmMDS analysis. Beta diversity between sites was higher than expected, indicating that the species turnover between sites contributed more to the total richness (gamma diversity) than the alpha diversity.

  1. The origin of the absorption spectra of porphyrin N- and dithiaporphyrin S-oxides in their neutral and protonated states.

    PubMed

    Bruhn, Torsten; Brückner, Christian

    2015-02-07

    meso-Tetraphenylporphyrin N-oxide (1) and meso-tetraphenyl-21,23-dithiaporphyrin S-oxide (3) possess optical spectra that are distinctly different from their parent porphyrins, meso-tetraphenylporphyrin (2) and meso-tetraphenyl-21,23-dithiaporphyrin (4), respectively. The hyperporphyrin spectra were reproduced and classified using TD CAM-B3LYP and SCS-CC2 computational methods. Calculations revealed the electronic and conformational influences of the N- and S-oxide functionalities. While the N-oxide under acidic conditions forms a dication with a UV-vis spectrum that is nearly indistinguishable from that of the diprotonated parent porphyrin, the diprotonated S-oxide possesses a much different UV-vis spectrum from diprotonated parent dithiaporphyrin. A computational study of the protonation events revealed the site and degree of protonation and rationalized the regular and hyperporphyrin UV-vis spectra of the neutral and protonated species, respectively. The study illuminates the electronic effects of the relatively rare modification of the inner porphyrin heteroatoms. It also illustrates a case in which TD CAM-B3LYP reaches its limits to make reliable predictions about the optical properties of a porphyrinoid, making the use of higher methods essential.

  2. Analysis of nonlinear optical properties in donor–acceptor materials

    SciTech Connect

    Day, Paul N.; Pachter, Ruth; Nguyen, Kiet A.

    2014-05-14

    Time-dependent density functional theory has been used to calculate nonlinear optical (NLO) properties, including the first and second hyperpolarizabilities as well as the two-photon absorption cross-section, for the donor-acceptor molecules p-nitroaniline and dimethylamino nitrostilbene, and for respective materials attached to a gold dimer. The CAMB3LYP, B3LYP, PBE0, and PBE exchange-correlation functionals all had fair but variable performance when compared to higher-level theory and to experiment. The CAMB3LYP functional had the best performance on these compounds of the functionals tested. However, our comprehensive analysis has shown that quantitative prediction of hyperpolarizabilities is still a challenge, hampered by inadequate functionals, basis sets, and solvation models, requiring further experimental characterization. Attachment of the Au{sub 2}S group to molecules already known for their relatively large NLO properties was found to further enhance the response. While our calculations show a modest enhancement for the first hyperpolarizability, the enhancement of the second hyperpolarizability is predicted to be more than an order of magnitude.

  3. Electron correlation effects and density analysis of the first-order hyperpolarizability of neutral guanine tautomers.

    PubMed

    Alparone, Andrea

    2013-08-01

    Dipole moments (μ), charge distributions, and static electronic first-order hyperpolarizabilities (β(μ)) of the two lowest-energy keto tautomers of guanine (7H and 9H) were determined in the gas phase using Hartree-Fock, Møller-Plesset perturbation theory (MP2 and MP4), and DFT (PBE1PBE, B97-1, B3LYP, CAM-B3LYP) methods with Dunning's correlation-consistent aug-cc-pVDZ and d-aug-cc-pVDZ basis sets. The most stable isomer 7H exhibits a μ value smaller than that of the 9H form by a factor of ca. 3.5. The β μ value of the 9H tautomer is strongly dependent on the computational method employed, as it dramatically influences the β(μ) (9H)/β(μ) (7H) ratio, which at the highest correlated MP4/aug-cc-pVDZ level is predicted to be ca. 5. The Coulomb-attenuating hybrid exchange-correlation CAM-B3LYP method is superior to the conventional PBE1PBE, B3LYP, and B97-1 functionals in predicting the β(μ) values. Differences between the largest diagonal hyperpolarizability components were clarified through hyperpolarizability density analyses. Dipole moment and first-order hyperpolarizability are molecular properties that are potentially useful for distinguishing the 7H from the 9H tautomer.

  4. Determination of Molecular Structure of Bisphenylene Homologues of BINOL-Based Phosphoramidites by Chiroptical Methods

    NASA Astrophysics Data System (ADS)

    Julínek, Ondřej; Setnička, Vladimír; Miklášová, Natalia; Putala, Martin; Ruud, Kenneth; Urbanová, Marie

    2009-09-01

    Vibrational (VCD), electronic circular dichroism (ECD), and IR absorption spectra together with transparent spectral region optical rotation (OR) of two derivatives of bisphenylene 1,1'-binaphthyl-based phosphoramidites containing three stereogenic axes were measured and the results were compared with simulated data obtained by ab initio calculations with density functional theory. An excellent agreement between experimental and predicted B3LYP/6-31G** and BPW91/6-31G** VCD spectra enabled the assignment of all VCD bands in the experimental spectra, while the Gibbs free energy of all the conformers allowed the determination of their relative populations. The calculation of ECD spectra showed that CAM-B3LYP/6-311G** provided results superior to those of B3LYP/6-311G**. The theoretical results for the OR at the B3LYP/6-311G** and CAM-B3LYP/6-311G** levels were in good agreement with experimental optical rotations, but exhibited lower sensitivity in determining particular conformers than VCD and ECD. By a careful comparison of experimental VCD, IR, and ECD spectra and OR with calculated data, it was possible to assign the absolute configuration of all three stereogenic axes and to determine the molecular structure of the studied bisphenylene 1,1'-binaphthyl-based phosphoramidites in solution with a high degree of confidence.

  5. Land Planarian Assemblages in Protected Areas of the Interior Atlantic Forest: Implications for Conservation

    PubMed Central

    Negrete, Lisandro; Colpo, Karine D.; Brusa, Francisco

    2014-01-01

    Land planarians are an interesting group of free-living flatworms that can be useful as bioindicators because of their high sensitivity to environmental changes and low dispersal capacity. In this study, we describe and compare assemblages of land planarians from areas with different conservation degrees of the Interior Atlantic Forest (Misiones, Argentina), and assess factors that could be related to their abundance and richness. Eight sites were tracked in search of land planarians in Reserva de Vida Silvestre Urugua-í (RVSU) and Campo Anexo Manuel Belgrano (CAMB). Diurnal and nocturnal surveys were performed in each site along nine sampling campaigns. We collected 237 individuals belonging to 18 species of the subfamily Geoplaninae. All sites were dominated by Geoplana sp. 1 and Pasipha hauseri. The richness estimators showed that there would be more species in RVSU than in CAMB. The abundance and richness of land planarians was high during the night and after rainfalls, suggesting an increased activity of flatworms under such conditions. The abundance and richness of land planarians were also related to the conservation condition of the sites. Disturbed sites showed less abundance and richness, and were segregated from non-disturbed ones by nmMDS analysis. Beta diversity between sites was higher than expected, indicating that the species turnover between sites contributed more to the total richness (gamma diversity) than the alpha diversity. PMID:24598934

  6. Does the ionization potential condition employed in QTP functionals mitigate the self-interaction error?

    NASA Astrophysics Data System (ADS)

    Ranasinghe, Duminda S.; Margraf, Johannes T.; Jin, Yifan; Bartlett, Rodney J.

    2017-01-01

    Though contrary to conventional wisdom, the interpretation of all occupied Kohn-Sham eigenvalues as vertical ionization potentials is justified by several formal and numerical arguments. Similarly, the performance of density functional approximations (DFAs) for fractionally charged systems has been extensively studied as a measure of one- and many-electron self-interaction errors (MSIEs). These complementary perspectives (initially recognized in ab initio dft) are shown to lead to the unifying concept that satisfying Bartlett's IP theorem in DFA's mitigates self-interaction errors. In this contribution, we show that the IP-optimized QTP functionals (reparameterization of CAM-B3LYP where all eigenvalues are approximately equal to vertical IPs) display reduced self-interaction errors in a variety of tests including the He2+ potential curve. Conversely, the MSIE-optimized rCAM-B3LYP functional also displays accurate orbital eigenvalues. It is shown that the CAM-QTP and rCAM-B3LYP functionals show improved dissociation limits, fundamental gaps and thermochemical accuracy compared to their parent functional CAM-B3LYP.

  7. Plant food resources exploited by Blue-and-Yellow Macaws (Ara ararauna, Linnaeus 1758) at an urban area in Central Brazil.

    PubMed

    Santos, A A; Ragusa-Netto, J

    2014-05-01

    In this study, we described the food plants available to Blue-and-Yellow Macaws (Ara ararauna), its feeding habits and the relationship between these parameters with feeding niche breadth. We established four transects, each one 12 km long, to sample fruiting plants and the feeding habits of this macaw (monthly 40 h, of observations), at the urban areas of Três Lagoas (Mato Grosso do Sul, Brazil). During all studied months, macaws foraged for palm fruits, mainly Syagrus oleracea and Acrocomia aculeata fruit pulp, both available all year, as well as Caryocar brasiliense and Anacardium occidentale seeds, in the wet season. The year-round feeding activity of macaws suggests Três Lagoas city as an adequate feeding area. The permanent availability of plant food resources, potentially, resulted from the diverse fruiting patterns of exotic and, mainly, native plant species, which provided a variety of suitable fruit patches.

  8. Free-living ixodid ticks in an urban Atlantic Forest fragment, state of Rio de Janeiro, Brazil.

    PubMed

    Pinheiro, Michele da Costa; Lourenço, Elizabete Captivo; Patrício, Priscilla Maria Peixoto; Sá-Hungaro, Iwine Joyce Barbosa de; Famadas, Kátia Maria

    2014-01-01

    As a consequence of the importance of ticks in forests in protected areas, was conducted survey of species of free-living ticks in the Natural Park Municipal Curió, state of Rio de Janeiro, Brazil. Monthly samples were taken by dragging method, dry ice traps and visual search in two transects. Adults and nymphs of Amblyomma cajennense (n= 147), Amblyomma brasiliense (n= 4) and Amblyomma parvum (n= 1) were collected. This is the first occurrence of A. parvum in the state. No correlation was found between the abundance of stages of A. cajennense and rainfall, temperature and relative humidity. The highest abundances of adults were in the months of January and May, and nymphs in September and October. The low diversity of parasites on Curió Park can be attributed to the proximity of households with pets, which would also explain the higher abundance of A. cajennense that is commonly found in areas impacted by anthropogenic pressure.

  9. [Eosinophilic pneumonia in response to cutaneous larva migrans syndrome--a case report].

    PubMed

    Darocha, Szymon; Wawrzyńska, Liliana; Oniszh, Karina; Dziewulska, Barbara

    2011-01-01

    Cutaneous larva migrans is a parasitic dermatosis imported by travelers returning from tropical and subtropical regions. In cutaneous larva migrans syndrome humans are incidental hosts and the larvae are unable to complete their natural cycle. Adult hookworms live in the intestines of dogs and cats, shedding eggs in feces that hatch and mature into larvae that can remain infective for months in the soil. Larvae penetrate the skin after contact with infected soil and cause an itchy creeping eruption. Cutaneous larva migrans is not usually associated with systemic symptoms and is rarely accompanied by peripheral blood eosinophilia. We report a patient who had both cutaneous larva migrans syndrome caused by Ancylostoma brasiliense and eosinophilic pneumonia after returning from Sri Lanka. The patient has been applied intravenous corticosteroids and local treatment with albendazole ointment with a very good clinical response.

  10. Egg-laying butterflies distinguish predaceous ants by sight.

    PubMed

    Sendoya, Sebastián F; Freitas, André V L; Oliveira, Paulo S

    2009-07-01

    Information about predation risks is critical for herbivorous insects, and natural selection favors their ability to detect predators before oviposition and to select enemy-free foliage when offspring mortality risk is high. Food plants are selected by ovipositing butterflies, and offspring survival frequently varies among plants because of variation in the presence of predators. Eunica bechina butterflies oviposit on Caryocar brasiliense, an ant-defended plant. Experiments with dried Camponotus and Cephalotes ants pinned to leaves revealed that butterflies use ant size and form as visual cues to avoid ovipositing on plant parts occupied by ants more likely to kill larval offspring. Presence of sap-sucking bugs did not affect butterfly oviposition. This is the first demonstration that visual recognition of predators can mediate egg-laying decisions by an insect herbivore and that an insect will discriminate among different species of potential predators. This unusual behavioral capability permits specialization on a risky, ant-defended food plant.

  11. Welwitschiaceae from the Lower Cretaceous of northeastern Brazil.

    PubMed

    Dilcher, David L; Bernardes-De-Oliveira, Mary E; Pons, Denise; Lott, Terry A

    2005-08-01

    Welwitschiaceae, a family in the Gnetales, is known today from only one extant species, Welwitschia mirabilis. This species is distributed in the Namibian desert, along the western coast of southern Africa, about 10 km inland from the coast. Very little is known about the fossil record of this family. Lower Cretaceous megafossils of various organs, assigned to Welwitschiaceae, are presented here. These fossils include young stems with paired cotyledons attached (Welwitschiella austroamericana n. gen. et sp.), isolated leaves (Welwitschiophyllum brasiliense n. gen. et sp.), and axes bearing male cones (Welwitschiostrobus murili n. gen. et sp.). They were collected in the Crato Formation, which is dated by palynomorphs and ostracods as Late Aptian (114 to 112 million years ago). These sediments are exposed in the Araripe Basin of northeastern Brazil. This study brings together new information of the megafossil record of Welwitschia-like plants and also reports of pollen said to be similar to that of Welwitschia from Lower Cretaceous sediments.

  12. Design and synthesis of natural product derivatives with selective and improved cytotoxicity based on a sesquiterpene scaffold.

    PubMed

    Zhang, Yang; Zhang, Zhuowei; Wang, Bo; Liu, Ling; Che, Yongsheng

    2016-04-15

    Brasilamide E (1) is a bisabolane sesquiterpenoid isolated from the solid-substrate fermentation cultures of a plant endophytic fungus Paraconiothyrium brasiliense. The compound specifically inhibited proliferation of the MCF-7 cells, but did not show cytotoxicity towards the negative controls HaCaT and NIH3T3 cells (IC50>50 μM). To improve its potency while maintain selectivity, a total of 27 derivatives of 1 were designed, synthesized, and evaluated for in vitro cytotoxicity against six tumor cell lines and the negative control NIH3T3 cells. Among these compounds, compound 12b showed significantly improved potency against the MCF-7, HeLa, and HO8910 cells with IC50 values of 0.13-0.25 μM compared to 1 (IC50 8.47-18.00 μM), and remained nontoxic to the NIH3T3 cells.

  13. Antibacterial activity of crude extracts from Mexican medicinal plants and purified coumarins and xanthones.

    PubMed

    Yasunaka, Kakuko; Abe, Fumiko; Nagayama, Ariaki; Okabe, Hikaru; Lozada-Pérez, Lucio; López-Villafranco, Edith; Muñiz, Elizabeth Estrada; Aguilar, Abigail; Reyes-Chilpa, Ricardo

    2005-02-28

    Thirty-two extracts from 22 Mexican medicinal plants of 15 different families were assayed to determine their antibacterial activity against Escherichia coli and Staphylococcus aureus. Seventeen plants showed antibacterial activity, while five plants showed no activity against both bacteria. All of the extracts showed higher activity against Staphylococcus aureus (methicillin-sensitive and methicillin-resistant) than against Escherichia coli, except one. Among the plants examined, Bursera simaruba (L.) Sarg. (Burseraceae), Haematoxylum brasiletto H. Karst. (Fabaceae), Calophyllum brasiliense Cambess. (Clusiaceae), and Mammea americana L. (Clusiaceae) were highly active against Staphylococcus aureus. Coumarins (mammea A/BA and mammea A/AA) and xanthones, namely jacareubin and 1,3,5,6-tetrahydroxy-2-(3,3-dimethylallyl) xanthone, were isolated as the principle compounds from the last two plants.

  14. Direct Dynamics Simulation of Dissociation of the [CH3--I--OH]- Ion-Molecule Complex

    SciTech Connect

    Xie, Jing; McClellan, Miranda; Sun, Rui; Kohale, Swapnil C.; Govind, Niranjan; Hase, William L.

    2015-02-05

    Direct dynamics simulations were used to study dissociation of the [CH3--I--OH]- complex ion, which was observed in a previous study of the OH- + CH3I gas phase reaction (J. Phys. Chem. A 2013, 117, 7162). Restricted B97-1 simulations were performed to study dissociation at 65, 75 and 100 kcal/mol and the [CH3--I--OH]- ion dissociated exponentially, in accord with RRKM theory. For these energies the major dissociation products are CH3I + OH-, CH2I- + H2O, and CH3OH + I-. Unrestricted B97-1 and restricted and unrestricted CAM-B3LYP simulations were also performed at 100 kcal/mol to compare with the restricted B97-1 results. The {CH3I + OH-}:{CH2I- + H2O}:{CH3OH + I-} product ratio is 0.72 : 0.15 : 0.13, 0.81 : 0.05 : 0.14, 0.71 : 0.19 : 0.10 , and 0.83 : 0.13 : 0.04 for the restricted B97-1, unrestricted B97-1, restricted CAM-B3LYP, and unrestricted CAM-B3LYP simulations, respectively. Other product channels found are CH2 + I- + H2O, CH2 + I-(H2O), CH4 + IO-, CH3 - + IOH, and CH3 + IOH-. The CH3 - + IOH singlet products are only given by the restricted B97-1 simulation and the lower energy CH3 + IOH- doublet products are only formed by the unrestricted B97-1 simulation. Also studied were the direct and indirect atomic-level mechanisms for forming CH3I + OH-, CH2I- + H2O, and CH3OH + I-. The majority of CH3I + OH- were formed through a direct mechanism. For both CH2I- + H2O and CH3OH + I-, the direct mechanism is overall more important than the indirect mechanisms, with the round-about like mechanism the most important indirect mechanism at high excitation energies. Mechanism comparisons between the B97-1 and CAM-B3LYP simulations showed that formation of the CH3OH---I- complex is favored for the B97-1 simulations, while formation of the HO----HCH2I complex is favored for the CAM-B3LYP simulations. The unrestricted simulations give a higher percentage of indirect mechanisms than the restricted simulations. The possible role of the self-interaction error in the

  15. Improving Hydrological Models by Applying Air Mass Boundary Identification in a Precipitation Phase Determination Scheme

    NASA Astrophysics Data System (ADS)

    Feiccabrino, James; Lundberg, Angela; Sandström, Nils

    2013-04-01

    inversion) of air in the vertical profile between the lower cold air mass and the warm air mass above. The warm air forced up often cools to its condensation temperature, becoming the main cause of winter precipitation. A common exception comes with cold air mass boundaries (CAMB) not having a frontal inversion in the vertical profile. Therefore, CAMB precipitation occurs under very different lower tropospheric conditions, than other precipitation. Changes in continuous hourly AOS temperature and wind could be used to identify different types of surface air mass boundaries. When identified rain and snow observations occurring immediately before CAMB were separated from all other observations, the TS and TR values -1° C, 3° C respectively, were found to be 1° C cooler than the TS and TR for non-CAMB observations. Analyzing CAMB separately reduced total misclassified precipitation from 7.0% to 5.4% (23% improvement) in the PPTZ. However, this tool only allows a statistically better chance for correct precipitation phase determination; it is incapable of adjustments for deviations from an average vertical temperature lapse rate.

  16. Sedimentary facies and stratigraphic architecture in coarse-grained deltas: Anatomy of the Cenozoic Camaná Formation, southern Peru (16°25‧S to 17°15‧S)

    NASA Astrophysics Data System (ADS)

    Alván, Aldo; von Eynatten, Hilmar

    2014-10-01

    In the external forearc of southern Peru (Arequipa region), the sedimentary facies and the stratigraphic architecture of the Cenozoic Camaná Formation are presented in the context of tectono-eustatic controls. The Camaná Formation is defined as ∼500 m thick coarse-grained deltaic complex that accumulated in a fault-bounded elongated depression extending from the Coastal Cordillera in the east to the offshore Mollendo Basin in the west and likely up to the Peruvian Trench. Based on the analysis of facies associations, we propose a refined stratigraphic scheme of the Camaná Basin fill. The Camaná Formation was formerly divided into the Camaná “A” and Camaná “B” units (CamA and CamB, respectively). We reinterpret the stratigraphic position and the timing of the CamA to CamB boundary, and define three sub-units for CamA, i.e. sub-units A1, A2, and A3. Each depositional unit shows individual stacking patterns, which are linked with particular shoreline trajectories through time. Strata of A1 form the basal succession of the Camaná Formation and consist of distributary channels and mouth bars, unconformably overlain by beds of A2. A2 consists of delta front deposits arranged in voluminous clinothems that reflect a progradational downstepping complex. A3 consists of delta front sandstones to prodelta siltstones arranged in retrogradational onlapping geometry. A pebbly intercalation in proximal onlapping A3 deposits is interpreted to reflect pulses of uplift in the hinterland. The overlying CamB unit is characterized by a thick alternation of fluvio-deltaic conglomerates and sand bars. The ages of the individual units of the Camaná Formation are not yet well defined. Based on the available information and stratigraphic correlations we tentatively assign A1 to the Late Oligocene, A2 to the Early Miocene, A3 to the late Early Miocene to early Middle Miocene, and CamB to the Late Miocene to? early Pliocene. The sub-units A1 and A2 represent a regressive

  17. Antimycobacterial and HIV-1 Reverse Transcriptase Activity of Julianaceae and Clusiaceae Plant Species from Mexico

    PubMed Central

    Gómez-Cansino, Rocio; Espitia-Pinzón, Clara Inés; Campos-Lara, María Guadalupe; Guzmán-Gutiérrez, Silvia Laura; Segura-Salinas, Erika; Echeverría-Valencia, Gabriela; Torras-Claveria, Laura; Cuevas-Figueroa, Xochitl Marisol; Reyes-Chilpa, Ricardo

    2015-01-01

    The extracts of 14 Julianaceae and 5 Clusiaceae species growing in Mexico were tested in vitro (50 µg/mL) against Mycobacterium tuberculosis H37Rv and HIV reverse transcriptase (HIV-RT). The Julianaceae bark and leaf extracts inhibited M. tuberculosis (>84.67%) and HIV-RT (<49.89%). The Clusiaceae leaves extracts also inhibited both targets (>58.3% and >67.6%), respectively. The IC50 values for six selected extracts and their cytotoxicity (50 µg/mL) to human macrophages were then determined. Amphipterygium glaucum, A. molle, and A. simplicifolium fairly inhibited M. tuberculosis with IC50 of 1.87–2.35 µg/mL; but their IC50 against HIV-RT was 59.25–97.83 µg/mL. Calophyllum brasiliense, Vismia baccifera, and Vismia mexicana effect on M. tuberculosis was noteworthy (IC50 3.02–3.64 µg/mL) and also inhibited RT-HIV (IC50 26.24–35.17 µg/mL). These 6 extracts (50 µg/mL) presented low toxicity to macrophages (<23.8%). The HPLC profiles of A. glaucum, A. molle, and A. simplicifolium indicated that their antimycobacterial activity cannot be related to masticadienonic, 3α, or 3β-hydromasticadienonic acids, suggesting that other compounds may be responsible for the observed activity or this might be a synergy result. The anti-HIV-RT and antimycobacterial activities induced by C. brasiliense can be attributed to the content of calanolides A, B, as well as soulatrolide. PMID:25983849

  18. Failures of TDDFT in describing the lowest intramolecular charge-transfer excitation in para-nitroaniline

    NASA Astrophysics Data System (ADS)

    Eriksen, Janus J.; Sauer, Stephan P. A.; Mikkelsen, Kurt V.; Christiansen, Ove; Jensen, Hans Jørgen Aa.; Kongsted, Jacob

    2013-07-01

    We investigate the failure of time-dependent density functional theory (TDDFT) with the CAM-B3LYP exchange-correlation (xc) functional coupled to the polarisable embedding (PE) scheme (PE-CAM-B3LYP) in reproducing the solvatochromic shift of the lowest intense charge-transfer excitation in para-nitroaniline (pNA) in water by comparing with results obtained with the coupled cluster singles and doubles (CCSD) model also coupled to the polarisable embedding scheme (PE-CCSD). We determine the amount of charge separation in the ground and excited charge-transfer state with both methods by calculating the electric dipole moments in the gas phase and for 100 solvent configurations. We find that CAM-B3LYP overestimates the amount of charge separation inherent in the ground state and TDDFT/CAM-B3LYP drastically underestimates this amount in the excited charge-transfer state. As the errors in the solvatochromatic shift are found to be inverse proportional to the change in dipole moment upon excitation, we conclude that the flaws in the description of the solvatochromic shift of this excitation are related to TDDFT itself and how it responds to the solvent effects modelled by the PE scheme. We recommend therefore to benchmark results of TDDFT calculations with CAM-B3LYP for intramolecular charge-transfer excitations in molecular systems similar to pNA against higher level ab initio wave function methods, like, e.g. CCSD, prior to their use. Using the calculated change in dipole moment upon excitation as a measure for charge-transfer character, we furthermore confirm that the difference between excitation energies calculated with TDDFT and with the Tamm-Dancoff approximation (TDA) to TDDFT is indeed correlated with the charge-transfer character of a given electronic transition both in vacuo and in solution. This is supported by a corresponding correlation between the change in dipole moment and the size of the Λ index diagnostic for the investigated CT excitation.

  19. Comparative Assessment of DFT Performances in Ru- and Rh-Promoted σ-Bond Activations.

    PubMed

    Sun, Yuanyuan; Hu, Lianrui; Chen, Hui

    2015-04-14

    In this work, the performances of 19 density functional theory (DFT) methods are calibrated comparatively on Ru- and Rh-promoted σ-bond (C-H, O-H, and H-H) activations. DFT calibration reference is generated from explicitly correlated coupled cluster CCSD(T)-F12 calculations, and the 4s4p core-valence correlation effect of the two 4d platinum group transition metals is also included. Generally, the errors of DFT methods for calculating energetics of Ru-/Rh-mediated reactions appear to correlate more with the magnitude of energetics itself than other factors such as metal identity. For activation energy calculations, the best performing functionals for both Ru and Rh systems are MN12SX < CAM-B3LYP < M06-L < MN12L < M06 < ωB97X < B3LYP < LC-ωPBE (in the order of increasing mean unsigned deviations, MUDs, of less than 2 kcal/mol). For reaction energy calculations, best functionals with MUDs less than 2 kcal/mol are PBE0 < CAM-B3LYP ≈ N12SX. The effect of the DFT empirical dispersion correction on the performance of the DFT methods is beneficial for most density functionals tested in this work, reducing their MUDs to different extents. After including empirical dispersion correction, ωB97XD, B3LYP-D3, and CAM-B3LYP-D3 (PBE0-D3, B3LYP-D3, and ωB97XD) are the three best performing DFs for activation energy (reaction energy) calculations, from which B3LYP-D3 and ωB97XD can notably be recommended uniformly for both the reaction energy and reaction barrier calculations. The good performance of B3LYP-D3 in quantitative description of the energetic trends further adds value to B3LYP-D3 and singles this functional out as a reasonable choice in the Ru/Rh-promoted σ-bond activation processes.

  20. CosmoSIS: A System for MC Parameter Estimation

    SciTech Connect

    Zuntz, Joe; Paterno, Marc; Jennings, Elise; Rudd, Douglas; Manzotti, Alessandro; Dodelson, Scott; Bridle, Sarah; Sehrish, Saba; Kowalkowski, James

    2015-01-01

    Cosmological parameter estimation is entering a new era. Large collaborations need to coordinate high-stakes analyses using multiple methods; furthermore such analyses have grown in complexity due to sophisticated models of cosmology and systematic uncertainties. In this paper we argue that modularity is the key to addressing these challenges: calculations should be broken up into interchangeable modular units with inputs and outputs clearly defined. We present a new framework for cosmological parameter estimation, CosmoSIS, designed to connect together, share, and advance development of inference tools across the community. We describe the modules already available in Cosmo- SIS, including camb, Planck, cosmic shear calculations, and a suite of samplers. We illustrate it using demonstration code that you can run out-of-the-box with the installer available at http://bitbucket.org/joezuntz/cosmosis.

  1. Simple implementation of general dark energy models

    SciTech Connect

    Bloomfield, Jolyon K.; Pearson, Jonathan A. E-mail: jonathan.pearson@durham.ac.uk

    2014-03-01

    We present a formalism for the numerical implementation of general theories of dark energy, combining the computational simplicity of the equation of state for perturbations approach with the generality of the effective field theory approach. An effective fluid description is employed, based on a general action describing single-scalar field models. The formalism is developed from first principles, and constructed keeping the goal of a simple implementation into CAMB in mind. Benefits of this approach include its straightforward implementation, the generality of the underlying theory, the fact that the evolved variables are physical quantities, and that model-independent phenomenological descriptions may be straightforwardly investigated. We hope this formulation will provide a powerful tool for the comparison of theoretical models of dark energy with observational data.

  2. Density functional theory study on oligosilane-functionalized C60 fullerene

    NASA Astrophysics Data System (ADS)

    Yoshizawa, Saori; Abe, Shigeaki; Mutoh, Mami; Kusaka, Teruo; Nakamura, Mariko; Yoshida, Yasuhiro; Iida, Junichiro; Kawabata, Hiroshi; Tachikawa, Hiroto

    2017-01-01

    Oligosilane-functionalized C60 fullerenes [namely, C60-(SiH2) n -H, n = 1-4] have been investigated by the density functional theory (DFT) method to elucidate the structures and electronic states of oligosilane-radical added fullerene. The DFT calculation showed that oligosilane radicals bind to the carbon atom of C60 in the on-top site, and a strong Si-C heterojunction is formed. The binding energies of oligosilane radicals to C60 were calculated to be 24.6-28.2 kcal/mol at the CAM-B3LYP/6-311G(d,p) level. The electronic states of oligosilane-functionalized fullerenes C60-(SiH2) n -H are discussed on the basis of theoretical results.

  3. CosmoSIS: Modular cosmological parameter estimation

    SciTech Connect

    Zuntz, J.; Paterno, M.; Jennings, E.; Rudd, D.; Manzotti, A.; Dodelson, S.; Bridle, S.; Sehrish, S.; Kowalkowski, J.

    2015-06-09

    Cosmological parameter estimation is entering a new era. Large collaborations need to coordinate high-stakes analyses using multiple methods; furthermore such analyses have grown in complexity due to sophisticated models of cosmology and systematic uncertainties. In this paper we argue that modularity is the key to addressing these challenges: calculations should be broken up into interchangeable modular units with inputs and outputs clearly defined. Here we present a new framework for cosmological parameter estimation, CosmoSIS, designed to connect together, share, and advance development of inference tools across the community. We describe the modules already available in CosmoSIS, including CAMB, Planck, cosmic shear calculations, and a suite of samplers. Lastly, we illustrate it using demonstration code that you can run out-of-the-box with the installer available at http://bitbucket.org/joezuntz/cosmosis

  4. CMB and matter power spectra with non-linear dark-sector interactions

    NASA Astrophysics Data System (ADS)

    vom Marttens, R. F.; Casarini, L.; Hipólito-Ricaldi, W. S.; Zimdahl, W.

    2017-01-01

    An interaction between dark matter and dark energy, proportional to the product of their energy densities, results in a scaling behavior of the ratio of these densities with respect to the scale factor of the Robertson-Walker metric. This gives rise to a class of cosmological models which deviate from the standard model in an analytically tractable way. In particular, it becomes possible to quantify the role of potential dark-energy perturbations. We investigate the impact of this interaction on the structure formation process. Using the (modified) CAMB code we obtain the CMB spectrum as well as the linear matter power spectrum. It is shown that the strong degeneracy in the parameter space present in the background analysis is considerably reduced by considering Planck data. Our analysis is compatible with the ΛCDM model at the 2σ confidence level with a slightly preferred direction of the energy flow from dark matter to dark energy.

  5. Theoretical study of the optical, electronic, and charge-transfer properties of 1,2,4,5-tetrakis(phenylethynyl)benzene derivatives for solar cell applications

    NASA Astrophysics Data System (ADS)

    Liang, Dadong; Tang, Shanshan; Kang, Lijuan; Liu, Junbo; Jin, Ruifa

    2013-02-01

    A series of 1,2,4,5-tetrakis(phenylethynyl)benzene derivatives has been investigated at the CAM-B3LYP/6-31G(d) and TD-CAM-B3LYP/6-31 + G(d,p) levels to design materials with high performance with respect to suitable frontier molecular orbitals (FMOs), broad absorption spectra, and better and balanced charge-transfer properties. The calculated results reveal that the molecule possessing benzene has the largest torsion angle of these derivatives. Different branches have a slight influence on the distributions of the FMOs of the molecules. 2-vinyl-thieno[3,2-b]thiophene branches display a small HOMO-LUMO gap corresponding to red shifts of the absorption spectra. These molecules are potential ambipolar charge-transport materials under the appropriate operating conditions.

  6. An improved method for thin layer chromatographic analysis of saponins.

    PubMed

    Sharma, Om P; Kumar, Neeraj; Singh, Bikram; Bhat, Tej K

    2012-05-01

    Analysis of saponins by thin layer chromatography (TLC) is reported. The solvent system was n-butanol:water:acetic acid (84:14:7). Detection of saponins on the TLC plates after development and air-drying was done by immersion in a suspension of sheep erythrocytes, followed by washing off the excess blood on the plate surface. Saponins appeared as white spots against a pink background. The protocol provided specific detection of saponins in the saponins enriched extracts from Aesculusindica (Wall. ex Camb.) Hook.f., Lonicera japonica Thunb., Silene inflata Sm., Sapindusmukorossi Gaertn., Chlorophytum borivilianum Santapau & Fernandes, Asparagusadscendens Roxb., Asparagus racemosus Willd., Agave americana L., Camellia sinensis [L.] O. Kuntze. The protocol is convenient, inexpensive, does not require any corrosive chemicals and provides specific detection of saponins.

  7. Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences

    SciTech Connect

    Ai Yuejie; Zhang Feng; Cui Ganglong; Fang Weihai; Luo Yi

    2010-08-14

    2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized {sup 1}{pi}{pi}* excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed.

  8. Label-free functional nucleic acid sensors for detecting target agents

    DOEpatents

    Lu, Yi; Xiang, Yu

    2015-01-13

    A general methodology to design label-free fluorescent functional nucleic acid sensors using a vacant site approach and an abasic site approach is described. In one example, a method for designing label-free fluorescent functional nucleic acid sensors (e.g., those that include a DNAzyme, aptamer or aptazyme) that have a tunable dynamic range through the introduction of an abasic site (e.g., dSpacer) or a vacant site into the functional nucleic acids. Also provided is a general method for designing label-free fluorescent aptamer sensors based on the regulation of malachite green (MG) fluorescence. A general method for designing label-free fluorescent catalytic and molecular beacons (CAMBs) is also provided. The methods demonstrated here can be used to design many other label-free fluorescent sensors to detect a wide range of analytes. Sensors and methods of using the disclosed sensors are also provided.

  9. Experimental and DFT studies on the vibrational, electronic spectra and NBO analysis of thiamethoxam

    NASA Astrophysics Data System (ADS)

    Zhang, Fang; Zhang, Yu; Ni, Haiwei; Ma, Kuirong; Li, Rongqing

    2014-01-01

    Vibrational and electronic spectral measurements were performed for 3-(2-chloro-1,3-thiazol-5-ylmethyl)-5-methyl-1,3,5-oxadiazinan-4-ylidene(nitro) amine (thiamethoxam). Optimized geometrical structure and harmonic vibrational frequencies were calculated with ab initio RHF and DFT (B3LYP, CAMB3LYP, M06 and PBE1PBE) methods with 6-311++G (d, p) basis set. Complete assignments of the observed spectra were proposed. The absorption spectra of the compound were computed in gas-phase using TD-B3LYP/6-311++G (d, p) approach and H2O solution using PCM-TD-B3LYP/6-311++G (d, p) approach. The calculated results matched well with the experimental values. Temperature dependence of thermodynamic parameters in the range of 100-1000 K were determined. The bond orbital occupancies, contribution from parent natural bond orbital (NBO), the natural atomic hybrids was discussed.

  10. Experimental and DFT studies on the vibrational, electronic spectra and NBO analysis of thiamethoxam.

    PubMed

    Zhang, Fang; Zhang, Yu; Ni, Haiwei; Ma, Kuirong; Li, Rongqing

    2014-01-24

    Vibrational and electronic spectral measurements were performed for 3-(2-chloro-1,3-thiazol-5-ylmethyl)-5-methyl-1,3,5-oxadiazinan-4-ylidene(nitro) amine (thiamethoxam). Optimized geometrical structure and harmonic vibrational frequencies were calculated with ab initio RHF and DFT (B3LYP, CAMB3LYP, M06 and PBE1PBE) methods with 6-311++G (d, p) basis set. Complete assignments of the observed spectra were proposed. The absorption spectra of the compound were computed in gas-phase using TD-B3LYP/6-311++G (d, p) approach and H2O solution using PCM-TD-B3LYP/6-311++G (d, p) approach. The calculated results matched well with the experimental values. Temperature dependence of thermodynamic parameters in the range of 100-1000 K were determined. The bond orbital occupancies, contribution from parent natural bond orbital (NBO), the natural atomic hybrids was discussed.

  11. Electric field gradients of transition metal complexes from density functional theory: assessment of functionals, geometries and basis sets.

    PubMed

    Bjornsson, Ragnar; Bühl, Michael

    2010-06-14

    Electric field gradients (EFGs) were computed for the first-row transition metal nuclei in Cr(C(6)H(6))(CO)(3), MnO(3)F, Mn(CO)(5)H, MnCp(CO)(3), Co(CO)(4)H, Co(CO)(3)(NO) and VCp(CO)(4), for which experimental gas-phase data (in form of nuclear quadrupole coupling constants) are available from microwave spectroscopy. A variety of exchange-correlation functionals were assessed, among which range-separated hybrids (such as CAM-B3LYP or LC-omegaPBE) perform best, followed by global hybrids (such as B3LYP and PBE0) and gradient-corrected functionals (such as BP86). While large basis sets are required on the metal atom for converged EFGs, smaller basis sets can be employed on the ligands. In most cases, EFGs show little sensitivity toward the geometrical parameters.

  12. Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences

    NASA Astrophysics Data System (ADS)

    Ai, Yue-Jie; Zhang, Feng; Cui, Gang-Long; Luo, Yi; Fang, Wei-Hai

    2010-08-01

    2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized π1π∗ excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed.

  13. Biotransformation of flavone by CYP105P2 from Streptomyces peucetius.

    PubMed

    Niraula, Narayan Prasad; Bhattarai, Saurabh; Lee, Na-Rae; Sohng, Jae Kyung; Oh, Tae-Jin

    2012-08-01

    Biocatalytic transfer of oxygen in isolated cytochrome P450 or whole microbial cells is an elegant and efficient way to achieve selective hydroxylation. Cytochrome P450 CYP105P2 was isolated from Streptomyces peucetius that showed a high degree of amino acid identity with hydroxylases. Previously performed homology modeling, and subsequent docking of the model with flavone, displayed a reasonable docked structure. Therefore, in this study, in a pursuit to hydroxylate the flavone ring, CYP105P2 was co-expressed in a two-vector system with putidaredoxin reductase (camA) and putidaredoxin (camB) from Pseudomonas putida for efficient electron transport. HPLC analysis of the isolated product, together with LCMS analysis, showed a monohydroxylated flavone, which was further established by subsequent ESI/MS-MS. A successful 10.35% yield was achieved with the whole-cell bioconversion reaction in Escherichia coli. We verified that CYP105P2 is a potential bacterial hydroxylase.

  14. Computational engineering of low bandgap copolymers

    PubMed Central

    Wykes, Michael; Milián-Medina, Begoña; Gierschner, Johannes

    2013-01-01

    We present a conceptual approach to low bandgap copolymers, in which we clarify the physical parameters which control the optical bandgap, develop a fundamental understanding of bandgap tuning, unify the terminology, and outline the minimum requirements for accurate prediction of polymer bandgaps from those of finite length oligomers via extrapolation. We then test the predictive power of several popular hybrid and long-range corrected (LC) DFT functionals when applied to this task by careful comparison to experimental studies of homo- and co-oligomer series. These tests identify offset-corrected M06HF, with 100% HF exchange, as a useful alternative to the poor performance of tested hybrid and LC functionals with lower fractions of HF exchange (B3LYP, CAM-B3LYP, optimally-tuned LC-BLYP, BHLYP), which all significantly overestimate changes in bandgap as a function of system size. PMID:24790963

  15. Theoretical study of a novel imino bridged pillar[5]arene derivative

    NASA Astrophysics Data System (ADS)

    Xie, Ju; Zuo, Tongfei; Huang, Zhiling; Huan, Long; Gu, Qixin; Gao, Chenxi; Shao, Jingjing

    2016-10-01

    In this paper, we report a novel imino bridged pillar[5]arene derivative (P5N) for the first time. Four conformers (P5N0, P5N1, P5N12, and P5N13, arising due to the different orientation of Nsbnd H bond of imino bridging group) are obtained by quantum chemical calculations at the CAM-B3LYP/6-31+G(d, p) level of theory. The geometries, energies, electronic structures, and absorption spectra of P5N conformers as well as pillar[5]arene (P5) are discussed in detail. The inclusion complexes of paraquat (Pq) with P5N and P5, respectively, are also obtained at the same level of theory. Compared to P5, P5N exhibits better performance in inclusion complexation toward Pq.

  16. First hyperpolarizability of cyclooctatetraene modulated by alkali and alkaline earth metals.

    PubMed

    Roy, Ria Sinha; Mondal, Avijit; Nandi, Prasanta K

    2017-03-01

    In the present investigation, the first hyperpolarizability of alkali and alkaline earth metal derivatives of cyclooctatetraene (COT) has been calculated using BHHLYP and CAM-B3LYP functional for 6-311++G(d,p), 6-311++G(3df,3pd), and aug-pc 2 basis sets. Introduction of Na/K atoms at the axial position of COT and Li, Na, K/Be, Mg, Ca metal atoms and cyanide groups at the equatorial sites leads to lager enhancement of first hyperpolarizability. The ring charge density can account for the variation of first hyperpolarizability. The two state model has been invoked to explain the variation of first hyperpolarizability.

  17. CosmoSIS: Modular cosmological parameter estimation

    DOE PAGES

    Zuntz, J.; Paterno, M.; Jennings, E.; ...

    2015-06-09

    Cosmological parameter estimation is entering a new era. Large collaborations need to coordinate high-stakes analyses using multiple methods; furthermore such analyses have grown in complexity due to sophisticated models of cosmology and systematic uncertainties. In this paper we argue that modularity is the key to addressing these challenges: calculations should be broken up into interchangeable modular units with inputs and outputs clearly defined. Here we present a new framework for cosmological parameter estimation, CosmoSIS, designed to connect together, share, and advance development of inference tools across the community. We describe the modules already available in CosmoSIS, including CAMB, Planck, cosmicmore » shear calculations, and a suite of samplers. Lastly, we illustrate it using demonstration code that you can run out-of-the-box with the installer available at http://bitbucket.org/joezuntz/cosmosis« less

  18. Non-linear optical study of BODIPY-benzimidazole conjugate by solvatochromic, Z-scan and theoretical methods

    NASA Astrophysics Data System (ADS)

    Thakare, Shrikant S.; Sreenath, Mavila C.; Chitrambalam, Subramaniyan; Joe, Isaac H.; Sekar, Nagaiyan

    2017-02-01

    BODIPY chromophore flanked with the benzimidazole moiety at 2-position has been investigated for its nonlinear optical (NLO) properties. Charge transfer character developed by the unsymmetrical substitution on the molecular framework and the solvatochromic behaviour of this dye inspired us to study its NLO characteristics. NLO response has been measured using solvatochromic method as well as the Z scan technique. The values obtained for nonlinear absorption coefficient (β) and third order susceptibility χ(3) are -7.45 × 10-12 and 3.85 × 10-13 respectively. Quantum chemical calculations have also been performed to estimate the NLO properties theoretically by using DFT method with three functionals viz B3LYP, BHHLYP and CAMB3LYP with 6-311 G (d,p) basis set. The results obtained from the DFT method are in well accordance with those produced from solvatochromic method.

  19. A sequential MC/TD-DFT study of the solvatochromic shift of the pyridinium- N-phenoxide betaine dye in water using standard and long-range corrected functionals

    NASA Astrophysics Data System (ADS)

    Oliveira, Leonardo B. A.; Fonseca, Tertius L.; Coutinho, Kaline; Canuto, Sylvio

    2011-10-01

    Solvatochromic shifts of the π-π∗ and n-π∗ transitions for the pyridinium-N-phenoxide [2-(pyridinium-1-yl)phenolate] betaine changing from vacuum to water, have been investigated using Monte Carlo simulations and time-dependent density functional theory schemes using standard and long-range corrected functionals. The classical Boltzmann distribution of the interring twist angle obtained from the calculated free energy agrees with a Car-Parrinello distribution. For the calculated spectral shifts BHandHLYP/6-311+G(2d,p) performs better than the CAM-B3LYP/6-311+G(2d,p) or LC-ωPBE/6-311+G(2d,p) model but the experimental shift is very well reproduced only after the inclusion of solute polarization and proper consideration of the twist geometry relaxation associated with the intramolecular charge transfer.

  20. Density functional theory calculations on (2e)-3-(3-Bromo-4-methoxyphenyl)-1-(pyridin-2-yl) prop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Öner, Nazmiye; Tamer, Ömer; Başoǧlu, Adil; Avcı, Davut; Atalay, Yusuf

    2017-02-01

    In this paper, quantum chemical calculations of (2e)-3-(3-Bromo-4-methoxyphenyl) -1-(pyridin-2-yl)prop-2-en-1-one were performed by using B3LYP and CAMB3LYP levels of density functional theory (DFT) with 6-311++G(d, p) basis set. Geometric parameters of the title molecule in the ground state were found to be in good agreement with experimental data. 13C and 1H NMR chemical shifts were calculated within GIAO approach which is one of the most common approaches. The frontier molecular orbitals (HOMO and LUMO) were simulated by the same levels. Nonlinear optical parameters (NLO) were also evaluated by determining of dipole moment, polarizability and first hyperpolarizability. All of calculations were carried out Gaussian 09 package program.

  1. A ligation-triggered DNAzyme cascade for amplified fluorescence detection of biological small molecules with zero-background signal.

    PubMed

    Lu, Li-Min; Zhang, Xiao-Bing; Kong, Rong-Mei; Yang, Bin; Tan, Weihong

    2011-08-03

    Many types of fluorescent sensing systems have been reported for biological small molecules. Particularly, several methods have been developed for the recognition of ATP or NAD(+), but they only show moderate sensitivity, and they cannot discriminate either ATP or NAD(+) from their respective analogues. We have addressed these limitations and report here a dual strategy which combines split DNAzyme-based background reduction with catalytic and molecular beacon (CAMB)-based amplified detection to develop a ligation-triggered DNAzyme cascade, resulting in ultrahigh sensitivity. First, the 8-17 DNAzyme is split into two separate oligonucleotide fragments as the building blocks for the DNA ligation reaction, thereby providing a zero-background signal to improve overall sensitivity. Next, a CAMB strategy is further employed for amplified signal detection achieved through cycling and regenerating the DNAzyme to realize the true enzymatic multiple turnover (one enzyme catalyzes the cleavage of several substrates) of catalytic beacons. This combination of zero-background signal and signal amplification significantly improves the sensitivity of the sensing systems, resulting in detection limits of 100 and 50 pM for ATP and NAD(+), respectively, much lower than those of previously reported biosensors. Moreover, by taking advantage of the highly specific biomolecule-dependence of the DNA ligation reaction, the developed DNAzyme cascades show significantly high selectivity toward the target cofactor (ATP or NAD(+)), and the target biological small molecule can be distinguished from its analogues. Therefore, as a new and universal platform for the design of DNA ligation reaction-based sensing systems, this novel ligation-triggered DNAzyme cascade method may find a broad spectrum of applications in both environmental and biomedical fields.

  2. The Nature of the Donor Motif in Acceptor-Bridge-Donor Dyes as an Influence in the Electron Photo-Injection Mechanism in DSSCs.

    PubMed

    Zarate, Ximena; Schott-Verdugo, Stephan; Rodriguez-Serrano, Angela; Schott, Eduardo

    2016-03-10

    The combination and balance of acceptor(A)-bridge-donor(D) architecture of molecules confer suitable attributes and/or properties to act as efficient light-harvesting and sensitizers in dye sensitized solar cells (DSSCs). An important process in a DSSC performance is the electron photoinjection (PI) mechanism which can take place either via type I (indirect), that consists in injecting from the excited state of the dye to the semiconductor, or type II (direct), where the PI is from the ground state of the dye to the semiconductor upon photoexcitation. Here, we present a computational study about the role of the donor motif in the PI mechanisms displayed from a family of 11 A-bridge-D structured dyes to a (TiO2)15 anatase cluster. To this end, different donor motifs (D1-D11) were evaluated while the A and bridge motifs remained the same. All the computations were carried out within the DFT framework, using the B3LYP, PW91, PBE, M06L and CAM-B3LYP functionals. The 6-31G(d) basis set was employed for nonmetallic atoms and the LANL2DZ pseudopotential for Ti atoms. The solvation effects were incorporated using the polarized continuum model (PCM) for acetonitrile. As benchmark systems, alizarin and naphthalenediol dyes were analyzed, as they are known to undergo Type I and Type II PI pathways in DSSCs, respectively. Donors in the studied family of dyes could influence to drive Type I or II PI since it was found that D2 could show some Type II PI route, showing a new absorption band, although with CAM-B3LYP this shows a very low oscillator strength, while the remaining dyes behave according to Type I photoinjectors. Finally, the photovoltaic parameters that govern the light absorption process were evaluated, as the use of these criteria could be applied to predict the efficiency of the studied dyes in DSSCs devices.

  3. Density functional theory based generalized effective fragment potential method

    SciTech Connect

    Nguyen, Kiet A. E-mail: ruth.pachter@wpafb.af.mil; Pachter, Ruth E-mail: ruth.pachter@wpafb.af.mil; Day, Paul N.

    2014-06-28

    We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes.

  4. Pharmacokinetics and tissue distribution after intravenous administration of a single dose of amphotericin B cochleates, a new lipid-based delivery system.

    PubMed

    Segarra, Ignacio; Movshin, Diane A; Zarif, Leila

    2002-08-01

    Model independent pharmacokinetic analysis of intravenous (iv) amphotericin B cochleates (CAMB), a new lipid-based drug delivery system, in mice (0.625 mg/kg) shows a two-phase disposition profile in blood [area under the curve of concentration versus time from time zero to infinity (AUC(0-infinity)) = 1.01 microg. h/mL, half-life (t((1/2))) = 11.68 h, volume of distribution at steady state (V(ss)) = 9.59 L/kg, clearance (CL) = 10.36 mL/min/kg and mean residence time from time 0 to infinity (MRT(0-infinity)) = 15.41 h). In target tissues, maximum time (t(max)) ranged from 2 min (spleen and lung) to 10 min (liver) and lungs presented the highest AMB concentration (16.4 microg. h/g) followed by liver (8.56 microg/g), and spleen (6.63 microg/g). In addition, liver and spleen presented the longest elution half-life (75.03 and 66.71 h, respectively), MRT(0-infinity) (98.4 and 86.3 h, respectively), and AMB exposure:liver AUC(0-infinity) = 474 and 116.4 microg. h/g for the spleen. The large V(ss) and the extensive tissue AUC indicate large and efficient ability of cochleates to penetrate and deliver AMB. Differences in tissue uptake mechanism and pharmacokinetic data suggest a crucial role of macrophages in CAMB clearance from blood as well as an essential role of the liver and the spleen in AMB distribution to target tissues.

  5. Testing the ultra-light axion hypothesis with CMB-SIV

    NASA Astrophysics Data System (ADS)

    Grin, Daniel; Hlozek, Renee; Marsh, David

    2017-01-01

    Measurements of cosmic microwave background (CMB) anisotropies provide strong evidence for the existence of dark matter and dark energy. They can also test its composition, probing the energy density and particle mass of different dark-matter and dark-energy components. CMB data have already shown that ultra-light axions (ULAs) with mass in the range 10-32 eV→10-26 eV compose a fraction <0.01 of the cosmological critical density. Here, the sensitivity of a proposed CMB-Stage IV (CMB-S4) experiment (assuming a 1 arcmin beam and <1 μK-arcmin noise levels over a sky fraction of 0.4) to the density of ULAs and other dark-sector components is assessed. CMB-S4 data should be ˜10 times more sensitive to the ULA energy-density than Planck data alone, across a wide range of ULA masses 10-32CAMB code (a modification to the CAMB Boltzmann code), presented here for public use.

  6. Assessment of new DFT methods for predicting vibrational spectra and structure of cisplatin: Which density functional should we choose for studying platinum(II) complexes?

    NASA Astrophysics Data System (ADS)

    Malik, Magdalena; Michalska, Danuta

    Ten different DFT methods, including several recently developed functionals have been tested for their performances in prediction of infrared and Raman spectra and molecular structure of cisplatin. The assessed DFT methods cover the range from meta-GGA to hybrid, double hybrid and long-range corrected hybrid models (M06-L, M06, M06-2X, PBE0, mPW1PW, B3LYP, B2PLYP, CAM-B3LYP, ωB97XD and LC-ωPBE). The calculated structural parameters and theoretical spectra have been compared to the corresponding experimental data. It is shown that the LC-ωPBE scheme is superior to other DFT methods in predicting the geometry of cisplatin. Unfortunately, the M06-L, M06-2X and B3LYP functionals are deficient in the evaluation of the strength of two Pt ← NH3 coordination bonds in cisplatin (the calculated bond lengths are too long and the Pt-N stretching frequencies are underestimated). Both the PBE0 and mPW1PW functionals, in conjunction with the LanL2TZ(f) basis set for Pt give very similar theoretical results and seem to be the best methods for predicting the IR and Raman spectra of cisplatin. The long-range corrected functionals (LC-ωPBE, ωB97XD and CAM-B3LYP) have shown good performances in predicting the frequencies of Pt-ligand vibrations and are promising new tools for theoretical study of novel platinum(II) compounds.

  7. The structure and UV spectroscopy of benzene-water (Bz-W6) clusters using time-dependent density functional theory.

    PubMed

    Sharma, Divya; Paterson, Martin J

    2014-11-01

    DFT and MP2 calculations are performed to obtain optimized ground state geometries and binding energies of the cage and the prism conformers of water W6 clusters and Bz-W6 clusters using the aug-cc-pVDZ basis set. The cage conformer of Bz-W6 system is found to be more stable than prism conformer for all range of DFT functionals and MP2. Time dependent-DFT is then used to study UV spectroscopy of Bz, water W6 clusters and Bz-W6 clusters at both the MP2 and wB97XD optimized ground state geometries using the B3LYP, CAM-B3LYP and M06-2X functionals with 6-31++G(d,p) and aug-cc-pVTZ basis sets. Our results predict minor differences in the UV spectroscopy of cage and prism conformers W6 and Bz-W6 clusters that may be observable with high-resolution spectroscopy. The M06-2X and CAM-B3LYP functionals perform consistently with each other. Benzene-mediated excitations of the water W6 cluster towards longer wavelengths above 170 nm are noticed in both the cage and prism geometries of Bz-W6. Benzene is found to be influenced after interacting with the cage and prism W6 geometries, and is seen to undergo a red shift in the main π→π* electronic transition, in which the degeneracy is slightly broken. Charge transfer (CT) states and diffuse Rydberg-type states are also found to play an important role in the spectroscopy of such systems.

  8. A relativistic time-dependent density functional study of the excited states of the mercury dimer

    SciTech Connect

    Kullie, Ossama E-mail: ossama.kullie@unistra.fr

    2014-01-14

    In previous works on Zn{sub 2} and Cd{sub 2} dimers we found that the long-range corrected CAMB3LYP gives better results than other density functional approximations for the excited states, especially in the asymptotic region. In this paper, we use it to present a time-dependent density functional (TDDFT) study for the ground-state as well as the excited states corresponding to the (6s{sup 2} + 6s6p), (6s{sup 2} + 6s7s), and (6s{sup 2} + 6s7p) atomic asymptotes for the mercury dimer Hg{sub 2}. We analyze its spectrum obtained from all-electron calculations performed with the relativistic Dirac-Coulomb and relativistic spinfree Hamiltonian as implemented in DIRAC-PACKAGE. A comparison with the literature is given as far as available. Our result is excellent for the most of the lower excited states and very encouraging for the higher excited states, it shows generally good agreements with experimental results and outperforms other theoretical results. This enables us to give a detailed analysis of the spectrum of the Hg{sub 2} including a comparative analysis with the lighter dimers of the group 12, Cd{sub 2}, and Zn{sub 2}, especially for the relativistic effects, the spin-orbit interaction, and the performance of CAMB3LYP and is enlightened for similar systems. The result shows, as expected, that spinfree Hamiltonian is less efficient than Dirac-Coulomb Hamiltonian for systems containing heavy elements such as Hg{sub 2}.

  9. Identification and characterization of L-arabonate dehydratase, L-2-keto-3-deoxyarabonate dehydratase, and L-arabinolactonase involved in an alternative pathway of L-arabinose metabolism. Novel evolutionary insight into sugar metabolism.

    PubMed

    Watanabe, Seiya; Shimada, Naoko; Tajima, Kunihiko; Kodaki, Tsutomu; Makino, Keisuke

    2006-11-03

    Azospirillum brasiliense possesses an alternative pathway of L-arabinose metabolism, different from the known bacterial and fungal pathways. In the preceding articles, we identified and characterized L-arabinose-1-dehydrogenase and alpha-ketoglutaric semialdehyde dehydrogenase, which catalyzes the first and final reaction steps in this pathway, respectively (Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 2612-2623 and Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 28876-28888). We here report the remaining three enzymes, L-arabonate dehydratase, L-2-keto-3-deoxyarabonate (L-KDA) dehydratase, and L-arabinolactonase. N-terminal amino acid sequences of L-arabonate dehydratase and L-KDA dehydratase purified from A. brasiliense cells corresponded to those of AraC and AraD genes, which form a single transcriptional unit together with the L-arabinose-1-dehydrogenase gene. Furthermore, the L-arabinolactonase gene (AraB) was also identified as a component of the gene cluster. Genetic characterization of the alternative L-arabinose pathway suggested a significant evolutional relationship with the known sugar metabolic pathways, including the Entner-Doudoroff (ED) pathway and the several modified versions. L-arabonate dehydratase belongs to the ILVD/EDD family and spectrophotometric and electron paramagnetic resonance analysis revealed it to contain a [4Fe-4S](2+) cluster. Site-directed mutagenesis identified three cysteine ligands essential for cluster coordination. L-KDA dehydratase was sequentially similar to DHDPS/NAL family proteins. D-2-Keto-3-deoxygluconate aldolase, a member of the DHDPS/NAL family, catalyzes the equivalent reaction to L-KDA aldolase involved in another alternative L-arabinose pathway, probably associating a unique evolutional event between the two alternative L-arabinose pathways by mutation(s) of a common ancestral enzyme. Site-directed mutagenesis revealed a unique catalytic amino acid residue in L

  10. The Colletotrichum boninense species complex

    PubMed Central

    Damm, U.; Cannon, P.F.; Woudenberg, J.H.C.; Johnston, P.R.; Weir, B.S.; Tan, Y.P.; Shivas, R.G.; Crous, P.W.

    2012-01-01

    Although only recently described, Colletotrichum boninense is well established in literature as an anthracnose pathogen or endophyte of a diverse range of host plants worldwide. It is especially prominent on members of Amaryllidaceae, Orchidaceae, Proteaceae and Solanaceae. Reports from literature and preliminary studies using ITS sequence data indicated that C. boninense represents a species complex. A multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3, CAL) of 86 strains previously identified as C. boninense and other related strains revealed 18 clades. These clades are recognised here as separate species, including C. boninense s. str., C. hippeastri, C. karstii and 12 previously undescribed species, C. annellatum, C. beeveri, C. brassicicola, C. brasiliense, C. colombiense, C. constrictum, C. cymbidiicola, C. dacrycarpi, C. novae-zelandiae, C. oncidii, C. parsonsiae and C. torulosum. Seven of the new species are only known from New Zealand, perhaps reflecting a sampling bias. The new combination C. phyllanthi was made, and C. dracaenae Petch was epitypified and the name replaced with C. petchii. Typical for species of the C. boninense species complex are the conidiogenous cells with rather prominent periclinal thickening that also sometimes extend to form a new conidiogenous locus or annellations as well as conidia that have a prominent basal scar. Many species in the C. boninense complex form teleomorphs in culture. Taxonomic novelties: New combination - Colletotrichum phyllanthi (H. Surendranath Pai) Damm, P.F. Cannon & Crous. Name replacement - C. petchii Damm, P.F. Cannon & Crous. New species - C. annellatum Damm, P.F. Cannon & Crous, C. beeveri Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. brassicicola Damm, P.F. Cannon & Crous, C. brasiliense Damm, P.F. Cannon, Crous & Massola, C. colombiense Damm, P.F. Cannon, Crous, C. constrictum Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. cymbidiicola Damm, P.F. Cannon

  11. When Genome-Based Approach Meets the “Old but Good”: Revealing Genes Involved in the Antibacterial Activity of Pseudomonas sp. P482 against Soft Rot Pathogens

    PubMed Central

    Krzyżanowska, Dorota M.; Ossowicki, Adam; Rajewska, Magdalena; Maciąg, Tomasz; Jabłońska, Magdalena; Obuchowski, Michał; Heeb, Stephan; Jafra, Sylwia

    2016-01-01

    Dickeya solani and Pectobacterium carotovorum subsp. brasiliense are recently established species of bacterial plant pathogens causing black leg and soft rot of many vegetables and ornamental plants. Pseudomonas sp. strain P482 inhibits the growth of these pathogens, a desired trait considering the limited measures to combat these diseases. In this study, we determined the genetic background of the antibacterial activity of P482, and established the phylogenetic position of this strain. Pseudomonas sp. P482 was classified as Pseudomonas donghuensis. Genome mining revealed that the P482 genome does not contain genes determining the synthesis of known antimicrobials. However, the ClusterFinder algorithm, designed to detect atypical or novel classes of secondary metabolite gene clusters, predicted 18 such clusters in the genome. Screening of a Tn5 mutant library yielded an antimicrobial negative transposon mutant. The transposon insertion was located in a gene encoding an HpcH/HpaI aldolase/citrate lyase family protein. This gene is located in a hypothetical cluster predicted by the ClusterFinder, together with the downstream homologs of four nfs genes, that confer production of a non-fluorescent siderophore by P. donghuensis HYST. Site-directed inactivation of the HpcH/HpaI aldolase gene, the adjacent short chain dehydrogenase gene, as well as a homolog of an essential nfs cluster gene, all abolished the antimicrobial activity of the P482, suggesting their involvement in a common biosynthesis pathway. However, none of the mutants showed a decreased siderophore yield, neither was the antimicrobial activity of the wild type P482 compromised by high iron bioavailability. A genomic region comprising the nfs cluster and three upstream genes is involved in the antibacterial activity of P. donghuensis P482 against D. solani and P. carotovorum subsp. brasiliense. The genes studied are unique to the two known P. donghuensis strains. This study illustrates that mining of

  12. Natural products isolated from Mexican medicinal plants: novel inhibitors of sulfotransferases, SULT1A1 and SULT2A1.

    PubMed

    Mesía-Vela, S; Sańchez, R I; Estrada-Muñiz, E; Alavez-Solano, D; Torres-Sosa, C; Jiménez, M; Estrada; Reyes-Chilpa, R; Kauffman, F C

    2001-11-01

    Calophyllum brasiliense, Lonchocarpus oaxacensis, and Lonchocarpus guatemalensis are used in Latin American folk medicine. Four natural xanthones, an acetylated derivative, and two coumarins were obtained from C. brasiliense. Two flavanones were extracted from L. oaxacensis and one chalcone from L guatemalensis. These compounds were tested as substrates and inhibitors for two recombinant sulfotransferases (SULTs) involved in the metabolism of many endogenous compounds and foreign chemicals. Assays were performed using recombinant phenolsulfotransferase (SULT1A1) and hydroxysteroidsulfotransferase (SULT2A1). Three of the five xanthones, one of the flavonoids and the coumarins tested were substrates for SULT1A1. None of the xanthones or the flavonoids were sulfonated by SULT2A1, whereas the coumarin mammea A/BA was a substrate for this enzyme. The natural xanthones reversibly inhibited SULT1A1 with IC50 values ranging from 1.6 to 7 microM whereas much higher amounts of these compounds were required to inhibit SULT2A1 (IC50 values of 26-204 microM). The flavonoids inhibited SULT1A1 with IC50 values ranging from 9.5 to 101 microM, which compared with amounts needed to inhibit SULT2A1 (IC50 values of 11 to 101 microM). Both coumarins inhibited SULT1A1 with IC50 values of 47 and 185 pM, and SULT2A1 with IC50 values of 16 and 31 microM. The acetylated xanthone did not inhibit either SULT1AI or SULT2A1 activity. Rotenone from a commercial source had potency comparable to that of the flavonoids isolated from Lonchocarpus for inhibiting both SULTs. The potency of this inhibition depends on the position and number of hydroxyls. The results indicate that SULT1A1, but not SULT2A1, is highly sensitive to inhibition by xanthones. Conversely, SULT2A1 is 3-6 times more sensitive to coumarins than SULT1A1. The flavonoids are non-specific inhibitors of the two SULTs. Collectively, the results suggest that these types of natural products have the potential for important

  13. Antioxidant Properties of Brazilian Tropical Fruits by Correlation between Different Assays

    PubMed Central

    Pereira Lima, Giuseppina Pace; Fabris, Sabrina

    2013-01-01

    Four different assays (the Folin-Ciocalteu, DPPH, enzymatic method, and inhibitory activity on lipid peroxidation) based on radically different physicochemical principles and normally used to determine the antioxidant activity of food have been confronted and utilized to investigate the antioxidant activity of fruits originated from Brazil, with particular attention to more exotic and less-studied species (jurubeba, Solanum paniculatum; pequi, Caryocar brasiliense; pitaya, Hylocereus undatus; siriguela, Spondias purpurea; umbu, Spondias tuberosa) in order to (i) verify the correlations between results obtained by the different assays, with the final purpose to obtain more reliable results avoiding possible measuring-method linked mistakes and (ii) individuate the more active fruit species. As expected, the different methods give different responses, depending on the specific assay reaction. Anyhow all results indicate high antioxidant properties for siriguela and jurubeba and poor values for pitaya, umbu, and pequi. Considering that no marked difference of ascorbic acid content has been detected among the different fruits, experimental data suggest that antioxidant activities of the investigated Brazilian fruits are poorly correlated with this molecule, principally depending on their total polyphenolic content. PMID:24106692

  14. Antioxidant properties of Brazilian tropical fruits by correlation between different assays.

    PubMed

    Gregoris, Elena; Pereira Lima, Giuseppina Pace; Fabris, Sabrina; Bertelle, Mariangela; Sicari, Michela; Stevanato, Roberto

    2013-01-01

    Four different assays (the Folin-Ciocalteu, DPPH, enzymatic method, and inhibitory activity on lipid peroxidation) based on radically different physicochemical principles and normally used to determine the antioxidant activity of food have been confronted and utilized to investigate the antioxidant activity of fruits originated from Brazil, with particular attention to more exotic and less-studied species (jurubeba, Solanum paniculatum; pequi, Caryocar brasiliense; pitaya, Hylocereus undatus; siriguela, Spondias purpurea; umbu, Spondias tuberosa) in order to (i) verify the correlations between results obtained by the different assays, with the final purpose to obtain more reliable results avoiding possible measuring-method linked mistakes and (ii) individuate the more active fruit species. As expected, the different methods give different responses, depending on the specific assay reaction. Anyhow all results indicate high antioxidant properties for siriguela and jurubeba and poor values for pitaya, umbu, and pequi. Considering that no marked difference of ascorbic acid content has been detected among the different fruits, experimental data suggest that antioxidant activities of the investigated Brazilian fruits are poorly correlated with this molecule, principally depending on their total polyphenolic content.

  15. Phylogenetic Relationships Among Xiphinema and Xiphidorus Nematode Species from Brazil Inferred from 18S rDNA Sequences

    PubMed Central

    Oliveira, Claudio M. G.; Hübschen, Judith; Brown, Derek J. F.; Ferraz, Luiz C. C. B.; Wright, Frank; Neilson, Roy

    2004-01-01

    Maximum likelihood trees produced from 18S rDNA sequences separated 14 Xiphinema and five Xiphidorus nematode species from Brazil into distinct groups that concurred with their current morphological taxonomic status. Species belonging to the X. americanum group (X. brevicolle, X. diffusum, X. oxycaudatum, and X. peruvianum) formed a single group that was clearly separated from the other Xiphinema species. As with previous taxonomic studies that noted only minor morphological differences between putative X. americanum group species, separation of these species based upon 18S rDNA sequences was inconclusive. Thus it is probable that instead of comprising distinct species, the X. americanum group may in fact represent numerous morphotypes with large inter- and intra- population morphological variability that may be environmentally driven. Within the cluster representing non X. americanum group species, there was little statistical support to clearly separate species. However, three subgroups, comprising (i) the X. setariae/vulgare complex, (ii) X. ifacolum and X. paritaliae, and (iii) X. brasiliense and X. ensiculiferum were well resolved. PMID:19262801

  16. Analysis of phylogeny, distribution, and pathogenicity of Botryosphaeriaceae species associated with gummosis of Anacardium in Brazil, with a new species of Lasiodiplodia.

    PubMed

    Netto, Mariote S B; Lima, Waléria G; Correia, Kamila C; da Silva, Christiana F B; Thon, Michael; Martins, Ricardo B; Miller, Robert N G; Michereff, Sami J; Câmara, Marcos P S

    2017-04-01

    Netto, M. S. B., Lima, W. G., Correia, K. C., da Silva, C. F. B., Thon, M., Martins, R. B., Miller, R. N. G., Michereff, S. J., and Câmara, M. P. S. 2016. Analysis of phylogeny, distribution, and pathogenicity of Botryosphaeriaceae species associated with gummosis of Anacardium in Brazil, with a new species of Lasiodiplodia. We identified Botryosphaeriaceae species associated with gummosis on Anacardium in Brazil. Isolates were sampled and identified on the basis morphology and phylogeny, through analysis of a partial translation elongation factor 1-α sequence, ribosomal DNA internal transcribed spacers, and β-tubulin gene sequence. Ten taxa were identified, namely, Lasiodiplodia brasiliense, L. euphorbicola, L. gonubiensis, L. iraniensis, L. jatrophicola, L. gravistriata sp. nov., L. pseudotheobromae, L. theobromae, Neofusicoccum batangarum, and Pseudofusicoccum stromaticum. Lasiodiplodia theobromae has been previously reported in cashew and is the most prevalent species observed. All the other species are reported here for the first time on this host. All species of Botryosphaeriaceae were pathogenic on detached green cashew shoots. Differences in aggressiveness were observed among the species, with N. batangarum, L. iraniensis, L. jatrophicola, and L. gravistriata characterized as the most aggressive species, whilst L. euphorbicola and L. pseudotheobromae were identified as the least aggressive.

  17. Antiproliferative and proapoptotic activity of GUT-70 mediated through potent inhibition of Hsp90 in mantle cell lymphoma

    PubMed Central

    Jin, L; Tabe, Y; Kimura, S; Zhou, Y; Kuroda, J; Asou, H; Inaba, T; Konopleva, M; Andreeff, M; Miida, T

    2011-01-01

    Background: Mantle cell lymphoma (MCL) is an aggressive B-cell lymphoma with poor prognosis, requiring novel anticancer strategies. Methods: Mantle cell lymphoma cell lines with known p53 status were treated with GUT-70, a tricyclic coumarin derived from Calophyllum brasiliense, and the biological and biochemical consequences of GUT-70 were studied. Results: GUT-70 markedly reduced cell proliferation/viability through G1 cell cycle arrest and increased apoptosis, with greater sensitivity in mutant (mt)-p53-expressing MCL cells than in wild-type (wt)-p53-bearing cells. Mechanistically, GUT-70 showed binding affinity to heat-shock protein 90 (Hsp90) and ubiquitin-dependent proteasomal degradation of Hsp90 client proteins, including cyclin D1, Raf-1, Akt, and mt-p53. Depletion of constitutively overexpressed cyclin D1 by GUT-70 was accompanied by p27 accumulation and decreased Rb phosphorylation. GUT-70 induced mitochondrial apoptosis with Noxa upregulation and Mcl-1 downregulation in mt-p53 cells, but Mcl-1 accumulation in wt-p53 cells. Noxa and Mcl-1 were coimmunoprecipitated, and activated BAK. Treatment with a combination of GUT-70 and bortezomib or doxorubicin had synergistic antiproliferative effects in MCL cells that were independent of p53 status. Conclusion: GUT-70 has pronounced antiproliferative effects in MCL with mt-p53, a known negative prognostic factor for MCL, through Hsp90 inhibition. These findings suggest that GUT-70 has potential utility for the treatment of MCL. PMID:21139584

  18. Expression levels of antimicrobial peptide tachyplesin I in transgenic Ornithogalum lines affect the resistance to Pectobacterium infection.

    PubMed

    Lipsky, Alexander; Joshi, Janak Raj; Carmi, Nir; Yedidia, Iris

    2016-11-20

    The genus Ornithogalum includes several ornamental species that suffer substantial losses from bacterial soft rot caused by Pectobacteria. The absence of effective control measures for use against soft rot bacteria led to the initiation of a project in which a small antimicrobial peptide from an Asian horseshoe crab, tachyplesin (tpnI), was introduced into two commercial cultivars: O. dubium and O. thyrsoides. Disease severity and bacterial colonization were examined in transgenic lines expressing this peptide. Disease resistance was evaluated in six lines of each species by measuring bacterial proliferation in the plant tissue. Three transgenic lines of each species were subjected to further analysis in which the expression level of the transgene was evaluated using RT-PCR and qRT-PCR. The development of disease symptoms and bacterial colonization of the plant tissue were also examined using GFP-expressing strain of P. carotovorum subsp. brasiliense Pcb3. Confocal-microscopy imaging revealed significantly reduced quantities of bacterial cells in the transgenic plant lines that had been challenged with the bacterium. The results clearly demonstrate that tpnI expression reduces bacterial proliferation, colonization and disease symptom (reduced by 95-100%) in the transgenic plant tissues. The quantity of tpnI transcripts, as measured by qRT-PCR, was negatively correlated with the protection afforded to the plants, as measured by the reduced severity of disease symptoms in the tissue.

  19. Microbial diversity in a bagasse-based compost prepared for the production of Agaricus brasiliensis

    PubMed Central

    Silva, Cristina Ferreira; Azevedo, Raquel Santos; Braga, Claudia; da Silva, Romildo; Dias, Eustáquio Souza; Schwan, Rosane Freitas

    2009-01-01

    Edible mushrooms are renowned for their nutritional and medicinal properties and are thus of considerable commercial importance. Mushroom production depends on the chemical composition of the basic substrates and additional supplements employed in the compost as well as on the method of composting. In order to minimise the cost of mushroom production, considerable interest has been shown in the use of agro-industrial residues in the preparation of alternative compost mixtures. However, the interaction of the natural microbiota present in agricultural residues during the composting process greatly influences the subsequent colonisation by the mushroom. The aim of the present study was to isolate and identify the microbiota present in a sugar cane bagasse and coast-cross straw compost prepared for the production of Agaricus brasilienses. Composting lasted for 14 days, during which time the substrates and additives were mixed every 2 days, and this was followed by a two-step steam pasteurisation (55 - 65°C; 15 h each step). Bacteria, (mainly Bacillus and Paenibacillus spp. and members of the Enterobacteriaceae) were the predominant micro-organisms present throughout the composting process with an average population density of 3 x 108 CFU/g. Actinomycetes, and especially members of the genus Streptomyces, were well represented with a population density of 2 - 3 x 108 CFU/g. The filamentous fungi, however, exhibited much lower population densities and were less diverse than the other micro-organisms, although Aspergillus fumigatus was present during the whole composting process and after pasteurisation. PMID:24031404

  20. Cytotoxic, Virucidal, and Antiviral Activity of South American Plant and Algae Extracts

    PubMed Central

    Faral-Tello, Paula; Mirazo, Santiago; Dutra, Carmelo; Pérez, Andrés; Geis-Asteggiante, Lucía; Frabasile, Sandra; Koncke, Elina; Davyt, Danilo; Cavallaro, Lucía; Heinzen, Horacio; Arbiza, Juan

    2012-01-01

    Herpes simplex virus type 1 (HSV-1) infection has a prevalence of 70% in the human population. Treatment is based on acyclovir, valacyclovir, and foscarnet, three drugs that share the same mechanism of action and of which resistant strains have been isolated from patients. In this aspect, innovative drug therapies are required. Natural products offer unlimited opportunities for the discovery of antiviral compounds. In this study, 28 extracts corresponding to 24 plant species and 4 alga species were assayed in vitro to detect antiviral activity against HSV-1. Six of the methanolic extracts inactivated viral particles by direct interaction and 14 presented antiviral activity when incubated with cells already infected. Most interesting antiviral activity values obtained are those of Limonium brasiliense, Psidium guajava, and Phyllanthus niruri, which inhibit HSV-1 replication in vitro with 50% effective concentration (EC50) values of 185, 118, and 60 μg/mL, respectively. For these extracts toxicity values were calculated and therefore selectivity indexes (SI) obtained. Further characterization of the bioactive components of antiviral plants will pave the way for the discovery of new compounds against HSV-1. PMID:22619617

  1. Ticks (Acari: Ixodidae) identified from prey-predator interactions via faecal analysis of Brazilian wild carnivores.

    PubMed

    Martins, Thiago F; Diniz-Reis, Thaís R; Libardi, Gustavo S; Percequillo, Alexandre R; Verdade, Luciano M; Matushima, Eliana R; Labruna, Marcelo B

    2015-05-01

    Between July 2008 and May 2010, we conducted a trophic study on 12 Brazilian wild carnivore species through their faecal analysis in a silvicultural landscape at Angatuba municipality, southern São Paulo state. Predator faeces was identified by morphology, predator hair, and surrounding tracks; prey remnants within faeces were used for morphological identification of the prey. Among the recovered ectoparasites, there were 89 specimens of six tick species in 21 (4.0%) out of 523 analysed samples. Ticks were identified to species level, based on external morphological characters, as following: adults of Amblyomma ovale and Amblyomma sculptum; nymphs of Amblyomma brasiliense, Amblyomma calcaratum, Amblyomma dubitatum, A. ovale, and Ixodes schulzei; and larvae of Amblyomma sp. and Ixodes sp. Generally, the recovered immature ticks were associated with consumed prey (small birds or small mammals), whereas adults were associated with the predator itself, ingested during its self-grooming. Our data show that faeces is an additional information source on ticks in Brazil and which may provide information on ectoparasite-predator-prey interactions.

  2. Nymphs of the genus Amblyomma (Acari: Ixodidae) of Brazil: descriptions, redescriptions, and identification key.

    PubMed

    Martins, Thiago F; Onofrio, Valeria C; Barros-Battesti, Darci M; Labruna, Marcelo B

    2010-06-01

    Together with the larval stage, the nymphal stage of ticks of the genus Amblyomma are the most aggressive ticks for humans entering areas inhabited by wildlife and some domestic animals in Brazil. However, due to the absence of morphological descriptions of the nymphal stage of most Brazilian Amblyomma species, plus the lack of an identification key, little or nothing is known about the life history of Amblyomma spp. nymphs in the country. In the present study, morphological description of the nymphal stage, illustrating important external characters through scanning electron microscopy, is provided for nymphs of 15 Amblyomma species that occur in Brazil, for which the nymphal stage had never been described: A. aureolatum, A. auricularium, A. calcaratum, A. coelebs, A. fuscum, A. humerale, A. incisum, A. latepunctatum, A. naponense, A. nodosum, A. ovale, A. pacae, A. pseudoconcolor, A. scalpturatum, A. varium. In addition, the nymphal stage of 12 Amblyomma species, which had been previously described, are redescribed: A. brasiliense, A. cajennense, A. dissimile, A. dubitatum, A. longirostre, A. oblongoguttatum, A. parkeri, A. parvum, A. romitii, A. rotundatum, A. tigrinum, A. triste. The descriptions and redescriptions totalized 27 species. Only 2 species (A. geayi, A. goeldii) out of the 29 Amblyomma species established in Brazil are not included in the present study. A dichotomous identification key is included to support taxonomic identification of the nymphal stage of 27 Amblyomma species established in Brazil.

  3. Evaluation of the Effects of Some Brazilian Medicinal Plants on the Production of TNF- α and CCL2 by THP-1 Cells.

    PubMed

    Gusman, Grasielle S; Campana, Priscilla R V; Castro, Luciano C; Castilho, Rachel O; Teixeira, Mauro M; Braga, Fernão C

    2015-01-01

    Several plant species are traditionally used in Brazil to treat various inflammatory diseases. Tumor necrosis factor- (TNF-) α and chemokine (C-C motif) ligand 2 (CCL2) are key inflammatory mediators in diseases like rheumatoid arthritis and atherosclerosis, respectively; nevertheless, only a few extracts have been assayed against these targets. We herein report the effect of 19 plant extracts on TNF-α and CCL2 release by lipopolysaccharide- (LPS-) stimulated THP-1 cells, a human monocytic leukemia cell line, along with their radical scavenging activity on DPPH. The extracts of Caryocar brasiliense, Casearia sylvestris, Coccoloba cereifera, and Terminalia glabrescens inhibited TNF-α production in a concentration-dependent manner. Fractionation of these extracts potentiated the anti-TNF-α effect, which was shown to concentrate in polar fractions, mainly composed by polyphenols. Significant CCL2 inhibition was elicited by Lippia sidoides and Terminalia glabrescens extracts, whose fractionation resulted in highly active low polar fractions. All assayed extracts showed strong radical scavenging activity, but antioxidant activity did not correlate with inhibition of TNF-α or CCL2 production. Our results allowed identifying extracts with selective capacity to block cytokine production; therefore, further purification of these extracts may yield molecules that could be useful in the treatment of chronic inflammatory diseases.

  4. Inhibition of gastric H+,K+-ATPase activity by flavonoids, coumarins and xanthones isolated from Mexican medicinal plants.

    PubMed

    Reyes-Chilpa, Ricardo; Baggio, Cristiane Hatsuko; Alavez-Solano, Dagoberto; Estrada-Muñiz, Elizabeth; Kauffman, Frederick C; Sanchez, Rosa I; Mesia-Vela, Sonia

    2006-04-21

    Medicinal plants are commonly used in Latin American folk medicine for the treatment of gastric problems. In order to understand the properties of some of their chemical constituents, four natural xanthones, an acetylated derivative, two coumarins (mammea A/BA and mammea C/OA) isolated from Calophyllum brasiliense Cambess and two flavonoids (minimiflorin and mundulin) isolated from Lonchocarpus oaxacensis Pittier, and the chalcone lonchocarpin isolated from Lonchocarpus guatemalensis Benth were tested for their activities on gastric H+,K+-ATPase isolated from dog stomach. All the compounds tested inhibited H+,K+-ATPase activity with varied potency. The xanthones inhibited the H+,K+-ATPase with IC50 values ranging from 47 microM to 1.6 mM. Coumarins inhibited H+,K+-ATPase with IC50 values of 110 and 638 microM. IC50 values for the flavonoids ranged from 9.6 to 510 microM among which minimiflorin was the most potent. The results suggest that H+,K+-ATPase is sensitive to inhibition by several types of structurally different natural compounds. The potency of the effects on gastric H+,K+-ATPase depends on the presence, position and number of hydroxyls groups in the molecule. Collectively, these results suggest a potential for important pharmacological and toxicological interactions by these types of natural products at the level of H+,K+-ATPase which may explain, at least in part, the gastroprotective properties, indicated by traditional medicine, of the plants from which these compounds were isolated.

  5. A Contribution to the Taxonomy of the Genus Xiphinema Cobb, 1913

    PubMed Central

    Cohn, E.; Sher, S. A.

    1972-01-01

    In a comparative study of different populations of Xiphinema, the significance of the female gonad structure in species determination is stressed, and monodelphic, pseudomonodelphic, and didelphic forms in the genus are defined. X. chambersi is redescribed and illustrated, X. ensiculiferum and X. krugi are redefined, and X. ensiculiferoides n.sp. and X. orthotenum n.sp. are described. Proposed new synonymies are: X. itanhaense = X. brasiliense; X. bulgariensis and X. conurum = X. italiae; X. ifacolum = X. basiri; X. macrostylum = X. ensiculiferum; X. truncatum = X. elongatum; and X. vulgare = X. setariae. X. yapoense is considered species inquirenda and X. obtusum a nomen dubium. The following eight subgenera of the genus Xiphinema are proposed: Radiphinema n. subg., Krugiphinema n. subg., Xiphinema n. subg., Elongiphinema n. subg., Halliphinema n. subg., Basiphinema n. subg., Rotundiphinema n. subg., and Diversiphinema n. subg. A key to the subgenera of Xiphinema is presented, plus a list of 50 species in the genus, their synonyms, and 10 species inquirendae. PMID:19319244

  6. Evaluation of the Effects of Some Brazilian Medicinal Plants on the Production of TNF-α and CCL2 by THP-1 Cells

    PubMed Central

    Gusman, Grasielle S.; Campana, Priscilla R. V.; Castro, Luciano C.; Castilho, Rachel O.; Teixeira, Mauro M.; Braga, Fernão C.

    2015-01-01

    Several plant species are traditionally used in Brazil to treat various inflammatory diseases. Tumor necrosis factor- (TNF-) α and chemokine (C-C motif) ligand 2 (CCL2) are key inflammatory mediators in diseases like rheumatoid arthritis and atherosclerosis, respectively; nevertheless, only a few extracts have been assayed against these targets. We herein report the effect of 19 plant extracts on TNF-α and CCL2 release by lipopolysaccharide- (LPS-) stimulated THP-1 cells, a human monocytic leukemia cell line, along with their radical scavenging activity on DPPH. The extracts of Caryocar brasiliense, Casearia sylvestris, Coccoloba cereifera, and Terminalia glabrescens inhibited TNF-α production in a concentration-dependent manner. Fractionation of these extracts potentiated the anti-TNF-α effect, which was shown to concentrate in polar fractions, mainly composed by polyphenols. Significant CCL2 inhibition was elicited by Lippia sidoides and Terminalia glabrescens extracts, whose fractionation resulted in highly active low polar fractions. All assayed extracts showed strong radical scavenging activity, but antioxidant activity did not correlate with inhibition of TNF-α or CCL2 production. Our results allowed identifying extracts with selective capacity to block cytokine production; therefore, further purification of these extracts may yield molecules that could be useful in the treatment of chronic inflammatory diseases. PMID:25878716

  7. Neoproterozoic and Paleozoic accretionary orogens exposed at different crustal levels

    NASA Astrophysics Data System (ADS)

    Kroener, A.

    2002-12-01

    Accretionary orogens in the upper crust are dominated by trench and forearc deposits, obducted ophiolite fragments, exotic terranes and well defined structural boundaries such as major shear zones. The Neoproterozoic Arabian-Nubian shield (ANS) of western Arabia and NE Africa, the huge terrain of the Neoproterozoic to Palaeozoic Central Asian mobile belt (CAMB) and the present Indonesian Archipelago are prime examples of such orogens. In the ANS and CAMB, field relationships, rock associations, differences in structural style and metamorphic grade, and geochronology have led to the recognition of terrane assemblages that are related to processes of lateral accretion as now observed in the southwest Pacific and lasting for several hundred my. In the ANS, ocean crust and arc formation began about 900 Ma ago, and terrane accretion was completed by ~600 Ma, whereas in the CAMB the oldest oceanic crust formed some 1000 Ma ago, and terrane accretion continued into the late Palaeozoic. Typical rock associations are trench and forearc sediments, island-arc volcanics, calc-alkaline granitoids, dismembered ophiolite suites and gneissic rocks (microcontinents?) constituting exotic terranes and mostly of distinctly older age and more complex tectono-metamorphic history than the surrounding lower grade rocks. Shear zones frequently separate the terranes and in the ANS also constitue seismic discontinuities extending to the lower crust. The middle to lower crustal high grade assemblages of the Neoproterozoic Mozambique belt (MB) of East Africa, Madagascar, southernmost India, Sri Lanka and East Antarctica are considered to be a deep crustal analogue to the upper crustal accretionary belts described above. Typical characteristics are (1) voluminous calc-alkaline granitoid suites, now layered gneisses, and interpreted as root zones of arc terranes, (2) tectonic interdigitation of Archaean to Palaeoproterozoic gneisses with Neoproterozoic rocks, probably brought about during

  8. Production of ω-hydroxy palmitic acid using CYP153A35 and comparison of cytochrome P450 electron transfer system in vivo.

    PubMed

    Jung, Eunok; Park, Beom Gi; Ahsan, Md Murshidul; Kim, Joonwon; Yun, Hyungdon; Choi, Kwon-Young; Kim, Byung-Gee

    2016-12-01

    Bacterial cytochrome P450 enzymes in cytochrome P450 (CYP)153 family were recently reported as fatty acid ω-hydroxylase. Among them, CYP153As from Marinobacter aquaeolei VT8 (CYP153A33), Alcanivorax borkumensis SK2 (CYP153A13), and Gordonia alkanivorans (CYP153A35) were selected, and their specific activities and product yields of ω-hydroxy palmitic acid based on whole cell reactions toward palmitic acid were compared. Using CamAB as redox partner, CYP153A35 and CYP153A13 showed the highest product yields of ω-hydroxy palmitic acid in whole cell and in vitro reactions, respectively. Artificial self-sufficient CYP153A35-BMR was constructed by fusing it to the reductase domain of CYP102A1 (i.e., BM3) from Bacillus megaterium, and its catalytic activity was compared with CYP153A35 and CamAB systems. Unexpectedly, the system with CamAB resulted in a 1.5-fold higher yield of ω-hydroxy palmitic acid than that using A35-BMR in whole cell reactions, whereas the electron coupling efficiency of CYP153A35-BM3 reductase was 4-fold higher than that of CYP153A35 and CamAB system. Furthermore, various CamAB expression systems according to gene arrangements of the three proteins and promoter strength in their gene expression were compared in terms of product yields and productivities. Tricistronic expression of the three proteins in the order of putidaredoxin (CamB), CYP153A35, and putidaredoxin reductase (CamA), i.e., A35-AB2, showed the highest product yield from 5 mM palmitic acid for 9 h in batch reaction owing to the concentration of CamB, which is the rate-limiting factor for the activity of CYP153A35. However, in fed-batch reaction, A35-AB1, which expressed the three proteins individually using three T7 promoters, resulted with the highest product yield of 17.0 mM (4.6 g/L) ω-hydroxy palmitic acid from 20 mM (5.1 g/L) palmitic acid for 30 h.

  9. Different proton transfer channels for the transformation of zwitterionic alanine-(H₂O)(n=2-4) to nonzwitterionic alanine-(H₂O)(n=2-4): a density functional theory study.

    PubMed

    Ojha, Animesh K; Bhunia, Snehasis

    2014-03-01

    We report here the various possibilities of proton transfer between the zwitterionic and the non-zwetterionic form of alanine (Ala) via (H₂O)(n=2-4) clusters by calculating the transition state structures of zwitterionic alanine (ZAla)-(H₂O)(n=2-4) and non-zwitterionic alanine (Ala)-(H₂O)(n=2-4) complexes at B3LYP/6-311++G(d,p) and CAM-B3LYP/6-311++G(d,p) level of theory. In order to determine the most feasible channel for proton transfer, the barrier energy corresponding to each channel was calculated. For the transformation of ZAla-(H₂O)(n=2) to Ala-(H₂O)(n=2), we identified eight channels for proton transfer. The lowest barrier energy (2.57 kcal mol⁻¹) channel, where ZAla-(H₂O)(n=2) transforms to Ala-(H₂O)(n=2) via triple proton transfer, is said to be the energetically most feasible channel. The values of barrier energy corresponding to the least energy pathway for proton transfer were calculated to be 1.14 and 9.82 kcal mol⁻¹ for n = 3 and n = 4 complexes, respectively, at B3LYP/6-311++G(d,p) level of theory. For complex n = 3, the structure where proton transfer takes place directly from -NH₃⁺ to -COO⁻ has the lowest energy pathway. However, the complexes for n = 2 and 3--the channels where proton transferred from -NH₃⁺ to -COO⁻ via two water molecules have the lowest barrier energy. For each n, the values of barrier energy calculated at CAM-B3LYP/6-311++G(d,p) level of theory were always less compared those calculated at B3LYP/6-311++G(d,p) level of theory. The value of rate constants corresponding to each proton transfer channel was also calculated.

  10. Prediction of two-photon absorption enhancement in red fluorescent protein chromophores made from non-canonical amino acids.

    PubMed

    Salem, M Alaraby; Twelves, Isaac; Brown, Alex

    2016-09-21

    Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool known for deep tissue penetration and little cellular damage. Being less sensitive than the one-photon microscopy alternatives, a protein with a large two-photon absorption (TPA) cross-section is needed. Here, we use time-dependent density functional theory (TD-DFT) at the B3LYP and CAM-B3LYP/6-31+G(d,p) levels of theory to screen twenty-two possible chromophores that can be formed upon replacing the amino-acid Tyr66 that forms the red fluorescent protein (RFP) chromophore with a non-canonical amino acid. The two-level model for TPA was used to assess the properties (i.e., transition dipole moment, permanent dipole moment difference, and the angle between them) leading to the TPA cross-sections determined via response theory. Computing TPA cross-sections with B3LYP and CAM-B3LYP yields similar overall trends. Results using both functionals agree that the RFP-derived model of the Gold Fluorescent Protein chromophore (Model 20) has the largest intrinsic TPA cross-section at the optimized geometry. TPA was further computed for selected chromophores following conformational changes: variation of both the dihedral angle of the acylimine moiety and the tilt and twist angles between the rings of the chromophore. The TPA cross-section assumed an oscillatory trend with the rotation of the acylimine dihedral, and the TPA is maximized in the planar conformation for almost all models. Model 21 (a hydroxyquinoline derivative) is shown to be comparable to Model 20 in terms of TPA cross-section. The conformational study on Model 21 shows that the acylimine angle has a much stronger effect on the TPA than its tilt and twist angles. Having an intrinsic TPA ability that is more than 7 times that of the native RFP chromophore, Models 20 and 21 appear to be very promising for future experimental investigation.

  11. Second-order nonlinear optical properties of dithienophenazine and TTF derivatives: A butterfly effect of dimalononitrile substitutions.

    PubMed

    Muhammad, Shabbir

    2015-06-01

    Using density functional theory (DFT) methods, the nonlinear optical (NLO) properties have been calculated with strong donor-π-conjugation-acceptor configurations. The static first hyperpolarizability (β0) and dynamic (frequency dependent) electric field induced second harmonic generation (EFISHG) first hyperpolarizability (μβ) are calculated for all designed systems. Our DFT calculations show dithienophenazine merged TTF (2) holds larger β0 amplitudes (β0=21.04×10(3)a.u.) as compared to its corresponding compounds of TTF merged-difurophenazine (1), dicyclopentaphenazine (3) and dipyrrolophenazine (4) derivatives having β0 amplitudes of 16.25×10(3), 12.69×10(3), and 18.38×10(3)a.u., respectively. Furthermore, substitution of dimalononitrile [C(CN)2]2 groups at acceptor end of these compounds results in new derivatives 1a-4a, respectively. Interestingly, a butterfly effect on first hyperpolarizability of all systems 1a-4a has been spotted, which not only results in their robustly larger β0 amplitudes but also changes the increasing order of β0 amplitudes from systems 3<1<4<2 to 1a<2a<3a<4a at both PBE0/6-31G* and CAM-B3LYP/6-31+G* levels of theory. For example, the increase in β0 amplitudes of systems 1a, 2a, 3a and 4a are 3, 3, 5, and 19 times as compared with their corresponding non dimalononitrile derivatives at PBE0/6-31G* level of theory, respectively. Remarkably, unlike the static first hyperpolarizability, the dynamic EFISHG hyperpolarizability (μβω) has the largest value for system 4a with its amplitudes of 1378.59×10(-46) and 1349.40×10(-46)esu, at PBE0/6-31G* and CAM-B3LYP/6-31+G* levels of theory, respectively. TD-DFT calculations have been performed to trace the origin of first hyperpolarizability. It has been found that the lower transition energy and higher oscillator strengths cause robustly large amplitudes especially in systems 3a and 4a, which consequently stems in strong donor-π-conjugation-acceptor configuration of these

  12. Computational studies of the electronic absorption spectrum of [(2,2';6',2″-terpyridine)-Pt(II)-OH] [7,7,8,8-tetracyanoquinodimethane] complex.

    PubMed

    Rabaâ, Hassan; Taubert, Stefan; Sundholm, Dage

    2013-11-27

    The electronic excitation spectrum of the [(2,2';6',2″-terpyridine)-platinum(II)-OH] [7,7,8,8-tetracyanoquinodimethane] ([Pt(trpy)OH]TCNQ) complex has been studied at the linear-response approximate coupled-cluster singles and doubles (CC2) level using triple-ζ basis sets augmented with polarization functions (TZVP). The calculated ultraviolet-visible (UV-vis) spectrum of the [Pt(trpy)OH]TCNQ complex is compared with the UV-vis spectrum measured for [Pt(tbtrpy)OH]TCNQ (tbtrpy = 4,4',4″-(t)Bu3-2,2';6',2″-terpyridine) in dichloromethane (CH2Cl2) solution. The UV-vis spectrum is also compared with the calculated UV-vis spectra of [Pt(trpy)OH](+) and of the neutral and negatively charged TCNQ species. In contrast to previous interpretations, the CC2 calculations suggest that the [Pt(trpy)OH]TCNQ complex is dissociated into [Pt(trpy)OH](+) and TCNQ(-) when dissolved in CH2Cl2. The computed electronic excitation energies of [Pt(trpy)OH](+) provide information about the charge-transfer excitations between the Pt(II) metal center and the ligands. The UV-vis spectra were also calculated at the linear-response time-dependent density functional theory (TDDFT) level using the B3LYP, BHLYP, and CAM-B3LYP functionals in combination with TZVP quality basis sets. For the TCNQ species, the TDDFT calculations yield slightly smaller excitation energies than obtained at the CC2 level, whereas for [Pt(trpy)OH](+) the CC2 excitation energies are slightly smaller than the TDDFT ones. For the [Pt(trpy)OH]TCNQ complex, the B3LYP calculations yield spurious low-lying excited states rendering the spectral assignment using B3LYP data difficult. The low-energy part of the electronic excitation spectrum for the [Pt(trpy)OH]TCNQ complex calculated at the BHLYP and CAM-B3LYP levels is reminiscent of the CC2 one because the larger amount of Hartree-Fock exchange and the long-range correction of the potential blue shifts the excitation energies.

  13. Computational Investigation on the Spectroscopic Properties of Thiophene Based Europium β-Diketonate Complexes.

    PubMed

    Greco, Claudio; Moro, Giorgio; Bertini, Luca; Biczysko, Malgorzata; Barone, Vincenzo; Cosentino, Ugo

    2014-02-11

    The adiabatic transition energies from the lowest triplet states of four Europium tris β-diketonate/phenantroline complexes have been determined in vacuo and in dicholomethane solution by the ΔSCF approach at the density functional theory level, using the PBE1PBE and the CAM-B3LYP hybrid functionals. The calculated adiabatic transition energies have been compared with the experimental 0-0 transitions of each complex determined from phosphorescence spectra of the corresponding Gd(3+) complexes and followed by direct comparison between simulated and experimental spectra line shapes. For compound 1, the Eu(TTA)3Phen system, triplet states other than the lowest one and conformational isomers other than the one present in the crystallographic structure have been considered. In the crystallographic structure, this compound presents three quasi-degenerate low energy triplet states, differing for the TTA ligand where the two unpaired electrons are localized and showing close adiabatic transition energies. For compound 1, the lowest triplet states of the four investigated conformational isomers show similar characteristics and close adiabatic transition energies. On the basis of these results, an investigation of compounds 2-4 (Eu(Br-TTA)3Phen, Eu(DTDK)3Phen, and Eu(MeT-TTA)3) has been performed by considering only the isomer present in the crystallographic structure and only the lowest triplet state of each compound. For compounds 1-3, the energies of the lowest triplet states calculated by both functionals in solution including zero-point energy corrections well reproduce the experimental trends as well as the values of the adiabatic transition energies: CAM-B3LYP, the best performing functional, provides energies of the lowest triplet state with deviations from experiments lower than 1200 cm(-1). Also, the calculated vibrationally resolved phosphorescence spectra and UV-vis absorptions well reproduce the main features of their experimental counterparts. Significant

  14. Simulating One-Photon Absorption and Resonance Raman Scattering Spectra Using Analytical Excited State Energy Gradients within Time-Dependent Density Functional Theory

    SciTech Connect

    Silverstein, Daniel W.; Govind, Niranjan; van Dam, Hubertus J. J.; Jensen, Lasse

    2013-12-10

    A parallel implementation of analytical time-dependent density functional theory gradients is presented for the quantum chemistry program NWChem. The implementation is based on the Lagrangian approach developed by Furche and Ahlrichs. To validate our implementation, we first calculate the Stokes shifts for a range of organic dye molecules using a diverse set of exchange-correlation functionals (traditional density functionals, global hybrids, and range-separated hybrids) followed by simulations of the one-photon absorption and resonance Raman scattering spectrum of the phenoxyl radical, the well-studied dye molecule rhodamine 6G, and a molecular host–guest complex (TTFcCBPQT4+). The study of organic dye molecules illustrates that B3LYP and CAM-B3LYP generally give the best agreement with experimentally determined Stokes shifts unless the excited state is a charge transfer state. Absorption, resonance Raman, and fluorescence simulations for the phenoxyl radical indicate that explicit solvation may be required for accurate characterization. For the host–guest complex and rhodamine 6G, it is demonstrated that absorption spectra can be simulated in good agreement with experimental data for most exchange-correlation functionals. Finally, however, because one-photon absorption spectra generally lack well-resolved vibrational features, resonance Raman simulations are necessary to evaluate the accuracy of the exchange-correlation functional for describing a potential energy surface.

  15. Computational Studies on Optoelectronic and Nonlinear Properties of Octaphyrin Derivatives

    PubMed Central

    Islam, Nasarul; Lone, Irfan H.

    2017-01-01

    The electronic and nonlinear optical (NLO) properties of octaphyrin derivatives were studied by employing the DFT/TDFT at CAM-B3LYP/6-311++G (2d, 2p) level of the theory. Thiophene, phenyl, methyl and cyano moieties were substituted on the molecular framework of octaphyrin core, in order to observe the change in optoelectronic and nonlinear response of these systems. The frontier molecular orbital studies and values of electron affinity reveals that the studied compounds are stable against the oxygen and moisture present in air. The calculated ionization energies, adiabatic electron affinity and reorganization energy values indicate that octaphyrin derivatives can be employed as effective n-type material for Organic Light Emitting Diodes (OLEDs). This character shows an enhancement with the introduction of an electron withdrawing group in the octaphyrin framework. The polarizability and hyperpolarizability values of octaphyrin derivatives demonstrate that they are good candidates for NLO devices. The nonlinear response of these systems shows enhancement on the introduction of electron donating groups on octaphyrin moiety. However, these claims needs further experimental verification. PMID:28321394

  16. Harmonic Vibrational Frequencies: Approximate Global Scaling Factors for TPSS, M06, and M11 Functional Families Using Several Common Basis Sets.

    PubMed

    Kashinski, D O; Chase, G M; Nelson, R G; Di Nallo, O E; Scales, A N; VanderLey, D L; Byrd, E F C

    2017-03-23

    We propose new approximate global multiplicative scaling factors for the DFT calculation of ground state harmonic vibrational frequencies using functionals from the TPSS, M06, and M11 functional families with standard correlation consistent cc-pVxZ and aug-cc-pVxZ (x = D, T, and Q), 6-311G split valence family, Sadlej and Sapporo polarized triple-ζ basis sets. Results for B3LYP, CAM-B3LYP, B3PW91, PBE, and PBE0 functionals with these basis sets are also reported. A total of 99 harmonic frequencies were calculated for 26 gas-phase organic and nonorganic molecules typically found in detonated solid propellant residue. Our proposed approximate multiplicative scaling factors are determined using a least-squares approach comparing the computed harmonic frequencies to experimental counterparts well established in the scientific literature. A comparison of our work to previously published global scaling factors is made to verify method reliability and the applicability of our molecular test set.

  17. Mocking the weak lensing universe: The LensTools Python computing package

    NASA Astrophysics Data System (ADS)

    Petri, A.

    2016-10-01

    We present a newly developed software package which implements a wide range of routines frequently used in Weak Gravitational Lensing (WL). With the continuously increasing size of the WL scientific community we feel that easy to use Application Program Interfaces (APIs) for common calculations are a necessity to ensure efficiency and coordination across different working groups. Coupled with existing open source codes, such as CAMB (Lewis et al., 2000) and Gadget2 (Springel, 2005), LensTools brings together a cosmic shear simulation pipeline which, complemented with a variety of WL feature measurement tools and parameter sampling routines, provides easy access to the numerics for theoretical studies of WL as well as for experiment forecasts. Being implemented in PYTHON (Rossum, 1995), LensTools takes full advantage of a range of state-of-the art techniques developed by the large and growing open-source software community (Jones et al., 2001; McKinney, 2010; Astrophy Collaboration, 2013; Pedregosa et al., 2011; Foreman-Mackey et al., 2013). We made the LensTools code available on the Python Package Index and published its documentation on http://lenstools.readthedocs.io.

  18. Time variation of the fine structure constant in the early universe and the Bekenstein model

    NASA Astrophysics Data System (ADS)

    Mosquera, M. E.; Scóccola, C. G.; Landau, S. J.; Vucetich, H.

    2008-02-01

    Aims:We calculate the bounds on the variation in the fine structure constant at the time of primordial nucleosynthesis and at the time of neutral hydrogen formation. We used these bounds and other bounds from the late universe to test the Bekenstein model. Methods: We modified the Kawano code, CAMB, and CosmoMC to include the possible variation in the fine structure constant. We used observational primordial abundances of D, ^4He, and ^7Li, recent data from the cosmic microwave background, and the 2dFGRS power spectrum, to obtain bounds on the variation in α. We calculated a piecewise solution to the scalar field equation of the Bekenstein model in two different regimes: i) matter and radiation, ii) matter and cosmological constant. We match both solutions with the appropriate boundary conditions. We performed a statistical analysis, using the bounds obtained from the early universe and other bounds from the late universe to constrain the free parameters of the model. Results: Results are consistent with no variation in α for the early universe. Limits on α are inconsistent with the scale length of the theory l being larger than the Planck scale. Conclusions: In order to fit all observational and experimental data, the assumption l > Lp implied in Bekenstein's model has to be relaxed.

  19. Constraints on variation in α and me from WMAP 7-year data

    NASA Astrophysics Data System (ADS)

    Landau, S. J.; Scóccola, G.

    2010-07-01

    Aims: We update the constraints on the time variation of the fine structure constant α and the electron mass me, using the latest CMB data, including the 7-yr release of WMAP. Methods: We made statistical analyses of the variation of each one of the constants and of their joint variation, together with the basic set of cosmological parameters. We used a modified version of CAMB and COSMOMC to account for these possible variations. Results: We present bounds on the variation of the constants for different data sets, and show how results depend on them. When using the latest CMB data plus the power spectrum from Sloan Digital Sky Survey LRG, we find that α/α_0 = 0.986 ± 0.007 at 1-σ level, when the 6 basic cosmological parameters were fitted, and only variation in α was allowed. The constraints in the case of variation of both constants are α/α_0 = 0.986 ± 0.009 and me/me0 = 0.999 ± 0.035. In the case of only variation in me, the bound is m e/me0 = 0.964 ± 0.025.

  20. Homogeneous catalysis on the gas-phase dehydration reaction of tertiary alcohols by hydrogen bromide. Density functional theory calculation

    NASA Astrophysics Data System (ADS)

    Maldonado, Alexis; Rosas, Felix; Mora, Jose R.; Brusco, Yannely; Córdova-Sintjago, Tania C.; Chuchani, Gabriel

    2015-02-01

    The gas-phase thermal dehydration mechanism of tert-butanol, 2-methyl-2-butanol, 2-methyl-2-pentanol and 2,3-dimethyl-2-butanol by homogeneous catalysis of hydrogen bromide was examined by density functional theory calculations with the hybrid functionals: M062X, CAMB3LYP and WB97XD. Reasonable agreements were found between theoretical and experimental enthalpy values at the WB97XD/6-311++G(d,p) level. The dehydration mechanism of tert-butanol with and without catalysis was evaluated in order to examine the catalyst effect on the mechanism. The elimination reaction without catalysis involves a four-membered transition state (TS), while the reaction with catalysis involves a six-membered TS. The mechanism without catalysis has enthalpy activation over 150 kJ mol-1 greater than the catalysed reaction. In all these reactions, the elongation of the C-O bond is significant in the TS. The un-catalysed reaction is controlled by breaking of C-O bond, and it was found to be more synchronous (Sy ≈ 0.91) than the hydrogen bromide catalysed reactions (Sy ≈ 0.75-0.78); the latter reactions are dominated by the three reaction coordinates associated with water formation. No significant effect on the enthalpies of activation was observed when the size of the alkyl chain was increased.

  1. First principles calculations of a H2 molecule inside boron-nitrogen nanotubes

    NASA Astrophysics Data System (ADS)

    Belmiloud, Yamina; Djitli, Wassila; Abdeldjebar, Hasnia; Abdelatif, Mohamed Lamine; Tangour, Bahoueddine; Brahimi, Meziane

    2017-01-01

    DFT/B3LYP and CAM-B3LYP/6-311G(d,p) calculations have been performed to study a H2 molecule inside boron-nitrogen nanotubes (BNNT) (2,2), (3,3), (4,4) and (5,5). H2 is introduced perpendicular and parallel to the axis of nanotubes. The main difference relatively to CNTs is the disappearance of the Hsbnd H bond activation zone in the BNNTs because of the absence of interactions between the π electrons and hydrogen. The most important phenomenon is the shortening of the Hsbnd H bond by the interaction of the hydrogen with the repulsive zone of the van der Waals potential of the BNNT walls. This led to the appearance of a dipole moment in the inclusion complex H2@BNNT. The most important consequence of the existence of this dipole moment is that the IR activation of the Hsbnd H vibration becomes intense. This vibration frequency may be used for detecting or assaying the H2 contained in the nanotubes or to deduce BNNT's diameter. In this work we have examined also the consequence of the BNNT flattening on bandgap, our results show that flattening causes the reduction of a BNNT bandgap.

  2. A Theoretical Study of Ene Reactions in Solution: A Solution-Phase Translational Entropy Model.

    PubMed

    Zhao, Liu; Li, Shi-Jun; Fang, De-Cai

    2015-12-01

    Several density functional theory (DFT) methods, such as CAM-B3LYP, M06, ωB97x, and ωB97xD, are used to characterize a range of ene reactions. The Gibbs free energy, activation enthalpy, and entropy are calculated with both the gas- and solution-phase translational entropy; the results obtained from the solution-phase translational entropies are quite close to the experimental measurements, whereas the gas-phase translational entropies do not perform well. For ene reactions between the enophile propanedioic acid (2-oxo-1,3-dimethyl ester) and π donors, the two-solvent-involved explicit+implicit model can be employed to obtain accurate activation entropies and free-energy barriers, because the interaction between the carbonyl oxygen atom and the solvent in the transition state is strengthened with the formation of C-C and O-H bonds. In contrast, an implicit solvent model is adequate to calculate activation entropies and free-energy barriers for the corresponding reactions of the enophile 4-phenyl-1,2,4-triazoline-3,5-dione.

  3. Experimental, DFT and molecular docking studies on 2-(2-mercaptophenylimino)-4-methyl-2H-chromen-7-ol

    NASA Astrophysics Data System (ADS)

    Singh, Ashok Kumar; Singh, Ravindra Kumar

    2016-10-01

    A new coumarin derivative 2-(2-mercaptophenylimino)-4-methyl-2H-chromen-7-ol (COMSB) was synthesized and characterized with the help of 1H,13C NMR, FT-IR, FT-Raman and mass spectrometry. All quantum calculations were performed at DFT level of theory using B3LYP functional and 6-31G (d,p) as basis set. The UV-Vis spectrum studied by TD-DFT theory, with a hybrid exchange-correlation functional using Coulomb-attenuating method (CAM-B3LYP) in solvent phase gives similar pattern of bands, at energies and is consistent with that of experimental findings. The detailed analysis of vibrational (IR and Raman) spectra and their assignments has been done by computing Potential Energy Distribution (PED) using Gar2ped. Intra-molecular interactions were analyzed by 'Atoms in molecule' (AIM) approach. Computed first static hyperpolarizability (β0 = 8.583 × 10-30 esu) indicates non-linear optical (NLO) response of the molecule. Molecular docking studies show that the title molecule may act as potential acetylcholine esterase (AChE) inhibitor.

  4. Modeling the Galaxy-Halo Connection: An open-source approach with Halotools

    NASA Astrophysics Data System (ADS)

    Hearin, Andrew

    2016-03-01

    Although the modern form of galaxy-halo modeling has been in place for over ten years, there exists no common code base for carrying out large-scale structure calculations. Considering, for example, the advances in CMB science made possible by Boltzmann-solvers such as CMBFast, CAMB and CLASS, there are clear precedents for how theorists working in a well-defined subfield can mutually benefit from such a code base. Motivated by these and other examples, I present Halotools: an open-source, object-oriented python package for building and testing models of the galaxy-halo connection. Halotools is community-driven, and already includes contributions from over a dozen scientists spread across numerous universities. Designed with high-speed performance in mind, the package generates mock observations of synthetic galaxy populations with sufficient speed to conduct expansive MCMC likelihood analyses over a diverse and highly customizable set of models. The package includes an automated test suite and extensive web-hosted documentation and tutorials (halotools.readthedocs.org). I conclude the talk by describing how Halotools can be used to analyze existing datasets to obtain robust and novel constraints on galaxy evolution models, and by outlining the Halotools program to prepare the field of cosmology for the arrival of Stage IV dark energy experiments.

  5. Investigation of intermolecular interactions between single walled nanotubes and conjugated oligomers using the dispersion-corrected DFT methods

    NASA Astrophysics Data System (ADS)

    Lagowski, Jolanta B.; Aljohani, Suad; Khan, M. Zahidul H.; Zhao, Yuming

    The area of carbon nanotubes (CNT)-polymer composites has been progressing rapidly in recent years. Pure CNT and CNT-polymer composites have many useful (industry related) properties: ranging from electronic electrical conductivity to superior strength. However the full potential of using CNTs as reinforcements (in say a polymer matrix) has been severely limited because of complications associated with the dispersion of CNTs. CNTs tend to entangle with each other forming materials that have properties that fall short of the expectations. The goal of this work is to identify the type of conjugated oligomers that are best suited for the dispersion of single walled CNT (SWCNT). For this purpose, various methods of dispersion corrected density functional theory (DFT-D/B97D, /WB97XD, /CAM-B3LYP) have been used to investigate the interaction between the SWCNT and the organic conjugated oligomers with different end groups (aldehyde (ALD) and dithiafulvenyl (DTF)). We investigate the effect of intermolecular interactions on the structure, polarity and energetics of the oligomers and SWCNT combinations. The comparison of results obtained using different DFT approximations is made. Our results show that DFT-endcapped oligomer interact more strongly with CNT than ALD-endcapped oligomer. The financial support from NSERC, SACBC and Memorial University and the computational resources from Compute Canada were received.

  6. Synthesis, electronic structure and spectral fluorescent properties of vinylogous merocyanines derived from 1,3-dialkyl-benzimidazole and malononitrile

    NASA Astrophysics Data System (ADS)

    Kulinich, Andrii V.; Mikitenko, Elena K.; Ishchenko, Alexander A.

    2017-01-01

    A vinylogous series of merocyanines were synthesized with 1,3-dibutyl-benzimidazole and malononitrile residues as the donor and acceptor terminal groups. These dyes do not comprise carbonyl groups, which are prone to the strong specific solvation by polar solvents up to hydrogen bond formation, and nevertheless they possess distinct reversed solvatochromism, i.e. their molecules have very high dipolarity. At that, they are soluble in a wide range of solvents from n-hexane to ethanol and do not aggregate readily. They were studied thoroughly by UV/Vis, fluorescence, IR, and NMR spectroscopy methods. Their structure and spectral properties in the ground and excited fluorescent states were modelled at the DFT level both in vacuum and in solvents of various polarities by using the PCM solvent field simulation. The calculations were performed using several hybrid functionals (B3LYP, CAM-B3LYP, and wB97XD) and the split-valence 6-31G (d,p) basis set.

  7. Computing UV/vis spectra using a combined molecular dynamics and quantum chemistry approach: bis-triazin-pyridine (BTP) ligands studied in solution.

    PubMed

    Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J

    2016-03-21

    We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution.

  8. Simulated evolution of fluorophores for light emitting diodes

    SciTech Connect

    Shu, Yinan; Levine, Benjamin G.

    2015-03-14

    Organic light emitting diodes based on fluorophores with a propensity for thermally activated delayed fluorescence (TADF) are able to circumvent limitations imposed on device efficiency by spin statistics. Molecules with a propensity for TADF necessarily have two properties: a small gap between the lowest lying singlet and triplet excited states and a large transition dipole moment for fluorescence. In this work, we demonstrate the use of a genetic algorithm to search a region of chemical space for molecules with these properties. This algorithm is based on a flexible and intuitive representation of the molecule as a tree data structure, in which the nodes correspond to molecular fragments. Our implementation takes advantage of hybrid parallel graphics processing unit accelerated computer clusters to allow efficient sampling while retaining a reasonably accurate description of the electronic structure (in this case, CAM-B3LYP/6-31G{sup ∗∗}). In total, we have identified 3792 promising candidate fluorophores from a chemical space containing 1.26 × 10{sup 6} molecules. This required performing electronic structure calculations on only 7518 molecules, a small fraction of the full space. Several novel classes of molecules which show promise as fluorophores are presented.

  9. Synthesis, X-ray, NMR, FT-IR, UV/vis, DFT and TD-DFT studies of N-(4-chlorobutanoyl)-N'-(2-, 3- and 4-methylphenyl)thiourea derivatives.

    PubMed

    Abosadiya, Hamza M; Anouar, El Hassane; Hasbullah, Siti Aishah; Yamin, Bohari M

    2015-06-05

    A new isomers of thiourea derivatives, namely N-(4-chlorobutanoyl)-N'-(2-methylphenyl)-thiourea (1a), N-(4-chlorobutanoyl)-N'-(3-methylphenyl)thiourea (1b) and N-(4-chlorobutanoyl)-N'-(4-methylphenyl)thiourea (1c) have been synthesized by refluxing mixture of equimolar amounts of 4-chlorobutanoylisothiocyanate with 2, 3 or 4-toluidine, respectively. The three isomers were characterized by spectroscopic (UV/vis, FT-IR and NMR) and X-ray crystallography techniques. To investigate the isomerization effect on spectroscopic data, DFT and TD-DFT calculations have been carried out using five hybrid functionals (B3LYP, B3P86, CAM-B3LYP, M06-2X and PBE0) to predict UV/vis absorption bands (n→π∗ and π→π∗), (1)H and (13)C NMR chemical shifts, FT-IR vibration modes and X-ray parameters (bonds, bond angles and torsion angles) for 1a, 1b and 1c isomers. The results showed that the isomerization effect is significant on λ(MAX) absorption bands, while for IR and NMR the effect is negligible. In accordance with previous studies, B3LYP, B3P86 and PBE0 gave the most reliable to predict the excitation energies of thiourea derivatives.

  10. Benchmarking DFT and semi-empirical methods for a reliable and cost-efficient computational screening of benzofulvene derivatives as donor materials for small-molecule organic solar cells

    NASA Astrophysics Data System (ADS)

    Tortorella, Sara; Mastropasqua Talamo, Maurizio; Cardone, Antonio; Pastore, Mariachiara; De Angelis, Filippo

    2016-02-01

    A systematic computational investigation on the optical properties of a group of novel benzofulvene derivatives (Martinelli 2014 Org. Lett. 16 3424-7), proposed as possible donor materials in small molecule organic photovoltaic (smOPV) devices, is presented. A benchmark evaluation against experimental results on the accuracy of different exchange and correlation functionals and semi-empirical methods in predicting both reliable ground state equilibrium geometries and electronic absorption spectra is carried out. The benchmark of the geometry optimization level indicated that the best agreement with x-ray data is achieved by using the B3LYP functional. Concerning the optical gap prediction, we found that, among the employed functionals, MPW1K provides the most accurate excitation energies over the entire set of benzofulvenes. Similarly reliable results were also obtained for range-separated hybrid functionals (CAM-B3LYP and wB97XD) and for global hybrid methods incorporating a large amount of non-local exchange (M06-2X and M06-HF). Density functional theory (DFT) hybrids with a moderate (about 20-30%) extent of Hartree-Fock exchange (HFexc) (PBE0, B3LYP and M06) were also found to deliver HOMO-LUMO energy gaps which compare well with the experimental absorption maxima, thus representing a valuable alternative for a prompt and predictive estimation of the optical gap. The possibility of using completely semi-empirical approaches (AM1/ZINDO) is also discussed.

  11. Molecular structure, vibrational spectra, NLO and MEP analysis of bis[2-hydroxy-кO-N-(2-pyridyl)-1-naphthaldiminato-кN]zinc(II)

    NASA Astrophysics Data System (ADS)

    Tanak, Hasan; Toy, Mehmet

    2013-11-01

    The molecular geometry and vibrational frequencies of bis[2-hydroxy-кO-N-(2-pyridyl)-1-naphthaldiminato-кN]zinc(II) in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-311G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The energetic and atomic charge behavior of the title compound in solvent media has been examined by applying the Onsager and the polarizable continuum model. To investigate second order nonlinear optical properties of the title compound, the electric dipole (μ), linear polarizability (α) and first-order hyperpolarizability (β) were computed using the density functional B3LYP and CAM-B3LYP methods with the 6-31+G(d) basis set. According to our calculations, the title compound exhibits nonzero (β) value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential (MEP), frontier molecular orbitals, and thermodynamic properties were performed at B3LYP/6-311G(d,p) level of theory.

  12. Benzylammonium Thermometer Ions: Internal Energies of Ions Formed by Low Temperature Plasma and Atmospheric Pressure Chemical Ionization.

    PubMed

    Stephens, Edward R; Dumlao, Morphy; Xiao, Dan; Zhang, Daming; Donald, William A

    2015-12-01

    The extent of internal energy deposition upon ion formation by low temperature plasma and atmospheric pressure chemical ionization was investigated using novel benzylammonium thermometer ions. C-N heterolytic bond dissociation enthalpies of nine 4-substituted benzylammoniums were calculated using CAM-B3LYP/6-311++G(d,p), which was significantly more accurate than B3LYP/6-311++G(d,p), MP2/6-311++G(d,p), and CBS-QB3 for calculating the enthalpies of 20 heterolytic dissociation reactions that were used to benchmark theory. All 4-substituted benzylammonium thermometer ions fragmented by a single pathway with comparable dissociation entropies, except 4-nitrobenzylammonium. Overall, the extent of energy deposition into ions formed by low temperature plasma was significantly lower than those formed by atmospheric pressure chemical ionization under these conditions. Because benzylamines are volatile, this new suite of thermometer ions should be useful for investigating the extent of internal energy deposition during ion formation for a wide range of ionization methods, including plasma, spray and laser desorption-based techniques. Graphical Abstract ᅟ.

  13. Hydrogen atom addition to the surface of graphene nanoflakes: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto

    2017-02-01

    Polycyclic aromatic hydrocarbons (PAHs) provide a 2-dimensional (2D) reaction surface in 3-dimensional (3D) interstellar space and have been utilized as a model of graphene surfaces. In the present study, the reaction of PAHs with atomic hydrogen was investigated by means of density functional theory (DFT) to systematically elucidate the binding nature of atomic hydrogen to graphene nanoflakes. PAHs with n = 4-37 were chosen, where n indicates the number of benzene rings. Activation energies of hydrogen addition to the graphene surface were calculated to be 5.2-7.0 kcal/mol at the CAM-B3LYP/6-311G(d,p) level, which is almost constant for all PAHs. The binding energies of hydrogen atom were slightly dependent on the size (n): 14.8-28.5 kcal/mol. The absorption spectra showed that a long tail is generated at the low-energy region after hydrogen addition to the graphene surface. The electronic states of hydrogenated graphenes were discussed on the basis of theoretical results.

  14. Improvement of photovoltaic performance by substituent effect of donor and acceptor structure of TPA-based dye-sensitized solar cells.

    PubMed

    Inostroza, Natalia; Mendizabal, Fernando; Arratia-Pérez, Ramiro; Orellana, Carlos; Linares-Flores, Cristian

    2016-01-01

    We report a computational study of a series of organic dyes built with triphenylamine (TPA) as an electron donor group. We designed a set of six dyes called (TPA-n, where n = 0-5). In order to enhance the electron-injection process, the electron-donor effect of some specific substituent was studied. Thus, we gave insights into the rational design of organic TPA-based chromophores for use in dye-sensitized solar cells (DSSCs). In addition, we report the HOMO, LUMO, the calculated excited state oxidized potential E(dye*)(eV) and the free energy change for electron-injection ΔGinject(eV), and the UV-visible absorption bands for TPA-n dyes by a time-dependent density functional theory (TDDFT) procedure at the B3LYP and CAM-B3LYP levels with solvent effect. The results demonstrate that the introduction of the electron-acceptor groups produces an intramolecular charge transfer showing a shift of the absorption wavelengths of TPA-n under studies. Graphical Abstract Several organic dyes TPA-n with different donors and acceptors are modeled. A strong conjugation acrros the donor and anchoring groips (TPA-n) bas been studied. Candidate TPA-3 shows a promising results.

  15. Importance of Solvation in Understanding the Chiroptical Spectra of Natural Products in Solution Phase: Garcinia Acid Dimethyl Ester

    PubMed Central

    Polavarapu, Prasad L.; Scalmani, Giovanni; Hawkins, Edward K.; Rizzo, Carmelo; Jeirath, Neha; Ibnusaud, Ibrahim; Habel, Deenamma; Nair, Divya Sadasivan; Haleema, Simimole

    2013-01-01

    The optical rotatory dispersion (ORD), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD) spectra of (+)-garcinia acid dimethyl ester have been measured and analyzed by comparison with the corresponding spectra predicted by quantum chemical methods for (2S,3S)-garcinia acid dimethyl ester. For solution-phase calculations the recently developed continuous surface charge polarizable continuum model (PCM) has been used. It is found that gas-phase predictions and PCM predictions at the B3LYP/aug-cc-pVDZ level yield nearly mirror-image ECD spectra in the 190–250 nm region for the same absolute configuration and that gas-phase ECD predictions lead to incorrect absolute configuration. At the CAM-B3LYP/aug-cc-pVDZ level, however, gas-phase predictions and PCM predictions of ECD in the 190–250 nm region are not so different, but PCM predictions provide better agreement with the experimental observations. For carbonyl stretching vibrations, the vibrational band positions predicted at the B3LYP/aug-cc-pVDZ level in gas-phase calculations differ significantly from the corresponding experimentally observed band positions, and this discrepancy has also been corrected by the use of PCM. In addition, the solution-phase VCD predictions provided better agreement (with experimental VCD observations) than gas-phase VCD predictions. These observations underscore the importance of including solvent effects in quantum chemical calculations of chiroptical spectroscopic properties. PMID:21114277

  16. Exchange interaction between the triplet exciton and the localized spin in copper-phthalocyanine

    SciTech Connect

    Wu, Wei

    2014-06-14

    Triplet excitonic state in the organic molecule may arise from a singlet excitation and the following inter-system crossing. Especially for a spin-bearing molecule, an exchange interaction between the triplet exciton and the original spin on the molecule can be expected. In this paper, such exchange interaction in copper-phthalocyanine (CuPc, spin-1/2 ) was investigated from first-principles by using density-functional theory within a variety of approximations to the exchange correlation, ranging from local-density approximation to long-range corrected hybrid-exchange functional. The magnitude of the computed exchange interaction is in the order of meV with the minimum value (1.5 meV, ferromagnetic) given by the long-range corrected hybrid-exchange functional CAM-B3LYP. This exchange interaction can therefore give rise to a spin coherence with an oscillation period in the order of picoseconds, which is much shorter than the triplet lifetime in CuPc (typically tens of nanoseconds). This implies that it might be possible to manipulate the localized spin on Cu experimentally using optical excitation and inter-system crossing well before the triplet state disappears.

  17. Regioselective ω-hydroxylation of medium-chain n-alkanes and primary alcohols by CYP153 enzymes from Mycobacterium marinum and Polaromonas sp. strain JS666.

    PubMed

    Scheps, Daniel; Malca, Sumire Honda; Hoffmann, Helen; Nestl, Bettina M; Hauer, Bernhard

    2011-10-07

    The oxofunctionalization of saturated hydrocarbons is an important goal in basic and applied chemistry. Biocatalysts like cytochrome P450 enzymes can introduce oxygen into a wide variety of molecules in a very selective manner, which can be used for the synthesis of fine and bulk chemicals. Cytochrome P450 enzymes from the CYP153A subfamily have been described as alkane hydroxylases with high terminal regioselectivity. Here we report the product yields resulting from C(5)-C(12) alkane and alcohol oxidation catalyzed by CYP153A enzymes from Mycobacterium marinum (CYP153A16) and Polaromonas sp. (CYP153A P. sp.). For all reactions, byproduct formation is described in detail. Following cloning and expression in Escherichia coli, the activity of the purified monooxygenases was reconstituted with putidaredoxin (CamA) and putidaredoxin reductase (CamB). Although both enzyme systems yielded primary alcohols and α,ω-alkanediols, each one displayed a different oxidation pattern towards alkanes. For CYP153A P. sp. a predominant ω-hydroxylation activity was observed, while CYP153A16 possessed the ability to catalyze both ω-hydroxylation and α,ω-dihydroxylation reactions.

  18. On the potential application of DFT methods in predicting the interaction-induced electric properties of molecular complexes. Molecular H-bonded chains as a case of study.

    PubMed

    Zawada, Agnieszka; Kaczmarek-Kędziera, Anna; Bartkowiak, Wojciech

    2012-07-01

    A detailed analysis of the selected DFT functionals for the calculations of interaction-induced dipole moment, polarizability and first-order hyperpolarizability has been carried out. The hydrogen-bonded model chains consisting of HF, H(2)CO and H(3)N molecules have been chosen as a case study. The calculations of the components of the static electric properties using the diffuse Dunning's basis set (aug-cc-pVDZ) have been performed employing different types of density functionals (B3LYP, LC-BLYP, PBE0, M06-2X and CAM-B3LYP). Obtained results have been compared with those gained at the CCSD(T) level of theory. The counterpoise correction scheme, namely site-site function counterpoise, has been applied in order to eliminate basis set superposition error. The performed tests allow to conclude that the DFT functionals can provide a useful tool for prediction of the interaction-induced electric properties, however a caution has to be urged to their decomposition to the two- and many-body terms.

  19. Population structure of the Brazilian southern green stink bug, Nezara viridula

    PubMed Central

    Sosa-Gómez, Daniel R.; da Silva, José Jairo; Costa, Fernando; Binneck, Eliseu; Marin, Silvana R. R.; Nepomuceno, Alexandre L.

    2005-01-01

    The Southern Green Stink Bug, Nezara viridula (L.) (Heteroptera: Pentatomidae), is a cosmopolitan and economically important pest to several crops. Studies on N. viridula migration and population structure have been neglected. We studied geographically distinct Brazilian N. viridula populations to assess their variability and to determine gene flow among them. DNA from specimens collected on soybean fields were subjected to RAPD analysis to determine genetic similarity and population structure parameters. All N. viridula populations studied were genetically distinct from the others. The maximum similarity occurred between populations from Londrina and Sertanópolis (Parana State). The Cruz Alta population was the most divergent from the others. Despite the short distance between Cambé and Londrina (ca. 29 km), and the absence of geographic barriers, both populations clustered in different groups and the estimated gene flow index (Nm) among them was 2.02, indicating relatively restricted migration. The estimated overall index, Nm was 1.41 suggesting that N. viridula is a better flier than the Neotropical Brown stink bug, Euschistus heros (Nm =0.83). PMID:17119605

  20. Synthesis, spectral analysis and quantum chemical studies on molecular geometry of (2E,6E)-2,6-bis(2-chlorobenzylidene)cyclohexanone: Experimental and theoretical approaches

    NASA Astrophysics Data System (ADS)

    Verma, Anil Kumar; Bishnoi, Abha; Fatma, Shaheen

    2016-07-01

    (2E,6E)-2,6-bis(2-chlorobenzylidene) cyclohexanone was synthesized and characterized by proton and carbon nuclear magnetic resonance, infrared, ultraviolet-visible, mass spectral analysis and X-ray crystallography techniques. Quantum Chemical calculations were done using Becke3-Lee-Yang-Parr with 6-31, 6-311, 6-311 + and 6-311++G (d, p) as basis sets and CAM-B3LYP with 6-31G(d,p) as the basis set. A good correlation between calculated and experimental spectroscopic data has been accomplished. Ultraviolet-Visible spectrum of the molecule was recorded in the region 200-500 nm and the electronic properties and composition were obtained using Time Dependent Density Functional Theory method. X-ray parameters (bonds, bond angles and torsion angles), Electric dipole moment, Mulliken atomic charges, polarizability and first static hyperpolarizability values have been calculated. Hyperconjugative interactions were studied with the help of natural bond orbital analysis. The thermodynamic properties of the compound were calculated at different temperatures.

  1. [Development of indicators for evaluating public dental healthcare services].

    PubMed

    Bueno, Vera Lucia Ribeiro de Carvalho; Cordoni Júnior, Luiz; Mesas, Arthur Eumann

    2011-07-01

    The objective of this article is to describe and analyze the development of indicators used to identify strengths and deficiencies in public dental healthcare services in the municipality of Cambé, Paraná. The methodology employed was a historical-organizational case study. A theoretical model of the service was developed for evaluation planning. To achieve this, information was collected from triangulation of methods (interviews, document analysis and observation). A matrix was then developed which presents analysis dimensions, criteria, indicators, punctuation, parameters and sources of information. Three workshops were staged during the process with local service professionals in order to verify whether both the logical model and the matrix represented the service adequately. The period for collecting data was from November 2006 through July, 2007. As a result, a flowchart of the organization of the public dental health service and a matrix with two-dimensional analysis, twelve criteria and twenty-four indicators, was developed. The development of indicators favoring the participation of people involved with the practice has enabled more comprehensive and realistic evaluation planning.

  2. TD-DFT investigation of the magnetic circular dichroism spectra of some purine and pyrimidine bases of nucleic acids.

    PubMed

    Fahleson, Tobias; Kauczor, Joanna; Norman, Patrick; Santoro, Fabrizio; Improta, Roberto; Coriani, Sonia

    2015-05-28

    We present a computational study of the magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil, thymine, and cytosine, using the B3LYP and CAM-B3LYP functionals. Solvent effects are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In general, the computed spectra are found to be in good agreement with the experimental ones, apart from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine bases are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific, but they do not in general alter the qualitative shape of the spectra. The bands are dominated by the bright π → π* transitions, and our calculations in solution nicely reproduce their energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n → π* excitations, but they are too weak to be observed in the experiment.

  3. A theoretical study on the electronic structures and equilibrium constants evaluation of Deferasirox iron complexes.

    PubMed

    Salehi, Samie; Saljooghi, Amir Shokooh; Izadyar, Mohammad

    2016-10-01

    Elemental iron is essential for cellular growth and homeostasis but it is potentially toxic to the cells and tissues. Excess iron can contribute in tumor initiation and tumor growth. Obviously, in iron overload issues using an iron chelator in order to reduce iron concentration seems to be vital. This study presents the density functional theory calculations of the electronic structure and equilibrium constant for iron-deferasirox (Fe-DFX) complexes in the gas phase, water and DMSO. A comprehensive study was performed to investigate the Deferasirox-iron complexes in chelation therapy. Calculation was performed in CAMB3LYP/6-31G(d,p) to get the optimized structures for iron complexes in high and low spin states. Natural bond orbital and quantum theory of atoms in molecules analyses was carried out with B3LYP/6-311G(d,p) to understand the nature of complex bond character and electronic transition in complexes. Electrostatic potential effects on the complexes were evaluated using the CHelpG calculations. The results indicated that higher affinity for Fe(III) is not strictly a function of bond length but also the degree of Fe-X (X=O,N) covalent bonding. Based on the quantum reactivity parameters which have been investigated here, it is possible reasonable design of the new chelators to improve the chelator abilities.

  4. Benchmark, DFT assessments, cooperativity, and energy decomposition analysis of the hydrogen bonds in HCN/HNC oligomeric complexes.

    PubMed

    de Oliveira, Paulo McMiller C; Silva, Juliana A B; Longo, Ricardo L

    2017-02-01

    Hydrogen cyanide (HCN) and its tautomer hydrogen isocyanide (HNC) are relevant for extraterrestrial chemistry and possible relation to the origin of biomolecules. Several processes and reactions involving these molecules depend on their intermolecular interactions that can lead to aggregates and liquids especially due to the hydrogen bonds. It is thus important to comprehend, to describe, and to quantify their hydrogen bonds, mainly their nature and the cooperativity effects. A systematic study of all linear complexes up to pentamers of HCN and HNC is presented. CCSD(T)/CBS energy calculations, with and without basis set superposition error (BSSE) corrections for energies and geometries, provided a suitable set of benchmarks. Approximated methods based on the density functional theory (DFT) such as BP86, PBE, TPSS, B3LYP, CAM-B3LYP with and without dispersion corrections and long-range corrections, were assessed to describe the interaction energies and cooperativity effects. These assessments are relevant to select DFT functionals for liquid simulations. Energy decomposition analysis was performed at the PBE/STO-TZ2P level and provided insights into the nature of the hydrogen bonds, which are dominated by the electrostatic component. In addition, several linear relationships between the various energy components and the interaction energy were obtained. The cooperativity energy was also found to be practically linear with respect to the interaction energy, which may be relevant for designing and/or correcting empirical force fields. Graphical Abstract Hydrogen bonds in HCN/HNC oligomeric complexesᅟ.

  5. Solvent effects on static polarizability, static first hyperpolarizability and one- and two-photon absorption properties of functionalized triply twisted Möbius annulenes: a DFT study.

    PubMed

    Alam, Md Mehboob; Kundi, Varun; Thankachan, Pompozhi Protasis

    2016-08-21

    The present work aims to study solvent effects on the polarizability (α), static first hyperpolarizability (β) and one- and two-photon absorption (OPA and TPA) properties of a new class of molecules viz. triply twisted Möbius annulenes, recently studied by us in vacuum phase [Kundi et al., Phys. Chem. Chem. Phys., 2015, 17, 6827]. We have employed linear and quadratic response theories within the framework of time-dependent density functional theory with the CAM-B3LYP functional and a cc-pVDZ basis set to calculate different parameters. The microscopic details of the said properties have been studied using a two-state model (2SM) approach, which performs very well in the case of β and TPA of the first excited state of all the systems. However for the second excited state, the 2SM results are far from those of response theory. In fact, in comparison to response theory, 2SM predicts an opposite trend for the TP activity of some of the model systems, indicating a significant contribution from the other higher excited states. The anomaly between the 2SM approach and response theory has been resolved by incorporating three states in the calculations.

  6. Chelation behavior of various flavonols and transfer of flavonol-chelated zinc(II) to alanylaspartic dipeptide: A PCM/DFT investigation

    NASA Astrophysics Data System (ADS)

    Yasarawan, Nuttawisit; Thipyapong, Khajadpai; Ruangpornvisuti, Vithaya

    2016-03-01

    Alanylaspartic dipeptide (AlaAsp) and zinc(II)-flavonol complex could represent a metal-binding site in proteins and a metal-ion releasing agent, respectively. Chelation of zinc(II) by either AlaAsp or flavonol ligands in aqueous solution has been examined using DFT methods with polarizable continuum model (PCM/DFT). Coordination geometry, complexation stoichiometry, coordination bond strength, preferable metal-binding site on ligands and effect of water coordination on the stability of complexes have been addressed. In several cases, the long-range corrected density functional CAM-B3LYP allows the most accurate prediction of both structural and spectroscopic data. The preferential transfer of flavonol-chelated zinc(II) to AlaAsp under solvation is attainable through the ligand-exchange reaction. The energy barrier of such reaction is significantly dependent on the degree of hydrogen bonding within the transition state. In summary, either hydroxylation or methoxylation at particular positions on the 3-hydroxyflavone backbone significantly affects the reactivity of flavonol chelates in the metal-ion transfer.

  7. Assignment of the Q-bands of the chlorophylls: coherence loss via Qx - Qy mixing.

    PubMed

    Reimers, Jeffrey R; Cai, Zheng-Li; Kobayashi, Rika; Rätsep, Margus; Freiberg, Arvi; Krausz, Elmars

    2013-09-26

    We provide a new and definitive spectral assignment for the absorption, emission, high-resolution fluorescence excitation, linear dichroism, and/or magnetic circular dichroism spectra of 32 chlorophyllides in various environments. This encompases all data used to justify previous assignments and provides a simple interpretation of unexplained complex decoherence phenomena associated with Qx → Qy relaxation. Whilst most chlorophylls conform to the Gouterman model and display two independent transitions Qx (S2) and Qy (S1), strong vibronic coupling inseparably mixes these states in chlorophyll-a. This spreads x-polarized absorption intensity over the entire Q-band system to influence all exciton-transport, relaxation and coherence properties of chlorophyll-based photosystems. The fraction of the total absorption intensity attributed to Qx ranges between 7% and 33%, depending on chlorophyllide and coordination, and is between 10% and 25% for chlorophyll-a. CAM-B3LYP density-functional-theory calculations of the band origins, relative intensities, vibrational Huang-Rhys factors, and vibronic coupling strengths fully support this new assignment.

  8. A highly selective fluorescent chemosensor for Mg2+ ion in aqueous solution using density function theory calculations

    NASA Astrophysics Data System (ADS)

    Jamshidi, Morteza; Rezaei, Omid; Belverdi, Ali Rezaei; Malekian, Sajad; Belverdi, Amin Rezaei

    2016-11-01

    Magnesium is one of the most common metal cations that contributes to the metabolism cycle of living beings as a biological ion so sensing magnesium ions is of great importance. As a catalyst, magnesium plays an essential part in a large number of cellular processes such as enzymatic biochemical reactions, and cell proliferation. Recently chemosensors are widely used in the detection of metal cations. In this study, the sensing ability of Isatin-3-(7‧-Methoxychromone-3‧-methylidene) (HL) ligands for the bivalent Mg+2 and Ca+2 cations was studied and compared using density function theory (DFT) method. The main inconvenient factor to detect magnesium is the Ca+2 cation. The calculations were performed using the CAM-B3LYP method on an aqueous environment. The analysis of optical data, including fluorescent and electronic absorption and emission indicates more sensitivity and selectivity for the detection of Mg+2 compared to Ca+2 in a way that energy gap changes of the [HL + Mg] and [HL + Ca] complexes are 0.155 eV and 0.054 eV respectively.

  9. Bond Length Alternation of Conjugated Oligomers: Wave Function and DFT Benchmarks.

    PubMed

    Jacquemin, Denis; Adamo, Carlo

    2011-02-08

    We have computed the bond length alternation (BLA) in a series of π-conjugated quasilinear chains containing from two to six unit cells. Several structures (eight oligomeric sets including three conformers of polyacetylene, polymethineimine, polysilaacetylene, etc.) have been considered to cover the possible evolutions of the BLA with increasing chain length. Three objectives have been tackled: (1) the computation of accurate reference values using the CCSD(T) theory; (2) an evaluation of the performances of other electron correlated wave function approaches (MPn, SCS-MP2, CCSD, etc.); (3) the benchmarking of several DFT functionals, including global, range-separated, and double hybrids. It turns out that the SCS-MP2 approach is, on average, an efficient scheme in terms of its accuracy/cost ratio. Among the selected DFT approaches, no single functional emerges as uniformly accurate for all oligomeric series and chain lengths, but BHHLYP, M06-2X, and CAM-B3LYP could be reasonable choices for long oligomers.

  10. Paleoindian demography and the extraterrestrial impact hypothesis.

    PubMed

    Buchanan, Briggs; Collard, Mark; Edinborough, Kevan

    2008-08-19

    Recently it has been suggested that one or more large extraterrestrial (ET) objects struck northern North America 12,900 +/- 100 calendar years before present (calBP) [Firestone RB, et al. (2007) Proc Natl Acad Sci USA 104: 16016-16021]. This impact is claimed to have triggered the Younger Dryas major cooling event and resulted in the extinction of the North American megafauna. The impact is also claimed to have caused major cultural changes and population decline among the Paleoindians. Here, we report a study in which approximately 1,500 radiocarbon dates from archaeological sites in Canada and the United States were used to test the hypothesis that the ET resulted in population decline among the Paleoindians. Following recent studies [e.g., Gamble C, Davies W, Pettitt P, Hazelwood L, Richards M (2005) Camb Archaeol J 15:193-223), the summed probability distribution of the calibrated dates was used to identify probable changes in human population size between 15,000 and 9,000 calBP. Subsequently, potential biases were evaluated by modeling and spatial analysis of the dated occupations. The results of the analyses were not consistent with the predictions of extraterrestrial impact hypothesis. No evidence of a population decline among the Paleoindians at 12,900 +/- 100 calBP was found. Thus, minimally, the study suggests the extraterrestrial impact hypothesis should be amended.

  11. Extending the Coyote emulator to dark energy models with standard w0-wa parametrization of the equation of state

    NASA Astrophysics Data System (ADS)

    Casarini, L.; Bonometto, S. A.; Tessarotto, E.; Corasaniti, P.-S.

    2016-08-01

    We discuss an extension of the Coyote emulator to predict non-linear matter power spectra of dark energy (DE) models with a scale factor dependent equation of state of the form w = w0+(1-a)wa. The extension is based on the mapping rule between non-linear spectra of DE models with constant equation of state and those with time varying one originally introduced in ref. [40]. Using a series of N-body simulations we show that the spectral equivalence is accurate to sub-percent level across the same range of modes and redshift covered by the Coyote suite. Thus, the extended emulator provides a very efficient and accurate tool to predict non-linear power spectra for DE models with w0-wa parametrization. According to the same criteria we have developed a numerical code that we have implemented in a dedicated module for the CAMB code, that can be used in combination with the Coyote Emulator in likelihood analyses of non-linear matter power spectrum measurements. All codes can be found at https://github.com/luciano-casarini/pkequal.

  12. Electronic Absorption Spectra of Tetrapyrrole-Based Pigments via TD-DFT: A Reduced Orbital Space Study.

    PubMed

    Shrestha, Kushal; Virgil, Kyle A; Jakubikova, Elena

    2016-07-28

    Tetrapyrrole-based pigments play a crucial role in photosynthesis as principal light absorbers in light-harvesting chemical systems. As such, accurate theoretical descriptions of the electronic absorption spectra of these pigments will aid in the proper description and understanding of the overall photophysics of photosynthesis. In this work, time-dependent density functional theory (TD-DFT) at the CAM-B3LYP/6-31G* level of theory is employed to produce the theoretical absorption spectra of several tetrapyrrole-based pigments. However, the application of TD-DFT to large systems with several hundreds of atoms can become computationally prohibitive. Therefore, in this study, TD-DFT calculations with reduced orbital spaces (ROSs) that exclude portions of occupied and virtual orbitals are pursued as a viable, computationally cost-effective alternative to conventional TD-DFT calculations. The effects of reducing orbital space size on theoretical spectra are qualitatively and quantitatively described, and both conventional and ROS results are benchmarked against experimental absorption spectra of various tetrapyrrole-based pigments. The orbital reduction approach is also applied to a large natural pigment assembly that comprises the principal light-absorbing component of the reaction center in purple bacteria. Overall, we find that TD-DFT calculations with proper and judicious orbital space reductions can adequately reproduce conventional, full orbital space, TD-DFT results of all pigments studied in this work.

  13. Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?

    PubMed

    Fouda, Adam; Ryde, Ulf

    2016-11-08

    We have examined how the self-interaction error in density-functional theory (DFT) calculations affects energies calculated on large systems (600-1000 atoms) involving several charged groups. We employ 18 different quantum mechanical (QM) methods, including Hartree-Fock, as well as pure, hybrid, and range-separated DFT methods. They are used to calculate reaction and activation energies for three different protein models in vacuum, in a point-charge surrounding, or with a continuum-solvent model. We show that pure DFT functionals give rise to a significant delocalization of the charges in charged groups in the protein, typically by ∼0.1 e, as evidenced from the Mulliken charges. This has a clear effect on how the surroundings affect calculated reaction and activation energies, indicating that these methods should be avoided for DFT calculations on large systems. Fortunately, methods such as CAM-B3LYP, BHLYP, and M06-2X give results that agree within a few kilojoules per mole, especially when the calculations are performed in a point-charge surrounding. Therefore, we recommend these methods to estimate the effect of the surroundings with large QM systems (but other QM methods may be used to study the intrinsic reaction and activation energies).

  14. Loophole-free Quantum Steering

    NASA Astrophysics Data System (ADS)

    Ramelow, Sven; Wittmann, Bernhard; Steinlechner, Fabian; Langford, Nathan K.; Brunner, Nicolas; Wiseman, Howard; Ursin, Rupert; Zeilinger, Anton

    2012-02-01

    Experiments testing quantum mechanics have provided increasing evidence against local realistic theories. However, a conclusive test that simultaneously closes all major loopholes (the locality, freedom-of-choice, and detection loopholes) remains an open challenge. An important class of local realistic theories can be tested with the concept of ``steering.'' Schr"odinger introduced this term for entanglement seemingly allowing to remotely steer the state of a distant system [1]. Einstein called this ``spooky action at a distance.'' Steering was recently formalized by deriving steering inequalities allowing experimental tests. Here, we present the first loophole-free steering experiment [2]. We use entangled photons shared between two distant laboratories and close all loopholes by a large separation, ultra-fast switching and quantum random number generation, and high, overall detection efficiency. Beside its foundational importance loop-hole-free steering is relevant for is relevant for device-independent certification of quantum entanglement. [4pt] [1] E. Schr"odinger, Proc. Camb. , Phil. Soc. 31, 553 (1935) [0pt] [2] B. Wittmann, S. Ramelow, F. Steinlechner, N. K. Langford, N. Brunner, H. Wiseman, R. Ursin, A. Zeilinger, arXiv:1111.0760, (2011)

  15. Many-body Green's function GW and Bethe-Salpeter study of the optical excitations in a paradigmatic model dipeptide.

    PubMed

    Faber, C; Boulanger, P; Duchemin, I; Attaccalite, C; Blase, X

    2013-11-21

    We study within the many-body Green's function GW and Bethe-Salpeter formalisms the excitation energies of a paradigmatic model dipeptide, focusing on the four lowest-lying local and charge-transfer excitations. Our GW calculations are performed at the self-consistent level, updating first the quasiparticle energies, and further the single-particle wavefunctions within the static Coulomb-hole plus screened-exchange approximation to the GW self-energy operator. Important level crossings, as compared to the starting Kohn-Sham LDA spectrum, are identified. Our final Bethe-Salpeter singlet excitation energies are found to agree, within 0.07 eV, with CASPT2 reference data, except for one charge-transfer state where the discrepancy can be as large as 0.5 eV. Our results agree best with LC-BLYP and CAM-B3LYP calculations with enhanced long-range exchange, with a 0.1 eV mean absolute error. This has been achieved employing a parameter-free formalism applicable to metallic or insulating extended or finite systems.

  16. Ab Initio Geometry and Bright Excitation of Carotenoids: Quantum Monte Carlo and Many Body Green’s Function Theory Calculations on Peridinin

    PubMed Central

    Coccia, Emanuele; Varsano, Daniele; Guidoni, Leonardo

    2016-01-01

    In this letter, we report the singlet ground state structure of the full carotenoid peridinin by means of variational Monte Carlo (VMC) calculations. The VMC relaxed geometry has an average bond length alternation of 0.1165(10) Å, larger than the values obtained by DFT (PBE, B3LYP, and CAM-B3LYP) and shorter than that calculated at the Hartree–Fock (HF) level. TDDFT and EOM-CCSD calculations on a reduced peridinin model confirm the HOMO–LUMO major contribution of the Bu+-like (S2) bright excited state. Many Body Green’s Function Theory (MBGFT) calculations of the vertical excitation energy of the Bu+-like state for the VMC structure (VMC/MBGFT) provide an excitation energy of 2.62 eV, in agreement with experimental results in n-hexane (2.72 eV). The dependence of the excitation energy on the bond length alternation in the MBGFT and TDDFT calculations with different functionals is discussed. PMID:26580027

  17. APEX-CAMBIUM: A Case Study in Advantages and Challenges of International Cooperation for the International Space Station

    NASA Technical Reports Server (NTRS)

    Cox, David; Buckley, Nicole

    2008-01-01

    It is generally agreed that space science benefits from an international collaboration. There are different mechanisms to make this happen but to recognize opportunities requires a keen awareness of the activities, people and respective strengths. Apex- Cambium is a joint Canadian Space Agency (CSA)-National Aeronautics and Space Administration (NASA) initiative. It was made possible in large part through the good relations and shared willingness to meet a common objective, that of doing exciting science in space. The actual mechanics of bringing an international project together can be divided into two perspectives: programmatic and implementation. The programmatic component includes recognizing complementarities, bringing science together, and the need to have Agencies approve and accept joint responsibility for the mission. The implementation component involves working to define science requirements, available resources and assigning individual responsibilities while keeping the overall success criteria as a collective objective. The APEX-CAMB11.JM mission will be described from the point of view of both CSA and NASA. Suggestions on how to facilitate these types of initiatives will be provided and highlights of the APEX-Cambium collaboration will be provided.

  18. Exchange interaction between the triplet exciton and the localized spin in copper-phthalocyanine.

    PubMed

    Wu, Wei

    2014-06-14

    Triplet excitonic state in the organic molecule may arise from a singlet excitation and the following inter-system crossing. Especially for a spin-bearing molecule, an exchange interaction between the triplet exciton and the original spin on the molecule can be expected. In this paper, such exchange interaction in copper-phthalocyanine (CuPc, spin-½) was investigated from first-principles by using density-functional theory within a variety of approximations to the exchange correlation, ranging from local-density approximation to long-range corrected hybrid-exchange functional. The magnitude of the computed exchange interaction is in the order of meV with the minimum value (1.5 meV, ferromagnetic) given by the long-range corrected hybrid-exchange functional CAM-B3LYP. This exchange interaction can therefore give rise to a spin coherence with an oscillation period in the order of picoseconds, which is much shorter than the triplet lifetime in CuPc (typically tens of nanoseconds). This implies that it might be possible to manipulate the localized spin on Cu experimentally using optical excitation and inter-system crossing well before the triplet state disappears.

  19. Quantitative Trait Loci for Yield and Yield-Related Traits in Spring Barley Populations Derived from Crosses between European and Syrian Cultivars

    PubMed Central

    Krystkowiak, Karolina; Sawikowska, Aneta; Frohmberg, Wojciech; Górny, Andrzej; Kędziora, Andrzej; Jankowiak, Janusz; Józefczyk, Damian; Karg, Grzegorz; Andrusiak, Joanna; Krajewski, Paweł; Szarejko, Iwona; Surma, Maria; Adamski, Tadeusz; Guzy-Wróbelska, Justyna; Kuczyńska, Anetta

    2016-01-01

    In response to climatic changes, breeding programmes should be aimed at creating new cultivars with improved resistance to water scarcity. The objective of this study was to examine the yield potential of barley recombinant inbred lines (RILs) derived from three cross-combinations of European and Syrian spring cultivars, and to identify quantitative trait loci (QTLs) for yield-related traits in these populations. RILs were evaluated in field experiments over a period of three years (2011 to 2013) and genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers; a genetic map for each population was constructed and then one consensus map was developed. Biological interpretation of identified QTLs was achieved by reference to Ensembl Plants barley gene space. Twelve regions in the genomes of studied RILs were distinguished after QTL analysis. Most of the QTLs were identified on the 2H chromosome, which was the hotspot region in all three populations. Syrian parental cultivars contributed alleles decreasing traits' values at majority of QTLs for grain weight, grain number, spike length and time to heading, and numerous alleles increasing stem length. The phenomic and molecular approaches distinguished the lines with an acceptable grain yield potential combining desirable features or alleles from their parents, that is, early heading from the Syrian breeding line (Cam/B1/CI08887//CI05761) and short plant stature from the European semidwarf cultivar (Maresi). PMID:27227880

  20. Degenerate two-photon absorption in all-trans retinal: nonlinear spectrum and theoretical calculations.

    PubMed

    Vivas, M G; Silva, D L; Misoguti, L; Zaleśny, R; Bartkowiak, W; Mendonca, C R

    2010-03-18

    In this work we investigate the degenerate two-photon absorption spectrum of all-trans retinal in ethanol employing the Z-scan technique with femtosecond pulses. The two-photon absorption (2PA) spectrum presents a monotonous increase as the excitation wavelength approaches the one-photon absorption band and a peak at 790 nm. We attribute the 2PA band to the mixing of states (1)B(u)(+)-like and |S(1)>, which are strongly allowed by one- and two-photon, respectively. We modeled the 2PA spectrum by using the sum-over-states approach and obtained spectroscopic parameters of the electronic transitions to |S(1)>, |S(2)> ("(1)B(u)(+)"), |S(3)>, and |S(4)> singlet-excited states. The results were compared with theoretical predictions of one- and two-photon transition calculations using the response functions formalism within the density functional theory framework with the aid of the CAM-B3LYP functional.

  1. The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part I: gas phase.

    PubMed

    Davari, Mehdi D; Ferrer, Francisco J Avila; Morozov, Dmitry; Santoro, Fabrizio; Groenhof, Gerrit

    2014-10-20

    In this work we present the vibrationally resolved optical absorption spectrum of p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI), the green fluorescent protein (GFP) chromophore, computed at several levels of theory, including time-dependent DFT with various functionals and basis sets, CASSCF, CASPT2 and XMCQDPT2. We also investigated what happens to the spectrum if the ground- and excited-state geometries are optimized at different levels of theory (mixed approach), as has been used previously. The vibrationally resolved absorption spectra obtained by DFT, CASPT2 and XMCQDPT2 are very similar and consist of a main absorption peak and a shoulder that is ∼1500 cm(-1) higher in energy. The vibrational progression increases moderately with temperature. These spectra are in qualitative agreement with experimental action spectra, but much narrower and lack the long tail in the blue, even at high temperatures. Because our calculated emission spectra, which are equally narrow, are in good agreement with the emission of green fluorescent protein at 253 K, we argue that the action spectrum are too broad to be considered as the absorption spectrum. The CASSCF method and the mixed approaches overestimate the vibrational progressions with respect to CAM-B3LYP, CASPT2 and XMCQDPT2, due to inaccuracies in the geometric S0 →S1 displacements. Finally, we computed the vibronic spectra of four chromophore analogues with different substitutions on the rings and found that these substitutions hardly affect the lineshape in vacuum.

  2. [Prevalence of tobacco use and associated factors among women in Paraná State, Brazil].

    PubMed

    Scarinci, Isabel C; Bittencourt, Lorna; Person, Sharina; Cruz, Regina C; Moysés, Simone Tetu

    2012-08-01

    This study aimed to estimate the prevalence of tobacco use and to describe the demographic profile of female smokers in Paraná State, Brazil. The study used a cross-sectional population-based design with cluster sampling (n = 2,153) of women 18 years or older in seven cities. Prevalence of smoking was 13.4%, ranging from 10% in Cascavel to 19% in Irati. According to multivariate analysis, city of residence, marital status, and schooling were significantly associated with tobacco use. Women in Irati (OR = 2.08; 95%CI: 1.22-3.54) were more likely to smoke than those in Cambé. Married women and widows were less likely to smoke (OR = 0.47; 95%CI: 0.30-0.73 and OR = 0.43; 95%CI: 0.22-0.87) than single women. Women living with a partner (but not married) were more likely to smoke than single women (OR = 2.49; 95%CI: 1.12-5.53), and women with university degrees were less likely to smoke than those with eight years of school or less (OR = 0.41; 95%CI: 0.22-0.87). The results confirm the need for tobacco control programs that take gender and regional differences into account.

  3. Crystal structure, spectroscopic investigations and quantum chemical calculation studies of (3aR,6S,7aR)-7a-bromo-6-methyl-2-[(4-methylphenyl)sulfonyl]-1,2,3,6,7,7a-hexahydro-3a,6-epoxyisoindole: A combined experimental and theoretical studies

    NASA Astrophysics Data System (ADS)

    Alaşalvar, Can; Demircan, Aydın; Koşar, Başak; Pekacar, Ali İhsan; Büyükgüngör, Orhan

    2016-11-01

    The crystal structure and spectroscopic properties of (3aR,6S,7aR)-7a-bromo-6-methyl-2-[(4-methylphenyl)sulfonyl]-1,2,3,6,7,7a-hexahydro-3a,6-epoxyisoindole were determined by X-ray diffraction, IR and 13CNMR and 1H NMR spectroscopy techniques. We investigate molecular and crystal structure of the new sulfonamide, which was derived from an environmental friendly cyclization reaction in water. This work allow to the development of a stereo-selective tandem allylamine isomerization/Diels Alder cyclo-addition sequence led to rapid assembly of complex nitrogen containing heterocycles. The molecular geometry from X-ray determination, vibrational frequencies and NMR shifts values of the title compound in the ground state have been calculated by using CAM-B3LYP and B3LYP methods with 6-311++G(d,p) basis sets. The calculated results show that the optimized geometry can well regenerate the crystal structure and theoretical vibrational frequencies and chemical shift data are in good agreement with experimental data. Besides, it is examined nonlinear optic properties, molecular electrostatic potential map and HOMO-LUMO orbitals of the molecule.

  4. Photoisomerization among ring-open merocyanines. II. A computational study

    NASA Astrophysics Data System (ADS)

    Walter, Christof; Ruetzel, Stefan; Diekmann, Meike; Nuernberger, Patrick; Brixner, Tobias; Engels, Bernd

    2014-06-01

    The photochemical isomerization of the trans-trans-cis to the trans-trans-trans isomer of the merocyanine form of 6-nitro BIPS, which has been studied with femtosecond transient absorption spectroscopy [S. Ruetzel, M. Diekmann, P. Nuernberger, C. Walter, B. Engels, and T. Brixner, J. Chem. Phys. 140, 224310 (2014)], is investigated using time-dependent density functional theory in conjunction with polarizable continuum models. Benchmark calculations against SCS-ADC(2) evaluate the applicability of the CAM-B3LYP functional. Apart from a relaxed scan in the ground state with additional computation of the corresponding excitation energies, which produces the excited-state surface vertical to the ground-state isomerization coordinate, a relaxed scan in the S1 gives insight into the geometric changes orthogonal to the reaction coordinate and the fluorescence conditions. The shape of the potential energy surface (PES) along the reaction coordinate is found to be highly sensitive to solvation effects, with the method of solvation (linear response vs. state-specific) being critical. The shape of the PES as well as the computed harmonic frequencies in the S1 minima are in line with the experimental results and offer a straightforward interpretation.

  5. Photoisomerization among ring-open merocyanines. II. A computational study.

    PubMed

    Walter, Christof; Ruetzel, Stefan; Diekmann, Meike; Nuernberger, Patrick; Brixner, Tobias; Engels, Bernd

    2014-06-14

    The photochemical isomerization of the trans-trans-cis to the trans-trans-trans isomer of the merocyanine form of 6-nitro BIPS, which has been studied with femtosecond transient absorption spectroscopy [S. Ruetzel, M. Diekmann, P. Nuernberger, C. Walter, B. Engels, and T. Brixner, J. Chem. Phys. 140, 224310 (2014)], is investigated using time-dependent density functional theory in conjunction with polarizable continuum models. Benchmark calculations against SCS-ADC(2) evaluate the applicability of the CAM-B3LYP functional. Apart from a relaxed scan in the ground state with additional computation of the corresponding excitation energies, which produces the excited-state surface vertical to the ground-state isomerization coordinate, a relaxed scan in the S1 gives insight into the geometric changes orthogonal to the reaction coordinate and the fluorescence conditions. The shape of the potential energy surface (PES) along the reaction coordinate is found to be highly sensitive to solvation effects, with the method of solvation (linear response vs. state-specific) being critical. The shape of the PES as well as the computed harmonic frequencies in the S1 minima are in line with the experimental results and offer a straightforward interpretation.

  6. Multiple lensing of the cosmic microwave background anisotropies

    SciTech Connect

    Calabrese, M.; Fabbian, G.; Baccigalupi, C.; Carbone, C.; Baldi, M. E-mail: carmelita.carbone@brera.inaf.it E-mail: marco.baldi5@unibo.it

    2015-03-01

    We study the gravitational lensing effect on the Cosmic Microwave Background (CMB) anisotropies performing a ray-tracing of the primordial CMB photons through intervening large-scale structures (LSS) distribution predicted by N-Body numerical simulations with a particular focus on the precise recovery of the lens-induced polarized counterpart of the source plane. We apply both a multiple plane ray-tracing and an effective deflection approach based on the Born approximation to deflect the CMB photons trajectories through the simulated lightcone. We discuss the results obtained with both these methods together with the impact of LSS non-linear evolution on the CMB temperature and polarization power spectra. We compare our results with semi-analytical approximations implemented in Boltzmann codes like, e.g., CAMB. We show that, with our current N-body setup, the predicted lensing power is recovered with good accuracy in a wide range of multipoles while excess power with respect to semi-analytic prescriptions is observed in the lensing potential on scales ℓ ∼> 3000. We quantify the impact of the numerical effects connected to the resolution in the N-Body simulation together with the resolution and band-limit chosen to synthesise the CMB source plane. We found these quantities to be particularly important for the simulation of B-mode polarization power spectrum.

  7. Evolution Under Environmental Stress at Macro- and Microscales

    PubMed Central

    Nevo, Eviatar

    2011-01-01

    Environmental stress has played a major role in the evolution of living organisms (Hoffman AA, Parsons PA. 1991. Evolutionary genetics and environmental stress. Oxford: Oxford University Press; Parsons PA. 2005. Environments and evolution: interactions between stress, resource inadequacy, and energetic efficiency. Biol Rev Camb Philos Soc. 80:589–610). This is reflected by the massive and background extinctions in evolutionary time (Nevo E. 1995a. Evolution and extinction. Encyclopedia of Environmental Biology. New York: Academic Press, Inc. 1:717–745). The interaction between organism and environment is central in evolution. Extinction ensues when organisms fail to change and adapt to the constantly altering abiotic and biotic stressful environmental changes as documented in the fossil record. Extreme environmental stress causes extinction but also leads to evolutionary change and the origination of new species adapted to new environments. I will discuss a few of these global, regional, and local stresses based primarily on my own research programs. These examples will include the 1) global regional and local experiment of subterranean mammals; 2) regional experiment of fungal life in the Dead Sea; 3) evolution of wild cereals; 4) “Evolution Canyon”; 5) human brain evolution, and 6) global warming. PMID:21979157

  8. Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration.

    PubMed

    Soniat, Marielle; Rogers, David M; Rempe, Susan B

    2015-07-14

    A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment.

  9. Serosurvey of antibodies against spotted fever group Rickettsia spp. in horse farms in Northern Paraná, Brazil.

    PubMed

    Tamekuni, Katia; Toledo, Roberta dos Santos; Silva Filho, Mauro de Freitas; Haydu, Valeska Bender; Pacheco, Richard Campos; Cavicchioli, José Henrique; Labruna, Marcelo Bahia; Dumler, John Stephen; Vidotto, Odilon

    2010-01-01

    Brazilian spotted fever (BSF) is an emerging disease most likely caused by Rickettsia rickettsii. The objective of the present study was to estimate the seroprevalence of BSF rickettsia infections in equines from six horse farms located in Londrina County, Paraná, Southern Brazil. Six owners of horse farms situated in Cambé, Santa Fé, Guaraci and Londrina municipalities participated in the study. All farms were located in areas where BSF has not been reported. A total of 273 horses were sampled and their sera were tested by indirect immunofluorescence assay (IFA) using R. rickettsii and R. parkeri antigens. Titers equal to and greater than 64 were considered positive. Of 273 sera tested, 15 (5.5%) reacted to R. rickettsii and 5 (1.8%) to R. parkeri. Five out of the six farms studied revealed seropositive animals and seropositivity rate ranged from 0 to 13%. The titers ranged from 64 to 512, and four samples had a titer of 512. Nine animals reacted to R. rickettsii with titers four-fold higher than those for R. parkeri. These results suggest that horses in Northern Paraná may have been exposed to rickettsiae identical or closely related to R. rickettsii.

  10. More about a successful vector-tensor theory of gravitation

    NASA Astrophysics Data System (ADS)

    Dale, R.; Sáez, D.

    2017-01-01

    The vector-tensor (VT) theory of gravitation revisited in this article was studied in previous papers, where it was proved that VT works and deserves attention. New observational data and numerical codes have motivated further development which is presented here. New research has been planed with the essential aim of proving that current cosmological observations, including Planck data, baryon acoustic oscillations (BAO), and so on, may be explained with VT, a theory which accounts for a kind of dark energy which has the same equation of state as vacuum. New versions of the codes CAMB and COSMOMC have been designed for applications to VT, and the resulting versions have been used to get the cosmological parameters of the VT model at suitable confidence levels. The parameters to be estimated are the same as in general relativity (GR), plus a new parameter D. For D = 0, VT linear cosmological perturbations reduces to those of GR, but the VT background may explain dark energy. The fits between observations and VT predictions lead to non vanishing |D| upper limits at the 1σ confidence level. The value D = 0 is admissible at this level, but this value is not that of the best fit in any case. Results strongly suggest that VT may explain current observations, at least, as well as GR; with the advantage that, as it is proved in this paper, VT has an additional parameter which facilitates adjustments to current observational data.

  11. Quantitative Trait Loci for Yield and Yield-Related Traits in Spring Barley Populations Derived from Crosses between European and Syrian Cultivars.

    PubMed

    Mikołajczak, Krzysztof; Ogrodowicz, Piotr; Gudyś, Kornelia; Krystkowiak, Karolina; Sawikowska, Aneta; Frohmberg, Wojciech; Górny, Andrzej; Kędziora, Andrzej; Jankowiak, Janusz; Józefczyk, Damian; Karg, Grzegorz; Andrusiak, Joanna; Krajewski, Paweł; Szarejko, Iwona; Surma, Maria; Adamski, Tadeusz; Guzy-Wróbelska, Justyna; Kuczyńska, Anetta

    2016-01-01

    In response to climatic changes, breeding programmes should be aimed at creating new cultivars with improved resistance to water scarcity. The objective of this study was to examine the yield potential of barley recombinant inbred lines (RILs) derived from three cross-combinations of European and Syrian spring cultivars, and to identify quantitative trait loci (QTLs) for yield-related traits in these populations. RILs were evaluated in field experiments over a period of three years (2011 to 2013) and genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers; a genetic map for each population was constructed and then one consensus map was developed. Biological interpretation of identified QTLs was achieved by reference to Ensembl Plants barley gene space. Twelve regions in the genomes of studied RILs were distinguished after QTL analysis. Most of the QTLs were identified on the 2H chromosome, which was the hotspot region in all three populations. Syrian parental cultivars contributed alleles decreasing traits' values at majority of QTLs for grain weight, grain number, spike length and time to heading, and numerous alleles increasing stem length. The phenomic and molecular approaches distinguished the lines with an acceptable grain yield potential combining desirable features or alleles from their parents, that is, early heading from the Syrian breeding line (Cam/B1/CI08887//CI05761) and short plant stature from the European semidwarf cultivar (Maresi).

  12. Molecular anions of polydeprotonated naphthalenes: An investigation on the metastability and deprotonation energies using nuclear-charge stabilization method

    SciTech Connect

    Sangwan, Poonam; Vikas E-mail: qlabspu@yahoo.com

    2016-01-28

    The dianions and trianions of doubly- and triply-deprotonated naphthalenes are investigated using density functional theory (DFT) computations employing hybrid, long-range, and dispersion corrected exchange-correlation functionals. The investigated polyanionic species are found to be metastable with negative electron affinity and are further treated using a nuclear-charge stabilization method. The tunneling lifetimes of these anionic species were estimated to be a few femtoseconds. Notably, the deprotonated energies (DPEs) of naphthalene leading to the formation of triply deprotonated trianions are observed to be affected by the metastability of the dianions and trianions. For the deprotonation of doubly deprotonated dianions, the DPE calculated using the improved methodology based on the stabilization method is found to be nearly 100 kcal/mol more than that computed using the conventional procedure. Though the various DFT approximations employed are in a good agreement for predicting the lifetimes of the metastable species but in the prediction of electron-affinities and deprotonation energies, the dispersion-corrected DFT-D3 significantly disagrees with the long-range corrected DFT methods employing cam-B3LYP and ωB97XD exchange-correlation functionals.

  13. Effect of the crystalline environment on the third-order nonlinear optical properties of L-arginine phosphate monohydrate: a theoretical study.

    PubMed

    Valverde, Clodoaldo; Rodrigues, Rosemberg F N; Machado, Daniel F S; Baseia, Basílio; de Oliveira, Heibbe C B

    2017-04-01

    A supermolecular approach combined with an iterative electrostatic scheme was employed to investigate the nonlinear optical properties of the hybrid L-arginine phosphate monohydrate crystal, the procedure being aided by DFT calculations. The supermolecular scheme basically treated the molecules surrounding the unit cell as point charges; this approximation results in rapid convergence, making it a feasible method. DFT functionals of different flavors were considered: B3LYP, B2PLYP, CAM-B3LYP, ωB97, and M06HF, utilizing the 6-311 + G(d) basis set. All functionals gave sufficiently accurate values for the dipole moment (μ) with respect to the experimental value 32(2) D. For the average linear polarizability ([Formula: see text]) and the total first hyperpolarizability (β tot), good agreement was observed between the DFT-calculated values and MP2-derived results reported in the literature. For the second hyperpolarizability, both static and dynamic regimes were considered. The point-charge embedding approach led to an attenuation of the second hyperpolarizability γ for all frequencies considered. Excitations of γ were not observed for frequencies smaller than 0.1 a.u. For the second hyperpolarizability (both static and dynamic), computational results showed that L-arginine phosphate monohydrate exhibits a large nonlinear optical effect, which implies the occurrence of microscopic third-order NLO behavior.

  14. Benzylammonium Thermometer Ions: Internal Energies of Ions Formed by Low Temperature Plasma and Atmospheric Pressure Chemical Ionization

    NASA Astrophysics Data System (ADS)

    Stephens, Edward R.; Dumlao, Morphy; Xiao, Dan; Zhang, Daming; Donald, William A.

    2015-12-01

    The extent of internal energy deposition upon ion formation by low temperature plasma and atmospheric pressure chemical ionization was investigated using novel benzylammonium thermometer ions. C-N heterolytic bond dissociation enthalpies of nine 4-substituted benzylammoniums were calculated using CAM-B3LYP/6-311++G(d,p), which was significantly more accurate than B3LYP/6-311++G(d,p), MP2/6-311++G(d,p), and CBS-QB3 for calculating the enthalpies of 20 heterolytic dissociation reactions that were used to benchmark theory. All 4-substituted benzylammonium thermometer ions fragmented by a single pathway with comparable dissociation entropies, except 4-nitrobenzylammonium. Overall, the extent of energy deposition into ions formed by low temperature plasma was significantly lower than those formed by atmospheric pressure chemical ionization under these conditions. Because benzylamines are volatile, this new suite of thermometer ions should be useful for investigating the extent of internal energy deposition during ion formation for a wide range of ionization methods, including plasma, spray and laser desorption-based techniques.

  15. Assessment of DFT methods for studying acid gas capture by ionic liquids.

    PubMed

    García, Gregorio; Atilhan, Mert; Aparicio, Santiago

    2015-10-28

    For the first time, this work reports an analysis of the performance of Density Functional methods for studying acid gas capture (CO2 and SO2) by ionic liquids (ILs). The considered functionals were selected as representatives of the available families: pure GGA (PBE and BLYP), hybrid (PBE0 and B3LYP), hybrid meta-GGA (M06, M06-2X and M06-HF), long range corrected (LC-PBEPBE, CAM-B3LYP, ωB97X) and dispersion corrected (PBE-D2, B3LYP-D2 and ωB97XD). Likewise, HF and MP2 were also applied. Binding energies of cation-anion interacting pairs as well as IL-CO2 and IL-SO2 systems were calculated for a set of 54 ILs and compared against MP2/aug-cc-pvDZ. Unlike previously reported DFT benchmarks on ILs, which calculated binding energies through single point calculations on fixed geometries, properties in this work were calculated for geometries optimized at each theoretical level. DFT functionals that are suitable for describing ion-ion and ion-gas interactions were identified, considering both Coulombic forces and dispersion interactions. The reported results allowed us to infer relationships to the rational design of ILs for acid gas capture.

  16. Vibrational, NMR and UV-Visible spectroscopic investigation, VCD and NLO studies on Benzophenone thiosemicarbazone using computational calculations

    NASA Astrophysics Data System (ADS)

    Moorthy, N.; Jobe Prabakar, P. C.; Ramalingam, S.; Periandy, S.; Parasuraman, K.

    2016-04-01

    In order to explore the unbelievable NLO property of prepared Benzophenone thiosemicarbazone (BPTSC), the experimental and theoretical investigation has been made. The theoretical calculations were made using RHF and CAM-B3LYP methods at 6-311++G(d,p) basis set. The title compound contains Cdbnd S ligand which helps to improve the second harmonic generation (SHG) efficiency. The molecule has been examined in terms of the vibrational, electronic and optical properties. The entire molecular behavior was studied by their fundamental IR and Raman wavenumbers and was compared with the theoretical aspect. The molecular chirality has been studied by performing vibrational circular dichroism (circularly polarized infrared radiation). The Mulliken charge levels of the compound ensure the perturbation of atomic charges according to the ligand. The molecular interaction of frontier orbitals emphasizes the modification of chemical properties of the compound through the reaction path. The enormous amount of NLO activity was induced by the Benzophenone in thiosemicarbazone. The Gibbs free energy was evaluated at different temperature and from which the enhancement of chemical stability was stressed. The VCD spectrum was simulated and the optical dichroism of the compound has been analyzed.

  17. Complex polarization propagator calculations of magnetic circular dichroism spectra

    NASA Astrophysics Data System (ADS)

    Solheim, Harald; Ruud, Kenneth; Coriani, Sonia; Norman, Patrick

    2008-03-01

    It is demonstrated that the employment of the nonlinear complex polarization propagator enables the calculation of the complete magnetic circular dichroism spectra of closed-shell molecules, including at the same time both the so-called Faraday A and B terms. In this approach, the differential absorption of right and left circularly polarized light in the presence of a static magnetic field is determined from the real part of the magnetic field-perturbed electric dipole polarizability. The introduction of the finite lifetimes of the electronically excited states into the theory results in response functions that are well behaved in the entire spectral region, i.e., the divergencies that are found in conventional response theory approaches at the transition energies of the system are not present. The applicability of the approach is demonstrated by calculations of the ultraviolet magnetic circular dichroism spectra of para-benzoquinone, tetrachloro-para-benzoquinone, and cyclopropane. The present results are obtained with the complex polarization propagator approach in conjunction with Kohn-Sham density functional theory and the standard adiabatic density functionals B3LYP, CAM-B3LYP, and BHLYP.

  18. Modelling the matrix shift on the vibrational frequency of ThO by DFT-D3 calculations

    NASA Astrophysics Data System (ADS)

    Kovács, Attila; Rode, Joanna E.

    2017-03-01

    Benchmark calculations with a goal to find dispersion-corrected DFT-D3 methods suitable for a reliable estimation of matrix shifts on the vibrational frequency were carried out on the ThO molecule in three rare gas (Rg = Ne, Ar, and Kr) matrices. The matrices were modelled by the explicit approach, in which a single and a double shell of Rg atoms around ThO was considered. The selection of exchange-correlation functionals was based on test calculations on triatomic ThO⋯ Rg models. The B3LYP, PBE0, CAM-B3LYP, and LC-ω PBE functionals were found to be the best suited for the estimation of matrix shifts. The single shell of Rg's around ThO accounted for a major part of the shifts; the addition of a second Rg shell resulted only in a minor improvement. Continuum solvation models considerably overestimated the effect of Rg matrices both when the whole matrix was treated by the model and when the first shell was treated explicitly and the rest with a continuum solvation model.

  19. Effects of delocalised π-electrons around the linear acenes ring (n = 1 to 7): an electronic properties through DFT and quantum chemical descriptors

    NASA Astrophysics Data System (ADS)

    Musa, A.; Saeed, M. A.; Shaari, A.; Sahnoun, Riadh; Lawal, M.

    2015-06-01

    Π-electrons in chemical structure are the unique part of the fundamental particles that modify many interesting properties among the organic semiconductor molecules. By comparing the ground state energy, electronic properties and chemical indices within RHF/6-311G, B3LYP/6-311(G), B3LYP/6-311G(d,p), MP2/6-311G* and Cam-B3LYP/aug-cc-pvdz basis set at level of the theory, we identify that the resonance and the inductive effect of the delocalisation of electrons around the acene molecules could be responsible for acenes electronic and chemical properties. The total energies, energy gaps, HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) energy gaps, electron affinity and ionisation potential are close to the experimental and theoretical results. Among the chemical indices, electrophilicity (ω), electronegativity (χ) and chemical hardness (η) observed to decrease as the acenes ring increasing, whereas the softness (S) and chemical potential (μ) increase with increasing the number of carbons around the acene molecules. The study is extended to electronics and chemical properties of the acene.

  20. The role of high-level calculations in the assignment of the Q-band spectra of chlorophyll

    NASA Astrophysics Data System (ADS)

    Reimers, Jeffrey R.; Cai, Zheng-Li; Kobayashi, Rika; Rätsep, Margus; Freiberg, Arvi; Krausz, Elmars

    2014-10-01

    We recently established a novel assignment of the visible absorption spectrum of chlorophyll-a that sees the two components Qx and Qy of the low-energy Q band as being intrinsically mixed by non-adiabatic coupling. This ended 50 years debate as to the nature of the Q bands, with prior discussion poised only in the language of the Born-Oppenheimer and Condon approximations. The new assignment presents significant ramifications for exciton transport and quantum coherence effects in photosystems. Results from state of the art electronic structure calculations have always been used to justify assignments, but quantitative inaccuracies and systematic failures have historically limited usefulness. We examine the role of CAM-B3LYP time-dependent density-functional theory (TD-DFT) and Symmetry Adapted Cluster-Configuration Interaction (SAC-CI) calculations in first showing that all previous assignments were untenable, in justifying the new assignment, in making some extraordinary predictions that were vindicated by the new assignment, and in then identifying small but significant anomalies in the extensive experimental data record.

  1. Adsorption-induced changes of intramolecular optical transitions: PTCDA/NaCl and PTCDA/KCl.

    PubMed

    Hochheim, Manuel; Bredow, Thomas

    2015-09-15

    Structural and optical properties of isolated perylene-3,4,9,10-tetracarboxylic acid dianhydride molecules adsorbed on (100) oriented NaCl and KCl surfaces were studied theoretically to analyze the recently observed red-shift of the optical excitation spectrum after adsorption (Müller et al., Phys. Rev. B, 2011, 83, 241203; Paulheim et al. Phys. Chem. Chem. Phys., 2013, 15, 4906). The ground-state structures were obtained by periodic dispersion-corrected density functional theory (DFT) calculations. For the excited-state calculations, nonperiodic time-dependent DFT methods were applied for a cluster model embedded in point charges. The range-separated hybrid functional CAM-B3LYP was used. Correlation-consistent basis sets were used and the calculated excitation energies were extrapolated to the complete basis set limit. The shift of the first optical excitation energy was analyzed in terms of electronic and geometric contributions. It was found that both the distortion of the molecule due to the interaction with the surface and the electrostatic potential of the surface play an important role.

  2. Intramolecular electronic couplings in class II/III organic mixed-valence systems of bis(1,4-dimethoxybenzene).

    PubMed

    Yang, Juanhua; Zhang, Weiwei; Si, Yubing; Zhao, Yi

    2012-12-06

    The intramolecular electronic couplings in organic mixed-valence systems [D-(ph)(n)-D](•+) (D = 2,5-dimethoxy-4-methylphenyl, n = 0, 1, and 2) are calculated by dominantly using density functional theory to investigate their dependence of functionals. Since these systems have the property that the charge is from localization to delocalization, the optimized structures are sensitive to the functionals. The geometric optimizations show that CAM-B3LYP and ωB97X-D functionals are good choices for delocalized systems and LC-ωPBE and M06HF are suitable for the systems from charge almost localization to localization. The calculations of electronic couplings demonstrate that the pure functional generally underestimates the electronic couplings whereas the pure HF overestimates them. Furthermore, the electronic couplings from the conventional generalized Mulliken-Hush method are very sensitive to the HF component in functionals, which makes it a challenge to accurately estimate the values. A new reduced two-state method is thus proposed to overcome the deficiency, and the obtained electronic couplings are less sensitive to the ω value in LC-ω PBE functional and they are also consistent with the experimental data.

  3. Design of Acceptors with Suitable Frontier Molecular Orbitals to Match Donors via Substitutions on Perylene Diimide for Organic Solar Cells

    PubMed Central

    Lv, Xiaoli; Li, Zhuoxin; Li, Songyang; Luan, Guoyou; Liang, Dadong; Tang, Shanshan; Jin, Ruifa

    2016-01-01

    A series of perylene diimide (PDI) derivatives have been investigated at the CAM-B3LYP/6-31G(d) and the TD-B3LYP/6-31+G(d,p) levels to design solar cell acceptors with high performance in areas such as suitable frontier molecular orbital (FMO) energies to match oligo(thienylenevinylene) derivatives and improved charge transfer properties. The calculated results reveal that the substituents slightly affect the distribution patterns of FMOs for PDI-BI. The electron withdrawing group substituents decrease the FMO energies of PDI-BI, and the electron donating group substituents slightly affect the FMO energies of PDI-BI. The di-electron withdrawing group substituents can tune the FMOs of PDI-BI to be more suitable for the oligo(thienylenevinylene) derivatives. The electron withdrawing group substituents result in red shifts of absorption spectra and electron donating group substituents result in blue shifts for PDI-BI. The –CN substituent can improve the electron transport properties of PDI-BI. The –CH3 group in different positions slightly affects the electron transport properties of PDI-BI. PMID:27187370

  4. Design of Acceptors with Suitable Frontier Molecular Orbitals to Match Donors via Substitutions on Perylene Diimide for Organic Solar Cells.

    PubMed

    Lv, Xiaoli; Li, Zhuoxin; Li, Songyang; Luan, Guoyou; Liang, Dadong; Tang, Shanshan; Jin, Ruifa

    2016-05-13

    A series of perylene diimide (PDI) derivatives have been investigated at the CAM-B3LYP/6-31G(d) and the TD-B3LYP/6-31+G(d,p) levels to design solar cell acceptors with high performance in areas such as suitable frontier molecular orbital (FMO) energies to match oligo(thienylenevinylene) derivatives and improved charge transfer properties. The calculated results reveal that the substituents slightly affect the distribution patterns of FMOs for PDI-BI. The electron withdrawing group substituents decrease the FMO energies of PDI-BI, and the electron donating group substituents slightly affect the FMO energies of PDI-BI. The di-electron withdrawing group substituents can tune the FMOs of PDI-BI to be more suitable for the oligo(thienylenevinylene) derivatives. The electron withdrawing group substituents result in red shifts of absorption spectra and electron donating group substituents result in blue shifts for PDI-BI. The -CN substituent can improve the electron transport properties of PDI-BI. The -CH₃ group in different positions slightly affects the electron transport properties of PDI-BI.

  5. A cosmology forecast toolkit — CosmoLib

    NASA Astrophysics Data System (ADS)

    Huang, Zhiqi

    2012-06-01

    The package CosmoLib is a combination of a cosmological Boltzmann code and a simulation toolkit to forecast the constraints on cosmological parameters from future observations. In this paper we describe the released linear-order part of the package. We discuss the stability and performance of the Boltzmann code. This is written in Newtonian gauge and including dark energy perturbations. In CosmoLib the integrator that computes the CMB angular power spectrum is optimized for a l-by-l brute-force integration, which is useful for studying inflationary models predicting sharp features in the primordial power spectrum of metric fluctuations. As an application, CosmoLib is used to study the axion monodromy inflation model that predicts cosine oscillations in the primordial power spectrum. In contrast to the previous studies by Aich et al. and Meerburg et al., we found no detection or hint of the osicllations. We pointed out that the CAMB code modified by Aich et al. does not have sufficient numerical accuracy. CosmoLib and its documentation are available at http://www.cita.utoronto.ca/~zqhuang/CosmoLib

  6. Simulation of the resonance Raman spectra for 5-halogenated (F, Cl, and Br) uracils.

    PubMed

    Sun, Shuai; Brown, Alex

    2015-04-30

    The resonance Raman spectra of the 5-halogenated (F, Cl, and Br) uracils are simulated via the Herzberg-Teller (HT) short-time dynamics formalism. The gradient of the S1 excited state is computed at the CAMB3LYP/aug-cc-pVTZ level of theory in the conductor-like polarizable continuum model for water (C-PCM, H2O), based on the equilibrium geometry determined using PBE0/aug-cc-pVTZ in H2O (C-PCM). The simulated resonance Raman spectra show good agreement with the experimental spectra in terms of both peak positions and intensities. The differences between the resonance Raman spectra of the three 5-halogenated uracils, caused by the effect of halogen substitution, are examined in terms of ground-state normal-mode eigenvectors and excited-state Cartesian gradients, according to the HT formalism. The differences in the normal-mode eigenvectors and excited-state Cartesian gradients between 5-fluorouracil and 5-chlorouracil are used to interpret the dissimilarity between their resonance Raman spectra. Meanwhile, the similarity between the spectra of 5-chlorouracil and 5-bromouracil is explained by the correspondence between their normal modes and excited-state gradients.

  7. Effective field theory of cosmic acceleration: Constraining dark energy with CMB data

    NASA Astrophysics Data System (ADS)

    Raveri, Marco; Hu, Bin; Frusciante, Noemi; Silvestri, Alessandra

    2014-08-01

    We introduce EFTCAMB/EFTCosmoMC as publicly available patches to the commonly used camb/CosmoMC codes. We briefly describe the structure of the codes, their applicability and main features. To illustrate the use of these patches, we obtain constraints on parametrized pure effective field theory and designer f(R) models, both on ΛCDM and wCDM background expansion histories, using data from Planck temperature and lensing potential spectra, WMAP low-ℓ polarization spectra (WP), and baryon acoustic oscillations (BAO). Upon inspecting the theoretical stability of the models on the given background, we find nontrivial parameter spaces that we translate into viability priors. We use different combinations of data sets to show their individual effects on cosmological and model parameters. Our data analysis results show that, depending on the adopted data sets, in the wCDM background case these viability priors could dominate the marginalized posterior distributions. Interestingly, with Planck +WP+BAO+lensing data, in f(R) gravity models, we get very strong constraints on the constant dark energy equation of state, w0∈(-1,-0.9997) (95% C.L.).

  8. The origin of the unusual broad and intense visible absorption of tetrathiafulvalene-annulated zinc porphyrazine: a density functional theory study.

    PubMed

    Tao, Wei; Kan, Yu-He; Wu, Shui-Xing; Li, Hai-Bin; Yan, Li-Kai; Sun, Shi-Ling; Su, Zhong-Min

    2012-03-01

    The vertical excitation energies of tetrathiafulvalene (TTF)-annulated zinc porphyrazine (ZnPzTTF) were investigated using time-dependent density functional theory (TDDFT) calculations and compared to the experimental UV-vis spectra. To examine the effects of the aza substitutions and TTF groups on the molecular properties, zinc complexes of porphyrin (ZnP), porphyrazine (ZnPz) and tetraTTF-annulated porphyrin (ZnPTTF) were also selected for comparison. It was shown that numerous electronic transitions with TTF-to-porphyrin or porphyrazine charge transfer character exist and the Q band of ZnPzTTF is dominated by TTF-to-porphyrazine charge transfer transition mixed with porphyrazine core unit itself except for classic porphyrazine π→π* transitions. The Q band of ZnPzTTF mixes with other configurations, which breaks down the Gouterman's classic four-orbital model for the spectral interpretation. The data suggest that TDDFT/SAOP performs best for Q and B bands of ZnPzTTF with the maximum error in excitation energy being 0.17 eV. The CAM-B3LYP, ωB97XD and M06-2X calculations qualitatively predict that the low-lying electronic transitions of ZnPzTTF with TTF-to-porphyrazine charge transfer character located below the Q band. The broad and intense red-shifted Q band suggests that ZnPzTTF can be a candidate for dye-sensitized solar cells.

  9. The role of high-level calculations in the assignment of the Q-band spectra of chlorophyll

    SciTech Connect

    Reimers, Jeffrey R.; Cai, Zheng-Li; Kobayashi, Rika; Rätsep, Margus; Freiberg, Arvi; Krausz, Elmars

    2014-10-06

    We recently established a novel assignment of the visible absorption spectrum of chlorophyll-a that sees the two components Q{sub x} and Q{sub y} of the low-energy Q band as being intrinsically mixed by non-adiabatic coupling. This ended 50 years debate as to the nature of the Q bands, with prior discussion poised only in the language of the Born-Oppenheimer and Condon approximations. The new assignment presents significant ramifications for exciton transport and quantum coherence effects in photosystems. Results from state of the art electronic structure calculations have always been used to justify assignments, but quantitative inaccuracies and systematic failures have historically limited usefulness. We examine the role of CAM-B3LYP time-dependent density-functional theory (TD-DFT) and Symmetry Adapted Cluster-Configuration Interaction (SAC-CI) calculations in first showing that all previous assignments were untenable, in justifying the new assignment, in making some extraordinary predictions that were vindicated by the new assignment, and in then identifying small but significant anomalies in the extensive experimental data record.

  10. Reliable modeling of the electronic spectra of realistic uranium complexes

    NASA Astrophysics Data System (ADS)

    Tecmer, Paweł; Govind, Niranjan; Kowalski, Karol; de Jong, Wibe A.; Visscher, Lucas

    2013-07-01

    We present an EOMCCSD (equation of motion coupled cluster with singles and doubles) study of excited states of the small [UO2]2+ and [UO2]+ model systems as well as the larger UVIO2(saldien) complex. In addition, the triples contribution within the EOMCCSDT and CR-EOMCCSD(T) (completely renormalized EOMCCSD with non-iterative triples) approaches for the [UO2]2+ and [UO2]+ systems as well as the active-space variant of the CR-EOMCCSD(T) method—CR-EOMCCSd(t)—for the UVIO2(saldien) molecule are investigated. The coupled cluster data were employed as benchmark to choose the "best" appropriate exchange-correlation functional for subsequent time-dependent density functional (TD-DFT) studies on the transition energies for closed-shell species. Furthermore, the influence of the saldien ligands on the electronic structure and excitation energies of the [UO2]+ molecule is discussed. The electronic excitations as well as their oscillator dipole strengths modeled with TD-DFT approach using the CAM-B3LYP exchange-correlation functional for the [UVO2(saldien)]- with explicit inclusion of two dimethyl sulfoxide molecules are in good agreement with the experimental data of Takao et al. [Inorg. Chem. 49, 2349 (2010), 10.1021/ic902225f].

  11. Spectroscopic, DFT and Z-scan supported investigation of dicyanoisophorone based push-pull NLOphoric styryl dyes

    NASA Astrophysics Data System (ADS)

    Erande, Yogesh; Sreenath, Mavila C.; Chitrambalam, Subramaniyan; Joe, Isaac H.; Sekar, Nagaiyan

    2017-04-01

    The dicyanoisophorone acceptor based NLOphores with Intramolecular Charge Transfer (ICT) character are newly synthesised, characterised and explored for linear and non linear optical (NLO) property investigation. Strong ICT character of these D-π-A styryl NLOphores is established with support of emission solvatochromism, polarity functions and Generalised Mulliken Hush (GMH) analysis. First, second and third order polarizability of these NLOphores is investigated by spectroscopic and TDDFT computational approach using CAM/B3LYP-6-311 + g (d, p) method. BLA and BOA values of these chromophores are evaluated from ground and excited state optimized geometries and found that the respective structures are approaching towards cyanine limit. Third order nonlinear susceptibility (X(3)) along with nonlinear absorption coefficient (β) and nonlinear refraction (n2) are evaluated for these NLOphores using Z-scan experiment. All four chromophores exhibit large polarization anisotropy (Δα), first order hyperpolarizability (β0), second order hyperpolarizability (γ) and third order nonlinear susceptibility (X(3)). TGA analysis proved these NLOphores are stable up to 320 °C and hence can be used in device fabrication.

  12. Structural and static electric response properties of highly symmetric lithiated silicon cages: theoretical predictions.

    PubMed

    Koukaras, Emmanuel N; Zdetsis, Aristides D; Karamanis, Panaghiotis; Pouchan, Claude; Avramopoulos, Aggelos; Papadopoulos, Manthos G

    2012-04-15

    It is shown by density functional theory calculations that high symmetry silicon cages can be designed by coating with Li atoms. The resulting highly symmetric lithiated silicon cages (up to D(5d) symmetry) are low-lying true minima of the energy hypersurface with binding energies of the order of 4.6 eV per Si atom and moderate highest occupied molecular orbital-lowest unoccupied molecular orbital gaps. Moreover, relying on a systematic study of the electric response properties obtained by ab initio (Hartree-Fock, MP2, and configuration interaction singles (CIS)) and density functional (B3LYP, B2PLYP, and CAM-B3LYP) methods, it is shown that lithium coating has a large impact on the magnitude of their second hyperpolarizabilities resulting to highly hyperpolarizable species. Such hyperpolarizable character is directly connected to the increase in the density of the low-lying excited states triggered by the interaction between the Si cage and the surrounding Li atoms.

  13. π-Extension of a 4-ethoxy-1,3-thiazole via aryl alkyne cross coupling: synthesis and exploration of the electronic structure.

    PubMed

    Habenicht, Stefanie H; Schramm, Stefan; Zhu, Mingming; Freund, Robert R A; Langenstück, Teresa; Strathausen, Rainer; Weiss, Dieter; Biskup, Christoph; Beckert, Rainer

    2015-11-01

    A series of four donor aryl alkynyl substituted thiazole derivatives 3a-d and three similar aryl donor-acceptor systems 6a-c have been synthesized. All compounds bear different electron-donating groups in the 5-position of the thiazole core. The influence of both electron donor strength and the additional phenylethynyl unit on photophysical properties, i.e. UV/Vis absorption, fluorescence emission and fluorescence lifetime, has been evaluated. Additionally, theoretical calculations have been performed at the CAM-B3LYP/6-31+G(d,p) level and good agreement with the experimental data has been achieved. The new derivatives synthesized via palladium catalyzed cross coupling are characterised by moderately strong emission between 474 and 538 nm (ΦF = 0.35-0.39) and Stokes' shifts ranging from 0.54 to 0.79 eV (4392-6351 cm(-1)). The smaller chromophores of type 6 exhibit modest to high fluorescence emission (ΦF = 0.45-0.76) between 470 and 529 nm and their Stokes' shifts range from 0.59 to 0.65 eV (4765-5251 cm(-1)).

  14. Microbial diversity in a bagasse-based compost prepared for the production of Agaricus brasiliensis.

    PubMed

    Silva, Cristina Ferreira; Azevedo, Raquel Santos; Braga, Claudia; da Silva, Romildo; Dias, Eustáquio Souza; Schwan, Rosane Freitas

    2009-07-01

    Edible mushrooms are renowned for their nutritional and medicinal properties and are thus of considerable commercial importance. Mushroom production depends on the chemical composition of the basic substrates and additional supplements employed in the compost as well as on the method of composting. In order to minimise the cost of mushroom production, considerable interest has been shown in the use of agro-industrial residues in the preparation of alternative compost mixtures. However, the interaction of the natural microbiota present in agricultural residues during the composting process greatly influences the subsequent colonisation by the mushroom. The aim of the present study was to isolate and identify the microbiota present in a sugar cane bagasse and coast-cross straw compost prepared for the production of Agaricus brasilienses. Composting lasted for 14 days, during which time the substrates and additives were mixed every 2 days, and this was followed by a two-step steam pasteurisation (55 - 65°C; 15 h each step). Bacteria, (mainly Bacillus and Paenibacillus spp. and members of the Enterobacteriaceae) were the predominant micro-organisms present throughout the composting process with an average population density of 3 x 10(8) CFU/g. Actinomycetes, and especially members of the genus Streptomyces, were well represented with a population density of 2 - 3 x 10(8) CFU/g. The filamentous fungi, however, exhibited much lower population densities and were less diverse than the other micro-organisms, although Aspergillus fumigatus was present during the whole composting process and after pasteurisation.

  15. Transporters in the Paracoccidioides brasiliensis transcriptome: insights on drug resistance.

    PubMed

    Costa, Christiane da Silva; Albuquerque, Flávia Caixeta; Andrade, Rosângela Vieira; Oliveira, Gina Camilo de; Almeida, Mauro Fernandes de; Brigido, Marcelo de Macedo; Maranhão, Andrea Queiroz

    2005-06-30

    In the struggle for life, the capacity of microorganisms to synthesize and secrete toxic compounds (inhibiting competitors) plays an important role in successful survival of these species. This ability must come together with the capability of being unaffected by these same compounds. Several mechanisms are thought to avoid the toxic effects. One of them is toxin extrusion from the intracellular environment to the outside vicinity, using special transmembrane proteins, referred to as transporters. These proteins are also important for other reasons, since most of them are involved in nutrient uptake and cellular excretion. In cancer cells and in pathogens, and particularly in fungi, some of these proteins have been pointed out as responsible for an important phenotype known as multidrug resistance (MDR). In the present study, we tried to identify in the Paracoccidioides brasiliensis transcriptome, transporter-ortholog genes from the two major classes: ATP binding cassette and major facilitator superfamily transporter. We found 22 groups with good similarity with other fungal ATP binding cassette transporters, and four Paracoccidioides brasilienses assembled expressed sequence tags that probably code for major facilitator superfamily proteins. We also focused on fungicide resistance orthologs already characterized in other pathogenic fungi. We were able to find homologs to C. albicans CDR1, CDR2, and MDR1, Saccharomyces cerevisiae PDR5 and Aspergillus AtrF genes, all of them related to azole resistance. As current treatment for paracoccidioidomycosis mainly uses azole derivatives, the presence of these genes can be postulated to play a similar role in P. brasiliensis, warning us for the possibility of resistant isolate emergence.

  16. Induction of reduced photorespiratory activity in submersed and amphibious aquatic macrophytes.

    PubMed

    Salvucci, M E; Bowes, G

    1981-02-01

    Incubation under water in a 30 C/14-hour or 12 C/10-hour photoperiod caused the CO(2) compensation points of 10 aquatic macrophytes to decrease below 25 or increase above 50 microliters CO(2) per liter, respectively. Submerged and aerial leaves of two amphibious angiosperms (Myriophyllum brasiliense and Proserpinaca palustris) maintained high compensation points when incubated in air but, when the submerged or aerial leaves of Proserpinaca were incubated under water, the compensation points dropped as low as 10. This suggests that, in addition to temperature and photoperiod, some factor associated with submergence regulates the compensation point of aquatic plants. In the high-compensation point plants, photorespiration, as a percentage of net photosynthesis, was equivalent to that in terrestrial C(3) plants. For Hydrilla verticillata, the decreasing CO(2) compensation points (110, 40, and 10) were associated with reduced photorespiration, as indicated by decreased O(2) inhibition, decreased rates of CO(2) evolution into CO(2)-free air, and increased net photosynthetic rates.The decrease in the CO(2) compensation points of Hydrilla, Egeria densa, and Cabomba caroliniana was accompanied by an increase in the activity of phosphoenolpyruvate, but not of ribulose bisphosphate, carboxylase. In Hydrilla, several C(4) enzymes also increased in activity to the following levels (micromoles per gram fresh weight per hour): pyruvate Pi dikinase (35), pyrophosphatase (716), adenylate kinase (525), NAD and NADP malate dehydrogenase (6565 and 30), NAD and NADP malic enzymes (239 and 44), and aspartate and alanine aminotransferases (357 and 85), whereas glycolate oxidase (6) and phosphoglycolate and phosphoglycerate phosphatases (76 and 32) showed no change. Glycolate dehydrogenase and phosphoenolpyruvate carboxykinase were undetectable. The reduced photorespiration in these plants may be due to increased CO(2) fixation via a C(4) acid pathway. However, for three Myriophyllum

  17. Assessing the extent of "conflict of use" in multipurpose tropical forest trees: a regional view.

    PubMed

    Herrero-Jáuregui, Cristina; Guariguata, Manuel R; Cárdenas, Dairon; Vilanova, Emilio; Robles, Marco; Licona, Juan Carlos; Nalvarte, Walter

    2013-11-30

    In the context of multiple forest management, multipurpose tree species which provide both timber and non-timber forest products (NTFP), present particular challenges as the potential of conflicting use for either product may be high. One key aspect is that the magnitude of conflict of use can be location specific, thus adding complexity to policy development. This paper focuses on the extent to which the potential for conflict of use in multipurpose tree species varies across the Amazonian lowland forests shared by Peru, Bolivia, Colombia, Ecuador and Venezuela, emphasizing the economic dimension of conflict. Based on a review of the current normative and regulatory aspects of timber and NTFP extraction in the five countries, the paper also briefly discusses the opportunities and constraints for harmonization of timber and NTFP management of multipurpose species across the region. It was found that about half of the 336 timber species reviewed across the five countries also have non-timber uses. Eleven timber species are multipurpose in all five countries: Calophyllum brasiliense, Cedrela odorata, Ceiba pentandra, Clarisia racemosa, Ficus insipida, Jacaranda copaia, Schefflera morototoni, Simarouba amara and Terminalia amazonia. Seven other multipurpose species occurred only in either Venezuela (Tabebuia impetiginosa, Spondias mombin, Pentaclethra macroloba, Copaifera officinalis, Chlorophora tinctoria, Carapa guianensis) or Ecuador (Tabebuia chrysantha). Four multipurpose tree species presented the highest potential of conflict of use across the region: Dipteryx odorata, Tabebuia serratifolia, Hymenaea courbaril and Myroxylon balsamum yet these were not evenly distributed across all five countries. None of the five studied countries have specific legislation to promote sustainable use of any of the multipurpose species reported here and thus mitigate potential conflict of use; nor documented management options for integration or else segregation of both their

  18. [Larva migrans].

    PubMed

    Chabasse, D; Le Clec'h, C; de Gentile, L; Verret, J L

    1995-01-01

    Larbish, cutaneous larva migrans or creeping eruption, is a serpiginous cutaneous eruption caused by skin penetration of infective larva from various animal nematodes. Hookworms (Ancylostoma brasiliense, A. caninum) are the most common causative parasites. They live in the intestines of dogs and cats where their ova are deposited in the animal feces. In sandy and shady soil, when temperature and moisture are elevated, the ova hatch and mature into infective larva. Infection occurs when humans have contact with the infected soil. Infective larva penetrate the exposed skin of the body, commonly around the feet, hands and buttocks. In humans, the larva are not able to complete their natural cycle and remain trapped in the upper dermis of the skin. The disease is widespread in tropical or subtropical regions, especially along the coast on sandy beaches. The diagnosis is easy for the patient who is returning from a tropical or subtropical climate and gives a history of beach exposure. The characteristic skin lesion is a fissure or erythematous cord which is displaced a few millimeters each day in a serpiginous track. Scabies, the larva currens syndrome due to Strongyloides stercoralis, must be distinguished from other creeping eruptions and subcutaneous swelling lesions caused by other nematodes or myiasis. Medical treatments are justified because it shortens the duration of the natural evolution of the disease. Topical tiabendazole is safe for localized invasions, but prolonged treatment may be necessary. Oral thiabendazole treatment for three days is effective, but sometimes is associated with adverse effects. Trials using albendazole for one or four consecutive days appear more efficacious. More recent trials using ivermectine showed that a single oral dose can cure 100% of the patients; thus, this drug looks very promising as a new form of therapy. Individual prophylaxis consists of avoiding skin contact with soil which has been contaminated with dog or cat feces

  19. Structure-activity relationship of (-) mammea A/BB derivatives against Leishmania amazonensis.

    PubMed

    Brenzan, Mislaine Adriana; Nakamura, Celso Vataru; Dias Filho, Benedito Prado; Ueda-Nakamura, Tânia; Young, Maria Claudia M; Côrrea, Arlene Gonçalves; Alvim, Joel; dos Santos, Adriana Oliveira; Cortez, Diógenes Aparício Garcia

    2008-11-01

    To study the structure-activity relationship of coumarin (-) mammea A/BB isolated from the CH(2)Cl(2) extract of Calophyllum brasiliense leaves, we evaluated the antileishmanial activity of natural, synthetic and derivatives of this coumarin, against promastigote and intracellular amastigote forms of Leishmania amazonensis, and their cytotoxicity to J774G8 murine macrophages. The derivatives were obtained by hydrogenation and methoxylation reactions. The compound structures were elucidated on the basis of spectroscopic data. The compounds 5,7-dihydroxy-8-(2-methylbutanoyl)-6-(3-methylbutyl)-4-phenyl-chroman-2-one (3), 7-hydroxy-5-methoxy-8-(2-methylbutanoyl)-6-(3-methylbut-2-en-1-yl)-4-phenylcoumarin (4) and 5,7-dimethoxy-8-(1-methoxy-2-methylbutyl)-6-(3-methylbut-2-en-1-yl)-4 phenylcoumarin (6) were more biologically active than the compound (-) mammea A/BB (1) (7.4 microM), with IC(50) values from 0.9, 2.4 and 1.9 microM respectively; compound (3) displayed the highest activity. The compounds mammea B/BB (2), 5,7-dimethoxy-8-(2-methylbutanoyl)-6-(3-methylbut-2-en-1-yl)-4-phenylcoumarin (5) and 5,7-dihydroxy-4-phenylcoumarin (7) were less active than (-) mammea A/BB (1), with IC(50) of 30.1, 15.1 and 60.2 microM respectively; compound (7) showed the lowest antileishmanial activity of all. Compounds (1), (3), (4) and (6) were active not only against promastigote forms of L. amazonensis, but also against intracellular amastigote forms with IC(50) of 14.3, 0.6, 34.0 and 22.2 microM, respectively. Interestingly, compound (3) showed the most antileishmanial activity of all. This study demonstrated that several aspects of the structure were important for antileishmanial activity.

  20. Initial conditions for accurate N-body simulations of massive neutrino cosmologies

    NASA Astrophysics Data System (ADS)

    Zennaro, M.; Bel, J.; Villaescusa-Navarro, F.; Carbone, C.; Sefusatti, E.; Guzzo, L.

    2017-04-01

    The set-up of the initial conditions in cosmological N-body simulations is usually implemented by rescaling the desired low-redshift linear power spectrum to the required starting redshift consistently with the Newtonian evolution of the simulation. The implementation of this practical solution requires more care in the context of massive neutrino cosmologies, mainly because of the non-trivial scale-dependence of the linear growth that characterizes these models. In this work, we consider a simple two-fluid, Newtonian approximation for cold dark matter and massive neutrinos perturbations that can reproduce the cold matter linear evolution predicted by Boltzmann codes such as CAMB or CLASS with a 0.1 per cent accuracy or below for all redshift relevant to non-linear structure formation. We use this description, in the first place, to quantify the systematic errors induced by several approximations often assumed in numerical simulations, including the typical set-up of the initial conditions for massive neutrino cosmologies adopted in previous works. We then take advantage of the flexibility of this approach to rescale the late-time linear power spectra to the simulation initial redshift, in order to be as consistent as possible with the dynamics of the N-body code and the approximations it assumes. We implement our method in a public code (REPS rescaled power spectra for initial conditions with massive neutrinos https://github.com/matteozennaro/reps) providing the initial displacements and velocities for cold dark matter and neutrino particles that will allow accurate, i.e. 1 per cent level, numerical simulations for this cosmological scenario.

  1. Copper(II) interacting with the non-steroidal antiinflammatory drug flufenamic acid: structure, antioxidant activity and binding to DNA and albumins.

    PubMed

    Tolia, Charikleia; Papadopoulos, Athanassios N; Raptopoulou, Catherine P; Psycharis, Vassilis; Garino, Claudio; Salassa, Luca; Psomas, George

    2013-06-01

    Copper(II) complexes with the non-steroidal antiinflammatory drug flufenamic acid (Hfluf) in the presence of N,N-dimethylformamide (DMF) or nitrogen donor heterocyclic ligands (2,2'-bipyridylamine (bipyam), 1,10-phenanthroline (phen), 2,2'-bipyridine (bipy) or pyridine (py)) have been synthesized and characterized. The crystal structures of [Cu2(fluf)4(DMF)2], 1, and [Cu(fluf)(bipyam)Cl], 2, have been determined by X-ray crystallography. Density functional theory (DFT) (CAM-B3LYP/LANL2DZ/6-31G**) was employed to determine the structure of complex 2 and its analogues (complexes [Cu(fluf)(phen)Cl], 3, [Cu(fluf)(bipy)Cl], 4 and [Cu(fluf)2(py)2], 5). Time-dependent DFT calculations of doublet-doublet transitions show that the lowest-energy band in the absorption spectrum of 2-5 has a mixed d-d/LMCT character. UV study of the interaction of the complexes with calf-thymus DNA (CT DNA) has shown that the complexes can bind to CT DNA with [Cu(fluf)(bipy)Cl] exhibiting the highest binding constant to CT DNA. The complexes can bind to CT DNA via intercalation as concluded by studying the cyclic voltammograms of the complexes in the presence of CT DNA solution and by DNA solution viscosity measurements. Competitive studies with ethidium bromide (EB) have shown that the complexes can displace the DNA-bound EB suggesting strong competition with EB. Flufenamic acid and its Cu(II) complexes exhibit good binding affinity to human or bovine serum albumin protein with high binding constant values. All compounds have been tested for their antioxidant and free radical scavenging activity as well as for their in vitro inhibitory activity against soybean lipoxygenase showing significant activity with [Cu(fluf)(phen)Cl] being the most active.

  2. Substituent Effects on the Absorption and Fluorescence Properties of Anthracene.

    PubMed

    Abou-Hatab, Salsabil; Spata, Vincent A; Matsika, Spiridoula

    2017-02-16

    Substitution can be used to efficiently tune the photophysical properties of chromophores. In this study, we examine the effect of substituents on the absorption and fluorescence properties of anthracene. The effects of mono-, di-, and tetrasubstitution of electron-donating and -withdrawing functional groups were explored. In addition, the influence of a donor-acceptor substituent pair and the position of substitution were investigated. Eleven functional groups were varied on positions 1, 2, and 9 of anthracene, and on position 6 of 2-methoxyanthracene and 2-carboxyanthracene. Moreover, the donor-acceptor pair NH2/CO2H was added on different positions of anthracene for additional studies of doubly substituted anthracenes. Finally, we looked into quadruple substitutions on positions 1,4,5,8 and 2,3,6,7. Vertical excitation energies and oscillator strengths were computed using density functional theory with the hybrid CAM-B3LYP functional and 6-311G(d) basis set. Correlations between the excitation energies or oscillator strengths of the low-lying bright La state and the Hammett sigma parameter, σp(+), of the substituents were examined. The energy is red-shifted for all cases of substitution. Oscillator strengths increase when substituents are placed along the direction of the transition dipole moment of the bright La excited state. Substitution of long chain conjugated groups significantly increases the oscillator strength in comparison to the cases for other substituents. In addition, the results of quadruply substituted geometries reveal symmetric substitution at the 1,4,5,8 positions significantly increases the oscillator strength and can lower the band gap compared to that of the unsubstituted anthracene molecule by up to 0.5 eV.

  3. DFT Study of the Structure, Reactivity, Natural Bond Orbital and Hyperpolarizability of Thiazole Azo Dyes

    PubMed Central

    Osman, Osman I.

    2017-01-01

    The structure, reactivity, natural bond orbital (NBO), linear and nonlinear optical (NLO) properties of three thiazole azo dyes (A, B and C) were monitored by applying B3LYP, CAM-B3LYP and ωB97XD functionals with 6-311++G** and aug-cc-pvdz basis sets. The geometrical parameters, dipole moments, HOMO-LUMO (highest occupied molecular orbital, lowest unoccupied molecular orbital) energy gaps, absorption wavelengths and total hyperpolarizabilities were investigated in carbon tetrachloride (CCl4) chloroform (CHCl3), dichloromethane (CH2Cl2) and dimethlysulphoxide (DMSO). The donor methoxyphenyl group deviates from planarity with the thiazole azo moiety by ca. 38°; while the acceptor dicyanovinyl, indandione and dicyanovinylindanone groups diverge by ca. 6°. The HOMOs for the three dyes are identical. They spread over the methoxyphenyl donor moiety, the thiazole and benzene rings as π-bonding orbitals. The LUMOs are shaped up by the nature of the acceptor moieties. The LUMOs of the A, B and C dyes extend over the indandione, malononitrile and dicyanovinylindanone acceptor moieties, respectively, as π-antibonding orbitals. The HOMO-LUMO splittings showed that Dye C is much more reactive than dyes A and B. Compared to dyes A and B, Dye C yielded a longer maximum absorption wavelength because of the stabilization of its LUMOs relative to those of the other two. The three dyes show solvatochromism accompanied by significant increases in hyperpolarizability. The enhancement of the total hyperpolarizability of C compared to those of A and B is due to the cumulative action of the long π-conjugation of the indanone ring and the stronger electron-withdrawing ability of the dicyanovinyl moiety that form the dicyanovinylindanone acceptor group. These findings are facilitated by a natural bond orbital (NBO) technique. The very high total hyperpolarizabilities of the three dyes define their potent nonlinear optical (NLO) behaviour. PMID:28157151

  4. A DFT study on the complex formation between desferrithiocin and metal ions (Mg(2+), Al(3+), Ca(2+), Mn(2+), Fe(3+), Co(2+), Ni(2+), Cu(2+), Zn(2+)).

    PubMed

    Kaviani, Sadegh; Izadyar, Mohammad; Housaindokht, Mohammad Reza

    2017-04-01

    In recent years, Metal-chelating compounds, namely siderphores have been considered very much because of their crucial role in various fields of the environmental researches. Their importance lies in the fact that they are able to be bonded to a variety of metals in addition to iron. A theoretical study on the structures of desferrithiocin siderphore coordinated to Mg(2+), Al(3+), Ca(2+), Mn(2+), Fe(3+), Co(2+), Ni(2+), Cu(2+) and Zn(2+) metal ions was carried out, using the CAM-B3LYP/6-31G(d) level of the theory in the water. In order to understand the factors which control the stability, reactivity and the strength of toxic metals excretion as well as microbial uptake of the metal-siderphore complexes, we examined the stability and binding energies of the desferrithiocin and various metal ions with different spin states. The binding affinity of desferrithiocin to Fe(3+) (log β2=23.88) showed that the desferrithiocin can scavenge the excess iron(III) from the labile sources. Also, the binding energy values were well described by addition of the dispersion-corrected D3 functional. Because of the importance of the charge transfer in the complex formation, donor-acceptor interaction energies were evaluated. Based on this analysis, an increase in the effective nuclear charge increases E(2) values. Vibrational analysis showed that the critical bonds (CO stretching and CH bending) are in the range of 1300-1800cm(-1). Finally, some probable correlations between the complexation behavior and quantum chemistry descriptors have been analyzed.

  5. Theoretical Studies on F(-) + NH2Cl Reaction: Nucleophilic Substitution at Neutral Nitrogen.

    PubMed

    Liu, Xu; Zhang, Jiaxu; Yang, Li; Sun, Rui

    2016-05-26

    The SN2 reactions at N center, denoted as SN2@N, has been recognized to play a significant role in carcinogenesis, although they are less studied and less understood. The potential energy profile for the model reaction of SN2@N, chloramine (NH2Cl) with fluorine anion (F(-)), has been characterized by extensive electronic structure calculations. The back-side SN2 channel dominates the reaction with the front-side SN2 channel becoming feasible at higher energies. The minimum energy pathway shows a resemblance to the well-known double-well potential model for SN2 reactions at carbon. However, the complexes involving nitrogen on both sides of the reaction barrier are characterized by NH---X (X = F or Cl) hydrogen bond and possess C1 symmetry, in contrast to the more symmetric ion-dipole carbon analogues. In the F(-) + NH2Cl system, the proton transfer pathway is found to become more competitive with the SN2 pathway than in the F(-) + CH3Cl system. The calculations reported here indicate that stationary point properties on the F(-) + NH2Cl potential energy surface are slightly perturbed by the theories employed. The MP2 and CAM-B3LYP, as well as M06-2X and MPW1K functionals give overall best agreement with the benchmark CCSD(T)/CBS energies for the major SN2 reaction channel, and are recommended as the preferred methods for the direct dynamics simulations to uncover the dynamic behaviors of the title reaction.

  6. Competing E2 and SN2 Mechanisms for the F(-) + CH3CH2I Reaction.

    PubMed

    Yang, Li; Zhang, Jiaxu; Xie, Jing; Ma, Xinyou; Zhang, Linyao; Zhao, Chenyang; Hase, William L

    2017-02-09

    Anti-E2, syn-E2, inv-, and ret-SN2 reaction channels for the gas-phase reaction of F(-) + CH3CH2I were characterized with a variety of electronic structure calculations. Geometrical analysis confirmed synchronous E2-type transition states for the elimination of the current reaction, instead of nonconcerted processes through E1cb-like and E1-like mechanisms. Importantly, the controversy concerning the reactant complex for anti-E2 and inv-SN2 paths has been clarified in the present work. A positive barrier of +19.2 kcal/mol for ret-SN2 shows the least feasibility to occur at room temperature. Negative activation energies (-16.9, -16.0, and -4.9 kcal/mol, respectively) for inv-SN2, anti-E2, and syn-E2 indicate that inv-SN2 and anti-E2 mechanisms significantly prevail over the eclipsed elimination. Varying the leaving group for a series of reactions F(-) + CH3CH2Y (Y = F, Cl, Br, and I) leads to monotonically decreasing barriers, which relates to the gradually looser TS structures following the order F > Cl > Br > I. The reactivity of each channel nearly holds unchanged except for the perturbation between anti-E2 and inv-SN2. RRKM calculation reveals that the reaction of the fluorine ion with ethyl iodide occurs predominately via anti-E2 elimination, and the inv-SN2 pathway is suppressed, although it is energetically favored. This phenomenon indicates that, in evaluating the competition between E2 and SN2 processes, the kinetic or dynamical factors may play a significant role. By comparison with benchmark CCSD(T) energies, MP2, CAM-B3LYP, and M06 methods are recommended to perform dynamics simulations of the title reaction.

  7. Computational study of the one- and two-photon absorption and circular dichroism of (L)-tryptophan.

    PubMed

    Guillaume, Maxime; Ruud, Kenneth; Rizzo, Antonio; Monti, Susanna; Lin, Zijing; Xu, Xuee

    2010-05-20

    A density functional theory (DFT) study of the one- and two-photon absorption and circular dichroism spectra of (l)-tryptophan in water is presented. The effects on the simulated spectra of conformational averaging, of solvent as described by the polarizable continuum model (PCM), and of the choice of exchange-correlation (XC) functional are analyzed. Conformational Maxwell-Boltzmann (MB) averaging is carried out at room temperature in the gas phase using the ten lowest-energy conformers in the gas phase, whereas in the solvent, the nine lowest zwitterionic conformers are determined in combination with a PCM continuum model and employed in the calculations. One- and two-photon absorption and circular dichroism spectra are calculated using time-dependent DFT with both the B3LYP and CAM-B3LYP XC functionals, including the 15 lowest excited electronic states in each case. The spectra are shown to be strongly influenced by all parameters of our computational models. Changing the XC functional yields large changes not only in the excitation energies but also in the transition dipole moments and the rotational strengths of each excited state. The inclusion of the effect of water solvation also yields different response properties for each excited state, as well as different ground-state equilibrium geometries for the gas and solvated phases. MB weights change significantly from the gas to the solvated phase, making the effect of conformational averaging strongly phase dependent. The study of all these effects highlights the importance of an accurate and reliable treatment of both ground and excited states when aiming at predicting experimental one- or two-photon spectra. However, the comparison between the MB weighted spectra and experiment for the linear spectroscopies turns out to be rather satisfactory, showing that our approach can yield at least information on the major features of the spectra.

  8. Rayleigh light scattering properties of atmospheric molecular clusters consisting of sulfuric acid and bases.

    PubMed

    Elm, Jonas; Norman, Patrick; Mikkelsen, Kurt V

    2015-06-28

    The Rayleigh light scattering properties of (H2SO4)a(NH3)b and (H2SO4)a((CH3)2NH)b atmospheric molecular clusters have been investigated using a response theory approach. Using density functional theory the molecular structures and stepwise formation free energies of clusters with a and b up to 4 have been re-investigated. The Rayleigh scattering intensities are calculated from the dipole polarizability tensor α using the CAM-B3LYP functional by applying linear response methods. The intrinsic scattering properties of (H2SO4)a(NH3)b and (H2SO4)a((CH3)2NH)b indicate that amine containing clusters scatter light significantly more efficiently then their ammonia containing counterparts. Using the Atmospheric Cluster Dynamics Code (ACDC) the steady state cluster concentrations are estimated and the effective scattering is calculated. The effective scattering is shown to be highly dependent on the estimated concentrations and indicates that there exist competitive pathways, such as nucleation and coagulation, which influence the cluster distributions. The frequency dependence of the scattering is found to depend on the cluster composition and show increased responses when clusters contain more bases than acid molecules. Based on structures obtained using semi-empirical molecular dynamics simulations the Rayleigh scattering properties of clusters with up to 20 acid-base pairs are evaluated. This study represents the first step towards gaining a fundamental understanding of the scattering properties of small atmospheric clusters in the ambient atmosphere.

  9. Non-equilibrium Thermodynamics of Rayleigh-Taylor instability

    NASA Astrophysics Data System (ADS)

    Sengupta, Tapan K.; Sengupta, Aditi; Shruti, K. S.; Sengupta, Soumyo; Bhole, Ashish

    2016-10-01

    Rayleigh-Taylor instability (RTI) has been studied here as a non-equilibrium thermodynamics problem. Air masses with temperature difference of 70K, initially with heavier air resting on lighter air isolated by a partition, are allowed to mix by impulsively removing the partition. This results in interface instabilities, which are traced here by solving two dimensional (2D) compressible Navier-Stokes equation (NSE), without using Boussinesq approximation (BA henceforth). The non-periodic isolated system is studied by solving NSE by high accuracy, dispersion relation preserving (DRP) numerical methods described in Sengupta T.K.: High Accuracy Computing Method (Camb. Univ. Press, USA, 2013). The instability onset is due to misaligned pressure and density gradients and is evident via creation and evolution of spikes and bubbles (when lighter fluid penetrates heavier fluid and vice versa, associated with pressure waves). Assumptions inherent in compressible formulation are: (i) Stokes' hypothesis that uses zero bulk viscosity assumption and (ii) the equation of state for perfect gas which is a consequence of equilibrium thermodynamics. Present computations for a non-equilibrium thermodynamic process do not show monotonic rise of entropy with time, as one expects from equilibrium thermodynamics. This is investigated with respect to the thought-experiment. First, we replace Stokes' hypothesis, with another approach where non-zero bulk viscosity of air is taken from an experiment. Entropy of the isolated system is traced, with and without the use of Stokes' hypothesis. Without Stokes' hypothesis, one notes the rate of increase in entropy to be higher as compared to results with Stokes' hypothesis. We show this using the total entropy production for the thermodynamically isolated system. The entropy increase from the zero datum is due to mixing in general; punctuated by fluctuating entropy due to creation of compression and rarefaction fronts originating at the interface

  10. Ionization potential and electron affinity for six common explosive compounds by DFT, MP2, and CBS-QB3

    SciTech Connect

    Cooper, Jason K.; Grant, Christian D.; Zhang, Jin Z.

    2012-07-20

    The vertical and adiabatic ionization potential (IPV and IPA) and vertical electron affinity (EAV) for six explosives (RDX, HMX, TNT, PETN, HMTD, and TATP) have been studied by ab initio computational methods. The IPV was calculated using MP2 and CBS-QB3 while the IPA was calculated with B3LYP, CAM-B3LYP, ω B97XD, B2PLYP, and MP2. RDX and TNT IPA’s were also reported using CBS -QB3. Excluding results by CBS-QB3, B3LYP and B2PLYPD provided superior and more consistent results for calculating the IP. The EAV were calculated using the same methods however B3LYP performed the worst in this case with MP2 and B2PLYPD predicting values closest to those made by CBS-QB3, which was used a reference due to lacking experimental data. Basis set effects were evaluated using 6- 31+G(d,p), 6-311+G(d,p), and 6-311+(3df,2p) for both IP and EA. 6-31+G(d,p) gave satisfactory results for calculating both IP however 6-311+G(3df,2p) had improved results in calculating the EA. The four nitro containing compounds had exothermic reduction potentials while the peroxides were unfavorable. Additionally, it was seen that RDX, HMX, TATP and HMTD were unstable in their reduced forms. Results are aimed to assist detection and screening methods.

  11. Interaction between transition metals and phenylalanine: a combined experimental and computational study.

    PubMed

    Elius Hossain, Md; Mahmudul Hasan, Md; Halim, M E; Ehsan, M Q; Halim, Mohammad A

    2015-03-05

    Some transition metal complexes of phenylalanine of general formula [M(C9H10NO2)2]; where M=Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) are prepared in aqueous medium and characterized by spectroscopic, thermo-gravimetric (TG) and magnetic susceptibility analysis. Density functional theory (DFT) has been employed calculating the equilibrium geometries and vibrational frequencies of those complexes at B3LYP level of theory using 6-31G(d) and SDD basis sets. In addition, frontier molecular orbital and time-dependent density functional theory (TD-DFT) calculations are performed with CAM-B3LYP/6-31+G(d,p) and B3LYP/SDD level of theories. Thermo-gravimetric analysis confirms the composition of the complexes by comparing the experimental and calculated data for C, H, N and metals. Experimental and computed IR results predict a significant change in vibrational frequencies of metal-phenylalanine complexes compared to free ligand. DFT calculation confirms that Mn, Co, Ni and Cu complexes form square planar structure whereas Zn adopts distorted tetrahedral geometry. The metal-oxygen bonds in the optimized geometry of all complexes are shorter compared to the metal-nitrogen bonds which is consistent with a previous study. Cation-binding energy, enthalpy and Gibbs free energy indicates that these complexes are thermodynamically stable. UV-vis and TD-DFT studies reveal that these complexes demonstrate representative metal-to-ligand charge transfer (MLCT) and d-d transitions bands. TG analysis and IR spectra of the metal complexes strongly support the absence of water in crystallization. Magnetic susceptibility data of the complexes exhibits that all except Zn(II) complex are high spin paramagnetic.

  12. Interaction between transition metals and phenylalanine: A combined experimental and computational study

    NASA Astrophysics Data System (ADS)

    Elius Hossain, Md.; Mahmudul Hasan, Md.; Halim, M. E.; Ehsan, M. Q.; Halim, Mohammad A.

    2015-03-01

    Some transition metal complexes of phenylalanine of general formula [M(C9H10NO2)2]; where M = Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) are prepared in aqueous medium and characterized by spectroscopic, thermo-gravimetric (TG) and magnetic susceptibility analysis. Density functional theory (DFT) has been employed calculating the equilibrium geometries and vibrational frequencies of those complexes at B3LYP level of theory using 6-31G(d) and SDD basis sets. In addition, frontier molecular orbital and time-dependent density functional theory (TD-DFT) calculations are performed with CAM-B3LYP/6-31+G(d,p) and B3LYP/SDD level of theories. Thermo-gravimetric analysis confirms the composition of the complexes by comparing the experimental and calculated data for C, H, N and metals. Experimental and computed IR results predict a significant change in vibrational frequencies of metal-phenylalanine complexes compared to free ligand. DFT calculation confirms that Mn, Co, Ni and Cu complexes form square planar structure whereas Zn adopts distorted tetrahedral geometry. The metal-oxygen bonds in the optimized geometry of all complexes are shorter compared to the metal-nitrogen bonds which is consistent with a previous study. Cation-binding energy, enthalpy and Gibbs free energy indicates that these complexes are thermodynamically stable. UV-vis and TD-DFT studies reveal that these complexes demonstrate representative metal-to-ligand charge transfer (MLCT) and d-d transitions bands. TG analysis and IR spectra of the metal complexes strongly support the absence of water in crystallization. Magnetic susceptibility data of the complexes exhibits that all except Zn(II) complex are high spin paramagnetic.

  13. Differential physiological and molecular response of barley genotypes to water deficit.

    PubMed

    de Mezer, Mateusz; Turska-Taraska, Anna; Kaczmarek, Zygmunt; Glowacka, Katarzyna; Swarcewicz, Barbara; Rorat, Tadeusz

    2014-07-01

    Changes in physiological parameters (relative water content (RWC), biomass, water use efficiency (WUE), net photosynthetic yield (PN) and quantum yield of PSII (Fv/Fm)), in proline and sugar content, and expression profile of genes reported to be associated with the barley response to water deficit, including LEA genes, NHX1, Hsdr4, BLT101 and genes encoding transcription factors (HvDREB1, HvABF1, HvABI5 and HvZIP1), were analyzed in seedlings of nine barley genotypes subjected to a progressive increase in water deficit. Seedlings of all genotypes wilted when the soil water content (SWC) declined from 65% (control conditions) to 10% (severe drought conditions), but recovered turgor within a few hours of re-watering. However, when severe drought conditions were prolonged for a week, large differences in survival characteristics were observed between genotypes after re-watering. Multivariate analysis of the changes in physiological and molecular characteristics allowed several different homogenous groups within the genotypes to be distinguished, depending on stress intensity. Furthermore, integration between the stress-response traits was found and was shown to vary depending on the genotype and the stress level. Based on analysis of physiological traits and survival characteristics, two barley genotypes with high adaptability to the stress conditions (cv. Saida and breeding line Cam/B1), and two with low adaptability (cv. Express and breeding line Harmal), were identified. In addition, only changes in expression of the genes HvZIP1, encoding a b-ZIP-type transcription factor, and Hsdr4, encoding a protein of unknown function, were shown to be linked with adaptability of barley to water deficit. In summary, physiological and molecular data revealed large, stress-level-dependent differences between the barley cultivars and breeding lines tested in their response to water deficit.

  14. Spectroscopic (FT-IR, FT-Raman, FT-NMR and UV-Vis) investigation on benzil dioxime using quantum computational methods

    NASA Astrophysics Data System (ADS)

    Bakkiyaraj, D.; Periandy, S.; Xavier, S.

    2016-03-01

    The spectral analysis of benzil dioxime is carried out using the FTIR, FT Raman, FT NMR and UV-Vis spectra of the compound with the help of quantum computations by density functional theories. The FT-IR (4000 - 400 cm-1) and FT-Raman (4000-100 cm-1) spectra are recorded in solid phase, the 1H and 13C NMR spectra in DMSO phase and the UV spectrum (200-400 nm) in ethanol phase. The different conformers of the compound and their minimum energies are studied by potential energy surface scan, using semi-empirical method PM6. The computed wavenumbers from different methods are scaled so as to agree with the experimental values and the scaling factors are reported. All the fundamental modes have been assigned based on the potential energy distribution (PED) values and the structure the molecule is analyzed interms of parameters like bond length, bond angle and dihedral angles predicted byB3LYP and CAM-B3LYP methods with cc-pVDZ basis sets. The values of dipole moment (μ), polarizability (α) and hyperpolarizability (β) of the molecule are reported, using which the non -linear optical property of the molecule is discussed. The HOMO-LUMO mappings are reported which reveals the different charge transfer possibilities within the molecule. The isotropic chemical shifts predicted for 1H and 13C atoms using gauge invariant atomic orbital (GIAO) theory show good agreement with experimental shifts and the same is discussed in comparison with atomic charges, predicted by Mullikan and APT charge analysis. NBO analysis is carried out to picture the probable electronic transitions in the molecule.

  15. Involvement of Phospholipase Cγ1 in Mouse Egg Activation Induced by a Truncated Form of the C-kit Tyrosine Kinase Present in Spermatozoa

    PubMed Central

    Sette, Claudio; Bevilacqua, Arturo; Geremia, Raffaele; Rossi, Pellegrino

    1998-01-01

    Microinjection of a truncated form of the c-kit tyrosine kinase present in mouse spermatozoa (tr-kit) activates mouse eggs parthenogenetically, and tr-kit– induced egg activation is inhibited by preincubation with an inhibitor of phospholipase C (PLC) (Sette, C., A. Bevilacqua, A. Bianchini, F. Mangia, R. Geremia, and P. Rossi. 1997. Development [Camb.]. 124:2267–2274). Co-injection of glutathione-S-transferase (GST) fusion proteins containing the src-homology (SH) domains of the γ1 isoform of PLC (PLCγ1) competitively inhibits tr-kit– induced egg activation. A GST fusion protein containing the SH3 domain of PLCγ1 inhibits egg activation as efficiently as the whole SH region, while a GST fusion protein containing the two SH2 domains is much less effective. A GST fusion protein containing the SH3 domain of the Grb2 adaptor protein does not inhibit tr-kit–induced egg activation, showing that the effect of the SH3 domain of PLCγ1 is specific. Tr-kit–induced egg activation is also suppressed by co-injection of antibodies raised against the PLCγ1 SH domains, but not against the PLCγ1 COOH-terminal region. In transfected COS cells, coexpression of PLCγ1 and tr-kit increases diacylglycerol and inositol phosphate production, and the phosphotyrosine content of PLCγ1 with respect to cells expressing PLCγ1 alone. These data indicate that tr-kit activates PLCγ1, and that the SH3 domain of PLCγ1 is essential for tr-kit–induced egg activation. PMID:9722617

  16. Comparative Ab-Initio Study of Substituted Norbornadiene-Quadricyclane Compounds for Solar Thermal Storage

    PubMed Central

    2016-01-01

    Molecular photoswitches that are capable of storing solar energy, so-called molecular solar thermal storage systems, are interesting candidates for future renewable energy applications. In this context, substituted norbornadiene-quadricyclane systems have received renewed interest due to recent advances in their synthesis. The optical, thermodynamic, and kinetic properties of these systems can vary dramatically depending on the chosen substituents. The molecular design of optimal compounds therefore requires a detailed understanding of the effect of individual substituents as well as their interplay. Here, we model absorption spectra, potential energy storage, and thermal barriers for back-conversion of several substituted systems using both single-reference (density functional theory using PBE, B3LYP, CAM-B3LYP, M06, M06-2x, and M06-L functionals as well as MP2 calculations) and multireference methods (complete active space techniques). Already the diaryl substituted compound displays a strong red-shift compared to the unsubstituted system, which is shown to result from the extension of the conjugated π-system upon substitution. Using specific donor/acceptor groups gives rise to a further albeit relatively smaller red-shift. The calculated storage energy is found to be rather insensitive to the specific substituents, although solvent effects are likely to be important and require further study. The barrier for thermal back-conversion exhibits strong multireference character and as a result is noticeably correlated with the red-shift. Two possible reaction paths for the thermal back-conversion of diaryl substituted quadricyclane are identified and it is shown that among the compounds considered the path via the acceptor side is systematically favored. Finally, the present study establishes the basis for high-throughput screening of norbornadiene-quadricyclane compounds as it provides guidelines for the level of accuracy that can be expected for key properties from

  17. Constraints on primordial magnetic fields from Planck data combined with the South Pole Telescope CMB B -mode polarization measurements

    NASA Astrophysics Data System (ADS)

    Zucca, Alex; Li, Yun; Pogosian, Levon

    2017-03-01

    A primordial magnetic field (PMF) present before recombination can leave specific signatures on the cosmic microwave background (CMB) fluctuations. Of particular importance is its contribution to the B-mode polarization power spectrum. Indeed, vortical modes sourced by the PMF can dominate the B-mode power spectrum on small scales, as they survive damping up to a small fraction of the Silk length. Therefore, measurements of the B-mode polarization at high ℓ , such as the one recently performed by the South Pole Telescope (SPT), have the potential to provide stringent constraints on the PMF. We use the publicly released SPT B-mode polarization spectrum, along with the temperature and polarization data from the Planck satellite, to derive constraints on the magnitude, the spectral index and the energy scale at which the PMF was generated. We find that, while Planck data constrains the magnetic amplitude to B1 Mpc<3.3 nG at the 95% confidence level (C.L.), the SPT measurement improves the constraint to B1 Mpc<1.5 nG . The magnetic spectral index, nB, and the time of the generation of the PMF are unconstrained. For a nearly scale-invariant PMF, predicted by the simplest inflationary magnetogenesis models, the bound from Planck +SPT is B1 Mpc<1.2 nG at 95% C.L. For PMF with nB=2 , which is expected for fields generated in post-inflationary phase transitions, the 95% C.L. bound is B1 Mpc<0.002 nG , corresponding to the magnetic fraction of the radiation density ΩB γ<10-3 or the effective field Beff<100 nG . The patches for the Boltzmann code camb and the Markov chain Monte Carlo engine CosmoMC, incorporating the PMF effects on CMB, are made publicly available.

  18. The study of ascorbate peroxidase, catalase and peroxidase during in vitro regeneration of Argyrolobium roseum.

    PubMed

    Habib, Darima; Chaudhary, Muhammad Fayyaz; Zia, Muhammad

    2014-01-01

    Here, we demonstrate the micropropagation protocol of Argyrolobium roseum (Camb.), an endangered herb exhibiting anti-diabetic and immune-suppressant properties, and antioxidant enzymes pattern is evaluated. Maximum callogenic response (60 %) was observed from leaf explant at 1.0 mg L(-1) 1-nephthalene acetic acid (NAA) and 0.5 mg L(-1) 6-benzyl aminopurine (BA) in Murashige and Skoog (MS) medium using hypocotyl and root explants (48 % each). Addition of AgNO3 and PVP in the culture medium led to an increase in callogenic response up to 86 % from leaf explant and 72 % from hypocotyl and root explants. The best shooting response was observed in the presence of NAA, while maximum shoot length and number of shoots were achieved based on BA-supplemented MS medium. The regenerated shoots were rooted and successfully acclimatized under greenhouse conditions. Catalase and peroxidase enzymes showed ascending pattern during in vitro plant development from seed while ascorbate peroxidase showed descending pattern. Totally reverse response of these enzymes was observed during callus induction from three different explants. During shoot induction, catalase and peroxidase increased at high rate while there was a mild reduction in ascorbate peroxidase activity. Catalase and peroxidase continuously increased; on the other hand, ascorbate peroxidase activity decreased during root development and acclimatization states. The protocol described here can be employed for the mass propagation and genetic transformation of this rare herb. This study also highlights the importance and role of ascorbate peroxidase, catalase, and peroxidase in the establishment of A. roseum in vitro culture through callogenesis and organogenesis.

  19. Theoretical study of chlordecone and surface groups interaction in an activated carbon model under acidic and neutral conditions.

    PubMed

    Gamboa-Carballo, Juan José; Melchor-Rodríguez, Kenia; Hernández-Valdés, Daniel; Enriquez-Victorero, Carlos; Montero-Alejo, Ana Lilian; Gaspard, Sarra; Jáuregui-Haza, Ulises Javier

    2016-04-01

    Activated carbons (ACs) are widely used in the purification of drinking water without almost any knowledge about the adsorption mechanisms of the persistent organic pollutants. Chlordecone (CLD, Kepone) is an organochlorinated synthetic compound that has been used mainly as agricultural insecticide. CLD has been identified and listed as a persistent organic pollutant by the Stockholm Convention. The selection of the best suited AC for this type of contaminants is mainly an empirical and costly process. A theoretical study of the influence of AC surface groups (SGs) on CLD adsorption is done in order to help understanding the process. This may provide a first selection criteria for the preparation of AC with suitable surface properties. A model of AC consisting of a seven membered ring graphene sheet (coronene) with a functional group on the edge was used to evaluate the influence of the SGs over the adsorption. Multiple Minima Hypersurface methodology (MMH) coupled with PM7 semiempirical Hamiltonian was employed in order to study the interactions of the chlordecone with SGs (hydroxyl and carboxyl) at acidic and neutral pH and different hydration conditions. Selected structures were re-optimized using CAM-B3LYP to achieve a well-defined electron density to characterize the interactions by the Quantum Theory of Atoms in Molecules approach. The deprotonated form of surface carboxyl and hydroxyl groups of AC models show the strongest interactions, suggesting a chemical adsorption. An increase in carboxylic SGs content is proposed to enhance CLD adsorption onto AC at neutral pH conditions.

  20. A new insight on the gas phase retro-Diels-Alder reaction of bicyclic compounds: density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Mora, Jose R.; Lezama, Jesús; Córdova-Sintjago, Tania C.; Chuchani, Gabriel

    2015-11-01

    The mechanisms of the gas-phase thermal decomposition of bicyclo[2.2.1]heptadiene and 3,7,7-trimethylbicyclo[2.2.1]hept-2-ene were examined by density functional theory calculations with the hybrid functionals: B3LYP, CAM-B3LYP, MPW1PW91, and PBEPBE. Reasonable agreements were found between theoretical and experimental values with the B3LYP hybrid functional. Three molecular concerted pathways for bicyclo[2.2.1]heptadiene decomposition are proposed. The retro-Diels-Alder (retro-DA) pathway yields cyclopentadiene and acetylene through a nearly synchronous transition state structure (Sy = 0.97). The other two reaction channels are stepwise with a common step with the formation of the intermediate bicyclo[4.1.0] heptadiene. This reaction is dominated by C-C bond breaking leading to the methylene migration by an early transition state in the reaction coordinate (Sy = 0.91). The rearrangements of the latter intermediate producing toluene were also studied. The retro-DA elimination of 3,7,7-trimethylbicyclo[2.2.1]hept-2-ene gives 1,5,5-trimethyl-cyclopenta-1,3-diene in a less synchronous process (Sy = 0.77). This fact may be due to the electronic effects of the methyl substituent. The latter product is unstable and undergoes methyl migrations to give a more stable isomer 1,2,3-trimethylcyclopenta-1,3-diene. The stepwise mechanism for the retro-DA reaction through a biradical intermediate appears to be unfavourable because the barrier is bigger than that for the concerted reaction.

  1. Benchmarking DFT and TD-DFT Functionals for the Ground and Excited States of Hydrogen-Rich Peptide Radicals.

    PubMed

    Riffet, Vanessa; Jacquemin, Denis; Cauët, Emilie; Frison, Gilles

    2014-08-12

    We assess the pros and cons of a large panel of DFT exchange-correlation functionals for the prediction of the electronic structure of hydrogen-rich peptide radicals formed after electron attachment on a protonated peptide. Indeed, despite its importance in the understanding of the chemical changes associated with the reduction step, the question of the attachment site of an electron and, more generally, of the reduced species formed in the gas phase through electron-induced dissociation (ExD) processes in mass spectrometry is still a matter of debate. For hydrogen-rich peptide radicals in which several positive groups and low-lying π* orbitals can capture the incoming electron in ExD, inclusion of full Hartree-Fock exchange at long-range interelectronic distance is a prerequisite for an accurate description of the electronic states, thereby excluding several popular exchange-correlation functionals, e.g., B3LYP, M06-2X, or CAM-B3LYP. However, we show that this condition is not sufficient by comparing the results obtained with asymptotically correct range-separated hybrids (M11, LC-BLYP, LC-BPW91, ωB97, ωB97X, and ωB97X-D) and with reference CASSCF-MRCI and EOM-CCSD calculations. The attenuation parameter ω significantly tunes the spin density distribution and the excited states vertical energies. The investigated model structures, ranging from methylammonium to hexapeptide, allow us to obtain a description of the nature and energy of the electronic states, depending on (i) the presence of hydrogen bond(s) around the cationic site(s), (ii) the presence of π* molecular orbitals (MOs), and (iii) the selected DFT approach. It turns out that, in the present framework, LC-BLYP and ωB97 yields the most accurate results.

  2. Extensive TD-DFT Benchmark: Singlet-Excited States of Organic Molecules.

    PubMed

    Jacquemin, Denis; Wathelet, Valérie; Perpète, Eric A; Adamo, Carlo

    2009-09-08

    Extensive Time-Dependent Density Functional Theory (TD-DFT) calculations have been carried out in order to obtain a statistically meaningful analysis of the merits of a large number of functionals. To reach this goal, a very extended set of molecules (∼500 compounds, >700 excited states) covering a broad range of (bio)organic molecules and dyes have been investigated. Likewise, 29 functionals including LDA, GGA, meta-GGA, global hybrids, and long-range-corrected hybrids have been considered. Comparisons with both theoretical references and experimental measurements have been carried out. On average, the functionals providing the best match with reference data are, one the one hand, global hybrids containing between 22% and 25% of exact exchange (X3LYP, B98, PBE0, and mPW1PW91) and, on the other hand, a long-range-corrected hybrid with a less-rapidly increasing HF ratio, namely LC-ωPBE(20). Pure functionals tend to be less consistent, whereas functionals incorporating a larger fraction of exact exchange tend to underestimate significantly the transition energies. For most treated cases, the M05 and CAM-B3LYP schemes deliver fairly small deviations but do not outperform standard hybrids such as X3LYP or PBE0, at least within the vertical approximation. With the optimal functionals, one obtains mean absolute deviations smaller than 0.25 eV, though the errors significantly depend on the subset of molecules or states considered. As an illustration, PBE0 and LC-ωPBE(20) provide a mean absolute error of only 0.14 eV for the 228 states related to neutral organic dyes but are completely off target for cyanine-like derivatives. On the basis of comparisons with theoretical estimates, it also turned out that CC2 and TD-DFT errors are of the same order of magnitude, once the above-mentioned hybrids are selected.

  3. Ultraviolet photodissociation action spectroscopy of gas-phase protonated quinoline and isoquinoline cations.

    PubMed

    Hansen, Christopher S; Blanksby, Stephen J; Trevitt, Adam J

    2015-10-21

    The gas-phase photodissociation action spectroscopy of protonated quinoline and isoquinoline cations (quinolineH(+) and isoquinolineH(+)) is investigated at ambient temperature. Both isomers exhibit vibronic detail and wavelength-dependent photoproduct partitioning across two broad bands in the ultraviolet. Photodissociation action spectra are reported spanning 370-285 nm and 250-220 nm and analysed with the aid of electronic structure calculations: TD-DFT (CAM-B3LYP/aug-cc-pVDZ) is used for spectra simulations and CBS-QB3 for dissociation enthalpies. It is shown that the action spectra are afforded predominantly by two-photon excitation. The first band is attributed to both the S1 ← S0 and S2 ← S0 electronic transitions in quinolineH(+), with a S1 ← S0 electronic origin assigned at 27,900 cm(-1). For isoquinolineH(+) the S1 ← S0 transition is observed with an assigned electronic origin at 27,500 cm(-1). A separate higher energy band is observed for both species, corresponding to the S3 ← S0 transition, with origins assigned at 42,100 cm(-1) and 42,500 cm(-1) for quinolineH(+) and isoquinolineH(+), respectively. Franck-Condon absorption simulations provide an explanation for some vibrational structure observed in both bands allowing several normal mode assignments. The nature of the electronic transitions is discussed and it is shown that the excited states active in the reported spectra should be of ππ* character with some degree of charge transfer from the homocycle to the heterocycle.

  4. Characterization of prepared In2O3 thin films: The FT-IR, FT-Raman, UV-Visible investigation and optical analysis

    NASA Astrophysics Data System (ADS)

    Panneerdoss, I. Joseph; Jeyakumar, S. Johnson; Ramalingam, S.; Jothibas, M.

    2015-08-01

    In this original work, the Indium oxide (In2O3) thin film is deposited cleanly on microscope glass substrate at different temperatures by spray pyrolysis technique. The physical properties of the films are characterized by XRD, SEM, AFM and AFM measurements. The spectroscopic investigation has been carried out on the results of FT-IR, FT-Raman and UV-Visible. XRD analysis exposed that the structural transformation of films from stoichiometric to non-stoichiometric orientation of the plane vice versa and also found that, the film is polycrystalline in nature having cubic crystal structure with a preferred grain orientation along (2 2 2) plane. SEM and AFM studies revealed that, the film with 0.1 M at 500 °C has spherical grains with uniform dimension. The complete vibrational analysis has been carried out and the optimized parameters are calculated using HF and DFT (CAM-B3LYP, B3LYP and B3PW91) methods with 3-21G(d,p) basis set. Furthermore, NMR chemical shifts are calculated by using the gauge independent atomic orbital (GIAO) technique. The molecular electronic properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, molecular electrostatic potential energy (MEP) analysis and Polarizability first order hyperpolarizability calculations are performed by time dependent DFT (TD-DFT) approach. The energy excitation on electronic structure is investigated and the assignment of the absorption bands in the electronic spectra of steady compound is discussed. The calculated HOMO and LUMO energies showed the enhancement of energy gap by the addition of substitutions with the base molecule. The thermodynamic properties (heat capacity, entropy, and enthalpy) at different temperatures are calculated and interpreted in gas phase.

  5. Comprehensive evaluation of medium and long range correlated density functionals in TD-DFT investigation of DNA bases and base pairs: gas phase and water solution study

    NASA Astrophysics Data System (ADS)

    Shukla, Manoj K.; Leszczynski, Jerzy

    2010-11-01

    A comprehensive analysis of the performance of the TD-DFT method using different density functionals including recently developed medium and long-range correlation corrected density functionals have been carried out for lower-lying electronic singlet valence transitions of nucleic acid bases and the Watson-Crick base pairs in the gas phase and in the water solution. The standard 6-311++G(d,p) basis set was used. Ground state geometries of bases and base pairs were optimized at the M05-2X/6-311++G(d,p) level. The nature of potential energy surfaces (PES) was ascertained through the harmonic vibrational frequency analysis; all geometries were found to be minima at the respective PES. Electronic singlet vertical transition energies were also computed at the CC2/def2-TZVP level in the gas phase. The effect of state-specific water solvation on TD-DFT computed transition energies was considered using the PCM model. For the isolated bases the performance of the B3LYP functional was generally found to be superior among all functionals, but it measurably fails for charge-transfer states in the base pairs. The CC2/def2-TZVP computed transition energies were also revealed to be inferior compared with B3LYP results for the isolated bases. The performance of the ωB97XD, CAM-B3LYP and BMK functionals were found to be similar and comparable with the CC2 results for the isolated bases. However, for the Watson-Crick adenine-thymine and guanine-cytosine base pairs the performance of the ωB97XD functional was found to be the best among all the studied functionals in the present work in predicting the locally excited transitions as well as charge transfer states.

  6. The Thermodynamic and Kinetic Properties of 2-Hydroxypyridine/2-Pyridone Tautomerization: A Theoretical and Computational Revisit

    PubMed Central

    Hejazi, Safiyah A.; Osman, Osman I.; Alyoubi, Abdulrahman O.; Aziz, Saadullah G.; Hilal, Rifaat H.

    2016-01-01

    The gas-phase thermal tautomerization reaction between 2-hydroxypyridine (2-HPY) and 2-pyridone (2-PY) was investigated by applying 6-311++G** and aug-cc-pvdz basis sets incorporated into some density functional theory (DFT) and coupled cluster with singles and doubles (CCSD) methods. The geometrical structures, dipole moments, HOMO-LUMO energy gaps, total hyperpolarizability, kinetics and thermodynamics functions were monitored against the effects of the corrections imposed on these functionals. The small experimental energy difference between the two tautomers of 3.23 kJ/mol; was a real test of the accuracy of the applied levels of theory. M062X and CCSD methods predicted the preference of 2-HPY over 2-PY by 5–9 kJ/mol; while B3LYP functional favoured 2-PY by 1–3 kJ/mol. The CAM-B3LYP and ωB97XD functionals yielded mixed results depending on the basis set used. The source of preference of 2-HPY is the minimal steric hindrance and electrostatic repulsion that subdued the huge hyperconjugation in 2-PY. A 1,3-proton shift intramolecular gas-phase tautomerization yielded a high average activation of 137.152 kJ/mol; while the intermolecular mixed dimer interconversion gave an average barrier height of 30.844 kJ/mol. These findings are boosted by a natural bond orbital (NBO) technique. The low total hyperpolarizabilities of both tautomers mark out their poor nonlinear optical (NLO) behaviour. The enhancement of the total hyperpolarizability of 2-HPY over that of 2-PY is interpreted by the bond length alternation. PMID:27854244

  7. DFT calculations on molecular structure, spectral analysis, multiple interactions, reactivity, NLO property and molecular docking study of flavanol-2,4-dinitrophenylhydrazone

    NASA Astrophysics Data System (ADS)

    Singh, Ravindra Kumar; Singh, Ashok Kumar

    2017-02-01

    A new flavanol-2,4-dinitrophenylhydrazone (FDNP) was synthesized and its structure was confirmed by FT-IR, FT-Raman, 1H NMR, mass spectrometry and elemental analysis. All quantum chemical calculations were carried out at level of density functional theory (DFT) with B3LYP functional using 6-311++ G (d,p) basis atomic set. UV-Vis absorption spectra for the singlet-singlet transition computed for fully optimized ground state geometry using Time-Dependent-Density Functional Theory (TD-DFT) with CAM-B3LYP functional was found to be in consistent with that of experimental findings. Analysis of vibrational (FT-IR and FT-Raman) spectrum and their assignments has been done by computing Potential Energy Distribution (PED) using Gar2ped. HOMO-LUMO analysis was performed and reactivity descriptors were calculated. Calculated global electrophilicity index (ω = 7.986 eV) shows molecule to be a strong electrophile. 1H NMR chemical shift calculated with the help of gauge-including atomic orbital (GIAO) approach shows agreement with experimental data. Various intramolecular interactions were analysed by AIM approach. DFT computed total first static hyperpolarizability (β0 = 189.03 × 10-30 esu) indicates that title molecule can be used as attractive future NLO material. Solvent induced effects on the NLO properties studied by using self-consistent reaction field (SCRF) method shows that β0 value increases with increase in solvent polarity. To study the thermal behaviour of title molecule, thermodynamic properties such as heat capacity, entropy and enthalpy change at various temperatures have been calculated and reported. Molecular docking results suggests title molecule to be a potential kinase inhibitor and might be used in future for designing of new anticancer drug.

  8. The shape of the CMB lensing bispectrum

    SciTech Connect

    Lewis, Antony; Challinor, Anthony; Hanson, Duncan E-mail: adc1000@ast.cam.ac.uk

    2011-03-01

    Lensing of the CMB generates a significant bispectrum, which should be detected by the Planck satellite at the 5-sigma level and is potentially a non-negligible source of bias for f{sub NL} estimators of local non-Gaussianity. We extend current understanding of the lensing bispectrum in several directions: (1) we perform a non-perturbative calculation of the lensing bispectrum which is ∼ 10% more accurate than previous, first-order calculations; (2) we demonstrate how to incorporate the signal variance of the lensing bispectrum into estimates of its amplitude, providing a good analytical explanation for previous Monte-Carlo results; and (3) we discover the existence of a significant lensing bispectrum in polarization, due to a previously-unnoticed correlation between the lensing potential and E-polarization as large as 30% at low multipoles. We use this improved understanding of the lensing bispectra to re-evaluate Fisher-matrix predictions, both for Planck and cosmic variance limited data. We confirm that the non-negligible lensing-induced bias for estimation of local non-Gaussianity should be robustly treatable, and will only inflate f{sub NL} error bars by a few percent over predictions where lensing effects are completely ignored (but note that lensing must still be accounted for to obtain unbiased constraints). We also show that the detection significance for the lensing bispectrum itself is ultimately limited to 9 sigma by cosmic variance. The tools that we develop for non-perturbative calculation of the lensing bispectrum are directly relevant to other calculations, and we give an explicit construction of a simple non-perturbative quadratic estimator for the lensing potential and relate its cross-correlation power spectrum to the bispectrum. Our numerical codes are publicly available as part of CAMB and LensPix.

  9. Quantitative trait loci for plant height in Maresi × CamB barley population and their associations with yield-related traits under different water regimes.

    PubMed

    Mikołajczak, Krzysztof; Kuczyńska, Anetta; Krajewski, Paweł; Sawikowska, Aneta; Surma, Maria; Ogrodowicz, Piotr; Adamski, Tadeusz; Krystkowiak, Karolina; Górny, Andrzej G; Kempa, Michał; Szarejko, Iwona; Guzy-Wróbelska, Justyna; Gudyś, Kornelia

    2017-02-01

    High-yielding capacity of the modern barley varieties is mostly dependent on the sources of semi-dwarfness associated with the sdw1/denso locus. The objective of the study was to identify quantitative trait loci (QTLs) associated with the plant height and yield potential of barley recombinant inbred lines (RILs) grown under various soil moisture regimes. The plant material was developed from a hybrid between the Maresi (European cv.) and CamB (Syrian cv.). A total of 103 QTLs affecting analysed traits were detected and 36 of them showed stable effects over environments. In total, ten QTLs were found to be significant only under water shortage conditions. Nine QTLs affecting the length of main stem were detected on 2H-6H chromosomes. In four of the detected QTLs, alleles contributed by Maresi had negative effects on that trait, the most significant being the QLSt-3H.1-1 in the 3H.1 linkage group. The close linkage between QTLs identified around the sdw1/denso locus, with positive alleles contributed by Maresi, indicates that the semi-dwarf cv. Maresi could serve as a donor of favourable traits resulting in grain yield improvement, also under water scarcity. Molecular analyses revealed that the Syrian cv. also contributed alleles which increased the yield potential. Available barley resources of genomic annotations were employed to the biological interpretation of detected QTLs. This approach revealed 26 over-represented Gene Ontology terms. In the projected support intervals of QGWSl-5H.3-2 and QLSt-5H.3 on the chromosome 5H, four genes annotated to 'response to stress' were found. It suggests that these QTL-regions may be involved in a response of plant to a wide range of environmental disturbances.

  10. Stokes’ and Lamb's viscous drag laws

    NASA Astrophysics Data System (ADS)

    Eames, I.; Klettner, C. A.

    2017-03-01

    Since Galileo used his pulse to measure the time period of a swinging chandelier in the 17th century, pendulums have fascinated scientists. It was not until Stokes' (1851 Camb. Phil. Soc. 9 8-106) (whose interest was spurred by the pendulur time pieces of the mid 19th century) treatise on viscous flow that a theoretical framework for the drag on a sphere at low Reynolds number was laid down. Stokes' famous drag law has been used to determine two fundamental physical constants—the charge on an electron and Avogadro's constant—and has been used in theories which have won three Nobel prizes. Considering its illustrious history it is then not surprising that the flow past a sphere and its two-dimensional analog, the flow past a cylinder, form the starting point of teaching flow past a rigid body in undergraduate level fluid mechanics courses. Usually starting with the two-dimensional potential flow past a cylinder, students progress to the three-dimensional potential flow past a sphere. However, when the viscous flow past rigid bodies is taught, the three-dimensional example of a sphere is first introduced, and followed by (but not often), the two-dimensional viscous flow past a cylinder. The reason why viscous flow past a cylinder is generally not taught is because it is usually explained from an asymptotic analysis perspective. In fact, this added mathematical complexity is why the drag on a cylinder was only solved in 1911, 60 years after the drag on a sphere. In this note, we show that the viscous flow past a cylinder can be explained without the need to introduce any asymptotic analysis while still capturing all the physical insight of this classic fluid mechanics problem.

  11. Synthesis, crystal structure and investigation of mononuclear copper(II) and zinc(II) complexes of a new carboxylate rich tripodal ligand and their interaction with carbohydrates in alkaline aqueous solution.

    PubMed

    Stewart, Christopher D; Pedraza, Mayra; Arman, Hadi; Fan, Hua-Jun; Schilling, Eduardo Luiz; Szpoganicz, Bruno; Musie, Ghezai T

    2015-08-01

    A new carboxylate rich asymmetric tripodal ligand, N-[2-carboxybenzomethyl]-N-[carboxymethyl]-β-alanine (H3camb), and its di-copper(II), (NH4)2[1]2, and di-zinc(II), ((CH3)4N)2[2]2, complexes have been synthesized as carbohydrate binding models in aqueous solutions. The ligand and complexes have been fully characterized using several techniques, including single crystal X-ray diffraction. The interactions of (NH4)2[1]2 and ((CH3)4N)2[2]2 with D-glucose, D-mannose, D-xylose and xylitol in aqueous alkaline media were investigated using UV-Vis and (13)C-NMR spectroscopic techniques, respectively. The molar conductance, NMR and ESI-MS studies indicate that the complexes dissociate in solution to produce the respective complex anions, 1(-) and 2(-). Complexes 1(-) and 2(-) showed chelating ability towards the naturally abundant and biologically relevant sugars, D-glucose, D-mannose, D-xylose, and xylitol. The complex ions bind to one molar equivalent of the sugars, even in the presence of stoichiometric excess of the substrates, in solution. Experimentally obtained spectroscopic data and computational results suggest that the substrates bind to the metal center in a bidentate fashion. Apparent binding constant values, pK(app), between the complexes and the substrates were determined and a specific mode of substrate binding is proposed. The pK(app) and relativistic density functional theory (DFT) calculated Gibbs free energy values indicate that D-mannose displayed the strongest interaction with the complexes. Syntheses, characterizations, detailed substrate binding studies using spectroscopic techniques, single crystal X-ray diffraction and geometry optimizations of the complex-substrates with DFT calculations are also reported.

  12. Ionization potential and electron affinity for six common explosive compounds by DFT, MP2, and CBS-QB3

    DOE PAGES

    Cooper, Jason K.; Grant, Christian D.; Zhang, Jin Z.

    2012-07-20

    The vertical and adiabatic ionization potential (IPV and IPA) and vertical electron affinity (EAV) for six explosives (RDX, HMX, TNT, PETN, HMTD, and TATP) have been studied by ab initio computational methods. The IPV was calculated using MP2 and CBS-QB3 while the IPA was calculated with B3LYP, CAM-B3LYP, ω B97XD, B2PLYP, and MP2. RDX and TNT IPA’s were also reported using CBS -QB3. Excluding results by CBS-QB3, B3LYP and B2PLYPD provided superior and more consistent results for calculating the IP. The EAV were calculated using the same methods however B3LYP performed the worst in this case with MP2 and B2PLYPDmore » predicting values closest to those made by CBS-QB3, which was used a reference due to lacking experimental data. Basis set effects were evaluated using 6- 31+G(d,p), 6-311+G(d,p), and 6-311+(3df,2p) for both IP and EA. 6-31+G(d,p) gave satisfactory results for calculating both IP however 6-311+G(3df,2p) had improved results in calculating the EA. The four nitro containing compounds had exothermic reduction potentials while the peroxides were unfavorable. Additionally, it was seen that RDX, HMX, TATP and HMTD were unstable in their reduced forms. Results are aimed to assist detection and screening methods.« less

  13. Adaptability in stone tool use by wild capuchin monkeys (Sapajus libidinosus).

    PubMed

    De Moraes, Bárbara Lins Caldas; Da Silva Souto, Antonio; Schiel, Nicola

    2014-10-01

    Capuchin monkeys are well known for population variation in the use of stone tools and the types of food items consumed. In order to determine adaptability in stone tool use, we investigated a never before studied population of wild capuchin monkey (Sapajus libidinosus) displaying terrestrial habits in a Caatinga environment. To carry out this study we recorded physical evidence of the use of stone tools as well as made direct observations through trap cameras. During a 15-month period, we studied a group of Sapajus libidinosus in Serra Talhada, Pernambuco, Brazil. In total, 257 anvils and 395 hammers were identified, characterized, and monitored. We identified five types of food items exploited at these "tool use sites": Syagrus oleracea (catolé palm), Manihot epruinosa (manioc), Pilosocereus pachycladus (facheiro), Tacinga inamoena (quípa), and Commiphora leptophloeos (imburana de cambão). Five hundred three video clips of capuchin monkeys were recorded, 43 of which involved the use of stone tools. The results indicated evidence of adaptability in tool use by the capuchins. We verified that the rigidity and size of the food item, along with the presence or absence of spines seem to influence the choice of stone tools made by the animals for processing the food. The recurring use of tools for the processing of cacti was especially noteworthy and it appears that the presence of spines predisposes the capuchins to use stones to process them. A significant difference was observed between the characteristics of the anvils and the weight of the hammers according to the food item consumed. The use of tools enabled the animals to access otherwise unavailable or difficult to acquire food items within a Caatinga habitat. Adaptability in the use of stone tools by the capuchin monkey population of Serra Talhada provides an example of the complexity that these primates demonstrate in food processing.

  14. Semi-analytical description of clumping factor and cosmic microwave background free-free distortions from reionization

    NASA Astrophysics Data System (ADS)

    Trombetti, T.; Burigana, C.

    2014-01-01

    The density contrast of the Universe, parametrized in terms of the matter power spectrum and its variance, can amplify the signal of the free-free process in the plasma. The damping of fluctuations on scales smaller than the dark matter particle free streaming scale corresponds to a suppression of the total matter power spectrum on large wavenumbers k. We derive the time evolution of the variance of the matter power spectrum for various cosmological models and parameters by numerically computing the power spectrum with a modified version of the Boltzmann code CAMB, for different values of the cut-off parameter kmax. Suitable analytical approximations of the numerical results are presented. We then characterize the cosmic microwave background (CMB) free-free spectral distortion accounting for the amplification effect coming from clumping factor. Indeed, the clumpiness, associated with the density contrast of the intergalactic medium, increases at decreasing redshift. The analysis is carried out for selected astrophysical and phenomenological cosmological reionization histories for which we evaluate the impact of the clumping factor on the free-free distortion and discuss the wavelength dependence of the predicted signal. Finally, we address a comparison with other classes of unavoidable CMB spectral distortions and future observational perspectives. While Comptonization from reionization is dominant at high frequencies, the free-free signal predicted in the considered models contributes to the distortion at a level of few (few tens) per cent at frequencies below ˜25 GHz (˜10 GHz) and represents the main signature below ˜4 GHz. The cosmological signal from the H I 21-cm background is found to prevail over the free-free distortion in a restricted, model-dependent frequency window between ˜0.1 and ˜0.2 GHz.

  15. Describing excited state relaxation and localization in TiO2 nanoparticles using TD-DFT

    DOE PAGES

    Berardo, Enrico; Hu, Han -Shi; van Dam, Hubertus J. J.; ...

    2014-02-26

    We have investigated the description of excited state relaxation in naked and hydrated TiO2 nanoparticles using Time-Dependent Density Functional Theory (TD-DFT) with three common hybrid exchange-correlation (XC) potentials; B3LYP, CAM-B3LYP and BHLYP. Use of TD-CAM-B3LYP and TD-BHLYP yields qualitatively similar results for all structures, which are also consistent with predictions of coupled cluster theory for small particles. TD-B3LYP, in contrast, is found to make rather different predictions; including apparent conical intersections for certain particles that are not observed with TD-CAM-B3LYP nor with TD-BHLYP. In line with our previous observations for vertical excitations, the issue with TD-B3LYP appears to be themore » inherent tendency of TD-B3LYP, and other XC potentials with no or a low percentage of Hartree-Fock Like Exchange, to spuriously stabilize the energy of charge-transfer (CT) states. Even in the case of hydrated particles, for which vertical excitations are generally well described with all XC potentials, the use of TD-B3LYP appears to result in CT-problems for certain particles. We hypothesize that the spurious stabilization of CT-states by TD-B3LYP even may drive the excited state optimizations to different excited state geometries than those obtained using TD-CAM-B3LYP or TD-BHLYP. In conclusion, focusing on the TD-CAM-B3LYP and TD-BHLYP results, excited state relaxation in naked and hydrated TiO2 nanoparticles is predicted to be associated with a large Stokes’ shift.« less

  16. Describing excited state relaxation and localization in TiO2 nanoparticles using TD-DFT

    SciTech Connect

    Berardo, Enrico; Hu, Han -Shi; van Dam, Hubertus J. J.; Shevlin, Stephen A.; Woodley, Scott M.; Kowalski, Karol; Zwijnenburg, Martijn A.

    2014-02-26

    We have investigated the description of excited state relaxation in naked and hydrated TiO2 nanoparticles using Time-Dependent Density Functional Theory (TD-DFT) with three common hybrid exchange-correlation (XC) potentials; B3LYP, CAM-B3LYP and BHLYP. Use of TD-CAM-B3LYP and TD-BHLYP yields qualitatively similar results for all structures, which are also consistent with predictions of coupled cluster theory for small particles. TD-B3LYP, in contrast, is found to make rather different predictions; including apparent conical intersections for certain particles that are not observed with TD-CAM-B3LYP nor with TD-BHLYP. In line with our previous observations for vertical excitations, the issue with TD-B3LYP appears to be the inherent tendency of TD-B3LYP, and other XC potentials with no or a low percentage of Hartree-Fock Like Exchange, to spuriously stabilize the energy of charge-transfer (CT) states. Even in the case of hydrated particles, for which vertical excitations are generally well described with all XC potentials, the use of TD-B3LYP appears to result in CT-problems for certain particles. We hypothesize that the spurious stabilization of CT-states by TD-B3LYP even may drive the excited state optimizations to different excited state geometries than those obtained using TD-CAM-B3LYP or TD-BHLYP. In conclusion, focusing on the TD-CAM-B3LYP and TD-BHLYP results, excited state relaxation in naked and hydrated TiO2 nanoparticles is predicted to be associated with a large Stokes’ shift.

  17. Comparative Ab-Initio Study of Substituted Norbornadiene-Quadricyclane Compounds for Solar Thermal Storage.

    PubMed

    Kuisma, Mikael J; Lundin, Angelica M; Moth-Poulsen, Kasper; Hyldgaard, Per; Erhart, Paul

    2016-02-25

    Molecular photoswitches that are capable of storing solar energy, so-called molecular solar thermal storage systems, are interesting candidates for future renewable energy applications. In this context, substituted norbornadiene-quadricyclane systems have received renewed interest due to recent advances in their synthesis. The optical, thermodynamic, and kinetic properties of these systems can vary dramatically depending on the chosen substituents. The molecular design of optimal compounds therefore requires a detailed understanding of the effect of individual substituents as well as their interplay. Here, we model absorption spectra, potential energy storage, and thermal barriers for back-conversion of several substituted systems using both single-reference (density functional theory using PBE, B3LYP, CAM-B3LYP, M06, M06-2x, and M06-L functionals as well as MP2 calculations) and multireference methods (complete active space techniques). Already the diaryl substituted compound displays a strong red-shift compared to the unsubstituted system, which is shown to result from the extension of the conjugated π-system upon substitution. Using specific donor/acceptor groups gives rise to a further albeit relatively smaller red-shift. The calculated storage energy is found to be rather insensitive to the specific substituents, although solvent effects are likely to be important and require further study. The barrier for thermal back-conversion exhibits strong multireference character and as a result is noticeably correlated with the red-shift. Two possible reaction paths for the thermal back-conversion of diaryl substituted quadricyclane are identified and it is shown that among the compounds considered the path via the acceptor side is systematically favored. Finally, the present study establishes the basis for high-throughput screening of norbornadiene-quadricyclane compounds as it provides guidelines for the level of accuracy that can be expected for key properties from

  18. Angola Seismicity MAP

    NASA Astrophysics Data System (ADS)

    Neto, F. A. P.; Franca, G.

    2014-12-01

    The purpose of this job was to study and document the Angola natural seismicity, establishment of the first database seismic data to facilitate consultation and search for information on seismic activity in the country. The study was conducted based on query reports produced by National Institute of Meteorology and Geophysics (INAMET) 1968 to 2014 with emphasis to the work presented by Moreira (1968), that defined six seismogenic zones from macro seismic data, with highlighting is Zone of Sá da Bandeira (Lubango)-Chibemba-Oncócua-Iona. This is the most important of Angola seismic zone, covering the epicentral Quihita and Iona regions, geologically characterized by transcontinental structure tectono-magmatic activation of the Mesozoic with the installation of a wide variety of intrusive rocks of ultrabasic-alkaline composition, basic and alkaline, kimberlites and carbonatites, strongly marked by intense tectonism, presenting with several faults and fractures (locally called corredor de Lucapa). The earthquake of May 9, 1948 reached intensity VI on the Mercalli-Sieberg scale (MCS) in the locality of Quihita, and seismic active of Iona January 15, 1964, the main shock hit the grade VI-VII. Although not having significant seismicity rate can not be neglected, the other five zone are: Cassongue-Ganda-Massano de Amorim; Lola-Quilengues-Caluquembe; Gago Coutinho-zone; Cuima-Cachingues-Cambândua; The Upper Zambezi zone. We also analyzed technical reports on the seismicity of the middle Kwanza produced by Hidroproekt (GAMEK) region as well as international seismic bulletins of the International Seismological Centre (ISC), United States Geological Survey (USGS), and these data served for instrumental location of the epicenters. All compiled information made possible the creation of the First datbase of seismic data for Angola, preparing the map of seismicity with the reconfirmation of the main seismic zones defined by Moreira (1968) and the identification of a new seismic

  19. The Role of Cytosine Methylation on Charge Transport through a DNA Strand

    SciTech Connect

    Qi, Jianqing; Govind, Niranjan; Anantram, M. P.

    2015-09-04

    Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modifi-cation remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Buttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. Specifically, we compare the results generated with the widely used B3LYP exchange-correlation (XC) functional and CAM-B3LYP based tuned range-separated hybrid density functional. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that with both functionals, the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and interstrand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital (HOMO) level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with both functionals. We also study the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit. Our results suggest that the effect of the two different functionals is to alter the on-site energies of the DNA bases at the HOMO level, while the transport properties don't depend much on the two functionals.

  20. Simulations of light induced processes in water based on ab initio path integrals molecular dynamics. II. Photoionization

    NASA Astrophysics Data System (ADS)

    Svoboda, Ondřej; Ončák, Milan; Slavíček, Petr

    2011-10-01

    We have applied ab initio based reflection principle to simulate photoelectron spectra of small water clusters, ranging from monomer to octamer. The role of quantum and thermal effects on the structure of the water photoelectron spectra is discussed within the ab initio path integral molecular dynamics (PIMD) framework. We have used the PIMD method with up to 40 beads to sample the ground state quantum distribution at temperature T = 180 K. We have thoroughly tested the performance of various density functionals (B3LYP, BHandHLYP, M06HF, BNL, LC-ωPBE, and CAM-B3LYP) for the ionization process description. The benchmarking based on a comparison of simulated photoelectron spectra to experimental data and high level equation-of-motion ionization potential coupled clusters with singles and doubles calculations has singled out the BHandHLYP and LC-ωPBE functionals as the most reliable ones for simulations of light induced processes in water. The good performance of the density functional theory functionals to model the water photoelectron spectra also reflects their ability to reliably describe open shell excited states. The width of the photoelectron spectrum converges quickly with the cluster size as it is controlled by specific interactions of local character. The peak position is, on the other hand, defined by long-range non-specific solvent effects; it therefore only slowly converges to the corresponding bulk value. We are able to reproduce the experimental valence photoelectron spectrum of liquid water within the combined model of the water octamer embedded in a polarizable dielectric continuum. We demonstrate that including the long-range polarization and the state-specific treatment of the solvent response are needed for a reliable liquid water ionization description.

  1. Post-Flight Microbial Analysis of Samples from the International Space Station Water Recovery System and Oxygen Generation System

    NASA Technical Reports Server (NTRS)

    Birmele, Michele N.

    2011-01-01

    The Regenerative, Environmental Control and Life Support System (ECLSS) on the International Space Station (ISS) includes the the Water Recovery System (WRS) and the Oxygen Generation System (OGS). The WRS consists of a Urine Processor Assembly (UPA) and Water Processor Assembly (WPA). This report describes microbial characterization of wastewater and surface samples collected from the WRS and OGS subsystems, returned to KSC, JSC, and MSFC on consecutive shuttle flights (STS-129 and STS-130) in 2009-10. STS-129 returned two filters that contained fluid samples from the WPA Waste Tank Orbital Recovery Unit (ORU), one from the waste tank and the other from the ISS humidity condensate. Direct count by microscopic enumeration revealed 8.38 x 104 cells per mL in the humidity condensate sample, but none of those cells were recoverable on solid agar media. In contrast, 3.32 x lOs cells per mL were measured from a surface swab of the WRS waste tank, including viable bacteria and fungi recovered after S12 days of incubation on solid agar media. Based on rDNA sequencing and phenotypic characterization, a fungus recovered from the filter was determined to be Lecythophora mutabilis. The bacterial isolate was identified by rDNA sequence data to be Methylobacterium radiotolerans. Additional UPA subsystem samples were returned on STS-130 for analysis. Both liquid and solid samples were collected from the Russian urine container (EDV), Distillation Assembly (DA) and Recycle Filter Tank Assembly (RFTA) for post-flight analysis. The bacterium Pseudomonas aeruginosa and fungus Chaetomium brasiliense were isolated from the EDV samples. No viable bacteria or fungi were recovered from RFTA brine samples (N= 6), but multiple samples (N = 11) from the DA and RFTA were found to contain fungal and bacterial cells. Many recovered cells have been identified to genus by rDNA sequencing and carbon source utilization profiling (BiOLOG Gen III). The presence of viable bacteria and fungi from WRS

  2. Composition and conservation of Orchidaceae on an inselberg in the Brazilian Atlantic Forest and floristic relationships with areas of Eastern Brazil.

    PubMed

    Pessanha, Alexandre Soares; Menini Neto, Luiz; Forzza, Rafaela Campostrini; Nascimento, Marcelo Trindade

    2014-06-01

    The Brazilian Atlantic Forest presents high levels of richness and endemism of several taxonomic groups. Within this forest, the Orchidaceae may be highlighted as the richest family of Angiosperms found there, and is highly threatened due to collection and habitat destruction. The inselbergs of the Brazilian Atlantic Forest are mostly unknown regarding their floristic composition, but the available information points to occurrence of endemic species, with adaptations to survive to this dry environment. The objectives of this study were to conduct a floristic survey of the Orchidaceae species on the Maciço do Itaoca, an inselberg located in the Northern region of the State of Rio de Janeiro, make a comparative analysis with other sites in Eastern Brazil, and discuss the geographic distribution, floristic relationships and conservation status of the orchid species present on the inselbergs. The floristic composition of the study area was compared with 24 other locations in Eastern Brazil (of which 13 are inselbergs) and the influence of the types of surrounding vegetation on the composition of the Orchidaceae flora on the inselbergs. On Maciço do Itaoca we recorded 18 species from 17 genera: Brasiliorchis picta, Brassavola tuberculata, Campylocentrum robustum; C sellowii, Catasetum luridum, Cattleya guttata, Cyclopogon congestus, Cyrtopodium glutiniferum, Leptotes bicolor, Lophiaris pumila, Miltonia moreliana, Oeceoclades maculata, Phymatochilum brasiliense, Prescottia plantaginifolia, Pseudolaelia vellozicola, Sarcoglottis fasciculata, Sophronitis cernua. and Vanilla chamissonis. The highest floristic similarity was with the Pedra da Botelha (0.43), an inselberg located in the North of Espírito Santo. This result is probably due to the similarity in altitude and distance from the coast in both areas despite the geographical distance between them. Apparently, little influence is exerted by the types of surrounding vegetation on the composition of the flora of

  3. Evaluation of the Linear and Second-Order NLO Properties of Molecular Crystals within the Local Field Theory: Electron Correlation Effects, Choice of XC Functional, ZPVA Contributions, and Impact of the Geometry in the Case of 2-Methyl-4-nitroaniline.

    PubMed

    Seidler, Tomasz; Stadnicka, Katarzyna; Champagne, Benoît

    2014-05-13

    The linear [χ((1))] and second-order nonlinear [χ((2))] optical susceptibilities of the 2-methyl-4-nitroaniline (MNA) crystal are calculated within the local field theory, which consists of first computing the molecular properties, accounting for the dressing effects of the surroundings, and then taking into account the local field effects. Several aspects of these calculations are tackled with the aim of monitoring the convergence of the χ((1)) and χ((2)) predictions with respect to experiment by accounting for the effects of (i) the dressing field within successive approximations, of (ii) the first-order ZPVA corrections, and of (iii) the geometry. With respect to the reference CCSD-based results, besides double hybrid functionals, the most reliable exchange-correlation functionals are LC-BLYP for the static χ((1)) and CAM-B3LYP (and M05-2X, to a lesser extent) for the dynamic χ((1)) but they strongly underestimate χ((2)). Double hybrids perform better for χ((2)) but not necessarily for χ((1)), and, moreover, their performances are much similar to MP2, which is known to slightly overestimate β, with respect to high-level coupled-clusters calculations and, therefore, χ((2)). Other XC functionals with less HF exchange perform poorly with overestimations/underestimations of χ((1))/χ((2)), whereas the HF method leads to underestimations of both. The first-order ZPVA corrections, estimated at the B3LYP level, are usually small but not negligible. Indeed, after ZPVA corrections, the molecular polarizabilities and first hyperpolarizabilities increase by 2% and 5%, respectively, whereas their impact is magnified on the macroscopic responses with enhancements of χ((1)) by up to 5% and of χ((2)) by as much as 10%-12% at λ = 1064 nm. The geometry plays also a key role in view of predicting accurate susceptibilities, particularly for push-pull π-conjugated compounds such as MNA. So, the geometry optimized using periodic boundary conditions is characterized

  4. Far-Ir Action Spectroscopy of Aminophenol and Ethylvanillin: Experiment and Theory

    NASA Astrophysics Data System (ADS)

    Yatsyna, Vasyl; Feifel, Raimund; Zhaunerchyk, Vitali; Bakker, Daniël; Rijs, Anouk

    2015-06-01

    Investigations of molecular structure and conformational isomerism are at the forefront of today's biophysics and biochemistry. In particular, vibrations excited by far-IR radiation can be highly sensitive to the molecular 3D structure as they are delocalized over large parts of the molecule. Current theoretical predictions of vibrational frequencies in the far-IR range are not accurate enough because of the non-local character and anharmonicity of these vibrations. Therefore experimental studies in the far-IR are vital to guide theory towards improved methodology. In this work we present the conformer-specific far-IR spectra of aminophenol and ethylvanillin molecules in the range of 220-800 wn utilizing ion-dip action spectroscopy carried out at the free electron laser FELIX in Nijmegen, Netherlands. The systems studied are aromatic molecules with important functional groups such as the hydroxyl (OH) and amino (NH_2) groups in aminophenol, and the hydroxyl, ethoxy (OCH_2CH_3) and formyl (CHO) groups in ethylvanillin. The experimental spectra show well resolved conformer-specific vibrational bands. In the case of ethylvanillin only two planar conformers have been observed under supersonic jet expansion conditions. Despite the fact that these conformers differ only in the position of oxygen of the formyl group with respect to ethoxy group, they are well distinguishable in far-IR spectra. The capability of numerical methods based on density functional theory (DFT) for predicting vibrational frequencies in this spectral region within the harmonic approximation has been investigated by using several hybrid-functionals such as B3LYP, PBE0, B2PLYP and CAM-B3LYP. An anharmonic correction based on vibrational second order perturbation theory approach was also applied. We have found that the methods we considered are well suited for the assignment of far-IR vibrational features except the modes which are strongly anharmonic, like the NH_2 wagging mode in aminophenol which

  5. Hydroxyl Radical (OH•) Reaction with Guanine in an Aqueous Environment: A DFT Study

    PubMed Central

    Kumar, Anil; Pottiboyina, Venkata; Sevilla, Michael D.

    2011-01-01

    The reaction of hydroxyl radical (OH•) with DNA accounts for about half of radiation-induced DNA damage in living systems. Previous literature reports point out that the reaction of OH• with DNA proceeds mainly through the addition of OH• to the C=C bond of the DNA bases. However, recently it has been reported that the principal reaction of OH• with dGuo (deoxyguanosine) is the direct hydrogen atom abstraction from its exocyclic amine group rather than addition of OH• to the C=C bond. In the present work, these two reaction pathways of OH• attack on guanine (G) in the presence of water molecules (aqueous environment) are investigated using the density functional theory (DFT) B3LYP method with 6-31G* and 6-31++G** basis sets. The calculations show that the initial addition of the OH• at C4=C5 double bond of guanine is barrier free and the adduct radical (G-OH•) has only a small activation barrier of ca. 1 – 6 kcal/mol leading to the formation of a metastable ion-pair intermediate (G•+---OH−). The formation of ion-pair is a result of the highly oxidizing nature of the OH• in aqueous media. The resulting ion-pair (G•+---OH−) deprotonates to form H2O and neutral G radicals favoring G(N1-H)• with an activation barrier of ca. 5 kcal/mol. The overall process from the G(C4)-OH• (adduct) to G(N1-H)• and water is found to be exothermic in nature by more than 13 kcal/mol. (G-OH•), (G•+---OH−), and G(N1-H)• were further characterized by the CAM-B3LYP calculations of their UV-visible spectra and good agreement between theory and experiment is achieved. Our calculations for the direct hydrogen abstraction pathway from N1 and N2 sites of guanine by the OH• show that this is also a competitive route to produce G(N2-H)•, G(N1-H)• and H2O. PMID:22050033

  6. Doping-enhanced hyperpolarizabilities of silicon clusters: A global ab initio and density functional theory study of Si10 (Li, Na, K)n (n = 1, 2) clusters

    NASA Astrophysics Data System (ADS)

    Karamanis, Panaghiotis; Marchal, Remi; Carbonniére, Philippe; Pouchan, Claude

    2011-07-01

    , BhandHLYP, PBE0, CAM-B3LYP, LC-BLYP, LC-BPW91) only B3PW91 and PBE0 out of the seven provided a consistent quantitative performance for both polarizabilities and hyperpolarizabilities with respect to the ab initio methods utilized here. On the other hand, the long range corrected functionals LC-(U)BLYP and LC-(U)BPW91 (μ = 0.47) failed to supply quantitatively accurate hyperpolarizability results in all the studied clusters while the CAM-(U)B3LYP functional performs satisfactory only in the case of the Na and K doped systems.

  7. Inactivation of Gating Currents of L-Type Calcium Channels

    PubMed Central

    Shirokov, Roman; Ferreira, Gonzalo; Yi, Jianxun; Ríos, Eduardo

    1998-01-01

    In studies of gating currents of rabbit cardiac Ca channels expressed as α1C/β2a or α1C/β2a/α2δ subunit combinations in tsA201 cells, we found that long-lasting depolarization shifted the distribution of mobile charge to very negative potentials. The phenomenon has been termed charge interconversion in native skeletal muscle (Brum, G., and E. Ríos. 1987. J. Physiol. (Camb.). 387:489–517) and cardiac Ca channels (Shirokov, R., R. Levis, N. Shirokova, and E. Ríos. 1992. J. Gen. Physiol. 99:863–895). Charge 1 (voltage of half-maximal transfer, V1/2 ≃ 0 mV) gates noninactivated channels, while charge 2 (V1/2 ≃ −90 mV) is generated in inactivated channels. In α1C/β2a cells, the available charge 1 decreased upon inactivating depolarization with a time constant τ ≃ 8, while the available charge 2 decreased upon recovery from inactivation (at −200 mV) with τ ≃ 0.3 s. These processes therefore are much slower than charge movement, which takes <50 ms. This separation between the time scale of measurable charge movement and that of changes in their availability, which was even wider in the presence of α2δ, implies that charges 1 and 2 originate from separate channel modes. Because clear modal separation characterizes slow (C-type) inactivation of Na and K channels, this observation establishes the nature of voltage-dependent inactivation of L-type Ca channels as slow or C-type. The presence of the α2δ subunit did not change the V1/2 of charge 2, but sped up the reduction of charge 1 upon inactivation at 40 mV (to τ ≃ 2 s), while slowing the reduction of charge 2 upon recovery (τ ≃ 2 s). The observations were well simulated with a model that describes activation as continuous electrodiffusion (Levitt, D. 1989. Biophys. J. 55:489–498) and inactivation as discrete modal change. The effects of α2δ are reproduced assuming that the subunit lowers the free energy of the inactivated mode. PMID:9607938

  8. Doping-enhanced hyperpolarizabilities of silicon clusters: a global ab initio and density functional theory study of Si10 (Li, Na, K)n (n=1, 2) clusters.

    PubMed

    Karamanis, Panaghiotis; Marchal, Remi; Carbonniére, Philippe; Pouchan, Claude

    2011-07-28

    in this work, (B3LYP, B3PW91, BhandHLYP, PBE0, CAM-B3LYP, LC-BLYP, LC-BPW91) only B3PW91 and PBE0 out of the seven provided a consistent quantitative performance for both polarizabilities and hyperpolarizabilities with respect to the ab initio methods utilized here. On the other hand, the long range corrected functionals LC-(U)BLYP and LC-(U)BPW91 (μ = 0.47) failed to supply quantitatively accurate hyperpolarizability results in all the studied clusters while the CAM-(U)B3LYP functional performs satisfactory only in the case of the Na and K doped systems.

  9. Measurements and implications of the SDSS DR7 galaxy angular power spectrum

    NASA Astrophysics Data System (ADS)

    Hayes, Brett P.

    We calculate the angular power spectrum of galaxies selected from the Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) by using a quadratic estimation method with KLcompression. The primary data sample includes over 18 million galaxies covering more than 5,700 square degrees after masking areas with bright objects, reddening greater than 0.2 magnitudes, and seeing of more than 1.5 arcseconds. We also construct a volume-limited sample of 3.2 million galaxies in the same area, consisting of galaxies with absolute r-band magnitudes Mr < --21.2 and photometric redshifts z < 0.4. We test for systematic effects by calculating the angular power spectrum on simulated data and by SDSS stripe, and we find that these measurements are minimally affected by seeing and reddening. We calculate the angular power spectrum for ℓ ≤ 200 multipoles by using 40 bands for the full area data, ℓ ≤ 1000 multipoles using 50 bands for individual stripes, and ℓ ≤ 1600 multipoles using 64 bands for a selected area near the North Galactic Pole at high resolution. We also calculate the angular power spectra for the main galaxy sample separated into 3 magnitude bins, as well as the volume-limited sample separated into 2 redshift shells and early- and late-type galaxies to examine the evolution of the angular power spectrum. We determine the theoretical linear angular power spectrum by projecting the 3D power spectrum to two dimensions for a basic comparison to our observational results for the SDSS DR7 main galaxy sample and subsamples separated by magnitude. For our high resolution and volume-limited samples, we generate nonlinear angular power spectra using CAMB nonlinear 3D matter power spectra for our projections. By minimizing the chi2 fit between these data and the theoretical angular power spectra, we measure a fit of Om = +0.18-0.11 with a linear bias of b = 0.94 +/- 0.04 for the entire SDSS DR7 main galaxy sample, Om = 0.267 +/- 0.038, Ob = 0.045 +/- 0.012, and b = 1

  10. Why do TD-DFT excitation energies of BODIPY/Aza-BODIPY families largely deviate from experiment? Answers from electron correlated and multireference methods.

    PubMed

    Momeni, Mohammad R; Brown, Alex

    2015-06-09

    The vertical excitation energies of 17 boron-dipyrromethene (BODIPY) core structures with a variety of substituents and ring sizes are benchmarked using time-dependent density functional theory (TD-DFT) with nine different functionals combined with the cc-pVTZ basis set. When compared to experimental measurements, all functionals provide mean absolute errors (mean AEs) greater than 0.3 eV, larger than the 0.1-0.3 eV differences typically expected from TD-DFT. Due to the high linear correlation of TD-DFT results with experiment, most functionals can be used to predict excitation energies if corrected empirically. Using the CAM-B3LYP functional, 0-0 transition energies are determined, and while the absolute difference is improved (mean AE = 0.478 eV compared to 0.579 eV), the correlation diminishes substantially (R(2) = 0.961 to 0.862). Two very recently introduced charge transfer (CT) indices, q(CT) and d(CT), and electron density difference (EDD) plots demonstrate that CT does not play a significant role for most of the BODIPYs examined and, thus, cannot be the source of error in TD-DFT. To assess TD-DFT methods, vertical excitation energies are determined utilizing TD-HF, configuration interaction CIS and CIS(D), equation of motion EOM-CCSD, SAC-CI, and Laplace-transform based local coupled-cluster singles and approximate doubles LCC2* methods. Moreover, multireference CASSCF and CASPT2 vertical excitation energies were also obtained for all species (except CASPT2 was not feasible for the four largest systems). The SAC-CI/cc-pVDZ, LCC2*/cc-pVDZ, and CASPT2/cc-pVDZ approaches are shown to have the smallest mean AEs of 0.154, 0.109, and 0.100 eV, respectively; the utility of the LCC2* approach is demonstrated for eight extended BODIPYs and aza-BODIPYs. We found that the problems with TD-DFT arise from difficulties in dealing with the differential electron correlation (as assessed by comparing CCS, CC2, LR-CCSD, CCSDR(T), and CCSDR(3) vertical excitation energies for

  11. Sticking to (first) principles: quantum molecular dynamics and Bayesian probabilistic methods to simulate aquatic pollutant absorption spectra.

    PubMed

    Trerayapiwat, Kasidet; Ricke, Nathan; Cohen, Peter; Poblete, Alex; Rudel, Holly; Eustis, Soren N

    2016-08-10

    This work explores the relationship between theoretically predicted excitation energies and experimental molar absorption spectra as they pertain to environmental aquatic photochemistry. An overview of pertinent Quantum Chemical descriptions of sunlight-driven electronic transitions in organic pollutants is presented. Second, a combined molecular dynamics (MD), time-dependent density functional theory (TD-DFT) analysis of the ultraviolet to visible (UV-Vis) absorption spectra of six model organic compounds is presented alongside accurate experimental data. The functional relationship between the experimentally observed molar absorption spectrum and the discrete quantum transitions is examined. A rigorous comparison of the accuracy of the theoretical transition energies (ΔES0→Sn) and oscillator strength (fS0→Sn) is afforded by the probabilistic convolution and deconvolution procedure described. This method of deconvolution of experimental spectra using a Gaussian Mixture Model combined with Bayesian Information Criteria (BIC) to determine the mean (μ) and standard deviation (σ) as well as the number of observed singlet to singlet transition energy state distributions. This procedure allows a direct comparison of the one-electron (quantum) transitions that are the result of quantum chemical calculations and the ensemble of non-adiabatic quantum states that produce the macroscopic effect of a molar absorption spectrum. Poor agreement between the vertical excitation energies produced from TD-DFT calculations with five different functionals (CAM-B3LYP, PBE0, M06-2X, BP86, and LC-BLYP) suggest a failure of the theory to capture the low energy, environmentally important, electronic transitions in our model organic pollutants. However, the method of explicit-solvation of the organic solute using the quantum Effective Fragment Potential (EFP) in a density functional molecular dynamics trajectory simulation shows promise as a robust model of the hydrated organic

  12. Simulations of light induced processes in water based on ab initio path integrals molecular dynamics. I. Photoabsorption

    NASA Astrophysics Data System (ADS)

    Svoboda, Ondřej; Ončák, Milan; Slavíček, Petr

    2011-10-01

    We have performed large-scale simulations of UV absorption spectra of water clusters (monomer to octamer) using a combination of ab initio path-integral molecular dynamics with reflection principle. The aim of the present work is four-fold: (1) To explore the transition from isolated molecules to bulk water from the perspective of UV photoabsorption. (2) To investigate quantum nuclear and thermal effects on the shape of the water UV spectra. (3) To make an assessment of the density functional theory functionals to be used for water excited states. (4) To check the applicability of the QM/MM schemes for a description of the UV absorption. Within the path integral molecular dynamics (PIMD)/reflection principle approach both the thermal and quantum vibrational effects including anharmonicities are accounted for. We demonstrate that shape of the spectra is primarily controlled by the nuclear quantum effects. The excited states and transition characteristics of the water clusters were calculated with the time-dependent density functional theory and equation-of-motion coupled clusters singles and doubles methods. Based on our benchmark calculations considering the whole UV spectrum we argue that the BHandHLYP method performs best among the 6 functionals tested (B3LYP, BHandHLYP, BNL, CAM-B3LYP, LC-ωPBE, and M06HF). We observe a gradual blueshift of the maximum of the first absorption peak with the increasing cluster size. The UV absorption spectrum for the finite size clusters (i.e., the peak centers, peak widths, and photoabsorption cross section) essentially converges into the corresponding bulk water spectrum. The effect of distant molecules accounted for within the polarizable continuum model is shown to be almost negligible. Using the natural transition orbitals we demonstrate that the first absorption band is formed by localized excitations while the second band includes delocalized excited states. Consequently, the QM/MM electrostatic embedding scheme can only be

  13. Nickel(II) Complex of a Hexadentate Ligand with Two o-Iminosemiquinonato(1-) π-Radical Units and Its Monocation and Dication.

    PubMed

    Ali, Akram; Dhar, Debanjan; Barman, Suman K; Lloret, Francesc; Mukherjee, Rabindranath

    2016-06-20

    Aerobic reaction of a hexadentate redox-active o-aminophenol-based ligand, H4L(3) = N,N'-bis(2-hydroxy-3,5-di-tert-butylphenyl)-2,2'-diamino(diphenyldithio)-ethane, in CH3OH with Ni(II)(O2CCH3)2·4H2O and Et3N afforded isolation of a reddish-brown crystalline solid [Ni(L(3))] 1. Cyclic voltammetry (CV) experiment exhibits two oxidative responses at E1/2 = 0.09 and 0.53 V vs SCE (saturated calomel electrode). Chemical oxidation of 1 in air by [Fe(III)(η(5)-C5H5)2][PF6] and AgBF4 in CH2Cl2 led to the isolation of one-electron oxidized species [1](1+) as purple [1][PF6]·CH2Cl2 and two-electron oxidized species [1](2+) as dark purple [1][BF4]2·CH2Cl2, respectively. X-ray crystallographic analysis at 100(2) K unambiguously established that the ligand is present in [Ni(II){(L(ISQ)O,N)(•-)}{(L(ISQ)O,N)(•-)}{(LS,S)(0)}] 1, [Ni(II){(L(IBQ)O,N)(0)}{(L(ISQ)O,N)(•-)}{(LS,S)(0)}][PF6]·CH2Cl2, and [Ni(II){(L(IBQ)O,N)(0)}{(L(IBQ)O,N)(0)}{(LS,S)(0)}][BF4]2·CH2Cl2, as monoanionic o-iminosemiquinonate(1-) π-radical (Srad = 1/2) (L(ISQ))(•-) and neutral o-iminoquinone (L(IBQ))(0) redox-levels. Complexes 1, [1][PF6]·CH2Cl2, and [1][BF4]2·CH2Cl2 possess an S = 2, 3/2, and 1 ground-state, respectively, established by temperature-dependent (2-300 K) magnetic behavior of 1 and [1][PF6]·CH2Cl2, and a μeff value of [1][BF4]2·CH2Cl2 at 300 K. Both 1 and [1][PF6]·CH2Cl2 exhibit ferromagnetic exchange-coupling between the two electrons of Ni(II) and two/one ligand π-radicals, respectively. The redox processes are shown to be ligand-based. Spectroscopic and redox properties, and density functional theory (DFT) calculations at the CAM-B3LYP-level of theory adequately describe the electronic structure of 1, [1](1+), and [1](2+). The observed UV-vis-NIR absorptions for 1, [1][PF6]·CH2Cl2, and [1][BF4]2·CH2Cl2 have been assigned, based on time-dependent (TD)-DFT calculations.

  14. Analyzing Planck and low redshift data sets with advanced statistical methods

    NASA Astrophysics Data System (ADS)

    Eifler, Tim

    -probe analysis proposed here we will use the existing CosmoLike software, a computationally efficient analysis framework that is unique in its integrated ansatz of jointly analyzing probes of large-scale structure (LSS) of the Universe. We plan to combine CosmoLike with publicly available CMB analysis software (Camb, CLASS) to include modeling capabilities of CMB temperature, polarization, and lensing measurements. The resulting analysis framework will be capable to independently and jointly analyze data from the CMB and from various probes of the LSS of the Universe. After completion we will utilize this framework to check for consistency amongst the individual probes and subsequently run a joint likelihood analysis of probes that are not in tension. The inclusion of Planck information in a joint likelihood analysis substantially reduces DES uncertainties in cosmological parameters, and allows for unprecedented constraints on parameters that describe astrophysics. In their recent review Observational Probes of Cosmic Acceleration (Weinberg et al 2013) the authors emphasize the value of a balanced program that employs several of the most powerful methods in combination, both to cross-check systematic uncertainties and to take advantage of complementary information. The work we propose follows exactly this idea: 1) cross-checking existing Planck results with alternative methods in the data analysis, 2) checking for consistency of Planck and DES data, and 3) running a joint analysis to constrain cosmology and astrophysics. It is now expedient to develop and refine multi-probe analysis strategies that allow the comparison and inclusion of information from disparate probes to optimally obtain cosmology and astrophysics. Analyzing Planck and DES data poses an ideal opportunity for this purpose and corresponding lessons will be of great value for the science preparation of Euclid and WFIRST.

  15. Possible Role of Ice in the Synthesis of Polymeric Compounds

    NASA Astrophysics Data System (ADS)

    Monnard, Pierre-Alain; Doerr, Mark; Loeffler, Philipp, M. G.

    -Crick base-pairing nucleobase were higher than in non-base-pairing systems cases where hydrogen bond based pairing is not favoured [7]-this was even the found for low H-bridging uridine monomers [7, 8]. The presence of templates fur-ther allows the synthesis of long complementary strands [9]. Thus, template-directed elongation of RNA in the eutectic phase of the water-ice system seems possible. Recently, Miller's group [10, 11] in San Diego further established that dilute solutions of ammo-nium cyanide maintained frozen at -78 C could promote the synthesis of nucleobases, although with rather low yields. The catalytic activity of a RNA-ligase ribozyme was also detected in the eutectic phase [12]. All the observations on the promotion of synthetic reactions in the eutectic phase in water-ice suggest that the cold conditions with transient thawing periods could have allowed the formation of RNA monomers on our Earth and possibly on other icy planets. [1] Ferris, J. P. Phil. Trans. R. Soc. B, 2006, 361, 1777. [2] Rajamani, S.; Vlassov, A.; Coombs, A.; F., O.; Deamer, D. W. Orig Life Evol Biosph, accepted2008, 38, 57. [3] Bada, J. L.; Bigham, C.; Miller, S. L. Proc. Nat. Acad Sci USA, 1994, 91, 1248. [4] Kanavarioti, A.; Monnard, P.-A.; Deamer, D. W. Astrobiology, 2001, 1, 271. [5] Monnard, P.-A.; Kanavarioti, A.; Deamer, D. W. J. Am. Chem. Soc., 2003, 125, 13734. [6] Dürr, M and Monnard, P.-A. in preparation. [7] Monnard, P.-A.; Szostak, J. W. J. Inorg. Biochem., 2008, 112, 1104. [8] Vogel, S. R.; Richert, C. Chem Commun (Camb), 2007, 1896. [9] Trinks, H.; Schroder, W.; Biebricher, C. K. Orig Life Evol Biosph, 2005, 35, 429. [10] Miyakawa, S.; Cleaves, H. J.; Miller, S. L. Orig. Life Evol Biosphere, 2002, 32, 195. [11] Miyakawa, S.; Cleaves, H. J.; Miller, S. L. Orig. Life Evol Biosphere, 2002, 32, 209. [12] Vlassov, A.; Johnston, B. H.; Landweber, L. F.; Kazakov, S. A. Nucl. Acids. Res., 2004, 32, 2966.

  16. PERSPECTIVE: Waorani at the head of the table: towards inclusive conservation in Yasuní

    NASA Astrophysics Data System (ADS)

    McSweeney, Kendra; Pearson, Zoe

    2009-09-01

    /2007 Oil development, indigenous organizations, and the politics of egalitarianism Camb. Anthropol. 26 34-6 Holt F L 2005 The catch-22 of conservation: indigenous peoples, biologists, and cultural change Hum. Ecol. 33 199-215 Kane J 1995 Savages (New York: Alfred A Knopf) Ma'anit A 2008 Costing the earth New Internationalist (413) 17-19 Martínez M O, Napolitano D A, MacLennan G J, O'Callaghan C, Ciborowski S and Fabregas X 2007 Impacts of petroleum activities for the Achuar people of the Peruvian Amazon: summary of existing evidence and research gaps Environ. Res. Lett. 2 045006 Napolitano D A and Ryan A S S 2007 The dilemma of contact: voluntary isolation and the impacts of gas exploitation on health and rights in the Kugapakori Nahua Reserve, Peruvian Amazon Environ. Res. Lett. 2 045005 Nygren A 2004 Contested lands and incompatible images: the political ecology of struggles over resources in Nicaragua's Indio-Maíz Reserve Soc. Nat. Resources 17 189-205 Peluso N and Watts D 2001 Violent environments Violent Environments ed N Peluso and D Watts (Ithaca, NY: Cornell University Press) pp 3-38 Rival L 2000 Marginality with a difference, or how the Huaorani preserve their sharing relations and naturalize outside powers Hunters and Gatherers in the Modern World: Conflict, Resistance, and Self-Determination ed P P Schweitzer, M Biesele and R K Hitchcock (New York: Berghahn) pp 244-63 Sawyer S 2003 Subterranean techniques: corporate environmentalism, oil operations, and social injustice in the Ecuadorian rain forest In Search of the Rainforest ed C Slater (Durham, NC: Duke University Press) pp 69-100 United Nations 2007 United Nations Declaration on the Rights of Indigenous Peoples Report of the Human Rights Council A/61/L.67 (New York: United Nations General Assembly)