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Sample records for brasiliense camb caryocaraceae

  1. Caryocar brasiliense camb protects against genomic and oxidative damage in urethane-induced lung carcinogenesis

    PubMed Central

    Colombo, N.B.R.; Rangel, M.P.; Martins, V.; Hage, M.; Gelain, D.P.; Barbeiro, D.F.; Grisolia, C.K.; Parra, E.R.; Capelozzi, V.L.

    2015-01-01

    The antioxidant effects of Caryocar brasiliense Camb, commonly known as the pequi fruit, have not been evaluated to determine their protective effects against oxidative damage in lung carcinogenesis. In the present study, we evaluated the role of pequi fruit against urethane-induced DNA damage and oxidative stress in forty 8-12 week old male BALB/C mice. An in vivo comet assay was performed to assess DNA damage in lung tissues and changes in lipid peroxidation and redox cycle antioxidants were monitored for oxidative stress. Prior supplementation with pequi oil or its extract (15 µL, 60 days) significantly reduced urethane-induced oxidative stress. A protective effect against DNA damage was associated with the modulation of lipid peroxidation and low protein and gene expression of nitric oxide synthase. These findings suggest that the intake of pequi fruit might protect against in vivo genotoxicity and oxidative stress. PMID:26200231

  2. Effect of a topical formulation containing Calophyllum brasiliense Camb. extract on cutaneous wound healing in rats.

    PubMed

    Lordani, T V A; Brenzan, M A; Cortez, L E R; Lordani, C R F; Honda, P A; Lonardoni, M V C; Cortez, D A G

    2015-01-01

    This study evaluated the wound healing effects of topical application of an emulsion containing the HPLC-standardised extract from Calophyllum brasiliense Cambess (Clusiaceae) leaves in rats. The macroscopic analysis demonstrated that the wounds treated with the C. brasiliense emulsion healed earlier than the wounds treated with emulsion base and Dersani®. The percentage of wound healing in the group treated with the C. brasiliense emulsion was significantly higher than in the other groups at 7 and 14 days. On day 14, the animals treated with the C. brasiliense emulsion exhibited a 90.67% reduction of the wound areas. The histological evaluation revealed that on day 21, the group treated with the C. brasiliense emulsion exhibited a significant increase in fibroblasts compared with the other groups. Thus, the C. brasiliense emulsion had healing properties in the topical treatment of wounds and accelerated the healing process.

  3. Chemopreventive effects of pequi oil (Caryocar brasiliense Camb.) on preneoplastic lesions in a mouse model of hepatocarcinogenesis.

    PubMed

    Palmeira, Simone M; Silva, Paula R P; Ferrão, Juliana S P; Ladd, Aliny A B L; Dagli, Maria L Z; Grisolia, Cesar K; Hernandez-Blazquez, Francisco J

    2016-07-01

    Pequi (Caryocar brasiliense Camb.), a fruit from Brazil's central region, was evaluated for its chemopreventive effects on preneoplastic liver lesions induced by the carcinogen diethylnitrosamine (DEN) in mice. BALB/c mice, 14 days of age, received an intraperitoneal injection at 10 µg/g of DEN. The mice received either of two doses of pequi oil (100 or 400 mg/kg) daily from the age of 30 days and were killed at the age of 189 days. Stereological parameters, including the volume density (Vv) and the total volume (Vtot) of the lesions (preneoplastic and adenomas), were measured and the expression of cytokeratins CK8/18 was evaluated. The total volume of lesions and adenomas was reduced by 51% in the group treated with the carcinogen and 400 mg/kg of pequi oil administered daily by an oral gavage for 25 consecutive weeks. In addition, some mice in this group did not develop lesions. Among the remaining preneoplastic lesions in this group, the number of remodelled profiles increased by 2.4-fold in the 400-mg pequi oil-treated mice relative to the 100-mg-treated mice. Our results show that pequi oil exerts a hepatoprotective effect against DEN-induced development of preneoplastic lesions and adenoma in mice and the potential for its use in the prevention of liver cancer. PMID:26287697

  4. Testing gravity with CAMB and CosmoMC

    SciTech Connect

    Hojjati, Alireza; Pogosian, Levon; Zhao, Gong-Bo E-mail: levon@sfu.ca

    2011-08-01

    We introduce a patch to the commonly used public codes CAMB and CosmoMC that allows the user to implement a general modification of the equations describing the growth of cosmological perturbations, while preserving the covariant conservation of the energy-momentum. This patch replaces the previously publicly released code MGCAMB, while also extending it in several ways. The new version removes the limitation of late-time-only modifications to the perturbed Einstein equations, and includes several parametrizations introduced in the literature. To demonstrate the use of the patch, we obtain joint constraints on the neutrino mass and parameters of a scalar-tensor gravity model from CMB, SNe and ISW data as measured from the correlation of CMB with large scale structure.

  5. Hypericum brasiliense plant extract neutralizes some biological effects of Bothrops jararaca snake venom.

    PubMed

    Assafim, Mariane; de Coriolano, Eduardo Coriolano; Benedito, Sérgio Eufrázio; Fernandes, Caio Pinho; Lobo, Jonathas Felipe Revoredo; Sanchez, Eladio Florez; Rocha, Leandro Machado; Fuly, André Lopes

    2011-01-01

    Alternative treatments for snake bite are currently being extensively studied, and plant metabolites are considered good candidates for such purpose. Here, the ability of a crude ethanolic extract of Hypericum brasiliense plant in neutralizing Bothrops jararaca snake venom was investigated by in vitro (coagulation, hemolysis or proteolysis) and in vivo (hemorrhage, lethality and edema) biological assays. We describe for the first time the ability of H. brasiliense extracts to inhibit some pharmacological effects of a Brazilian snake venom. Inhibitory assays were performed by incubating B. jararaca venom with H. brasiliense extracts for 30min at room temperature before the assays were performed. The results showed that H. brasiliense extracts impaired lethality, edema, hemorrhage, hemolysis, proteolysis as well as fibrinogen or plasma clotting induced by B. jararaca venom. This indicates that H. brasiliense extracts can provide promising agents to treat B. jararaca envenomation.

  6. 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

  7. Micropropagation of Calophyllum brasiliense (Cambess.) from nodal segments.

    PubMed

    Silveira, S S; Cordeiro-Silva, R; Degenhardt-Goldbach, J; Quoirin, M

    2016-05-01

    Micropropagation of Calophyllum brasiliense Cambess. (Clusiaceae) is a way to overcome difficulties in achieving large-scale plant production, given the recalcitrant nature of the seeds, irregular fructification and absence of natural vegetative propagation of the species. Cultures were established using nodal segments 2 cm in length, obtained from 1-2 year old seedlings, maintained in a greenhouse. Mercury chloride and Plant Preservative Mixture™ were used in the surface sterilizing stage, better results being achieved with Plant Preservative Mixture™ incorporation in culture medium, at any concentration. Polyvinylpyrrolidone, activated charcoal, cysteine, ascorbic acid or citric acid were added to the culture medium to avoid oxidation. After 30 days of culture, polyvinylpirrolidone and ascorbic acid gave better results, eliminating oxidation in most explants. For shoot multiplication, benzylaminopurine was used in concentrations of 4.4 and 8.8 µM in Woody Plant Medium, resulting in an average of 4.43 and 4.68 shoots per explant, respectively, after 90 days. Indole-3-butyric acid and α-naphthalene acetic acid were used to induce root formation, reaching a maximum rooting rate of 24% with 20µM α-naphthalene acetic acid. For acclimatization. the rooted plants were transferred to Plantmax® substrate and cultured in a greenhouse, reaching 79% of survival after 30 days and 60% after one year.

  8. 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.

  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. Micropropagation of Calophyllum brasiliense (Cambess.) from nodal segments.

    PubMed

    Silveira, S S; Cordeiro-Silva, R; Degenhardt-Goldbach, J; Quoirin, M

    2016-05-01

    Micropropagation of Calophyllum brasiliense Cambess. (Clusiaceae) is a way to overcome difficulties in achieving large-scale plant production, given the recalcitrant nature of the seeds, irregular fructification and absence of natural vegetative propagation of the species. Cultures were established using nodal segments 2 cm in length, obtained from 1-2 year old seedlings, maintained in a greenhouse. Mercury chloride and Plant Preservative Mixture™ were used in the surface sterilizing stage, better results being achieved with Plant Preservative Mixture™ incorporation in culture medium, at any concentration. Polyvinylpyrrolidone, activated charcoal, cysteine, ascorbic acid or citric acid were added to the culture medium to avoid oxidation. After 30 days of culture, polyvinylpirrolidone and ascorbic acid gave better results, eliminating oxidation in most explants. For shoot multiplication, benzylaminopurine was used in concentrations of 4.4 and 8.8 µM in Woody Plant Medium, resulting in an average of 4.43 and 4.68 shoots per explant, respectively, after 90 days. Indole-3-butyric acid and α-naphthalene acetic acid were used to induce root formation, reaching a maximum rooting rate of 24% with 20µM α-naphthalene acetic acid. For acclimatization. the rooted plants were transferred to Plantmax® substrate and cultured in a greenhouse, reaching 79% of survival after 30 days and 60% after one year. PMID:27143061

  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. Mevalonosomes: specific vacuoles containing the mevalonate pathway in Plocamium brasiliense cortical cells (Rhodophyta).

    PubMed

    Paradas, Wladimir Costa; Crespo, Thalita Mendes; Salgado, Leonardo Tavares; de Andrade, Leonardo Rodrigues; Soares, Angélica Ribeiro; Hellio, Claire; Paranhos, Ricardo Rogers; Hill, Lilian Jorge; de Souza, Geysa Marinho; Kelecom, Alphonse Germaine Albert Charles; Da Gama, Bernardo Antônio Perez; Pereira, Renato Crespo; Amado-Filho, Gilberto Menezes

    2015-04-01

    This paper has identified, for the first time in a member of the Rhodophyta, a vacuolar organelle containing enzymes that are involved in the mevalonate pathway-an important step in red algal isoprenoid biosynthesis. These organelles were named mevalonosomes (Mev) and were found in the cortical cells (CC) of Plocamium brasiliense, a marine macroalgae that synthesizes several halogenated monoterpenes. P. brasiliense specimens were submitted to a cytochemical analysis of the activity of the 3-hydroxy-3-methylglutaryl-CoA synthase (HMGS). Using transmission electron microscopy (TEM), we confirmed the presence of HMGS activity within the Mev. Because HMGS is necessary for the biosynthesis of halogenated monoterpenes, we isolated a hexanic fraction (HF) rich in halogenated monoterpenes from P. brasiliense that contained a pentachlorinated monoterpene as a major metabolite. Because terpenes are often related to chemical defense, the antifouling (AF) activity of pentachlorinated monoterpene was tested. We found that the settlement of the mussel Perna perna was reduced by HF treatment (2.25 times less than control; 40% and 90% of fouled surface, respectively; P = 0.001; F9,9 = 1.13). The HF (at 10 μg · mL(-1) ) also inhibited three species of fouling microalgae (Chlorarachnion reptans, Cylindrotheca cloisterium, and Exanthemachrysis gayraliae), while at a higher concentration (50 μg · mL(-1) ), it inhibited the bacteria Halomonas marina, Polaribacter irgensii, Pseudoalteromonas elyakovii, Shewanella putrefaciens, and Vibrio aestuarianus. The AF activity of P. brasiliense halogenated monoterpenes and the localization of HMGS activity inside Mev suggest that this cellular structure found in CC may play a role in thallus protection against biofouling. PMID:26986518

  13. Axonal degeneration in sheep caused by the ingestion of Halimium brasiliense.

    PubMed

    Riet-Correa, Franklin; Barros, Severo S; Méndez, Maria C; Gevehr-Fernandes, Cristina; Pereira Neto, Otaviano A; Soares, Marcio P; McGavin, M Donald

    2009-07-01

    Nervous system disease is reported in sheep from 2 farms in southern Brazil and in 33 farms in Uruguay. The illness was seasonal, occurring from May to November, during the growing season of Halimium brasiliense, and primarily affected sheep older than 3 years of age. Clinical signs included transient seizures that occurred mainly when sheep were disturbed or frightened. Most affected sheep recovered when removed to other pastures. Feeding trials produced clinical signs in 1 sheep after the ingestion of 2,117 g/kg of body weight of H. brasiliense over 142 days. Two sheep that had previously recovered from spontaneous toxicosis developed clinical signs after the ingestion of 263 g and 565 g of H. brasiliense per kg body weight given over 36 and 31 days, respectively. The main histologic lesion was vacuolation of the brain and spinal cord, with rare axonal spheroid formation. Transmission electron microscopy revealed segmental axonal swelling with degeneration and disappearance of the axonal organelles and vacuolation of the axoplasm. A pigment identified as ceroid was also present in neurons, astrocytes, and macrophages. These lesions suggested a novel morphologic manifestation of a toxic axonopathy. PMID:19564495

  14. 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

  15. Modeling of a violaxanthin-chlorophyll b chromophore pair in its LHCII environment using CAM-B3LYP.

    PubMed

    Kröner, Dominik; Götze, Jan Philipp

    2012-04-01

    Collecting energy for photosystem II is facilitated by several pigments, xanthophylls and chlorophylls, embedded in the light harvesting complex II (LHCII). One xanthophyll, violaxanthin (Vio), is loosely bound at a site close to a chlorophyll b (Chl). No final answer has yet been found for the role of this specific xanthophyll. We study the electronic structure of Vio in the presence of Chl and under the influence of the LHCII environment, represented by a point charge field (PCF). We compare the capability of the long range corrected density functional theory (DFT) functional CAM-B3LYP to B3LYP for the modeling of the UV/vis spectrum of the Vio+Chl pair. CAM-B3LYP was reported to allow for a very realistic reproduction of bond length alternation of linear polyenes, which has considerable impact on the carotenoid structure and spectrum. To account for the influence of the LHCII environment, the chromophore geometries are optimized using an ONIOM(DFT/6-31G(d):PM6) scheme. Our calculations show that the energies of the locally excited states are almost unaffected by the presence of the partner chromophore or the PCF. There are, however, indications for excitonic coupling of the Chl Soret band and Vio. We propose that Vio may accept energy from blue-light excited Chl.

  16. The antidepressant-like effect of Hedyosmum brasiliense and its sesquiterpene lactone, podoandin in mice: evidence for the involvement of adrenergic, dopaminergic and serotonergic systems.

    PubMed

    Gonçalves, Ana Elisa; Bürger, Cristiani; Amoah, Solomon K S; Tolardo, Rogério; Biavatti, Maique W; de Souza, Márcia M

    2012-01-15

    We have recently shown that the ethanol extract of the leaves of Hedyosmum brasiliense exhibits an antidepressant-like effect in the tail suspension and forced swimming tests in mice. The present study investigates the mechanisms involved in the antidepressant-like effect of H. brasiliense extract, together with the antidepressant potential of podoandin, an isolated sesquiterpenoid. H. brasiliense (50mg/kg, i.p.) and podoandin (10mg/kg, i.p.) decreased the immobility time in the forced swimming test, without any accompanying changes in ambulation in the open-field test. The anti-immobility effect of the H. brasiliense extract was prevented by pre-treating the mice with ondansetron, NAN 190, pindolol, prazosin, yohimbine, haloperidol, SCH23390, and sulpiride. On the other hand, pre-treating the mice with: p-chlorophenylalanine (4 consecutive days), ketanserin, naloxone, naltrindole, bicuculline, phaclofen, or l-arginine did not block the antidepressant-like effect of H. brasiliense. In addition, pre-treatment of the animals with methylene blue, NG-nitro-l-arginine or 7-nitroindazole, at subeffective doses, did not cause a synergistic effect with H. brasiliense extract at an effective dose in the forced swimming test. The anti-immobility effect of podoandin was also prevented by pre-treating the mice with NAN-190, ondansetron, prazosin, yohimbine, sulpiride and haloperidol. The results indicate that the antidepressant-like effect of H. brasiliense (and podoandin) is dependent on the serotonergic, noradrenergic and dopaminergic systems, but not on the GABAergic, opioid and oxidonitrergic systems. PMID:22115892

  17. Development and characterization of microsatellite markers for genetic analysis of a Brazilian endangered tree species Caryocar brasiliense.

    PubMed

    Collevatti, R G; Brondani, R V; Grattapaglia, D

    1999-12-01

    In this work we report the development and characterization of 10 microsatellite loci for the endangered tree species Caryocar brasiliense. Using genomic library enrichment, the efficiency of SSR marker development was 14.4% from sequencing data to operationally useful loci. Primer sequences for this set of 10 loci are made available together with their estimates of expected heterozygosity, probability of paternity exclusion and probability of identity. Mendelian inheritance and segregation was confirmed for all 10 loci in open-pollinated half-sib families as well as the absolute transferability of these 10 loci to five other species of the same genus. Number of alleles per locus ranged from 10 to 22 with a mean value of 16 and expected heterozygosity varying from 0.84 to 0.94. The combined probability of genetic identity was on the order of 10-17 clearly demonstrating that SSR multilocus genotypes are likely to be unique and capable of readily discriminating individuals of C. brasiliense. The very high combined probability of paternity exclusion (0.99999995) also indicates that these markers will permit detailed parentage studies in natural populations even in situations where both maternity and paternity are unknown. The battery of microsatellite markers developed and characterized in this study opens a new perspective for the generation of fundamental population genetic data for devising sound collection and conservation procedures for C. brasiliense and related species of the genus. PMID:10651920

  18. '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'.

  19. Evidences for multiple maternal lineages of Caryocar brasiliense populations in the Brazilian Cerrado based on the analysis of chloroplast DNA sequences and microsatellite haplotype variation.

    PubMed

    Collevatti, Rosane G; Grattapaglia, Dario; Hay, John D

    2003-01-01

    In this work we report on the phylogeography of the endangered tree species Caryocar brasiliense based on variability in two classes of maternally inherited chloroplast DNA sequences with different rates of molecular evolution. Eleven sequence haplotypes of a noncoding region between the genes trnT and trnF and 21 distinct 10-locus microsatellite haplotypes could be identified in a total of 160 individuals, collected in 10 widespread populations of C. brasiliense. An amova indicated that most of the variation can be attributed to differences among populations, both for DNA sequence (87.51%) and microsatellites (84.38%). Phylogeography based on a median-joining network analysis of the noncoding region showed a sharp difference from the analysis of microsatellite haplotypes. Nevertheless, both analyses indicated that multiple lineages may have contributed to the origin of C. brasiliense populations in Brazilian Cerrado. Incongruences in the microsatellite haplotypes network suggest that homoplasy, which emerged from recurrent and independent mutations, greatly influenced the evolution of the C. brasiliense chloroplast genome. We hypothesize that our results may show the outcome of the restriction of ancient relic populations to moist refugias during extended droughts coinciding with glaciation in the northern hemisphere. The subsequent spread to favourable areas throughout Central Brazil may have caused contact between different lineages during the interglacial periods. The extinction of megafauna dispersers in the last glaciation may have caused a restriction in seed movement and currently, gene flow has been occurring mainly by pollen movement.

  20. Traditional knowledge and uses of the Caryocar brasiliense Cambess. (Pequi) by "quilombolas" of Minas Gerais, Brazil: subsidies for sustainable management.

    PubMed

    Pinto, L C L; Morais, L M O; Guimarães, A Q; Almada, E D; Barbosa, P M; Drumond, M A

    2016-06-01

    Local knowledge of biodiversity has been applied in support of research focused on utilizing and management of natural resources and promotion of conservation. Among these resources, Pequi (Caryocar brasiliense Cambess.) is important as a source of income and food for communities living in the Cerrado biome. In Pontinha, a "quilombola" community, which is located in the central region of State of Minas Gerais, Brazil, an ethnoecological study about Pequi was conducted to support initiatives for generating income for this community. Data were collected through semi-structured interviews, participant observation, and crossing. The most relevant uses of Pequi were family food (97%), soap production (67%), oil production (37%), medical treatments (17%), and trade (3%). Bees were the floral visitors with the highest Salience Index (S=0.639). Among frugivores that feed on unfallen fruits, birds showed a higher Salience (S=0.359) and among frugivores who use fallen fruits insects were the most important (S=0.574). Borers (folivorous caterpillars) that attack trunks and roots were the most common pests cited. According to the respondents, young individuals of Pequi are the most affected by fire due to their smaller size and thinner bark. Recognition of the cultural and ecological importance of Pequi has mobilized the community, which has shown interest in incorporating this species as an alternative source of income. PMID:27058602

  1. 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.

  2. Plant phenolic acids affect the virulence of Pectobacterium aroidearum and P. carotovorum ssp. brasiliense via quorum sensing regulation.

    PubMed

    Joshi, Janak Raj; Burdman, Saul; Lipsky, Alexander; Yariv, Shaked; Yedidia, Iris

    2016-05-01

    Several studies have reported effects of the plant phenolic acids cinnamic acid (CA) and salicylic acid (SA) on the virulence of soft rot enterobacteria. However, the mechanisms involved in these processes are not yet fully understood. Here, we investigated whether CA and SA interfere with the quorum sensing (QS) system of two Pectobacterium species, P. aroidearum and P. carotovorum ssp. brasiliense, which are known to produce N-acyl-homoserine lactone (AHL) QS signals. Our results clearly indicate that both phenolic compounds affect the QS machinery of the two species, consequently altering the expression of bacterial virulence factors. Although, in control treatments, the expression of QS-related genes increased over time, the exposure of bacteria to non-lethal concentrations of CA or SA inhibited the expression of QS genes, including expI, expR, PC1_1442 (luxR transcriptional regulator) and luxS (a component of the AI-2 system). Other virulence genes known to be regulated by the QS system, such as pecS, pel, peh and yheO, were also down-regulated relative to the control. In agreement with the low levels of expression of expI and expR, CA and SA also reduced the level of the AHL signal. The effects of CA and SA on AHL signalling were confirmed in compensation assays, in which exogenous application of N-(β-ketocaproyl)-l-homoserine lactone (eAHL) led to the recovery of the reduction in virulence caused by the two phenolic acids. Collectively, the results of gene expression studies, bioluminescence assays, virulence assays and compensation assays with eAHL clearly support a mechanism by which CA and SA interfere with Pectobacterium virulence via the QS machinery.

  3. 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

  4. 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.

  5. 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.

  6. 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. PMID:26583523

  7. Transformation of the water soluble fraction from "alpeorujo" by Coriolopsis rigida: the role of laccase in the process and its impact on Azospirillum brasiliense survival.

    PubMed

    Saparrat, Mario C N; Jurado, Miguel; Díaz, Rosario; Romera, Inmaculada Garcia; Martínez, María Jesús

    2010-01-01

    The objective of this work was to evaluate the ability of the white rot basidiomycete Coriolopsis rigida to detoxify the water soluble fraction from "alpeorujo" (WSFA), a solid by-product produced by the olive oil extraction industry and characterized by a high concentration of phenols which limits its use as fertilizer and/or amendment. C. rigida reduced the phenol content in the liquid media supplemented with WSFA at 10 and 20% (v/v) after 15d of incubation. The analysis of WSFA toxicity after fungal treatment showed that C. rigida was responsible for a significant increase in the survival rate of Azospirillum brasiliense, a N(2) fixing soil rhizobacterium which promotes plant growth. Supplementation of culture medium with CuSO(4) (300 microM) resulted in strong laccase induction thus facilitating higher phenol reduction and detoxification of WSFA. In vitro reactions using a crude extracellular preparation from laccase-active C. rigida showed phenol removal as well as detoxification of the WSFA at 20%. These results suggest that C. rigida reduces the phenol content of the WSFA through the effect of laccase on free phenolic compounds consequently decreasing the toxic effect on A. brasiliense, which suggests that the enzyme plays an important role in the process. These findings have implications in the management and revalorization of olive-mill residues treated with laccase-producing fungi and their potential impact on integrative agricultural systems including organic residues and the co-inoculation with microorganisms which can facilitate the growth of plants of agricultural interest.

  8. Combining in vitro and in silico approaches to evaluate the multifunctional profile of rosmarinic acid from Blechnum brasiliense on targets related to neurodegeneration.

    PubMed

    Andrade, Juliana Maria de Mello; Dos Santos Passos, Carolina; Kieling Rubio, Maria Angélica; Mendonça, Jacqueline Nakau; Lopes, Norberto Peporine; Henriques, Amélia Teresinha

    2016-07-25

    Natural products are important sources of chemical diversity leading to unique scaffolds that can be exploited in the discovery of new drug candidates or chemical probes. In this context, chemical and biological investigation of ferns and lycophytes occurring in Brazil is an approach adopted by our research group aiming at discovering bioactive molecules acting on neurodegeneration targets. In the present study, rosmarinic acid (RA) isolated from Blechnum brasiliense showed an in vitro multifunctional profile characterized by antioxidant effects, and monoamine oxidases (MAO-A and MAO-B) and catechol-O-methyl transferase (COMT) inhibition. RA showed antioxidant effects against hydroxyl (HO(•)) and nitric oxide (NO) radicals (IC50 of 29.4 and 140 μM, respectively), and inhibition of lipid peroxidation (IC50 of 19.6 μM). In addition, RA inhibited MAO-A, MAO-B and COMT enzymes with IC50 values of 50.1, 184.6 and 26.7 μM, respectively. The MAO-A modulation showed a non-time-dependent profile, suggesting a reversible mechanism of inhibition. Structural insights on RA interactions with MAO-A and COMT were investigated by molecular docking. Finally, RA (up to 5 mM) demonstrated no cytotoxicity on polymorphonuclear rat cells. Taken together, our results suggest that RA may be exploited as a template for the development of new antioxidant molecules possessing additional MAO and COMT inhibition effects to be further investigated on in vitro and in vivo models of neurodegenerative diseases. PMID:27270453

  9. 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

  10. Bioactive Compounds Found in Brazilian Cerrado Fruits.

    PubMed

    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

  11. Identification of Ellagitannins and Flavonoids from Eugenia brasilienses Lam. (Grumixama) by HPLC-ESI-MS/MS.

    PubMed

    Teixeira, Luciane de Lira; Bertoldi, Fabiano Cleber; Lajolo, Franco Maria; Hassimotto, Neuza Mariko Aymoto

    2015-06-10

    The grumixama (Eugenia brasiliensis Lam.), also known as Brazilian cherry, is a fruit native to Brazil. This study identified the flavonoids in the flesh and seeds and ellagitannin in the flesh of purple and yellow varieties. The physicochemical characteristics and antioxidant capacity of these fruits were also evaluated. Anthocyanins and flavonols were found in high levels in the flesh of purple (32-180 mg 100 g(-1) FW) and yellow grumixama (13-41 mg 100 g(-1) FW), respectively. The major flavonoids identified were cyanidin 3-glucoside and quercetin aglycone. Furthermore, ellagitannins were found in high levels in the flesh of purple (82-243 mg ellagic acid equiv 100 g(-1) FW) and yellow grumixama (92 mg ellagic acid equiv 100 g(-1) FW) and seeds (2220-2905 mg ellagic acid equiv 100 g(-1) FW). The ellagitannin profiles of both varieties were first characterized in which pedunculagin isomers, strictinin isomers, and ellagic acid galloyl hexoside were the major ellagitannins identified. In summary, both varieties of the grumixama fruit as well as the seeds could be good sources of bioactive compounds, mainly ellagitannins. PMID:25990484

  12. 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...

  13. 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

  14. Dietary carotenoid-rich oil supplementation improves exercise-induced anisocytosis in runners: influences of haptoglobin, MnSOD (Val9Ala), CAT (21A/T) and GPX1 (Pro198Leu) gene polymorphisms in dilutional pseudoanemia (sports anemia)

    PubMed Central

    2010-01-01

    Physical training induces beneficial adaptation, whereas exhaustive exercises increase reactive oxygen-species generation, thereby causing oxidative damage in plasma and erythrocytes, fractions susceptible to lipid peroxidation. Pequi (Caryocar brasiliense Camb.) is a Brazilian Cerrado fruit containing a carotenoid-rich oil. The aim was to investigate the effects of pequi-oil on exercise-induced oxidative damage in plasma and erythrocytes, after running in the same environment and undergoing weekly training under the same conditions as to type, intensity and length. Evaluations were accomplished after outdoor running on flat land before and after ingestion of 400 mg pequi-oil capsules for 14 days. Blood samples were taken after running and submitted to TBARS assay and erythrogram analysis. Haptoglobin, MnSOD (Val9Ala), CAT (21A/T) and GPX1 (Pro198Leu) gene polymorphisms were priorly investigated, so as to estimate genetic influence The reduction in erythrocytes, hemoglobin and hematocrit after pequi-oil treatment was notably associated with higher plasma expansion. Except for MCHC (mean corpuscular hemoglobin concentration) and RDW (red cell distribution width), the results were influenced by the polymorphisms studied. The best response to pequi-oil was presented by MnSOD Val/Val, CAT AA or AT genotypes and the GPX1 Pro allele. The significantly lower RDW and higher MHCH values were related to pequi-oil protective effects. Pequi oil, besides possessing other nutritional properties, showed protective blood effects. PMID:21637495

  15. [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). PMID:17352068

  16. 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.

  17. Label-free catalytic and molecular beacon containing an abasic site for sensitive fluorescent detection of small inorganic and organic molecules.

    PubMed

    Song, Panshu; Xiang, Yu; Xing, Hang; Zhou, Zhaojuan; Tong, Aijun; Lu, Yi

    2012-03-20

    In this work, two methods with complementary features, catalytic and molecular beacon (CAMB) and label-free fluorescent sensors using an abasic site, have been combined into new label-free CAMB sensors that possess advantages of each method. The label-free method using a dSpacer-containing molecular beacon makes CAMB more cost-effective and less interfering with the catalytic activity, while CAMB allows the label-free method to use true catalytic turnovers for signal amplifications, resulting in a new label-free CAMB sensor for Pb(2+) ion, with a detection limit of 3.8 nM while maintaining the same selectivity. Furthermore, by using CAMB to overcome the label-free method's limitation of requiring excess enzyme strands, a new label-free CAMB sensor using aptazyme is also designed to detect adenosine down to 1.4 μM, with excellent selectivity over other nucleosides.

  18. Calcium mass balances in bicarbonate hemodialysis.

    PubMed

    Basile, Carlo

    2011-01-01

    Dialysate calcium (Ca) concentration should be viewed as part of the integrated therapeutic regimen to control renal osteodystrophy and maintain normal mineral metabolism. The goals of this integrated approach are to keep the patient in a mild positive Ca mass balance (CaMB), to maintain normal serum Ca levels, to control plasma parathyroid hormone values to two to three times above normal levels, and to avoid soft-tissue calcifications. Thus, a correct net CaMB during hemodialysis (HD) is crucial in the treatment of renal osteodystrophy. Very few studies have been published which measured CaMBs in bicarbonate HD. This is mainly due to the technical difficulties in achieving an accurate measurement of CaMBs owing to the need for the collection of the total spent dialysate or of a proportional aliquot of it. Whereas no doubt exists about the fact that an inlet dialysate Ca concentration (CaD) of 1.75 mmol/L leads to a positive CaMB, more controversial is this issue, when dealing with a CaD of 1.50 mmol/L and, even more, when dealing with a CaD of 1.25 mmol/L. Another important issue is the appropriate CaD in long-hour slow-flow nocturnal HD. Finally, which CaMB should we study: ionized CaMB or total CaMB? This issue is largely discussed in the review.

  19. 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

  20. 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

  1. 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...

  2. Analyticity of strictly static and strictly stationary, inheriting and non-inheriting Einstein-Maxwell solutions

    NASA Astrophysics Data System (ADS)

    Tod, Paul

    2007-07-01

    Following the technique of Müller zum Hagen (Proc. Camb. Phil. Soc. 67: 415-421, 1970) we show that strictly static and strictly stationary solutions of the Einstein-Maxwell equations are analytic in harmonic coordinates. This holds whether or not the Maxwell field inherits the symmetry.

  3. "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…

  4. Catalytic and molecular beacons for amplified detection of metal ions and organic molecules with high sensitivity.

    PubMed

    Zhang, Xiao-Bing; Wang, Zidong; Xing, Hang; Xiang, Yu; Lu, Yi

    2010-06-15

    The catalytic beacon has emerged as a general platform for sensing metal ions and organic molecules. However, few reports have taken advantage of the true potential of catalytic beacons in signal amplification through multiple enzymatic turnovers, as existing designs require either equal concentrations of substrate and DNAzyme or an excess of DNAzyme in order to maintain efficient quenching, eliminating the excess of substrate necessary for multiple turnovers. On the basis of the large difference in the melting temperatures between the intramolecular molecular beacon stem and intermolecular products of identical sequences, we here report a general strategy of catalytic and molecular beacon (CAMB) that combines the advantages of the molecular beacon for highly efficient quenching with the catalytic beacon for amplified sensing through enzymatic turnovers. Such a CAMB design allows detection of metal ions such as Pb(2+) with a high sensitivity (LOD = 600 pM). Furthermore, the aptamer sequence has been introduced into DNAzyme to use the modified CAMB for amplified sensing of adenosine with similar high sensitivity. These results together demonstrate that CAMB provides a general platform for amplified detection of a wide range of targets.

  5. 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.

  6. Antinociceptive and anti-inflammatory effects of Caryocar coriaceum Wittm fruit pulp fixed ethyl acetate extract on zymosan-induced arthritis in rats.

    PubMed

    de Oliveira, Francisco Fábio Bezerra; de Araújo, Joana Cláudia Bezerra; Pereira, Anamaria Falcão; Brito, Gerly Anne Castro; Gondim, Delane Viana; Ribeiro, Ronaldo de Albuquerque; de Menezes, Irwin Rose Alencar; Vale, Mariana Lima

    2015-11-01

    The ethyl acetate extract from the fruit pulp of Caryocar coriaceum Wittm (Caryocaraceae), popularly known as pequi, has wide applications in popular medicine. Preclinical tests have demonstrated the therapeutic properties of the oil. We investigated the antinociceptive and anti-inflammatory effects of Pequi C. coriaceum Wittm ethyl acetate extract (PCCO) on zymosan-induced arthritis in rat knee joint. The animals were pretreated with PCCO for 7 consecutive days or with a single dose. Paw elevation time (PET), leukocyte infiltration, myeloperoxidase activity (MPO) and cytokine levels were assessed 4h after zymosan injection. Synovial tissue was harvested for immunohistochemical analysis, edema and vascular permeability. We observed a significant decrease in PET with PCCO pretreatment. PCCO showed a significant reduction of leukocyte migration and a decrease in MPO. Decreases were observed in cytokine release in the synovial fluid and TNF-α and cyclooxygenase-1 immunostaining in synovial tissue. Edema was inhibited by treatment with all doses of PCCO. The data suggest that PCCO exerts antinociceptive and anti-inflammatory effects on arthritis in rats.

  7. Antinociceptive and anti-inflammatory effects of Caryocar coriaceum Wittm fruit pulp fixed ethyl acetate extract on zymosan-induced arthritis in rats.

    PubMed

    de Oliveira, Francisco Fábio Bezerra; de Araújo, Joana Cláudia Bezerra; Pereira, Anamaria Falcão; Brito, Gerly Anne Castro; Gondim, Delane Viana; Ribeiro, Ronaldo de Albuquerque; de Menezes, Irwin Rose Alencar; Vale, Mariana Lima

    2015-11-01

    The ethyl acetate extract from the fruit pulp of Caryocar coriaceum Wittm (Caryocaraceae), popularly known as pequi, has wide applications in popular medicine. Preclinical tests have demonstrated the therapeutic properties of the oil. We investigated the antinociceptive and anti-inflammatory effects of Pequi C. coriaceum Wittm ethyl acetate extract (PCCO) on zymosan-induced arthritis in rat knee joint. The animals were pretreated with PCCO for 7 consecutive days or with a single dose. Paw elevation time (PET), leukocyte infiltration, myeloperoxidase activity (MPO) and cytokine levels were assessed 4h after zymosan injection. Synovial tissue was harvested for immunohistochemical analysis, edema and vascular permeability. We observed a significant decrease in PET with PCCO pretreatment. PCCO showed a significant reduction of leukocyte migration and a decrease in MPO. Decreases were observed in cytokine release in the synovial fluid and TNF-α and cyclooxygenase-1 immunostaining in synovial tissue. Edema was inhibited by treatment with all doses of PCCO. The data suggest that PCCO exerts antinociceptive and anti-inflammatory effects on arthritis in rats. PMID:26341615

  8. 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. PMID:27529792

  9. Macroergonomic analysis of an assembly sector of a furniture company.

    PubMed

    Cristiane, A A Z; Danielle, M D; Vanessa, C B

    2012-01-01

    From of Macroergonomic Analysis of Work were diagnosed the main ergonomics demands in a furniture company in the city of Cambé, Paraná. Through this method we could identify the most problematic points of the analyzed environment for posterior solutions of improvement with the objective of increasing the working and psychological quality of the employees, motivating their good performance and satisfaction. PMID:22317139

  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. 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.

  12. Computational studies on structure and spectroscopic properties of 4-(Boc-amino) pyridine

    NASA Astrophysics Data System (ADS)

    Vural, H.

    2015-12-01

    The molecular modeling of 4-(Boc-amino) pyridine was carried out using B3LYP, CAMB3LYP and PBE1PBE levels of density functional theory (DFT). The vibrational frequencies of the title molecule in the ground state were computed by using B3LYP, CAMB3LYP and PBE1PBE methods with the 6-31G + (d, p) basis set. Gauge-independent atomic orbital (GIAO) 1H and 13C nuclear magnetic resonance (NMR) chemical shift values of the 4-(Boc-amino) pyridine were calculated by using the DFT/B3LYP with 6-31G + (d, p) basis set. The solvent effect on the NMR spectra of the molecule was also examined using the B3LYP method by applying the integral equation formalism-polarized continuum model (IEF-PCM). The electronic properties, such as HOMO-LUMO energies, absorption wavelengths and excitation energy, were investigated by time dependent DFT (TD-DFT) method with IEF-PCM. The mulliken charges on the atoms and second-order interaction energies were derived from NBO analysis. To investigate the nonlinear optical (NLO) properties of the title molecule, the electric dipole moment, the mean polarizability and the mean first hyperpolarizability were computed by using the DFT method with B3LYP, CAM-B3LYP and PBE1PBE levels.

  13. 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. PMID:27135846

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. The ticks (Acari: Ixodida: Argasidae, Ixodidae) of Paraguay.

    PubMed

    Nava, S; Lareschi, M; Rebollo, C; Benítez Usher, C; Beati, L; Robbins, R G; Durden, L A; Mangold, A J; Guglielmone, A A

    2007-04-01

    The ticks reported in Paraguay, which are here reviewed, can be categorized as 'endemic or established' (Argas persicus or a sibling species, Ornithodoros hasei, O. rostratus, O. rudis, O. talaje/O. puertoricensis, Amblyomma aureolatum, Am. auricularium, Am. brasiliense, Am. cajennense, Am. calcaratum, Am. coelebs, Am. dissimile, Am. dubitatum, Am. incisum, Am. longirostre, Am. nodosum, Am. ovale, Am. pacae, Am. parvum, Am. pseudoconcolor, Am. rotundatum, Am. scutatum, Am. tigrinum, Am. triste, Dermacentor nitens, Haemaphysalis juxtakochi, H. leporispalustris, Ixodes loricatus, Rhipicephalus microplus, and Rh. sanguineus), 'probably endemic or established' (Ar. miniatus, Ar. monachus, Am. argentinae, Am. humerale, Am. naponense, Am. oblongoguttatum, Am. pseudoparvum, I. aragaoi/I. pararicinus, I. auritulus, I. luciae), or 'erroneously reported from Paraguay' (O. coriaceus, Am. americanum and Am. maculatum). Most Paraguayan tick collections have been made in the Chaco phyto-geographical domain, in the central part of the country. Argas persicus or a related species, Am. cajennense, D. nitens, Rh. microplus and Rh. sanguineus are important parasites of domestic animals. Ornithodoros rudis, Am. aureolatum, Am. brasiliense, Am. cajennense, Am. coelebs, Am. incisum, Am. ovale and Am. tigrinum have all been collected from humans. In terms of public health, the collections of Am. cajennense and Am. triste from humans may be particularly significant, as these species are potential vectors of Rickettsia rickettsii and Ri. parkeri, respectively.

  19. 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

  20. Phytochemical Analysis and Antifungal Activity of Extracts from Leaves and Fruit Residues of Brazilian Savanna Plants Aiming Its Use as Safe Fungicides.

    PubMed

    Breda, Caroline Alves; Gasperini, Alessandra Marcon; Garcia, Vera Lucia; Monteiro, Karin Maia; Bataglion, Giovana Anceski; Eberlin, Marcos Nogueira; Duarte, Marta Cristina Teixeira

    2016-08-01

    The increasing demand for safe food without preservatives or pesticides residues has encouraged several studies on natural products with antifungal activity and low toxicity. In this study, ethanolic extracts from leaves and fruit residues (peel and seeds) of three Brazilian savanna species (Acrocomia aculeata, Campomanesia adamantium and Caryocar brasiliense) were evaluated against phytopathogenic fungi. Additionally, the most active extract was chemically characterized by ESI-MS and its oral acute toxicity was evaluated. Extracts from C. brasiliense (pequi) peel and leaves were active against Alternaria alternata, Alternaria solani and Venturia pirina with minimal inhibitory concentrations between 350 and 1000 µg/mL. When incorporated in solid media, these extracts extended the lag phase of A. alternata and A. solani and reduced the growth rate of A. solani. Pequi peel extract showed better antifungal activity and their ESI-MS analysis revealed the presence of substances widely reported as antifungal such as gallic acid, quinic acid, ellagic acid, glucogalin and corilagin. The oral acute toxicity was relatively low, being considered safe for use as a potential natural fungicide. PMID:27169570

  1. Ghost dark energy models in specific modified gravity

    NASA Astrophysics Data System (ADS)

    Jawad, Abdul; Salako, Ines G.; Sohail, Ayesha

    2016-09-01

    The paper is devoted to the study of the cosmic acceleration through ghost dark energy models (its simple and generalized form) in the dynamical Chern-Simons modified gravity. In order to check the reliability of this scenario, we explore different cosmological parameters, such as deceleration, equation of state parameters and squared speed of sound. The cosmological planes ωD - 'D and r- s are also investigated in this framework. The obtained results are consistent with observational data of various schemes (WMAP+eCAMB+BAO+H0).

  2. 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.

  3. 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.

  4. Designing a whole-cell biotransformation system in Escherichia coli using cytochrome P450 from Streptomyces peucetius.

    PubMed

    Shrestha, Pramod; Oh, Tae-Jin; Sohng, Jae Kyung

    2008-06-01

    A biotransformation system was designed to co-express CYP107P3 (CSP4), cytochrome P450, from Streptomyces peuceticus, along with CamA (putidaredoxin reductase) and CamB (putidaredoxin) from Pseudomonas putida, the necessary reducing equivalents, in a class I type electron-transfer system in E. coli BL21 (DE3). This was carried out using two plasmids with different selection markers and compatible origins of replication. The study results showed that this biotransformation system was able to mediate the O-dealkylation of 7-ethoxycumarin. PMID:18259876

  5. Selective detection of toxic cyanogen gas in the presence of O2, and H2O molecules using a AlN nanocluster

    NASA Astrophysics Data System (ADS)

    Solimannejad, Mohammad; Kamalinahad, Saeedeh; Shakerzadeh, Ehsan

    2016-08-01

    The interaction of cyanogen molecule with Al12N12 nanocage has been studied using density functional theory (DFT) at CAM-B3LYP/6-31+G(d) level. Geometric, electronic structure and natural bond orbitals (NBO) analysis display that adsorption of cyanogen onto exterior surface of Al12N12 is physisorption with adsorption energy (Eads) equal to -55.36 kJ/mol. UV-vis study shows a high intensity peak in 388.9 nm due to interaction of gas with nanocage. It is expected that Al12N12 will be used in designing novel materials for potential applications to detect toxic cyanogen molecule.

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

    PubMed

    Kullie, Ossama

    2014-01-14

    In previous works on Zn2 and Cd2 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(2) + 6s6p), (6s(2) + 6s7s), and (6s(2) + 6s7p) atomic asymptotes for the mercury dimer Hg2. 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 Hg2 including a comparative analysis with the lighter dimers of the group 12, Cd2, and Zn2, 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 Hg2.

  7. Cosmic microwave background with Brans-Dicke gravity. I. Covariant formulation

    SciTech Connect

    Wu Fengquan; Qiang Lie; Wang Xin; Chen Xuelei

    2010-10-15

    In the covariant cosmological perturbation theory, a 1+3 decomposition ensures that all variables in the frame-independent equations are covariant and gauge invariant and that they have clear physical interpretations. We develop this formalism in the case of Brans-Dicke gravity, and apply this method to the calculation of CMB anisotropy and large scale structures. We modify the publicly available Boltzmann code CAMB to calculate numerically the evolution of the background and adiabatic perturbations, and obtain the temperature and polarization spectra of Brans-Dicke theory for both scalar and tensor modes; the tensor mode results for Brans-Dicke gravity are obtained numerically for the first time. We first present our theoretical formalism in detail, and then explicitly describe the techniques used in modifying the CAMB code. These techniques are also very useful for other gravity models. Next we compare the CMB and large scale structure spectra in Brans-Dicke theory with those in the standard general relativity theory. At last, we investigate the integrated Sachs-Wolfe effect and the CMB lensing effect in Brans-Dicke theory. Constraints on the Brans-Dicke model with current observational data are presented in a companion paper [F. Wu and X. Chen, following Article, Phys. Rev. D 82, 083003 (2010)] (paper II).

  8. 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. PMID:24598934

  9. Modeling emission features of salicylidene aniline molecular crystals: A QM/QM' approach.

    PubMed

    Presti, Davide; Labat, Frédéric; Pedone, Alfonso; Frisch, Michael J; Hratchian, Hrant P; Ciofini, Ilaria; Cristina Menziani, Maria; Adamo, Carlo

    2016-04-01

    A new computational protocol relying on the use of electrostatic embedding, derived from QM/QM' ONIOM calculations, to simulate the effect of the crystalline environment on the emission spectra of molecular crystals is here applied to the β-form of salicylidene aniline (SA). The first singlet excited states (S1 ) of the SA cis-keto and trans-keto conformers, surrounded by a cluster of other molecules representing the crystalline structure, were optimized by using a QM/QM' ONIOM approach with and without electronic embedding. The model system consisting of the central salicylidene aniline molecule was treated at the DFT level by using either the B3LYP, PBE0, or the CAM-B3LYP functional, whereas the real system was treated at the HF level. The CAM-B3LYP/HF level of theory provides emission energies in good agreement with experiment with differences of -20/-32 nm (cis-keto form) and -8/-14 nm (trans-keto form), respectively, whereas notably larger differences are obtained using global hybrids. Though such differences on the optical properties arise from the density functional choice, the contribution of the electronic embedding is rather independent of the functional used. This plays in favor of a more general applicability of the present protocol to other crystalline molecular systems. PMID:26919703

  10. Theoretical study on absorption and emission spectra of pyrrolo-C analogues

    NASA Astrophysics Data System (ADS)

    Liu, Hongxia; Liu, Jianhua; Yang, Yan; Li, Yan; Wang, Haijun

    2015-01-01

    Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we use theoretical calculations to investigate the structural and optical properties of Pyrrolo-C (PyC) and its analogues which are modified via the conjugation or fusion of different aromatic ring to the PyC core. We also consider the effects of aqueous solution and base pairing. The results show that the fluorescent pyrrolo-C analogues can pair with guanosine to form stable H-bonded WC base pairs. The calculated absorption peaks of modified deoxyribonucleosides agree well with the measured data. The absorption and emission maxima of the pyrrolo-C analogues are greatly red shifted compared with nature C. The solvent effects can induce wavelength blue shift and increase the oscillator strengths in both the absorption and emission spectra. With regard to the WC base pairs, the B3LYP functional reveals that the lowest energy transitions of modified GC base pairs are charge transfer excitation while the CAM-B3LYP functional predicts that all the lowest transitions are localised on the pyrrolo-C analogues. The M062X and CAM-B3LYP functionals show good agreement with respect to both the value of the lowest energy transitions as well as the oscillator strengths.

  11. Performance of DFT Methods in the Calculation of Optical Spectra of TCF-Chromophores

    SciTech Connect

    Andzelm, Jan; Rinderspacher, Berend C.; Rawlett, Adam M.; Dougherty, Joseph; Baer, Roi; Govind, Niranjan

    2009-10-01

    We present electronic structure calculations of the ultraviolet/visible (UV-Vis) spectra of highly active push-pull chromophores containing tricyanofuran (TCF) acceptor group. In particular, we have applied the recently developed long-range corrected Baer-Neuhauser-Livshits (BNL) exchange-correlation functional. The performance of this functional compares favorably with other density functional theory (DFT) approaches, including the CAM-B3LYP functional. The accuracy of UV-Vis results for these molecules is best at low values of attenuation parameters (γ) for both BNL and CAM-B3LYP functionals. The optimal value of γ is different for the charge-transfer (CT) and π-π* excitations. The BNL and PBE0 exchange correlation functionals capture the CT states particularly well while the π-π* excitations are less accurate and system dependent. Chromophore conformations, which considerably affect the molecular hyperpolarizability, do not significantly influence the UV-Vis spectra on average. As expected, the color of chromophores is a sensitive function of modifications to its conjugated framework, and is not significantly affected by increasing aliphatic chain length linking a chromophore to a polymer. For selected push-pull aryl-chromophores, we find a significant dependence of absorption spectra on the strength of diphenylaminophenyl donors.

  12. 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

  13. 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.

  14. Electronic structures and second hyperpolarizabilities of alkaline earth metal complexes end-capped with NA2 (A = H, Li, Na).

    PubMed

    Banerjee, Paramita; Nandi, Prasanta K

    2016-05-14

    The ground state structures and NLO properties of a number of alkaline earth metal complexes end-capped with NA2 groups (A = H, Li, Na) are calculated by employing the CAM-B3LYP, wB97XD and B2PLYP functionals along with MP2 and CCSD(T) for 6-311++G(d,p), 6-311++G(3df,3pd), aug-cc-pVTZ, aug-pc-2 and Hypol basis sets. The complexes are found to be significantly stable. The magnitude of second hyperpolarizability enhances appreciably with increase in the number of magnesium and calcium atoms in the chain, which has been indicated by the power law dependence γ = a + bn(c) with c values ranging from 2.4-4.3 for Mg and 2.4-3.7 for Ca complexes, respectively. The largest second-hyperpolarizability (10(9) au) is obtained for the complex Ca7(NNa2)2 at the CAM-B3LYP level. The two state model has been used to explain the variation of hyperpolarizabilities. PMID:27088138

  15. 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.

  16. Accuracy of Quantum Mechanically Derived Force-Fields Parameterized from Dispersion-Corrected DFT Data: The Benzene Dimer as a Prototype for Aromatic Interactions.

    PubMed

    Prampolini, Giacomo; Livotto, Paolo Roberto; Cacelli, Ivo

    2015-11-10

    A multilevel approach is presented to assess the ability of several popular dispersion corrected density functionals (M06-2X, CAM-B3LYP-D3, BLYP-D3, and B3LYP-D3) to reliably describe two-body interaction potential energy surfaces (IPESs). To this end, the automated Picky procedure ( Cacelli et al. J. Comput. Chem. 2012 , 33 , 1055 ) was exploited, which consists in parametrizing specific intermolecular force fields through an iterative approach, based on the comparison with quantum mechanical data. For each of the tested functionals, the resulting force field was employed in classical Monte Carlo and Molecular Dynamics simulations, performed on systems of up to 1000 molecules in ambient conditions, to calculate a number of condensed phase properties. The comparison of the resulting structural and dynamic properties with experimental data allows us to assess the quality of each IPES and, consequently, even the quality of the DFT functionals. The methodology is tested on the benzene dimer, commonly used as a benchmark molecule, a prototype of aromatic interactions. The best results were obtained with the CAM-B3LYP-D3 functional. Besides assessing the reliability of DFT functionals in describing aromatic IPESs, this work provides a further step toward a robust protocol for the derivation of sound force field parameters from quantum mechanical data. This method can be relevant in all those cases where standard force fields fail in giving accurate predictions.

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

    NASA Astrophysics Data System (ADS)

    Kullie, Ossama

    2014-01-01

    In previous works on Zn2 and Cd2 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 (6s2 + 6s6p), (6s2 + 6s7s), and (6s2 + 6s7p) atomic asymptotes for the mercury dimer Hg2. 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 Hg2 including a comparative analysis with the lighter dimers of the group 12, Cd2, and Zn2, 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 Hg2.

  18. Biodegradation of hexachlorobenzene by a constructed microbial consortium.

    PubMed

    Yan, Da-Zhong; Mao, Ling-Qi; Li, Cun-Zhi; Liu, Jun

    2015-02-01

    A consortium comprised of an engineered Escherichia coli DH5α and a natural pentachlorophenol (PCP) degrader, Sphingobium chlorophenolicum ATCC 39723, was assembled for degradation of hexachlorobenzene (HCB), a persistent organic pollutant. The engineered E. coli strain, harbouring a gene cassette (camA (+) camB (+) camC) that encodes the F87W/Y96F/L244A/V247L mutant of cytochrome P-450cam (CYP101), oxidised HCB to PCP. The resulting PCP was then further completely degraded by ATCC 39723. The results showed that almost 40 % of 4 μM HCB was degraded by the consortium at a rate of 0.033 nmol/mg (dry weight)/h over 24 h, accompanied by transient accumulation and immediate consumption of the intermediate PCP, detected by gas chromatography. In contrast, in the consortium comprised of Pseudomonas putida PaW340 harbouring camA (+) camB (+) camC and ATCC 39723, PCP accumulated in PaW340 cells but could not be further degraded, which may be due to a permeability barrier of Pseudomonas PaW340 for PCP transportation. The strategy of bacterial co-culture may provide an alternative approach for the bioremediation of HCB contamination.

  19. Optical Rotation from Coupled Cluster and Density Functional Theory: The Role of Basis Set Convergence.

    PubMed

    Haghdani, Shokouh; Åstrand, Per-Olof; Koch, Henrik

    2016-02-01

    We have calculated the electronic optical rotation of seven molecules using coupled cluster singles-doubles (CCSD) and the second-order approximation (CC2) employing the aug-cc-pVXZ (X = D, T, or Q) basis sets. We have also compared to time-dependent density functional theory (TDDFT) by utilizing two functionals B3LYP and CAM-B3LYP and the same basis sets. Using relative and absolute error schemes, our calculations demonstrate that the CAM-B3LYP functional predicts optical rotation with the minimum deviations compared to CCSD at λ = 355 and 589.3 nm. Furthermore, our results illustrate that the aug-cc-pVDZ basis set provides the optical rotation in good agreement with the larger basis sets for molecules not possessing small-angle optical rotation at λ = 589.3 nm. We have also performed several two-point inverse power extrapolations for the basis set convergence, i.e., OR(∞) + AX(-n), using the CC2 model at λ = 355 and 589.3 nm. Our results reveal that a two-point inverse power extrapolation with the aug-cc-pVTZ and aug-cc-pVQZ basis sets at n = 5 provides optical rotation deviations similar to those of aug-cc-pV5Z with respect to the basis limit.

  20. 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.

  1. First hyperpolarizability of polymethineimine with long-range corrected functionals

    NASA Astrophysics Data System (ADS)

    Jacquemin, Denis; Perpète, Eric A.; Medved', Miroslav; Scalmani, Giovanni; Frisch, Michael J.; Kobayashi, Rika; Adamo, Carlo

    2007-05-01

    Using the long-range corrected (LC) density functional theory (DFT) scheme introduced by Iikura et al. [J. Chem. Phys. 115, 3540 (2001)] and the Coulomb-attenuating model (CAM-B3LYP) of Yanai et al. [Chem. Phys. Lett. 393, 51 (2004)], we have calculated the longitudinal dipole moments and static electronic first hyperpolarizabilities of increasingly long polymehtineimine oligomers. For comparison purposes Hartree-Fock (HF), Møller-Plesset perturbation theory (MP2), and conventional pure and hybrid functionals have been considered as well. HF, generalized gradient approximation (GGA), and conventional hybrids provide too large dipole moments for long oligomers, while LC-DFT allows to reduce the discrepancy with respect to MP2 by a factor of 3. For the first hyperpolarizability, the incorrect evolution with the chain length predicted by HF is strongly worsened by BLYP, Perdew-Burke-Ernzerhof (PBE), and also by B3LYP and PBE0. On the reverse, LC-BLYP and LC-PBE hyperpolarizabilities are correctly predicted to be positive (but for the two smallest chains). Indeed, for medium and long oligomers LC hyperpolarizabilities are slightly smaller than MP2 hyperpolarizabilities, as it should be. CAM-B3LYP also strongly improves the B3LYP results, though a bit less impressively for small chain lengths. The present study demonstrates the efficiency of long-range DFT, even in very pathological cases.

  2. Optical Rotation Calculations for a Set of Pyrrole Compounds.

    PubMed

    Haghdani, Shokouh; Gautun, Odd R; Koch, Henrik; Åstrand, Per-Olof

    2016-09-22

    Optical rotation of 14 molecules containing the pyrrole group is calculated by employing both time-dependent density functional theory (TDDFT) with the CAM-B3LYP functional and the second-order approximate coupled-cluster singles and doubles (CC2) method. All optical rotations have been provided using the aug-cc-pVDZ basis set at λ = 589 nm. The two methods predict similar results for both sign and magnitude for the optical rotation of all molecules. The obtained signs are consistent with experiments as well, although several conformers for four molecules needed to be studied to reproduce the experimental sign. We have also calculated excitation energies and rotatory strengths for the six lowest lying electronic transitions for several conformers of the two smallest molecules and found that each rotatory strength has various contributions for each conformer which can cause different optical rotations for different conformers of a molecule. Our results illustrate that both methods are able to reproduce the experimental optical rotations, and that the CAM-B3LYP functional, the least computationally expensive method used here, is an applicable and reliable method to predict the optical rotation for these molecules in line with previous studies. PMID:27571252

  3. Biodegradation of hexachlorobenzene by a constructed microbial consortium.

    PubMed

    Yan, Da-Zhong; Mao, Ling-Qi; Li, Cun-Zhi; Liu, Jun

    2015-02-01

    A consortium comprised of an engineered Escherichia coli DH5α and a natural pentachlorophenol (PCP) degrader, Sphingobium chlorophenolicum ATCC 39723, was assembled for degradation of hexachlorobenzene (HCB), a persistent organic pollutant. The engineered E. coli strain, harbouring a gene cassette (camA (+) camB (+) camC) that encodes the F87W/Y96F/L244A/V247L mutant of cytochrome P-450cam (CYP101), oxidised HCB to PCP. The resulting PCP was then further completely degraded by ATCC 39723. The results showed that almost 40 % of 4 μM HCB was degraded by the consortium at a rate of 0.033 nmol/mg (dry weight)/h over 24 h, accompanied by transient accumulation and immediate consumption of the intermediate PCP, detected by gas chromatography. In contrast, in the consortium comprised of Pseudomonas putida PaW340 harbouring camA (+) camB (+) camC and ATCC 39723, PCP accumulated in PaW340 cells but could not be further degraded, which may be due to a permeability barrier of Pseudomonas PaW340 for PCP transportation. The strategy of bacterial co-culture may provide an alternative approach for the bioremediation of HCB contamination. PMID:25532745

  4. 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

  5. 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

  6. 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. PMID:25054511

  7. A contribution to the taxonomy of the genus xiphinema cobb, 1913.

    PubMed

    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.

  8. A toxic cyanobacterial bloom in an urban coastal lake, Rio Grande do Sul state, Southern Brazil

    PubMed Central

    de Carvalho, Luciana Retz; Pipole, Fernando; Werner, Vera Regina; Laughinghouse IV, Haywood Dail; de Camargo, Antonio Carlos M.; Rangel, Marisa; Konno, Katsuhiro; Sant’ Anna, Célia Leite

    2008-01-01

    Reports of cyanobacterial blooms developing worldwide have considerably increased, and, in most cases, the predominant toxins are microcystins. The present study reports a cyanobacterial bloom in Lake Violão, Torres, Rio Grande do Sul State, in January 2005. Samples collected on January 13, 2005, were submitted to taxonomical, toxicological, and chemical studies. The taxonomical analysis showed many different species of cyanobacteria, and that Microcystis protocystis and Sphaerocavum cf. brasiliense were dominant. Besides these, Microcystis panniformis, Anabaena oumiana, Cylindrospermopsis raciborskii, and Anabaenopsis elenkinii f. circularis were also present. The toxicity of the bloom was confirmed through intraperitoneal tests in mice, and chemical analyses of bloom extracts showed that the major substance was anabaenopeptin F, followed by anabaenopeptin B, microcystin-LR, and microcystin-RR. PMID:24031304

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. Stability and Teller's theorem: Fullerenes in the March model

    NASA Astrophysics Data System (ADS)

    Clougherty, Dennis P.; Zhu, Xiang

    1997-07-01

    We study C60 with the use of the March model [N. H. March, Proc. Camb. Philos. Soc. 48, 665 (1952)]. A spherical shell model is invoked to treat the nuclear potential, where the nuclear and core charges are smeared out into a shell of constant surface charge density. The valence electron distribution and the electrostatic potential are efficiently computed by integration of the Thomas-Fermi equation, subject to the shell boundary conditions. Total energy is numerically calculated over a range of shell radii, and the mechanical stability of the model is explored with attention to the constraints of Teller's theorem [E. Teller, Rev. Mod. Phys. 34, 627 (1962)]. The calculated equilibrium radius of the shell is in fair agreement with experiment.

  14. Polymer Optical Constants from Long-Range Corrected DFT Calculations.

    PubMed

    Maekawa, Shintaro; Moorthi, Krzysztof

    2016-03-10

    A methodology to calculate refractive indices of plastics based on the Lorentz-Lorenz equation has been proposed. The polarizability of the nonconjugated polymer repeat units is predicted using the long-range corrected functionals. The end effect corrections in repeat unit models are essential to achieve accuracy similar to that observed for molecular liquids (ca. 1% in mean absolute deviation). The functionals with 100% Hartree-Fock (HF) exchange in the long-range limit perform best for aromatic and other hydrogen-deficient compounds; the Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP) performs very well for hydrogen-rich (usually, fully saturated) compounds. Exceptionally good agreement is observed for the sets of wavelength-dependent refractive index data for polystyrene, poly(methyl methacrylate), and for poly(perfluoro-4-vinyloxy-1-butene) (CYTOP), for which the root-mean-square deviations are 0.004, 0.002, and 0.004, respectively.

  15. Electronic states of alkyl-radical-functionalized C20 fullerene using density functional theory

    NASA Astrophysics Data System (ADS)

    Abe, Shigeaki; Kawano, Shimpei; Toida, Yu; Nakamura, Mariko; Inoue, Satoshi; Sano, Hidehiko; Yoshida, Yasuhiro; Kawabata, Hiroshi; Tachikawa, Hiroto

    2016-03-01

    The structures and electronic states of alkyl-radical-functionalized C20 fullerenes (denoted by C20-R) have been investigated using density functional theory (DFT). The different alkyl radicals investigated were methyl, ethyl, propyl, and butyl radicals. The DFT calculation indicated that the alkyl radical binds to the carbon atom of C20 in the on-top site, thus forming a strong C-C single bond. The binding energies of the alkyl radicals to C20 were calculated to be 83.9-86.6 kcal/mol at the CAM-B3LYP/6-311G(d,p) level. The electronic states of the C20-R complex are discussed on the basis of the theoretical results.

  16. Calculation of low bandgap homopolymers: Comparison of TD-DFT methods with experimental oligomer series

    NASA Astrophysics Data System (ADS)

    Oliveira, Eliezer Fernando; Roldao, Juan Carlos; Milián-Medina, Begoña; Lavarda, Francisco Carlos; Gierschner, Johannes

    2016-02-01

    The performance of different DFT functionals (B3LYP, BHLYP, CAM-B3LYP, M06HF) on the prediction of vertical transition energies Evert of low bandgap homopolymers is tested against the experimentally available oligomer series (thienopyrazines and thienothiophenes). This allows for a detailed and accurate comparison on the consistency of DFT methods for chainlength evolution and polymer limit prediction, and for an understanding of geometry and time-dependent contributions to Evert by combinatorial analysis. Together with former studies on wide/medium bandgap polymers and low bandgap co-polymers, our results on low bandgap homopolymers suggest offset-corrected M06HF as the most viable method for time inexpensive and reliable prediction of semiconducting polymers at the moment.

  17. Fast and accurate CMB computations in non-flat FLRW universes

    SciTech Connect

    Lesgourgues, Julien; Tram, Thomas E-mail: thomas.tram@epfl.ch

    2014-09-01

    We present a new method for calculating CMB anisotropies in a non-flat Friedmann universe, relying on a very stable algorithm for the calculation of hyperspherical Bessel functions, that can be pushed to arbitrary precision levels. We also introduce a new approximation scheme which gradually takes over in the flat space limit and leads to significant reductions of the computation time. Our method is implemented in the Boltzmann code class. It can be used to benchmark the accuracy of the camb code in curved space, which is found to match expectations. For default precision settings, corresponding to 0.1% for scalar temperature spectra and 0.2% for scalar polarisation spectra, our code is two to three times faster, depending on curvature. We also simplify the temperature and polarisation source terms significantly, so the different contributions to the C{sub ℓ} 's are easy to identify inside the code.

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

    SciTech Connect

    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.

  19. 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. PMID:26434348

  20. Theoretical exploration of photoisomerization-switchable second-order nonlinear optical responses of two-dimendional λ- and w-shaped polyoxometalate derivatives of dithienylperfluorocyclopentene.

    PubMed

    Ma, Teng-Ying; Ma, Na-Na; Yan, Li-Kai; Zhang, Ting; Su, Zhong-Min

    2013-10-17

    The switchable second-order nonlinear optical (NLO) properties on two-dimensional (2D) molecules based on Lindqvist-type [Mo6O19](2-) and dithienylperfluorocyclopentene (DTE) have been investigated at density functional theory (DFT) level. The CAM-B3LYP and M06-2X functionals were employed to study the switching behavior on NLO properties by photoisomerization reaction. The βtot value of system 2c (closed-ring form) is 15920.5 au, which is 150.1 times larger than that of the corresponding open-ring form (system 2o). The time-dependent DFT calculations predict that the charge transfer from DTE to polyoxometalate, and DTE intramolecular charge transfer in closed-ring systems effectively improve the static first hyperpolarizability. Furthermore, the Λ-shaped systems possess a larger u value than those of W-shaped systems owing to different orientation for substituent groups.

  1. 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.

  2. 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.

  3. Modification of alkali metals on silicon-based nanoclusters: An enhanced nonlinear optical response

    NASA Astrophysics Data System (ADS)

    Li, Xiaojun; Han, Quan; Yang, Xiaohui; Song, Ruijuan; Song, Limei

    2016-08-01

    Structures, chemical stabilities and nonlinear optical properties of alkali metals-adsorbed niobium-doped silicon (M@SinNb+) clusters are investigated using the DFT methods. The alkali metals prefer energetically to be attached as bridged bond rather than M-Si single bond in most of optimized structures. Adsorption of alkali metals on doped silicon clusters gradually enhances their chemical stabilities with increasing cluster size. Noteworthily, the first hyperpolarizabilities (βtot) of the M@SinNb+ clusters, obtained by using the long-range corrected CAM-B3LYP functional, are large enough to establish their strong nonlinear optical behavior, especially for M@Si9Nb+ (M = Li, Na, and K), and the enhanced βtot ordering by alkali metals is Na > K > Li.

  4. 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

  5. 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.

  6. CosmoSIS: Modular cosmological parameter estimation

    DOE PAGES

    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, 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

  7. New density functional parameterizations to accurate calculations of electric field gradient variations among compounds.

    PubMed

    Santiago, Régis Tadeu; Haiduke, Roberto Luiz Andrade

    2015-10-30

    This research provides a performance investigation of density functional theory and also proposes new functional parameterizations to deal with electric field gradient (EFG) calculations at nuclear positions. The entire procedure is conducted within the four-component formalism. First, we noticed that traditional hybrid and long-range corrected functionals are more efficient in the description of EFG variations for a set of elements (indium, antimony, iodine, lutetium, and hafnium) among linear molecules. Thus, we selected the PBE0, B3LYP, and CAM-B3LYP functionals and promoted a reoptimization of their parameters for a better description of these EFG changes. The PBE0q variant developed here showed an overall promising performance in a validation test conducted with potassium, iodine, copper, and gold. In general, the correlation coefficients found in linear regressions between experimental nuclear quadrupole coupling constants and calculated EFGs are improved while the systematic EFG errors also decrease as a result of this reparameterization. PMID:26284820

  8. Quantum chemical characterization of N-(2-hydroxybenzylidene)acetohydrazide (HBAH): a detailed vibrational and NLO analysis.

    PubMed

    Tamer, Ömer; Avcı, Davut; Atalay, Yusuf

    2014-01-01

    The molecular modeling of N-(2-hydroxybenzylidene)acetohydrazide (HBAH) was carried out using B3LYP, CAMB3LYP and PBE1PBE levels of density functional theory (DFT). The molecular structure of HBAH was solved by means of IR, NMR and UV-vis spectroscopies. In order to find the stable conformers, conformational analysis was performed based on B3LYP level. A detailed vibrational analysis was made on the basis of potential energy distribution (PED). HOMO and LUMO energies were calculated, and the obtained energies displayed that charge transfer occurs in HBAH. NLO analysis indicated that HBAH can be used as an effective NLO material. NBO analysis also proved that charge transfer, conjugative interactions and intramolecular hydrogen bonding interactions occur through HBAH. Additionally, major contributions from molecular orbitals to the electronic transitions were investigated theoretically.

  9. 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.

  10. 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.

  11. Fourth level MSSM inflation from new flat directions

    SciTech Connect

    Choudhury, Sayantan; Pal, Supratik E-mail: supratik@isical.ac.in

    2012-04-01

    We propose a model of inflation driven by minimal extension of SUSY, commonly known as MSSM. Starting from gauge invariant flat directions in the n = 4 level comprising of QQQL,QuQd,QuLe and uude, we construct the inflaton potential and employ it to investigate for its consequences around the saddle point arising from the non-vanishing fourth derivative of the original potential. To this end, we derive the expressions for the important parameters in MSSM inflation using the loop corrected potential. We further estimate the observable parameters and find them to fit well with recent observational data from WMAP7 by using the code CAMB. We also explore the possibility of primordial black hole formation from our model. Finally, we analyze one loop RGE and compute different phenomenological parameters which could be precisely determined in LHC or future Linear Colliders.

  12. 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.

  13. 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. PMID:26900717

  14. Density functional theory based generalized effective fragment potential method

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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.

  15. 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

    2011-08-01

    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.

  16. 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}.

  17. 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

  18. 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

  19. 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

    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 HYS(T). 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

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

    PubMed

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

    2004-06-01

    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.

  1. 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

  2. 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

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

    PubMed

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

    2011-01-01

    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 flavicalcarcomb. n.; Bassus macadamiae Briceño and Sharkey 2000 to Lytopylus macadamiaecomb. n.; Metriosoma bicarinatum Enderlein 1920 to Lytopylus bicarinatumcomb. n.; Metriosoma brasiliense Enderlein 1920 to Lytopylus brasiliensecomb. n.; Bassus tayrona Campos 2007 to Lytopylus tayronacomb. n.; Microdus femoratus Cameron 1887 to Lytopylus femoratuscomb. n.; Microdus melanocephalus Cameron 1887 to Lytopylus melanocephaluscomb. n.; Bassus pastranai Blanchard 1952 to Lytopylus pastranaicomb. n.; Agathis nigrobalteata Cameron 1911 to Lytopylus nigrobalteatuscomb. n. Two keys to species of Lytopylus are presented, one interactive and the other static.

  4. 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

  5. Adaptive patterns of osmotic and ionic regulation, and the invasion of fresh water by the palaemonid shrimps.

    PubMed

    Freire, Carolina A; Cavassin, Fabiola; Rodrigues, Ellen N; Torres, Antonio H; McNamara, John C

    2003-11-01

    To evaluate trends in the osmoregulatory behavior of neotropical, palaemonid shrimps, we investigated osmotic and ionic regulatory patterns in five species of Palaemon or Macrobrachium. The species' life histories depend on saline water to differing degrees, their habitats ranging from the marine/intertidal (P. northropi), through estuaries (P. pandaliformis) to coastal, freshwater streams (M. olfersii, M. potiuna) and inland, continental river systems (M. brasiliense). Hemolymph osmolality, chloride, sodium and magnesium concentrations were measured in shrimps exposed to experimental media ranging from fresh water (<0.5 per thousand ) to concentrated seawater (42 per thousand ) for up to 10 days. The marine and estuarine Palaemon species exhibit well-developed hyper/hypo-osmotic, sodium and chloride regulatory capabilities in mid-range salinities, tending to hyperconform in low salinities. The freshwater Macrobrachium species show variable hyperosmotic, sodium and chloride regulatory capacities, tending to hypoconform or unable to survive at higher salinities. All species hyper-regulate magnesium in fresh water, but hyporegulate strongly in saline media. Palaemonids from the saline habitats show the strongest osmoregulatory capabilities, and fresh water may have been gradually invaded by ancestral species with similar regulatory capacity. However, this regulatory plasticity has been lost to varying degrees in extant freshwater species.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. Can Contemporary Density Functional Theory Predict Energy Spans in Molecular Catalysis Accurately Enough To Be Applicable for in Silico Catalyst Design? A Computational/Experimental Case Study for the Ruthenium-Catalyzed Hydrogenation of Olefins.

    PubMed

    Rohmann, Kai; Hölscher, Markus; Leitner, Walter

    2016-01-13

    The catalytic hydrogenation of cyclohexene and 1-methylcyclohexene is investigated experimentally and by means of density functional theory (DFT) computations using novel ruthenium Xantphos(Ph) (4,5-bis(diphenylphosphino)-9,9-dimethylxanthene) and Xantphos(Cy) (4,5-bis(dicyclohexylphosphino)-9,9-dimethylxanthene) precatalysts [Ru(Xantphos(Ph))(PhCO2)(Cl)] (1) and [Ru(Xantphos(Cy))(PhCO2)(Cl)] (2), the synthesis, characterization, and crystal structures of which are reported. The intention of this work is to (i) understand the reaction mechanisms on the microscopic level and (ii) compare experimentally observed activation barriers with computed barriers. The Gibbs free activation energy ΔG(⧧) was obtained experimentally with precatalyst 1 from Eyring plots for the hydrogenation of cyclohexene (ΔG(⧧) = 17.2 ± 1.0 kcal/mol) and 1-methylcyclohexene (ΔG(⧧) = 18.8 ± 2.4 kcal/mol), while the Gibbs free activation energy ΔG(⧧) for the hydrogenation of cyclohexene with precatalyst 2 was determined to be 21.1 ± 2.3 kcal/mol. Plausible activation pathways and catalytic cycles were computed in the gas phase (M06-L/def2-SVP). A variety of popular density functionals (ωB97X-D, LC-ωPBE, CAM-B3LYP, B3LYP, B97-D3BJ, B3LYP-D3, BP86-D3, PBE0-D3, M06-L, MN12-L) were used to reoptimize the turnover determining states in the solvent phase (DF/def2-TZVP; IEF-PCM and/or SMD) to investigate how well the experimentally obtained activation barriers can be reproduced by the calculations. The density functionals B97-D3BJ, MN12-L, M06-L, B3LYP-D3, and CAM-B3LYP reproduce the experimentally observed activation barriers for both olefins very well with very small (0.1 kcal/mol) to moderate (3.0 kcal/mol) mean deviations from the experimental values indicating for the field of hydrogenation catalysis most of these functionals to be useful for in silico catalyst design prior to experimental work. PMID:26713773

  11. 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.

  12. 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. PMID:27534378

  13. Theoretical study on the stability of double-decker type metal phthalocyanines, M(Pc)2 and M(Pc)2(+) (M = Ti, Sn and Sc): a critical assessment on the performance of density functionals.

    PubMed

    Sumimoto, Michinori; Kawashima, Yukio; Hori, Kenji; Fujimoto, Hitoshi

    2015-03-01

    We report the results of theoretical calculations on the optimized structures and relative energies between the D4d and D2 symmetry structures for double-decker type phthalocyanine compounds, Ti(Pc)2, Ti(Pc)2(+), Sn(Pc)2, Sn(Pc)2(+), Sc(Pc)2 and Sc(Pc)2(+), using eighteen types of functionals: B3LYP, B3PW91, B3P86, PBE1PBE, BHandHLYP, BPW91, BP86, M06, M06-2x, M06-HF, M06L, LC-BPW91, LC-ωPBE, CAM-B3LYP, B97D, ωB97, ωB97X and ωB97XD. Two phthalocyanine moieties are stacked in a face-to-face configuration in the D4d structure, but they are stapled by two σ-bonds in the D2 one. We found that the molecular symmetry of M(Pc)2 and M(Pc)2(+) depends on the balance between stabilization due to electron delocalization and exchange repulsion of π-electrons in the phthalocyanine moieties. We assessed the performance of the well-established functionals to select the appropriate functional for calculations on M(Pc)2 and M(Pc)2(+), and several important aspects came out. Generally, the hybrid GGA and hybrid meta-GGA functionals with 20-27% of the HF exchange term would give the molecular structures consistent with the experimental expectations for the double-decker type phthalocyanine compounds. Pure GGA and pure meta-GGA functionals (BPW91, BP86, M06L and B97D) have the tendency to overestimate the stability of the D4d structure. On the other hand, functionals including HF exchange for 50% and over or including long-range corrections (BHandHLYP, M06, M06-2x, M06-HF, LC-BPW91, LC-ωPBE, CAM-B3LYP, ωB97, ωB97X and ωB97XD) tend to overestimate the stability of the D2 structure. It should be emphasized that the B3LYP functional, one of the most commonly used hybrid GGA functionals with 20% HF exchange, cannot estimate the relative stability between the two molecular structures of Ti(Pc)2 appropriately. The calculation for the systems considered in this article required well-balanced treatment of the HF exchange with the accompanied exchange-correlation functional. Thus, as

  14. [Al2O4](-), a Benchmark Gas-Phase Class II Mixed-Valence Radical Anion for the Evaluation of Quantum-Chemical Methods.

    PubMed

    Kaupp, Martin; Karton, Amir; Bischoff, Florian A

    2016-08-01

    The radical anion [Al2O4](-) has been identified as a rare example of a small gas-phase mixed-valence system with partially localized, weakly coupled class II character in the Robin/Day classification. It exhibits a low-lying C2v minimum with one terminal oxyl radical ligand and a high-lying D2h minimum at about 70 kJ/mol relative energy with predominantly bridge-localized-hole character. Two identical C2v minima and the D2h minimum are connected by two C2v-symmetrical transition states, which are only ca. 6-10 kJ/mol above the D2h local minimum. The small size of the system and the absence of environmental effects has for the first time enabled the computation of accurate ab initio benchmark energies, at the CCSDT(Q)/CBS level using W3-F12 theory, for a class-II mixed-valence system. These energies have been used to evaluate wave function-based methods [CCSD(T), CCSD, SCS-MP2, MP2, UHF] and density functionals ranging from semilocal (e.g., BLYP, PBE, M06L, M11L, N12) via global hybrids (B3LYP, PBE0, BLYP35, BMK, M06, M062X, M06HF, PW6B95) and range-separated hybrids (CAM-B3LYP, ωB97, ωB97X-D, LC-BLYP, LC-ωPBE, M11, N12SX), the B2PLYP double hybrid, and some local hybrid functionals. Global hybrids with about 35-43% exact-exchange (EXX) admixture (e.g., BLYP35, BMK), several range hybrids (CAM-B3LYP, ωB97X-D, ω-B97), and a local hybrid provide good to excellent agreement with benchmark energetics. In contrast, too low EXX admixture leads to an incorrect delocalized class III picture, while too large EXX overlocalizes and gives too large energy differences. These results provide support for previous method choices for mixed-valence systems in solution and for the treatment of oxyl defect sites in alumosilicates and SiO2. Vibrational gas-phase spectra at various computational levels have been compared directly to experiment and to CCSD(T)/aug-cc-pV(T+d)Z data. PMID:27434425

  15. 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.

  16. Simulation of circularly polarized luminescence spectra using coupled cluster theory

    NASA Astrophysics Data System (ADS)

    McAlexander, Harley R.; Crawford, T. Daniel

    2015-04-01

    We report the first computations of circularly polarized luminescence (CPL) rotatory strengths at the equation-of-motion coupled cluster singles and doubles (EOM-CCSD) level of theory. Using a test set of eight chiral ketones, we compare both dipole and rotatory strengths for absorption (electronic circular dichroism) and emission to the results from time-dependent density-functional theory (TD-DFT) and available experimental data for both valence and Rydberg transitions. For two of the compounds, we obtained optimized geometries of the lowest several excited states using both EOM-CCSD and TD-DFT and determined that structures and EOM-CCSD transition properties obtained with each structure were sufficiently similar that TD-DFT optimizations were acceptable for the remaining test cases. Agreement between EOM-CCSD and the Becke three-parameter exchange function and Lee-Yang-Parr correlation functional (B3LYP) corrected using the Coulomb attenuating method (CAM-B3LYP) is typically good for most of the transitions, though agreement with the uncorrected B3LYP functional is significantly worse for all reported properties. The choice of length vs. velocity representation of the electric dipole operator has little impact on the EOM-CCSD transition strengths for nearly all of the states we examined. For a pair of closely related β, γ-enones, (1R)-7-methylenebicyclo[2.2.1]heptan-2-one and (1S)-2-methylenebicyclo[2.2.1]heptan-7-one, we find that EOM-CCSD and CAM-B3LYP agree with the energetic ordering of the two possible excited-state conformations, resulting in good agreement with experimental rotatory strengths in both absorption and emission, whereas B3LYP yields a qualitatively incorrect result for the CPL signal of (1S)-2-methylenebicyclo[2.2.1]heptan-7-one. Finally, we predict that one of the compounds considered here, trans-bicyclo[3.3.0]octane-3,7-dione, is unique in that it exhibits an achiral ground state and a chiral first excited state, leading to a strong CPL

  17. Simulation of circularly polarized luminescence spectra using coupled cluster theory

    SciTech Connect

    McAlexander, Harley R.; Crawford, T. Daniel

    2015-04-21

    We report the first computations of circularly polarized luminescence (CPL) rotatory strengths at the equation-of-motion coupled cluster singles and doubles (EOM-CCSD) level of theory. Using a test set of eight chiral ketones, we compare both dipole and rotatory strengths for absorption (electronic circular dichroism) and emission to the results from time-dependent density-functional theory (TD-DFT) and available experimental data for both valence and Rydberg transitions. For two of the compounds, we obtained optimized geometries of the lowest several excited states using both EOM-CCSD and TD-DFT and determined that structures and EOM-CCSD transition properties obtained with each structure were sufficiently similar that TD-DFT optimizations were acceptable for the remaining test cases. Agreement between EOM-CCSD and the Becke three-parameter exchange function and Lee-Yang-Parr correlation functional (B3LYP) corrected using the Coulomb attenuating method (CAM-B3LYP) is typically good for most of the transitions, though agreement with the uncorrected B3LYP functional is significantly worse for all reported properties. The choice of length vs. velocity representation of the electric dipole operator has little impact on the EOM-CCSD transition strengths for nearly all of the states we examined. For a pair of closely related β, γ-enones, (1R)-7-methylenebicyclo[2.2.1]heptan-2-one and (1S)-2-methylenebicyclo[2.2.1]heptan-7-one, we find that EOM-CCSD and CAM-B3LYP agree with the energetic ordering of the two possible excited-state conformations, resulting in good agreement with experimental rotatory strengths in both absorption and emission, whereas B3LYP yields a qualitatively incorrect result for the CPL signal of (1S)-2-methylenebicyclo[2.2.1]heptan-7-one. Finally, we predict that one of the compounds considered here, trans-bicyclo[3.3.0]octane-3,7-dione, is unique in that it exhibits an achiral ground state and a chiral first excited state, leading to a strong CPL

  18. Evaluation of the difference in the rate coefficients of F2 + NOx (x = 1 or 2) → F + FNOx by the stereochemical arrangement using the density functional theory.

    PubMed

    Tajima, Satomi; Hayashi, Toshio; Hori, Masaru

    2015-02-26

    The rate coefficient of F2 + NO → F + FNO is 2 to 5 orders of magnitude higher than that of F2 + NO2 → F + FNO2 even though bond energies of FNO and FNO2 only differ by ∼0.2 eV. To understand the cause of having different rate coefficients of these two reactions, the change in total energies was calculated by varying the stereochemical arrangement of F2 with respect to NOx (x = 1 or 2) by the density functional theory (DFT), using CAM-B3LYP/6-311 G+(d) in the Gaussian program. The permitted approaching angle between the x-axis and the plane consisting of O, N, F, and ϕ plays a key role to restrict the reaction of NO2 and F2 compared to the reaction of NO and F2. This restriction in the reaction space is considered to be the main cause of different rate coefficients depending on the selection of x = 1 or 2 of the reaction of F2 + NOx → F + FNOx, which was also confirmed by the difference in Si etch rate using the F formed by those reactions. PMID:25599135

  19. Study of the Effect of the Pulse Width of the Excitation Source on the Two-Photon Absorption and Two-Photon Circular Dichroism Spectra of Biaryl Derivatives.

    PubMed

    Vesga, Yuly; Hernandez, Florencio E

    2016-09-01

    Herein we report on the expanded theoretical calculations and the experimental measurements of the two-photon absorption (TPA) and two-photon circular dichroism (TPCD) spectra of a series of optically active biaryl derivatives (R-BINOL, R-VANOL, and R-VAPOL) using femtosecond pulses. The comparative analysis of the experimental TPCD spectra obtained with our tunable amplified femtosecond system with those previously measured in our group on the same series of compounds in the picosecond regime reveals a decrease in the amplitude of the signal and an improvement in matching with the theory in the former. These results can be explained based on the negligible contribution of excited state absorption (ESA) using femtosecond pulses compared to the picosecond regime. We show how ESA affects both the strength of the signal and the shape of the TPA and TPCD spectra. TPA and TPCD spectra were obtained using the double L-scan technique over a broad spectral range (450-750 nm) using 90 fs pulses at 50 Hz repetition rate produced by an amplified femtosecond system. The theoretical calculations were performed using modern analytical response theory within the time-dependent density functional theory (TD-DFT) approach using CAM-B3LYP and 6-311++G(d,p) basis sets. PMID:27525702

  20. 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

    2016-01-01

    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

  1. Surface study and sensing activity of nanotubular indium trioxide to NH3, H2S, NO2 and CO environmental pollutants

    NASA Astrophysics Data System (ADS)

    Zamani, Mehdi

    2016-02-01

    Molecular and electronic structures of nanotubular indium trioxide were studied using B3LYP and CAM-B3LYP density functional methods. Three nanotube models including nanotubes with closed ends (CENT), one opened end (OOENT) and two opened ends (TOENT) were considered. The highest occupied molecular orbital (HOMO) of CENT is distributed over the entire nanotube; while it is distributed on the end cap of OOENT. In both CENT and OOENT, the distribution of the lowest unoccupied molecular orbital (LUMO) is on the end caps. HOMO and LUMO of TOENT are distributed on the center of nanotube. The sensing activity of OOENT to environmental pollutants was evaluated regarding the interaction of nanotube with NH3, H2S, NO2 and CO molecules. Adsorptions over different positions of OOENT are exothermic and the NH3 adsorption is thermodynamically more favorable. The selectivity of OOENT toward gaseous pollutants is investigated as NH3 > H2S > CO > NO2. Interaction of NO2 and CO over the closed end (end cap) of nanotube is preferred; while adsorption of NH3 and H2S on the opened end is more favorable.

  2. Probing the linear and nonlinear optical properties of nitrogen-substituted carbon nanotube.

    PubMed

    Sun, Shi-Ling; Hu, Yang-Yang; Xu, Hong-Liang; Su, Zhong-Min; Hao, Li-Zhu

    2012-07-01

    In view of their intriguing structural and electrical properties, the linear and nonlinear optical (NLO) responses of six carbon nanotube (CNT) molecules substituted by nitrogen atoms at one end have been explored by using the CAM-B3LYP method. Molecules 1, 2 and 3 were obtained by increasing the lengths of the CNTs, and 1-Li, 2-Li and 3-Li were constructed by doping one Li atom into the N-substituted end of 1, 2 and 3 (mentioned above), respectively. Two effective approaches have been proposed to increase nonlinear optical properties(NLO): increasing the length of the CNT as well as doping one Li atom into the N-substituted end. The results show that both the linear polarizabilities (α(0)) and nonlinear first hyperpolarizabilities (β(tot)) values increase with increasing the lengths of the CNTs: 188 of 1 < 307 of 2 < 453 of 3 for α(0) and 477 of 1 < 2654 of 2 < 3906 au of 3 for β(tot). Significantly, compared with the non-doped CNTs, the β(tot) values are remarkably enhanced by doping one Li atom into the N-substituted end: 477 of 1 < 23258 of 1-Li, 2654 of 2 < 37244 of 2-Li, and 3906 of 3 < 72004 au of 3-Li. Moreover, the β(vec) values show a similar trend to the β(tot) values. Our results may be beneficial to experimentalists in exploring high-performance nonlinear optical materials based on CNT.

  3. 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.

  4. Elucidation of Photoisomerization-Related Structural Changes in an Acrylamide-Bridged Binaphthalene-Diazene Macrocyclic Chiroptical Switch by Experimental Electronic Circular Dichroism Spectra Simulation: Role of Dispersion Corrections.

    PubMed

    Kerner, Lukáš; Kicková, Anna; Filo, Juraj; Kedžuch, Stanislav; Putala, Martin

    2015-08-13

    Nondestructive readout of light-driven molecular memory devices can be achieved by monitoring the alterations in the chiroptical properties of 1,1'-binaphthalene as a conformationally responsive chiral group. In our system, this signaling unit is connected via acrylamide linkers to the receiving diphenyldiazene fragment, which undergoes significant geometrical changes upon (E)/(Z)-photoisomerization. The compound functions as a stable photochromic switch by alternating irradiation at 365/465 nm, with fully reversible modulation of circular dichroism (CD) signal intensity (up to 1:3) and extended thermal stability of the (Z)-isomer. According to molecular modeling, the acrylamide spacers are due to the imposed cyclic strain upon photoisomerization forced to switch amide conformations, which is markedly reflected in the CD spectra, whereas binaphthalene conformational changes are mostly neglected both by theory and by experiment. In CD simulation by TD-DFT, CAM-B3LYP outperforms B3LYP and M06 by means of similarity analysis, whereas the last mentioned functional also delivers satisfactory performance qualitatively. The inclusion of dispersion corrections during geometry optimization was crucial to retain consistency with the measured spectra. By carefully considering all relevant conformations of this 20-membered macrocycle, reasonable agreement with the experiment is reached not only for the CD simulation of the individual conformers but also of the photoisomerization process of their admixture. PMID:26172026

  5. Structure and electronic properties of azadirachtin.

    PubMed

    de Castro, Elton A S; de Oliveira, Daniel A B; Farias, Sergio A S; Gargano, Ricardo; Martins, João B L

    2014-02-01

    We performed a combined DFT and Monte Carlo (13)C NMR chemical-shift study of azadirachtin A, a triterpenoid that acts as a natural insect antifeedant. A conformational search using a Monte Carlo technique based on the RM1 semiempirical method was carried out in order to establish its preferred structure. The B3LYP/6-311++G(d,p), wB97XD/6-311++G(d,p), M06/6-311++G(d,p), M06-2X/6-311++G(d,p), and CAM-B3LYP/6-311++G(d,p) levels of theory were used to predict NMR chemical shifts. A Monte Carlo population-weighted average spectrum was produced based on the predicted Boltzmann contributions. In general, good agreement between experimental and theoretical data was obtained using both methods, and the (13)C NMR chemical shifts were predicted highly accurately. The geometry was optimized at the semiempirical level and used to calculate the NMR chemical shifts at the DFT level, and these shifts showed only minor deviations from those obtained following structural optimization at the DFT level, and incurred a much lower computational cost. The theoretical ultraviolet spectrum showed a maximum absorption peak that was mainly contributed by the tiglate group. PMID:24509732

  6. 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.

  7. Charge-transfer optical absorption mechanism of DNA:Ag-nanocluster complexes

    NASA Astrophysics Data System (ADS)

    Longuinhos, R.; Lúcio, A. D.; Chacham, H.; Alexandre, S. S.

    2016-05-01

    Optical properties of DNA:Ag-nanoclusters complexes have been successfully applied experimentally in Chemistry, Physics, and Biology. Nevertheless, the mechanisms behind their optical activity remain unresolved. In this work, we present a time-dependent density functional study of optical absorption in DNA:Ag4. In all 23 different complexes investigated, we obtain new absorption peaks in the visible region that are not found in either the isolated Ag4 or isolated DNA base pairs. Absorption from red to green are predominantly of charge-transfer character, from the Ag4 to the DNA fragment, while absorption in the blue-violet range are mostly associated to electronic transitions of a mixed character, involving either DNA-Ag4 hybrid orbitals or intracluster orbitals. We also investigate the role of exchange-correlation functionals in the calculated optical spectra. Significant differences are observed between the calculations using the PBE functional (without exact exchange) and the CAM-B3LYP functional (which partly includes exact exchange). Specifically, we observe a tendency of charge-transfer excitations to involve purines bases, and the PBE spectra error is more pronounced in the complexes where the Ag cluster is bound to the purines. Finally, our results also highlight the importance of adding both the complementary base pair and the sugar-phosphate backbone in order to properly characterize the absorption spectrum of DNA:Ag complexes.

  8. 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.

  9. 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. PMID:26907588

  10. 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.

  11. 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

  12. Importance of solvation in understanding the chiroptical spectra of natural products in solution phase: garcinia acid dimethyl ester.

    PubMed

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

    2011-03-25

    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

  13. 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.

  14. Addition reaction of alkyl radical to C60 fullerene: Density functional theory study

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2016-02-01

    Functionalized fullerenes are known as a high-performance molecules. In this study, the alkyl-functionalized fullerenes (denoted by R-C60) have been investigated by means of the density functional theory (DFT) method to elucidate the effects of functionalization on the electronic states of fullerene. Also, the reaction mechanism of alkyl radicals with C60 was investigated. The methyl, ethyl, propyl, and butyl radicals (denoted by n = 1-4, where n means the number of carbon atoms in the alkyl radical) were examined as alkyl radicals. The DFT calculation showed that the alkyl radical binds to the carbon atom of C60 at the on-top site, and a strong C-C single bond is formed. The binding energies of alkyl radicals to C60 were distributed in the range of 31.8-35.1 kcal mol-1 at the CAM-B3LYP/6-311G(d,p) level. It was found that the activation barrier exists before alkyl addition, the barrier heights were calculated to be 2.1-2.8 kcal mol-1. The electronic states of R-C60 complexes were discussed on the basis of the theoretical results.

  15. 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].

  16. Tuning the NLO properties of polymethineimine chains by chemical substitution

    NASA Astrophysics Data System (ADS)

    Medved', Miroslav; Jacquemin, Denis

    2013-03-01

    Structure and molecular electronic properties including dipole moment, polarizability and first hyperpolarizability of polymethineimine (PMI) oligomers (up to hexadecamers) and its experimentally known amino-, methyl-, and cyano-derivatives are investigated using several ab initio methods (HF, MP2 and DFT). It is shown that side-chain substitutions have significant effects both on the structure and molecular properties of PMI chains. Depending on the substitution, two types of structures have been identified. The first is characterized by a bent skeleton and encompasses PMI, polyacetonitrile (PAcN), and polycyanonitrile (PCN). The second, represented by polyaminonitrile (PAN), remains quasi-linear with the plane of the unit cell (UC) only slightly rotating around the longitudinal molecular axis. These structural differences are also reflected in molecular properties; while in case of PMI, PAcN, and PCN the longitudinal component of properties (reduced per UC) reaches its maximum value for medium-size oligomers and then decreases for longer chains, the linear and nonlinear properties of PAN steadily increase towards the polymeric limit. In addition, we have assessed the performances of long-range corrected DFT functionals (LR-DFT), namely LC-BLYP, CAM-B3LYP, and ωB97X within the present framework: they provide results in qualitative agreement with MP2, a success not reached with B3LYP.

  17. TD-DFT Benchmark on Inorganic Pt(II) and Ir(III) Complexes.

    PubMed

    Latouche, Camille; Skouteris, Dimitrios; Palazzetti, Federico; Barone, Vincenzo

    2015-07-14

    We report in the present paper a comprehensive investigation of representative Pt(II) and Ir(III) complexes with special reference to their one-photon absorption spectra employing methods rooted in density functional theory and its time dependent extension. We have compared nine different functionals ranging from generalized gradient approximation (GGA) to global or range-separated hybrids, and two different basis sets, including pseudopotentials for 4 iridium and 7 platinum complexes. It turns out that hybrid functionals with the same exchange part give comparable results irrespective of the specific correlation functional (i.e., B3LYP is very close to B3PW91 and PBE0 is very close to MPW1PW91). More recent functionals, such as CAM-B3LYP and M06-2X, overestimate excitation energies, whereas local functionals (BP86 -GGA-, M06-L -Meta GGA-) strongly underestimate transition energies with respect to experimental results. As expected, basis set effects are weak, and the use of a triple-ζ polarized (def2-TZVP) basis set does not significantly improve the computed excitation energies with respect to a classical double-ζ basis set (LANL2DZ) augmented by polarization functions, but it significantly raises the computational effort. PMID:26575764

  18. 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.

  19. Competition Between H2SO4(-)(CH3)3N and H2SO4-H2O Interactions: Theoretical Studies on the Clusters [(CH3)3N]·(H2SO4)·(H2O)(3-7).

    PubMed

    Xu, Zhen-Zhen; Fan, Hong-Jun

    2015-08-27

    The role of the nucleation of sulfuric acid with amines in aerosol formation and its implications for environment is one of the fundamental unsettled questions in atmospheric chemistry. We have investigated the cluster of [(CH3)3N]·(H2SO4)·(H2O)n (n = 3–7) by molecular dynamics to obtain configurational sampling combination with CAM-B3LYP/6-311G(d,p) level to locate the global and many local minima for each cluster size. According to the binding energies at the method of MP2/6-311++G(d,p), the total binding energies decrease with the increasing of the water molecules. For each global minimum, the average binding energies decrease from n = 3 to 4, then increase slowly. The protons of H2SO4 are preferred to transfer to the (CH3)3N to form ion-pair HSO4(–) and (CH3)3NH(+), and the (CH3)3NH(+) ions are coordinated at the first hydrated shell of HSO4(–) when n is between 3 and 5 and coordinated at the second or third hydrated shell when n is larger than 5.

  20. 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.

  1. 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.

  2. Assessment in the competition between steric and electronic effects in the elimination kinetic of hydrogen in 1,4-cyclohexadienes in the gas phase. Quantum chemical theory calculations

    NASA Astrophysics Data System (ADS)

    Ramírez, Beatriz; Córdova-Sintjago, Tania C.; Ruette, Fernando; Chuchani, Gabriel

    2015-02-01

    The mechanisms of gas-phase thermal decomposition of alkyl-substituted cyclohexadienes were studied by the means of quantum chemical calculations with theory levels Møller-Plesset pertubation theory (MP2) and density functional theory (DFT) (B3LYP, MPW1PW91, PBEPBE, ωB97XD, CAM-B3LYP, M06, and M062X) with 6-31G(d,p), 6-31++G(d,p) basis sets. The examination of the reaction pathways of each substrate demonstrated a molecular mechanism through six-membered cyclic boat-like transition state (TS) structure. An alkyl group substituent causes a detrimental effect on the reaction rate, compared to the parent compound 1,4-cyclohexadiene; however, the reaction was favoured in the case of 3,6-dimethyl substitution. The 3,6-dimethyl-1,4-cyclohexadiene compound has activation energy 11.2 kJ/mol lower than the reference compound, which overcomes the effect of the most negative entropy of activation in the series. The effects of alkyl substituents in these reactions suggest a complex combination of electronic and steric influence. These reactions are characterised as highly synchronous concerted, with small predominance of C-H bond breaking in the TS.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. A comparison of density functional theory and coupled cluster methods for the calculation of electric dipole polarizability gradients of methane

    NASA Astrophysics Data System (ADS)

    Paidarová, Ivana; Sauer, Stephan P. A.

    2012-12-01

    We have compared the performance of density functional theory (DFT) using five different exchange-correlation functionals with four coupled cluster theory based wave function methods in the calculation of geometrical derivatives of the polarizability tensor of methane. The polarizability gradients of hydrocarbons are important ingredients in the simulation of their electron energy loss spectra and reliable but cost-effective methods for obtaining the gradients need to be found. In the present work we present results of a systematic investigation on methane as a prototype molecule with special focus on DFT methods. The KT3, B3LYP, CAM-B3LYP, B97-2 and PBE0 DFT exchange-correlation functionals and the highly correlated wave function methods SOPPA(CCSD), CCSD-LR, CCSD and CCSD(T) were employed in combination with a series of eleven basis sets. Comparison of the DFT results with CCSD(T)/daug-cc-pVQZ reference values reveals that none of the investigated DFT approaches reaches the accuracy of correlated wave function based methods and that the best DFT results are obtained with the PBE0 exchange-correlation functional and Sadlej's polarized valence triple zeta basis set. The SOPPA(CCSD) method, on the other hand, produces results in close agreement with the more expensive pure coupled cluster methods.

  8. 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.

  9. Synthetic scope, computational chemistry and mechanism of a base induced 5-endo cyclization of benzyl alkynyl sulfides

    PubMed Central

    Motto, John M.; Castillo, Álvaro; Montemayer, Laura K.; Sheepwash, Erin E.

    2011-01-01

    We present an experimental and computational study of the reaction of aryl substituted benzyl 1-alkynyl sulfides with potassium alkoxide in acetonitrile, which produces 2-aryl 2,3-dihydrothiophenes in poor to good yields. The cyclization is most efficient with electron withdrawing groups on the aromatic ring. Evidence indicates there is rapid exchange of protons and tautomerism of the alkynyl unit prior to cyclization. Theoretical calculations were also conducted to help rationalize the base induced 5-endo cyclization of benzyl 1-propynyl sulfide (1a). The potential energy surface was calculated for the formation of 2,3-dihydrothiophene in a reaction of benzyl 1-propynyl sulfide (1a) with potassium methoxide. Geometries were optimized with CAM-B3LYP/6-311+G(d,p) in acetonitrile with the CPCM solvent model. It is significant that the benzyl propa-1,2-dien-1-yl sulfane (6) possessed a lower benzylic proton affinity than the benzyl prop-2-yn-1-yl sulfane (8) thus favoring the base induced reaction of the former. From benzyl(propa-1,2-dien-1-yl sulfane (6), 2,3-dihydrothiophene can be formed via a conjugate base that undergoes 5-endo-trig cyclization followed by a protonation step. PMID:21442022

  10. 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.

  11. Simulated evolution of fluorophores for light emitting diodes.

    PubMed

    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(∗∗)). In total, we have identified 3792 promising candidate fluorophores from a chemical space containing 1.26 × 10(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.

  12. Conically shaped drops in electric fields

    NASA Astrophysics Data System (ADS)

    Stone, Howard A.; Brenner, Michael P.; Lister, John R.

    1996-11-01

    When an electric field is applied to a dielectric liquid containing a suspended immiscible fluid drop, the drop deforms into a prolate ellipsoidal shape. Above a critical field strength the drop develops conical ends, as first observed by Zeleny [Phys. Rev. 10, 1 (1917)] and Wilson & Taylor [Proc. Camb. Phil. Soc. 22, 728 (1925)] for, respectively, the case of conducting drops and soap films in air. The case of two dielectric liquids was studied recently using a slender drop approximation by Li, Halsey & Lobkovsky [Europhys. Lett 27, 575 (1994)]. In this presentation we further develop the slender body approximation to obtain coupled ordinary differential equations for the electric field and the drop shape. Analytical formulae are derived which approximately give the cone angle as a function of the dielectric constant ratio between the two fluids, and the minimum applied electric field at which conical tips first form as a function of the dielectric constant ratio. Finally, drops shapes are calculated numerically and compared with the common prolate shape assumption.

  13. 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.

  14. 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.

  15. Cluster Regime—The New Regime Of Flowing Of Gas-Liquid Mixture In Vertical Columns (Based On Experimental Data)

    NASA Astrophysics Data System (ADS)

    Ozerov, A. Yu.

    2010-03-01

    For the revealing of the reasons of occurrence of discrete volcanic explosions of basalt magma the Complex Apparatus for Modeling Basaltic Eruptions (CAMBE) has been developed. It consists of two major systems—modeling and recording. The device is 18 meters high. During experiments gas-saturated model liquid acts from the saturator to the vertical transparent hose in which arising two-phase structures and its kinetics are studied. The experiments resulted in detecting and describing a new, never before known, mode of gas-liquid two-phase flow in a vertical column—defined here as cluster regime, which is characterized by regular alteration of dense gas bubble clusters separated from each other by the liquid not containing free gas phase. The mechanism of the cluster regime formation is conditioned by the processes of blocking of the hose working section by one big bubble or several smaller ones. It has been demonstrated that liquid, bubble, cluster and slug regime are regularly sequential and present polymorphic modifications of gas-saturated liquids migrating within vertically oriented conduits. Analysis of data on explosions at volcanoes, given the obtained experimental data on the mechanism of this process, allows concluding that realization of cluster or slug regimes in volcanic crater produces basaltic explosions.

  16. 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.

  17. 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

  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. PMID:24929382

  19. Cytisine basicity, solvation, logP, and logD theoretical determination as tool for bioavailability prediction.

    PubMed

    Pieńko, Tomasz; Grudzień, Monika; Taciak, Przemysław Paweł; Mazurek, Aleksander Paweł

    2016-01-01

    Cytisine, an α4β2 nicotinic receptor partial agonist, is a plant alkaloid widely used as a smoking cessation agent. Despite long history of use, knowledge on pharmacokinetics of cytisine still demands an extension. This work is aimed at theoretical determination of physicochemical parameters that affect the bioavailability of cytisine. The acidic dissociation constant, Gibbs free energy of solvation in water and n-octanol as well as n-octanol/water partition coefficient and n-octanol/water distribution coefficient of cytisine were calculated as quantities corresponding to its solubility and permeability. Cytisine structure was optimized with several quantum chemical methods-ab initio: HF and MP2, and DFT functionals (B3LYP, B3LYP-D3, CAM-B3LYP, M06-2X, TPSS, VSXC) with 6-311++G(d,p) basis set. Solvation of cytisine in water and n-octanol was determined with the SMD continuum model. It was shown that lipophilicity of cytisine depends on the pH of an environment. Protonated cytisine, the most populated state under acidic conditions, is characterized by enhanced hydrophilicity. Then neutral cytisine, dominating in a basic environment, demonstrates more lipophilic character. It appears that cytisine is very well soluble in the gastrointestinal (GI) tract fluids. Then the distribution of cytisine ought to occur very rapidly. However, permeability of cytisine through the mucous membrane of the GI tract may be limited, leading to the diminished bioavailability.

  20. 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). PMID:27227880

  1. Evolution under environmental stress at macro- and microscales.

    PubMed

    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.

  2. Bed-limited cracks in effective medium theory

    NASA Astrophysics Data System (ADS)

    Tod, S. R.

    2003-02-01

    An effective medium theory typically requires the description of a mean crack shape. In general, for simplicity, this is taken to be a flat, circular (`penny-shaped') crack. However, this places an unnecessary limitation on the theory, when it is perhaps more realistic to describe a crack in terms of having a bounded width and an otherwise ellipsoidal shape. The generalization of the method of smoothing, as proposed by Hudson (1994, Geophys. J. Int.,117, 555-561) , to extend his original model (Hudson, 1980. Math. proc. Camb. phil. Soc.,88, 371-384), has been used to study the role of the crack width and the ratio of the two larger dimensions in determining the properties of the effective medium. In general, this leads to a description of the medium as having orthorhombic symmetry, and provides a suitable description of a material where the crack dimensions are restricted in one direction owing to, for example, bed-limiting effects, while remaining unconfined in other directions. An elliptical flat crack limit is determined, analoguous to the circular crack description of the original Hudson model. In addition to the isolated crack description, the theory is extended to include the fluid flow mechanism of Tod (2001, Geophys. J. Int.,146, 249-263) that models the flow as being dominated by crack-to-crack flow and is valid for low matrix porosities and over a large range of frequencies, provided that the wavelength is much greater than the crack dimensions.

  3. 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

  4. 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.

  5. 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.

  6. Noncovalent interactions of metal cations and arenes probed with thallium(I) complexes.

    PubMed

    Jurca, Titel; Korobkov, Ilia; Gorelsky, Serge I; Richeson, Darrin S

    2013-05-20

    The synthesis, characterization, and computational analysis of Tl(I) complexes bearing the bis(imino)pyridine scaffold, [{ArN═CPh}2(NC5H3)]Tl(+)(OTf)(-) (Ar = 2,6-Et2C6H33, 2,5-(t)Bu2C6H3, 4), are reported. The cations of these species showed long Tl-N and Tl-OTf distances indicating only weak or no ligand coordination. Computational analysis of the interactions between the Tl cation and the ligands (orbital populations, bond order, and energy decomposition analysis) point to only minimal covalent interactions of the cation with the ligands. The weak ligand-to-metal donation allows for additional interactions between the Tl cation and arene rings that are either intramolecular, in the case of 3, or intermolecular. From benzene or toluene, 4 crystallizes with inverted sandwich structures having two [{(2,5-(t)Bu2C6H3)N═CPh}2(NC5H3)]Tl(+) cations bridged by either benzene or toluene. A density functional computational description of these Tl-arene contacts required exchange-correlation functionals with long-range exchange corrections (e.g., CAM-B3LYP or LC-PBE) and show that Tl-arene contacts are stabilized by noncovalent interactions.

  7. Paleoindian demography and the extraterrestrial impact hypothesis

    PubMed Central

    Buchanan, Briggs; Collard, Mark; Edinborough, Kevan

    2008-01-01

    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 ≈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. PMID:18697936

  8. 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.

  9. Electronic states of aryl radical functionalized graphenes: Density functional theory study

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2016-06-01

    Functionalized graphenes are known as a high-performance molecular device. In the present study, the structures and electronic states of the aryl radical functionalized graphene have been investigated by the density functional theory (DFT) method to elucidate the effects of functionalization on the electronic states of graphene (GR). Also, the mechanism of aryl radical reaction with GR was investigated. The benzene, biphenyl, p-terphenyl, and p-quaterphenyl radicals [denoted by (Bz) n (n = 1-4), where n means numbers of benzene rings in aryl radical] were examined as aryl radicals. The DFT calculation of GR-(Bz) n (n = 1-4) showed that the aryl radical binds to the carbon atom of GR, and a C-C single bond was formed. The binding energies of aryl radicals to GR were calculated to be ca. 6.0 kcal mol-1 at the CAM-B3LYP/6-311G(d,p) level. It was found that the activation barrier exists in the aryl radical addition: the barrier heights were calculated to be 10.0 kcal mol-1. The electronic states of GR-(Bz) n were examined on the basis of theoretical results.

  10. 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.

  11. 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.

  12. Quantitatively Correct UV-vis Spectrum of Ferrocene with TDB3LYP.

    PubMed

    Salzner, Ulrike

    2013-09-10

    The ultraviolet-visible light (UV-vis) absorption spectrum of ferrocene is modeled with time-dependent density functional theory employing LSDA, BLYP, B3LYP, and CAM-B3LYP functionals in combination with 6-31G*, 6-31+G*, CC-PVTZ, and aug-CC-PVTZ basis sets. With the exception of LSDA, all functionals predict a reasonable Fe-CP distance of ∼1.67 Å. Diffuse functions are essential for the strongly allowed states at high energy but of lesser consequence for the visible range of the spectrum. Dipole forbidden states are examined with vibrationally excited structures, obtained from the normal modes of the infrared (IR) spectrum. Despite earlier claims, TDB3LYP predicts the UV-vis spectrum of ferrocene quantitatively correct. TDBLYP predicts a large number of spurious charge-transfer states, TDCAM-B3LYP and TDwB97XD are correct in the low-energy region but overestimate the energy of strongest peak of the spectrum by 0.8 eV. The amount of charge transfer involved in "d-d transitions" is equal to that in "charge-transfer states".

  13. 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.

  14. Insights on the Auxochromic Properties of the Guanidinium Group.

    PubMed

    Antol, Ivana; Glasovac, Zoran; Margetić, Davor; Crespo-Otero, Rachel; Barbatti, Mario

    2016-09-15

    UV/vis spectra of phenylguanidine (PHGU) in the gas phase and in acetonitrile have been simulated by TD-DFT calculations. Several DFT hybrid and long-range corrected functionals were tested with respect to CASPT2 gas phase calculations. Solvent effects were considered using polarizable continuum model (PCM) and compared with the measured data in acetonitrile. Comparison with isoelectronic phenylurea and related phenyltiourea was done as well. The PBE0 and long-range corrected CAM-B3LYP functionals were selected to investigate the effect of protonation on the excitation energies and absorption intensities of PHGU and several guanidine derivatives with different aromatic chromophoric groups (naphthyl, anthracenyl, quinolinyl, anthraquinonyl, and coumarinyl). Also, the effect of complexation and specific interactions through hydrogen bonds with different anions was examined. It was shown that the protonation of the guanidine subunit shifts the low energy absorption bands toward higher energies (hypsochromic shift). The shift is reduced upon complexation with anions. In phenylguanidine salts, λmax values are correlated to the anion basicity and strength of H-bonding. The observed changes diminish upon increase of chromophoric size (naphthyl, anthracenyl). Theoretical predictions of UV/vis spectra correlate well with experimentally measured spectra of selected guanidine derivatives and their salts. PMID:27556411

  15. Evaluation of the difference in the rate coefficients of F2 + NOx (x = 1 or 2) → F + FNOx by the stereochemical arrangement using the density functional theory.

    PubMed

    Tajima, Satomi; Hayashi, Toshio; Hori, Masaru

    2015-02-26

    The rate coefficient of F2 + NO → F + FNO is 2 to 5 orders of magnitude higher than that of F2 + NO2 → F + FNO2 even though bond energies of FNO and FNO2 only differ by ∼0.2 eV. To understand the cause of having different rate coefficients of these two reactions, the change in total energies was calculated by varying the stereochemical arrangement of F2 with respect to NOx (x = 1 or 2) by the density functional theory (DFT), using CAM-B3LYP/6-311 G+(d) in the Gaussian program. The permitted approaching angle between the x-axis and the plane consisting of O, N, F, and ϕ plays a key role to restrict the reaction of NO2 and F2 compared to the reaction of NO and F2. This restriction in the reaction space is considered to be the main cause of different rate coefficients depending on the selection of x = 1 or 2 of the reaction of F2 + NOx → F + FNOx, which was also confirmed by the difference in Si etch rate using the F formed by those reactions.

  16. A comparative study of semi-squaraine and squaraine dyes using computational techniques: tuning the charge transfer/biradicaloid character by substitution.

    PubMed

    Puyad, Avinash L; Chaitanya, Gunturu Krishna; Prabhakar, Chetti; Bhanuprakash, Kotamarthi

    2013-01-01

    Semi-squaraines (SMSQ) are known as donor-acceptor (D-A) type molecules whereas squaraines (SQ), which differs from SMSQ by an extra donor group, are more or less biradicaloids in nature. The effect of the additional donor group in SQ, which changes the nature of the molecule, on geometrical and electronic structure are studied here and compared with the corresponding SMSQ. It is noticed from the geometrical parameters that, a strong resonance exists in SQ whereas disparity in carbon-carbon bond lengths of central C4 ring is seen in SMSQ dyes. The increasing and decreasing of antibonding interactions between central C4 ring and side donor groups cause destabilization of HOMO and stabilization of LUMO respectively in case of SQ compared to SMSQ molecules. This leads to decreasing the HOMO-LUMO gap and promotes biradicaloid character of SQ. The absorption maxima obtained by using TD-DFT method with BLYP, B3LYP, BHandHLYP, CAM-B3LYP and M06-2X functionals are not in good agreement with experimental results. On the other hand SAC-CI method gives better results for all the molecules. From this work we can evolve a design principle of these molecules which play a role as sensitizers in dye sensitized solar cells. PMID:22878861

  17. 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.

  18. Electronic states of aryl radical functionalized graphenes: Density functional theory study

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2016-06-01

    Functionalized graphenes are known as a high-performance molecular device. In the present study, the structures and electronic states of the aryl radical functionalized graphene have been investigated by the density functional theory (DFT) method to elucidate the effects of functionalization on the electronic states of graphene (GR). Also, the mechanism of aryl radical reaction with GR was investigated. The benzene, biphenyl, p-terphenyl, and p-quaterphenyl radicals [denoted by (Bz) n (n = 1–4), where n means numbers of benzene rings in aryl radical] were examined as aryl radicals. The DFT calculation of GR–(Bz) n (n = 1–4) showed that the aryl radical binds to the carbon atom of GR, and a C–C single bond was formed. The binding energies of aryl radicals to GR were calculated to be ca. 6.0 kcal mol‑1 at the CAM-B3LYP/6-311G(d,p) level. It was found that the activation barrier exists in the aryl radical addition: the barrier heights were calculated to be 10.0 kcal mol‑1. The electronic states of GR–(Bz) n were examined on the basis of theoretical results.

  19. 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.

  20. Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

    NASA Astrophysics Data System (ADS)

    Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

    2015-04-01

    In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

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

    NASA Astrophysics Data System (ADS)

    Sangwan, Poonam; Vikas

    2016-01-01

    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.

  2. Benzo[c][1,2,5]thiadiazole Donor-Acceptor Dyes: A Synthetic, Spectroscopic, and Computational Study.

    PubMed

    Barnsley, Jonathan E; Shillito, Georgina E; Larsen, Christopher B; van der Salm, Holly; Wang, Lei E; Lucas, Nigel T; Gordon, Keith C

    2016-03-24

    The synthesis, optical characterization and computational modeling of seven benzo[c][1,2,5]thiadiazole (BTD) donor-acceptor dyes are reported. These dyes have been studied using electrochemical analysis, electronic absorption, emission, and Raman and resonance Raman spectroscopies coupled with various density functional theoretical approaches. Crystal structure geometries on a number of these compounds are also reported. The optical spectra are dominated by low energy charge-transfer states; this may be modulated by the coupling between donor and acceptor through variation in donor energy, variation of the donor-acceptor torsion angle, and incorporation of an insulating bridge. These modifications result in a perturbation of the excitation energy for this charge-transfer transition of up to ∼2000 cm(-1). Emission spectra exhibit significant solvatochromisim, with Lippert-Mataga analysis yielding Δμ between 8 and 33 D. Predicted λmax, ε, and Raman cross sections calculated by M06L, B3LYP, PBE0, M06, CAM-B3LYP, and ωB97XD DFT functionals were compared to experimental results and analyzed using multivariate analysis, which shows that hybrid functionals with 20-27% HF best predict ground state absorption, while long-range corrected functionals best predict molecular polarizabilities. PMID:26918584

  3. DLISA: A DNAzyme-Based ELISA for Protein Enzyme-Free Immunoassay of Multiple Analytes.

    PubMed

    Hu, Rong; Liu, Tao; Zhang, Xiao-Bing; Yang, Yunhui; Chen, Tao; Wu, Cuichen; Liu, Yuan; Zhu, Guizhi; Huan, Shuangyan; Fu, Ting; Tan, Weihong

    2015-08-01

    A DNAzyme-based ELISA, termed DLISA, was developed as a novel protein enzyme-free, triply amplified platform, combining a catalytic and molecular beacon (CAMB) system with a cation exchange reaction for ultrasensitive multiplex fluorescent immunosorbent assay. Classical ELISA, which employs protein enzymes as biocatalysts to afford amplified signals, suffers from poor stability caused by the irreversible denaturation of these enzymes under harsh conditions, such as heat and acidity. Compared with proteins, nucleic acids are more stable and adaptable, and they can be easily produced using a commercial DNA synthesizer. Moreover, the catalytic and cleavage activities of DNAzyme can be achieved in solution; thus, no enzyme immobilization is needed for detection. Taken together, these attributes suggest that a DNAzyme-based ELISA detection approach will be more robust than current ELISA assays. Importantly, the proposed triply amplified DLISA immunoassay method shows ultrasensitive detection of such targets as human IgG with a detection limit of 2 fg/mL (3 × 10(-17) M), which is well within the range of many important disease biomarkers. DLISA can also be used to construct a sensing array for simultaneous multiplexed detection. With these merits, this high-throughput, stable, simple, sensitive, and low-cost multiplex fluorescence immunoassay shows promise for applications in clinical diagnosis.

  4. Pyrophosphate-regulated Zn(2+)-dependent DNAzyme activity: an amplified fluorescence sensing strategy for alkaline phosphatase.

    PubMed

    Kong, Rong-Mei; Fu, Ting; Sun, Ni-Na; Qu, Feng-Li; Zhang, Shu-Fang; Zhang, Xiao-Bing

    2013-12-15

    In this work, based on the fact that pyrophosphate (PPi) could regulate the activity of Zn(2+)-dependent DNAzyme, we for the first time report a fluorescence turn-on sensing system for alkaline phosphatase (ALP) with improved sensitivity via nonprotein-enzymatic signal amplification. A catalytic and molecular beacon (CAMB) design was employed to further improve its sensitivity. Taking advantage of the strong interactions between PPi and the Zn(2+), the cofactor Zn(2+) was caged, and the DNAzyme activity was effectively inhibited. The introduction of ALP, however, could catalyze the hydrolysis of PPi and release free Zn(2+), resulting in the activation of DNAzyme to catalyze the cleavage of the molecular beacon substrate with a remarkable increase of fluorescent signal. These optimized designs together allow a high sensitivity for ALP, with a detection limit of 20 pM observed, much lower than previously reported methods. It has also been used for detection of ALP in human serum with satisfactory results, demonstrating its potential applications in clinical diagnosis.

  5. Red Emitting Coumarins: Insights of Photophysical Properties with DFT Methods.

    PubMed

    Tathe, Abhinav B; Rhyman, Lydia; Ramasami, Ponnadurai; Sekar, Nagaiyan

    2015-07-01

    Red emitting dyes are of interest in various technological applications. Coumarins, though being an important class of fluorescent molecules, those with red emission, have been rarely studied theoretically. The structural and electronic aspects of three novel red emitting coumarins were studied using DFT and TD-DFT methods. The functionals employed were the hybrid functionals B3LYP, CAM-B3LYP, PBE0 and the highly parameterized empirical functional M06. The geometry at ground state reveals the electron donor N,N-diethylamino group is coplanar with the chromophoric system and the nitrile group induces a red shift to the absorption and emission. The electronic energies and dipole moments were solvent dependent. The basis sets and functionals were benchmarked for their performance with these molecules. B3LYP has been proved to be more efficient in computations whereas the basis sets do not have noticeable effect on the electronic properties. However, adding a polarization function to the basis set has improved the calculation of vertical excitation. The B3LYP functional gives maximum absolute deviation of 0.20 eV in calculating the vertical excitations and 0.18 eV for emission.

  6. 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.

  7. 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.

  8. 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.

  9. Spatial and Temporal Resolution of Three Sites Characterizing Lattice-Assisted Nuclear Reactions (LANR)

    NASA Astrophysics Data System (ADS)

    Swartz, Mitchell

    2008-03-01

    We present developing evidence that three different sites (physical locations in the solid state) are involved in lattice-assisted nuclear reactions (LANR). By expanding the equation first developed by Prof. David Nagel at ICCF-13ootnotetextNagel, D., ``Rates for LENRs at Surfaces'', ICCF-13, we correlate observations of excess heat and de novo helium-4 production to three different physical locations and to the optimal operating points (OOPs) which are now known to characterize LANR systemsootnotetextSwartz. M., G. Verner, ``Excess Heat from Low Electrical Conductivity Heavy Water Spiral-Wound Pd/D2O/Pt and Pd/D2O-PdCl2/Pt Devices'', ICCF-10 (Camb. MA), Proceedings of ICCF-10, (2003).. This observation will be shown to be consistent with our previous reports of distinct time constants which characterize the tardive thermal power regimeootnotetextSwartz. M., G. Verner, ``Dual Ohmic Controls Improve Understanding of `Heat after Death' '', Transactions American Nuclear Society, vol. 93, ISSN:0003-018X, 891-892 (2005) (`heat after death'), which results after all input electrical power is terminated to an active LANR device.

  10. Assessment of long-range corrected and conventional DFT functional for the prediction of second--order NLO properties and other molecular properties of N-(2-cyanoethyl)-N-butylaniline--a vibrational spectroscopy study.

    PubMed

    Anitha, K; Balachandran, V

    2015-07-01

    Vibrational spectral analysis and quantum chemical computations based on density functional theory have been performed on the N-(2-cyanoethyl)-N-butylaniline. The geometry, structural properties, intermolecular hydrogen bond, and harmonic vibrational frequencies of the title molecule have been investigated with the help of DFT (B3LYP) and LC-DFT (CAM-B3LYP) method. Molecular electrostatic potential (MEP) have been performed. The various intramolecular interactions have been exposed by natural bond orbital analysis. The distribution of atomic charges and bending of natural hybrid orbitals also reflect the presence of intramolecular hydrogen bonding. Global reactivity and local reactivity descriptors of the title molecule have been calculated. The analysis of the electron density of HOMO and LUMO gives an idea of the delocalization and low value of energy gap indicated the electron transport in the molecule and thereby NLO activity. The effect of solvent on second-order NLO properties has been studied using polarized continuum model (PCM) in the tetrahydrofuran (THF) solution. The solvent leads to a slight enhancement of the NLO responses for the studied complexes relevant to their NLO responses in gas phase. The electronic absorption spectra were investigated by the TDDFT methods. The frequency-dependent first hyperpolarizabilities of the N-(2-cyanoethyl)-N-butylaniline were also evaluated. The (1)H and (13)C NMR chemical shifts have been calculated by gauge-indepedent atomic orbital (GIAO) method with B3LYP/6-311++G(d, p) approach.

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

    PubMed

    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. Bayesian analysis of inflation: Parameter estimation for single field models

    SciTech Connect

    Mortonson, Michael J.; Peiris, Hiranya V.; Easther, Richard

    2011-02-15

    Future astrophysical data sets promise to strengthen constraints on models of inflation, and extracting these constraints requires methods and tools commensurate with the quality of the data. In this paper we describe ModeCode, a new, publicly available code that computes the primordial scalar and tensor power spectra for single-field inflationary models. ModeCode solves the inflationary mode equations numerically, avoiding the slow roll approximation. It is interfaced with CAMB and CosmoMC to compute cosmic microwave background angular power spectra and perform likelihood analysis and parameter estimation. ModeCode is easily extendable to additional models of inflation, and future updates will include Bayesian model comparison. Errors from ModeCode contribute negligibly to the error budget for analyses of data from Planck or other next generation experiments. We constrain representative single-field models ({phi}{sup n} with n=2/3, 1, 2, and 4, natural inflation, and 'hilltop' inflation) using current data, and provide forecasts for Planck. From current data, we obtain weak but nontrivial limits on the post-inflationary physics, which is a significant source of uncertainty in the predictions of inflationary models, while we find that Planck will dramatically improve these constraints. In particular, Planck will link the inflationary dynamics with the post-inflationary growth of the horizon, and thus begin to probe the ''primordial dark ages'' between TeV and grand unified theory scale energies.

  13. An experimental and density functional study on conformational and spectroscopic analysis of 5-methoxyindole-2-carboxylic acid.

    PubMed

    Cinar, Mehmet; Karabacak, Mehmet; Asiri, Abdullah M

    2015-02-25

    In this article, a brief conformational and spectroscopic characterization of 5-methoxyindole-2-carboxylic acid (5-MeOICA) via experimental techniques and applications of quantum chemical methods is presented. The conformational analysis of the studied molecule was determined theoretically using density functional computations for ground state, and compared with previously reported experimental findings. The vibrational transitions were examined by measured FT-IR and FT-Raman spectroscopic data, and also results obtained from B3LYP and CAM-B3LYP functionals in combination with 6-311++G(d,p) basis set. The recorded proton and carbon NMR spectra in DMSO solution were analyzed to obtain the exact conformation. Due to intermolecular hydrogen bondings, NMR calculations were performed for the dimeric form of 5-MeOICA and so chemical shifts of those protons were predicted more accurately. Finally, electronic properties of steady compound were identified by a comparative study of UV absorption spectra in ethanol and water solution and TD-DFT calculations. PMID:25255480

  14. Density functional theory study on the interaction of magnesium ions with graphene surface

    NASA Astrophysics Data System (ADS)

    Kato, Koichi; Iyama, Tetsuji; Tachikawa, Hiroto

    2014-02-01

    The interactions of magnesium species (Mg, Mg+, and Mg2+) with a graphene surface have been investigated by the density functional theory (DFT) method. The distances of Mg atoms from the graphene surface were calculated to be 1.80 Å (Mg2+), 2.16 Å (Mg+), and 4.17 Å (Mg) at the Coulomb-attenuating method (CAM)-B3LYP/6-31G(d) level. The binding nature of Mg ions (Mg2+ and Mg+) is caused by the charge transfer interaction, and the Mg atom interacts with the surface via van der Waals (vdW) force. The Mg ions can diffuse via the C-C bond center between hexagonal sites. The barrier heights for the diffusion of Mg2+ and Mg+ on the graphene surface were calculated to be 14.6 and 2.8 kcal/mol, respectively. On the other hand, the diffusion of Mg atoms proceeds with a very low barrier. The mechanism of the interaction of Mg with the graphene surface was discussed on the basis of theoretical results.

  15. 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.

  16. 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.

  17. Bicarbonate and Alkyl Carbonate Radicals: Structural Integrity and Reactions with Lipid Components.

    PubMed

    Bühl, Michael; DaBell, Peter; Manley, David W; McCaughan, Rory P; Walton, John C

    2015-12-30

    The elusive neutral bicarbonate radical and the carbonate radical anion form an acid/conjugate base pair. We now report experimental studies for a model of bicarbonate radical, namely, methyl carbonate (methoxycarbonyloxyl) radical, complemented by DFT computations at the CAM-B3LYP level applied to the bicarbonate radical itself. Methyl carbonate radicals were generated by UV irradiation of oxime carbonate precursors. Kinetic EPR was employed to measure rate constants and Arrhenius parameters for their dissociation to CO2 and methoxyl radicals. With oleate and cholesterol lipid components, methyl carbonate radicals preferentially added to their double bonds; with linoleate and linolenate substrates, abstraction of the bis-allylic H atoms competed with addition. This contrasts with the behavior of ROS such as hydroxyl radicals that selectively abstract allylic and/or bis-allylic H atoms. The thermodynamic and activation parameters for bicarbonate radical dissociation, obtained from DFT computations, predicted it would indeed have substantial lifetime in gas and nonpolar solvents. The acidity of bicarbonate radicals was also examined by DFT methods. A noteworthy linear relationship was discovered between the known pKa's of strong acids and the computed numbers of microsolvating water molecules needed to bring about their ionization. DFT computations with bicarbonate radicals, solvated with up to eight water molecules, predicted that only five water molecules were needed to bring about its complete ionization. On comparing with the correlation, this indicated a pKa of about -2 units. This marks the bicarbonate radical as the strongest known carboxylic acid.

  18. 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. PMID:27436622

  19. Reliable Modeling of the Electronic Spectra of Realistic Uranium Complexes

    SciTech Connect

    Tecmer, Pawel; Govind, Niranjan; Kowalski, Karol; De Jong, Wibe A.; Visscher, Lucas

    2013-07-21

    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 UV IO2(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 | CREOMCCSd(t) | for the UV IO2(saldien) molecule are investigated. The coupled cluster data was employed as benchmark to chose 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 [UV O2(saldien)]- with explicit inclusion of two DMSOs are in good agreement with the experimental data of Takao et al. [Inorg. Chem. 49, 2349-2359, (2010)].

  20. [Non-indigenous and non-specific parasitic nematodes--the background and the consequences].

    PubMed

    Okulewicz, Anna

    2009-01-01

    different climatic conditions contribute to introduction of non-native nematodes: Dirofilaria immitis--in dogs, D. repens or Ancylostoma brasiliense--in humans. PMID:20209803

  1. Inhibitory effect of sesquiterpene lactones and the sesquiterpene alcohol aromadendrane-4β,10α-diol on memory impairment in a mouse model of Alzheimer.

    PubMed

    Amoah, Solomon K S; Dalla Vecchia, Maria Tereza; Pedrini, Beatriz; Carnhelutti, Gabriela Lazzarotto; Gonçalves, Ana Elisa; Dos Santos, Diogo Adolfo; Biavatti, Maique W; de Souza, Márcia Maria

    2015-12-15

    Alzheimer's disease (AD), a progressive neurodegenerative disorder of the aged brain with no known cause or cures, has become a major medical and social problem for industrialized countries. Cerebral deposition of amyloid-β peptide (Aβ) is a critical feature of AD. The use of medicinal plants as an alternative form of prevention, or even as a possible treatment of AD, is therefore interesting areas of research. Sesquiterpene lactones and a sesquiterpene alcohol are compounds found in H. brasiliense that have several anti-oxidative and anti-inflammatory effects. In the present study, we investigated whether these compounds have neuroprotective effects in an amyloid-β peptide-induced Alzheimer's disease mouse model. Mice were injected with Aβ1-42 peptide intracerebroventricularly and were subsequently injected (i.c.v.) with 1µg/site of IGM-A (15-acetoxy-isogermafurenolide), IGM-H (15-hydroxy-isogermafurenolide), PDA (Podoandin), EHP (1,2-epoxy-10α-hydroxy-podoandin), HDS (13-hydroxy-8,9-dehydroshizukanolide), and ARD (aromadendrane-4β,10α-diol). Seven days after treatments the animals had their memory tested in the inhibitory avoidance. After the behavioral testing of animals the brains were removed and subjected to biochemical tests for oxidative stress. The results showed that ARD, HDS and PDA significantly ameliorated the Aβ1-42 peptide-induced memory impairment in the passive avoidance task (P<0.05). In addition, GSH activity was increased while the TBARS levels were decreased by treatment with these compounds. These results suggest that these compounds inhibit the cognitive deficit of animals induced peptide amyloid and may be potential candidates for Alzheimer's disease therapy.

  2. Oil rich in carotenoids instead of vitamins C and E as a better option to reduce doxorubicin-induced damage to normal cells of Ehrlich tumor-bearing mice: hematological, toxicological and histopathological evaluations.

    PubMed

    Miranda-Vilela, Ana Luisa; Grisolia, Cesar K; Longo, João Paulo F; Peixoto, Raphael C A; de Almeida, Marcos Célio; Barbosa, Lilian Carla P; Roll, Mariana M; Portilho, Flávia A; Estevanato, Luciana L C; Bocca, Anamélia L; Báo, Sônia N; Lacava, Zulmira G M

    2014-11-01

    The development of therapeutic strategies to attenuate chemotherapy toxicity represents an area of great interest in cancer research, and among them is nutritional therapy based on antioxidants. As research on this topic is still controversial and scarce, we aim to investigate the effects of antioxidant supplementation with vitamin C, vitamin E or pequi oil, a carotenoid-rich oil extracted from pequi (Caryocar brasiliense), on doxorubicin (DX)-induced oxidative damage to normal cells in Ehrlich solid tumor-bearing mice. Tumor weight and volume, histopathology, morphometry and immunohistochemistry were used to assess the treatments' efficacy in containing tumor aggressiveness and regression, while possible toxicity of treatments was assessed by animals' weight, morphological analysis of the heart, liver and kidneys, hemogram, and serum levels of total bilirubin, direct bilirubin, indirect bilirubin, aspartate aminotransferase (AST), alanine aminotransferase (ALT), gamma glutamyl transferase (GGT), alkaline phosphatase, creatinine and urea. Although all the chemotherapeutic treatments increased internal necrosis area and reduced the positive Ki-67 cells compared to non-treated tumors, the treatments with pequi oil provided before tumor inoculation (PTDX) or in continuous and concurrent administration with doxorubicin (PTPDX) were more effective in containing tumor growth, besides increasing lymphocyte-dependent immunity and reducing the adverse side effects associated with DX-induced oxidative damage to normal cells, mainly the PTDX treatment. Vitamins C and E given before tumor inoculation and chemotherapy were not successful against doxorubicin-induced cardiotoxicity, besides increasing doxorubicin-induced nephrotoxicity, indicating that, at least for doxorubicin, pequi oil instead of vitamins C and E would be the best option to reduce its adverse effects.

  3. 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

  4. 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

  5. [Arborescent species of the genus Blechnum (Blechnaceae: Pteridophyta)].

    PubMed

    Rolleri, Cristina H; Prada, Carmen; Gabriel, José María; Galán; Passarelli, Lilian M

    2013-03-01

    Although the genus Blechnum has been largely studied, problems of species characterization, nomenclature, classification and taxonomy remain unsolved. For these reasons, in this study we intend to deepen in the characterization of the arborescent group of Blechnum with a review of eight species: B. brasiliense, B. columbiense, B. cycadifolium, B. magellanicum, B. moritzianum, B. schomburgkii, B. tabulare and B. werckleanum.Type material and several collections from diverse herbaria were studied. For morphological studies we used both herbarium and fresh material collected by the authors in fieldwork between 2005 and 2010. Rhizomes, stipes, vascularization of costae, as well as several characters of the lamina, such as outline, division, venation, margin structure, epidermal patterns, stomata, presence and types ofhypodermis, and mesophyll ofpinnae were studied. Important aspects of the morphology of the sporophyte have been analyzed, and external characters have been correlated with internal diagnostic ones to use the most reliable external traits in keys and descriptions. Taxonomy has been updated, and corrections have been introduced to the species nomenclature and comments were included to summarize the current knowledge of the geographical distribution and ecology. The presence of B. tabulare in America is confirmed, and the taxonomy of the species is updated, since external and internal morphology indicated that other related, American and African species, such as B. spannagelii and B. madagascariense must be included under that name. Similar studies carried out on B. schomburgkii indicated that the name is a synonym of B. auratum subsp. auratum, while B. auratum subsp. columbiense is treated here as a well characterized species. Detailed study of numerous specimens allowed to characterize B. moritzianum, being the correct name to apply to the recently described B. yungense. A refreshed description of the species is presented together with a list of new

  6. [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

  7. Paradoxical effect of a pequi oil-rich diet on the development of atherosclerosis: balance between antioxidant and hyperlipidemic properties

    PubMed Central

    Aguilar, E.C.; Jascolka, T.L.; Teixeira, L.G.; Lages, P.C.; Ribeiro, A.C.C.; Vieira, E.L.M.; Peluzio, M.C.G.; Alvarez-Leite, J.I.

    2012-01-01

    Pequi is the fruit of Caryocar brasiliense and its oil has a high concentration of monounsaturated and saturated fatty acids, which are anti- and pro-atherogenic agents, respectively, and of carotenoids, which give it antioxidant properties. Our objective was to study the effect of the intake of a cholesterol-rich diet supplemented with pequi oil, compared to the same diet containing soybean oil, on atherosclerosis development, and oxidative stress in atherosclerosis-susceptible LDL receptor-deficient mice (LDLr−/−, C57BL/6-background). Female mice were fed a cholesterol-rich diet containing 7% soybean oil (Soybean group, N = 12) or 7% pequi oil (Pequi group, N = 12) for 6 weeks. The Pequi group presented a more atherogenic lipid profile and more advanced atherosclerotic lesions in the aortic root compared to the Soybean group. However, the Pequi group presented a less advanced lesion in the aorta than the Soybean group and showed lower lipid peroxidation (Soybean group: 50.2 ± 7.1; Pequi group: 30.0 ± 4.8 µmol MDA/mg protein) and anti-oxidized LDL autoantibodies (Soybean group: 35.7 ± 9.4; Pequi group: 15.6 ± 3.7 arbitrary units). Peritoneal macrophages from the Pequi group stimulated with zymosan showed a reduction in the release of reactive oxygen species compared to the Soybean group. Our data suggest that a pequi oil-rich diet slows atherogenesis in the initial stages, possibly due to its antioxidant activity. However, the increase of serum cholesterol induces a more prominent LDL migration toward the intimae of arteries, increasing the advanced atherosclerotic plaque. In conclusion, pequi oil associated with an atherogenic diet worsens the lipid profile and accelerates the formation of advanced atherosclerotic lesions despite its antioxidant action. PMID:22570088

  8. [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

  9. Does physical exposure throughout working life influence chair-rise performance in midlife? A retrospective cohort study of associations between work and physical function in Denmark

    PubMed Central

    Møller, Anne; Reventlow, Susanne; Hansen, Åse Marie; Andersen, Lars L; Siersma, Volkert; Lund, Rikke; Avlund, Kirsten; Andersen, Johan Hviid; Mortensen, Ole Steen

    2015-01-01

    Objectives Our aim was to study associations between physical exposures throughout working life and physical function measured as chair-rise performance in midlife. Methods The Copenhagen Aging and Midlife Biobank (CAMB) provided data about employment and measures of physical function. Individual job histories were assigned exposures from a job exposure matrix. Exposures were standardised to ton-years (lifting 1000 kg each day in 1 year), stand-years (standing/walking for 6 h each day in 1 year) and kneel-years (kneeling for 1 h each day in 1 year). The associations between exposure-years and chair-rise performance (number of chair-rises in 30 s) were analysed in multivariate linear and non-linear regression models adjusted for covariates. Results Mean age among the 5095 participants was 59 years in both genders, and, on average, men achieved 21.58 (SD=5.60) and women 20.38 (SD=5.33) chair-rises in 30 s. Physical exposures were associated with poorer chair-rise performance in both men and women, however, only associations between lifting and standing/walking and chair-rise remained statistically significant among men in the final model. Spline regression analyses showed non-linear associations and confirmed the findings. Conclusions Higher physical exposure throughout working life is associated with slightly poorer chair-rise performance. The associations between exposure and outcome were non-linear. PMID:26537502

  10. 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 Central

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

    2016-01-01

    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)4 N)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)4 N)2[2]2 with D-glucose, D-mannose, D-xylose and xylitol in aqueous alkaline media were investigated using UV–Vis and 13C-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, pKapp, between the complexes and the substrates were determined and a specific mode of substrate binding is proposed. The pKapp 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. PMID:25969174

  11. 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

  12. 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.

  13. 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.

  14. Type I collagen gel induces Madin-Darby canine kidney cells to become fusiform in shape and lose apical-basal polarity

    PubMed Central

    1989-01-01

    In the embryo, epithelia give rise to mesenchyme at specific times and places. Recently, it has been reported (Greenburg, G., and E. D. Hay. 1986. Dev. Biol. 115:363-379; Greenberg, G., and E. D. Hay. 1988. Development (Camb.). 102:605-622) that definitive epithelia can give rise to fibroblast-like cells when suspended within type I collagen gels. We wanted to know whether Madin-Darby canine kidney (MDCK) cells, an epithelial line, can form mesenchyme under similar conditions. Small explants of MDCK cells on basement membrane were suspended within or placed on top of extracellular matrix gels. MDCK cells on basement membrane gel are tall, columnar in shape, and ultrastructurally resemble epithelia transporting fluid and ions. MDCK explants cultured on type I collagen gel give rise to isolated fusiform-shaped cells that migrate over the gel surface. The fusiform cells extend pseudopodia and filopodia, lose cell membrane specializations, and develop an actin cortex around the entire cell. Unlike true mesenchymal cells, which express vimentin and type I collagen, fusiform cells produce both keratin and vimentin, continue to express laminin, and do not turn on type I collagen. Fusiform cells are not apically-basally polarized, but show mesenchymal cell polarity. Influenza hemagglutinin and virus budding localize to the front end or entire cell surface. Na,K-ATPase occurs intracellularly and also symmetrically distributes on the cell surface. Fodrin becomes diffusely distributed along the plasma membrane, ZO-1 cannot be detected, and desmoplakins distribute randomly in the cytoplasm. The loss of epithelial polarity and acquisition of mesenchymal cell polarity and shape by fusiform MDCK cells on type I collagen gel was previously unsuspected. The phenomenon may offer new opportunities for studying cytoplasmic and nuclear mechanisms regulating cell shape and polarity. PMID:2537838

  15. Conformational landscape and low lying excited states of imatinib.

    PubMed

    Vinţeler, Emil; Stan, Nicoleta-Florina; Luchian, Raluca; Căinap, Călin; Ramalho, João P Prates; Chiş, Vasile

    2015-04-01

    The conformational changes of imatinib (IMT) are crucial for understanding the ligand-receptor interaction and its mechanism of action [Agofonov et al. (2014) Nature Struct Mol Biol 21:848-853]. Therefore, here we investigated the free energy conformational landscape of the free IMT base, aiming to describe the three-dimensional structures and energetic stability of its conformers. Forty-five unique conformers, within an energy window of 4.8 kcal mol(-1) were identified by a conformational search in gas-phase, at the B3LYP/6-31G(d) theoretical level. Among these, the 20 most stable, as well as 4 conformers resulting from optimization of experimental structures found in the two known polymorphs of IMT and in the c-Abl complex were further refined using the 6-31+G(d,p) basis set and the polarizable continuum solvation model. The most stable conformers in gas-phase and water exhibit a V-shaped structure. The major difference between the most stable free conformers and the bioactive conformers consists in the relative orientation of the pyrimidine-pyridine groups responsible for hydrogen bonding interactions in the ATP-binding pocket. The ratio of mole fractions corresponding to the two known (α and β) polymorphic forms of IMT was estimated from the calculated thermochemical data, in quantitative agreement with the existing experimental data related to their solubility. The electronic absorption spectrum of this compound was investigated in water and explained based on the theoretical TD-DFT results, considering the Boltzmann population-averaged computed data at CAM-B3LYP/6-31+G(d,p) level of theory for the nine most stable conformers. PMID:25764326

  16. Gas-Phase Thermal Tautomerization of Imidazole-Acetic Acid: Theoretical and Computational Investigations.

    PubMed

    Aziz, Saadullah G; Osman, Osman I; Elroby, Shaaban A; Hilal, Rifaat H

    2015-11-04

    The gas-phase thermal tautomerization reaction between imidazole-4-acetic (I) and imidazole-5-acetic (II) acids was monitored using the traditional hybrid functional (B3LYP) and the long-range corrected functionals (CAM-B3LYP and ωB97XD) with 6-311++G** and aug-cc-pvdz basis sets. The roles of the long-range and dispersion corrections on their geometrical parameters, thermodynamic functions, kinetics, dipole moments, Highest Occupied Molecular Orbital-Lowest Unoccupied Molecular Orbital (HOMO-LUMO) energy gaps and total hyperpolarizability were investigated. All tested levels of theory predicted the preference of I over II by 0.750-0.877 kcal/mol. The origin of predilection of I is assigned to the H-bonding interaction (nN8→σ*O14-H15). This interaction stabilized I by 15.07 kcal/mol. The gas-phase interconversion between the two tautomers assumed a 1,2-proton shift mechanism, with two transition states (TS), TS1 and TS2, having energy barriers of 47.67-49.92 and 49.55-52.69 kcal/mol, respectively, and an sp³-type intermediate. A water-assisted 1,3-proton shift route brought the barrier height down to less than 20 kcal/mol in gas-phase and less than 12 kcal/mol in solution. The relatively high values of total hyperpolarizability of I compared to II were interpreted and discussed.

  17. 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

  18. Mechanism of dissolution of a lithium salt in an electrolytic solvent in a lithium ion secondary battery: a direct ab initio molecular dynamics (AIMD) study.

    PubMed

    Tachikawa, Hiroto

    2014-06-01

    The mechanism of dissolution of the Li(+) ion in an electrolytic solvent is investigated by the direct ab initio molecular dynamics (AIMD) method. Lithium fluoroborate (Li(+)BF4(-)) and ethylene carbonate (EC) are examined as the origin of the Li(+) ion and the solvent molecule, respectively. This salt is widely utilized as the electrolyte in the lithium ion secondary battery. The binding of EC to the Li(+) moiety of the Li(+)BF4(-) salt is exothermic, and the binding energies at the CAM-B3LYP/6-311++G(d,p) level for n=1, 2, 3, and 4, where n is the number of EC molecules binding to the Li(+) ion, (EC)n(Li(+)BF4(-)), are calculated to be 91.5, 89.8, 87.2, and 84.0 kcal mol(-1) (per EC molecule), respectively. The intermolecular distances between Li(+) and the F atom of BF4(-) are elongated: 1.773 Å (n=0), 1.820 Å (n=1), 1.974 Å (n=2), 1.942 Å (n=3), and 4.156 Å (n=4). The atomic bond populations between Li(+) and the F atom for n=0, 1, 2, 3, and 4 are 0.202, 0.186, 0.150, 0.038, and 0.0, respectively. These results indicate that the interaction of Li(+) with BF4(-) becomes weaker as the number of EC molecules is increased. The direct AIMD calculation for n=4 shows that EC reacts spontaneously with (EC)3(Li(+)BF4(-)) and the Li(+) ion is stripped from the salt. The following substitution reaction takes place: EC+(EC)3(Li(+)BF4(-))→(EC)4Li(+)-(BF4(-)). The reaction mechanism is discussed on the basis of the theoretical results. PMID:24616076

  19. 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

  20. 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.

  1. Disentangling vibronic and solvent broadening effects in the absorption spectra of coumarin derivatives for dye sensitized solar cells.

    PubMed

    Cerezo, Javier; Avila Ferrer, Francisco J; Santoro, Fabrizio

    2015-05-01

    We simulate from first-principles the absorption spectra of five structure-related coumarin derivatives utilized in dye sensitized solar cells (DSSCs), investigating the vibronic and solvent contributions to the position and width of the spectra in ethanol. Ground and excited state potential energy surfaces (PESs) are modeled by Density Functional Theory (DFT) and its time-dependent (TD) expression for the excited state (TD-DFT). The solute vibronic structure associated with the spectrum is calculated by a TD formalism, accounting for both Duschinsky and temperature effects, while solvent inhomogeneous broadening is evaluated according to Marcus' theory, computing the solvent reorganization energy by the state-specific implementation of the polarizable continuum model (PCM) within TD-DFT. We adopted both the standard hybrid PBE0 and the range separated CAM-B3LYP functionals showing that the latter performs better both concerning the vibronic and solvent-induced contributions to the absorption lineshape. The different predictions of the two functionals are then rationalized in terms of the charge transfer (CT) character of the transitions showing that, in this class of compounds, it is strongly dependent on the nuclear structure. Such a dependence introduces a bias in the PBE0 PES that has a drastic impact on the vibronic spectra. We show that both the intrinsic vibronic structure and the solvent broadening play a relevant role in differentiating the absorption width of the five dyes. In this sense, our results provide a guide to understand the sources of spectral broadening of this family of dyes, a valuable help for a rational design of new molecules to improve DSSC devices.

  2. On the Potential of Using the Al7 Superatom as an Excess Electron Acceptor To Construct Materials with Excellent Nonlinear Optical Properties.

    PubMed

    Huang, Shaoyuan; Liao, Kuntian; Peng, Bin; Luo, Qiong

    2016-05-01

    With the aid of density functional theory (DFT) calculations, we found that, when alkali metal approaches the Al7 superatom, its outermost s-value electron can be trapped by Al7 to give the superatom compound MAl7 (M = Li, Na, K) with an excess electron. Different analyses including natural bond orbital (NBO), electron localization function (ELF), and energy decomposition analysis (EDA) show that the resulting M-Al bond is strong and has a polar covalent character. The optimizations of self-assemblies (MAl7)n (n = 2, 3) have been performed to explore the stability of MAl7 in the solid state. The results reveal that only NaAl7 can keep its structural integrity as a building block upon self-assembling, while serious aggregations between Al7 clusters occur in the dimers and trimers of LiAl7 and KAl7, despite the fact that the Li-Al7 and K-Al7 bond energies are comparable to that of Na-Al7. Born-Oppenheimer molecular dynamics (BOMD) simulations for (NaAl7)n (n = 2, 3) indicate that these species are stable toward fragmentation at 300 K. The β0 values of (NaAl7)n (n = 1, 2, and 3) predicted at the CAM-B3LYP/6-311+G(3df) level of theory are in the range of 1.6 × 10(4)a.u. to 7.5 × 10(4) a.u.. This theoretical study implies that NaAl7 is a promising candidate for nolinear optical (NLO) materials. We provide theoretical evidence for the possibility of using the Al7 superatom as an excess electron acceptor to construct materials with excellent NLO properties. Further experimental research is invited.

  3. Diterpene production in Mycobacterium tuberculosis

    PubMed Central

    Prach, Lisa; Kirby, James; Keasling, Jay D.; Alber, Tom

    2011-01-01

    Diterpenes are a structurally diverse class of molecules common in plants, although they are very rarely found in bacteria. We report the identification in Mycobacterium tuberculosis (Mtb) of three diterpenes proposed to promote phagolysosome maturation arrest. MS analysis reveals that these diterpenes are novel compounds not previously identified in other organisms. The diterpene with highest abundance in Mtb has a mass fragmentation pattern identical to edaxadiene, which is produced in vitro from geranylgeranyl diphosphate by the enzymes Rv3377c and Rv3378c [Mann FM et al. (2009) J Am Chem Soc 131, 17526–17527]. A second diterpene found in Mtb has a similar mass spectrum, and is always observed in the same proportion relative to edaxadiene, indicating that it is a side product of the Rv3378c reaction in vivo. We name this second diterpene olefin edaxadiene B. The least abundant of the three diterpenes in Mtb extracts is tuberculosinol, a dephosphorylated side-product of the edaxadiene pathway intermediate produced by Rv3377c [Nakano C et al. (2009) Chembiochem 10, 2060–2071; Nakano C et al. (2005) Chem Commun (Camb) 8, 1016–1018]. A frameshift in Rv3377c in Mtb completely eliminates diterpene production, whereas expression of Rv3377c and Rv3378c in the nonpathogenic M. smegmatis is sufficient to produce edaxadiene and edaxadiene B. These studies define the pathway of edaxadiene and edaxadiene B biosynthesis in vivo. Rv3377c and Rv3378c are unique to Mtb and M. bovis, making them candidates for selective therapeutics and diagnostics. PMID:20670276

  4. Assessment of Franck-Condon Methods for Computing Vibrationally Broadened UV-vis Absorption Spectra of Flavin Derivatives: Riboflavin, Roseoflavin, and 5-Thioflavin.

    PubMed

    Karasulu, Bora; Götze, Jan Philipp; Thiel, Walter

    2014-12-01

    We address the performance of the vertical and adiabatic Franck-Condon (VFC/AFC) approaches combined with time-independent or time-dependent (TI/TD) formalisms in simulating the one-photon absorption spectra of three flavin compounds with distinct structural features. Calculations were done in the gas phase and in two solvents (water, benzene) for which experimental reference measurements are available. We utilized the independent mode displaced harmonic oscillator model without or with frequency alteration (IMDHO/IMDHO-FA) and also accounted for Duschinsky mixing effects. In the initial validation on the first excited singlet state of riboflavin, the range-separated functionals, CAM-B3LYP and ωB97xD, showed the best performance, but B3LYP also gave a good compromise between peak positions and spectral topology. Large basis sets were not mandatory to obtain high-quality spectra for the selected systems. The presence of a symmetry plane facilitated the computation of vibrationally broadened spectra, since different FC variants yield similar results and the harmonic approximation holds rather well. Compared with the AFC approach, the VFC approach performed equally well or even better for all three flavins while offering several advantages, such as avoiding error-prone geometry optimization procedures on excited-state surfaces. We also explored the advantages of curvilinear displacements and of a Duschinsky treatment for the AFC spectra in cases when a rotatable group is present on the chromophore. Taken together, our findings indicate that the combination of the VFC approach with the TD formalism and the IMDHO-FA model offers the best overall performance. PMID:26583238

  5. Photophysics of α-furil at room temperature and 77 K: Spectroscopic and quantum chemical studies.

    PubMed

    Kundu, Pronab; Chattopadhyay, Nitin

    2016-06-21

    Steady state and time resolved spectroscopic measurements have been exploited to assign the emissions from different conformations of α-furil (2, 2'-furil) in solution phase at room temperature as well as cryogen (liquid nitrogen, LN2) frozen matrices of ethanol and methylcyclohexane. Room temperature studies reveal a single fluorescence from the trans-planar conformer of the fluorophore or two fluorescence bands coming from the trans-planar and the relaxed skew forms depending on excitation at the nπ(∗) or the ππ(∗) absorption band, respectively. Together with the fluorescence bands, the LN2 studies in both the solvents unambiguously ascertain two phosphorescence emissions with lifetimes 5 ± 0.3 ms (trans-planar triplet) and 81 ± 3 ms (relaxed skew triplet). Quantum chemical calculations have been performed using density functional theory at CAM-B3LYP/6-311++G(∗∗) level to prop up the spectroscopic surveillance. The simulated potential energy curves (PECs) illustrate that α-furil is capable of giving two emissions from each of the S1 and the T1 states-one corresponding to the trans-planar and the other to the relaxed skew conformation. Contrary to the other 1,2-dicarbonyl molecular systems like benzil and α-naphthil, α-furil does not exhibit any fluorescence from its second excited singlet (S2) state. This is ascribed to the proximity of the minimum of the PEC of the S2 state and the hill-top of the PEC of the S1 state. PMID:27334172

  6. 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. PMID:26945637

  7. The solvatochromic, spectral, and geometrical properties of nifenazone: a DFT/TD-DFT and experimental study.

    PubMed

    Bani-Yaseen, Abdulilah Dawoud; Al-Balawi, Mona

    2014-08-01

    The solvatochromic, spectral, and geometrical properties of nifenazone (NIF), a pyrazole-nicotinamide drug, were experimentally and computationally investigated in several neat solvents and in hydro-organic binary systems such as water-acetonitrile and water-dioxane systems. The bathochromic spectral shift observed in NIF absorption spectra when reducing the polarity of the solvent was correlated with the orientation polarizability (Δf). Unlike aprotic solvents, a satisfactory correlation between λ(max) and Δf was determined (linear correlation of regression coefficient, R, equal to 0.93) for polar protic solvents. In addition, the medium-dependent spectral properties were correlated with the Kamlet-Taft solvatochromic parameters (α, β, and π*) by applying a multiple linear regression analysis (MLRA). The results obtained from this analysis were then employed to establish MLRA relationships for NIF in order to estimate the spectral shift in different solvents, which in turn exhibited excellent correlation (R > 0.99) with the experimental values of ν(max). Density functional theory (DFT) and time-dependent DFT theory calculations coupled with the integral equation formalism-polarizable continuum model (IEF-PCM) were performed to investigate the solvent-dependent spectral and geometrical properties of NIF. The calculations showed good and poor agreements with the experimental results using the CAM-B3LYP and B3LYP functionals, respectively. Experimental and theoretical results confirmed that the chemical properties of NIF are strongly dependent on the polarity of the chosen medium and its hydrogen bonding capability. This in turn supports the hypothesis of the delocalization of the electron density within the pyrazole ring of NIF.

  8. 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

    2015-03-01

    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.

  9. On the Potential of Using the Al7 Superatom as an Excess Electron Acceptor To Construct Materials with Excellent Nonlinear Optical Properties.

    PubMed

    Huang, Shaoyuan; Liao, Kuntian; Peng, Bin; Luo, Qiong

    2016-05-01

    With the aid of density functional theory (DFT) calculations, we found that, when alkali metal approaches the Al7 superatom, its outermost s-value electron can be trapped by Al7 to give the superatom compound MAl7 (M = Li, Na, K) with an excess electron. Different analyses including natural bond orbital (NBO), electron localization function (ELF), and energy decomposition analysis (EDA) show that the resulting M-Al bond is strong and has a polar covalent character. The optimizations of self-assemblies (MAl7)n (n = 2, 3) have been performed to explore the stability of MAl7 in the solid state. The results reveal that only NaAl7 can keep its structural integrity as a building block upon self-assembling, while serious aggregations between Al7 clusters occur in the dimers and trimers of LiAl7 and KAl7, despite the fact that the Li-Al7 and K-Al7 bond energies are comparable to that of Na-Al7. Born-Oppenheimer molecular dynamics (BOMD) simulations for (NaAl7)n (n = 2, 3) indicate that these species are stable toward fragmentation at 300 K. The β0 values of (NaAl7)n (n = 1, 2, and 3) predicted at the CAM-B3LYP/6-311+G(3df) level of theory are in the range of 1.6 × 10(4)a.u. to 7.5 × 10(4) a.u.. This theoretical study implies that NaAl7 is a promising candidate for nolinear optical (NLO) materials. We provide theoretical evidence for the possibility of using the Al7 superatom as an excess electron acceptor to construct materials with excellent NLO properties. Further experimental research is invited. PMID:27064431

  10. Photophysics of α-furil at room temperature and 77 K: Spectroscopic and quantum chemical studies

    NASA Astrophysics Data System (ADS)

    Kundu, Pronab; Chattopadhyay, Nitin

    2016-06-01

    Steady state and time resolved spectroscopic measurements have been exploited to assign the emissions from different conformations of α-furil (2, 2'-furil) in solution phase at room temperature as well as cryogen (liquid nitrogen, LN2) frozen matrices of ethanol and methylcyclohexane. Room temperature studies reveal a single fluorescence from the trans-planar conformer of the fluorophore or two fluorescence bands coming from the trans-planar and the relaxed skew forms depending on excitation at the nπ∗ or the ππ∗ absorption band, respectively. Together with the fluorescence bands, the LN2 studies in both the solvents unambiguously ascertain two phosphorescence emissions with lifetimes 5 ± 0.3 ms (trans-planar triplet) and 81 ± 3 ms (relaxed skew triplet). Quantum chemical calculations have been performed using density functional theory at CAM-B3LYP/6-311++G∗∗ level to prop up the spectroscopic surveillance. The simulated potential energy curves (PECs) illustrate that α-furil is capable of giving two emissions from each of the S1 and the T1 states - one corresponding to the trans-planar and the other to the relaxed skew conformation. Contrary to the other 1,2-dicarbonyl molecular systems like benzil and α-naphthil, α-furil does not exhibit any fluorescence from its second excited singlet (S2) state. This is ascribed to the proximity of the minimum of the PEC of the S2 state and the hill-top of the PEC of the S1 state.

  11. 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.

  12. Experimental and TD-DFT study of optical absorption of six explosive molecules: RDX, HMX, PETN, TNT, TATP, and HMTD.

    PubMed

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

    2013-07-25

    Time dependent density function theory (TD-DFT) has been utilized to calculate the excitation energies and oscillator strengths of six common explosives: RDX (1,3,5-trinitroperhydro-1,3,5-triazine), β-HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), TATP (triacetone triperoxide), HMTD (hexamethylene triperoxide diamine), TNT (2,4,6-trinitrotoluene), and PETN (pentaerythritol tetranitrate). The results were compared to experimental UV-vis absorption spectra collected in acetonitrile. Four computational methods were tested including: B3LYP, CAM-B3LYP, ωB97XD, and PBE0. PBE0 outperforms the other methods tested. Basis set effects on the electronic energies and oscillator strengths were evaluated with 6-31G(d), 6-31+G(d), 6-31+G(d,p), and 6-311+G(d,p). The minimal basis set required was 6-31+G(d); however, additional calculations were performed with 6-311+G(d,p). For each molecule studied, the natural transition orbitals (NTOs) were reported for the most prominent singlet excitations. The TD-DFT results have been combined with the IPv calculated by CBS-QB3 to construct energy level diagrams for the six compounds. The results suggest optimization approaches for fluorescence based detection methods for these explosives by guiding materials selections for optimal band alignment between fluorescent probe and explosive analyte. Also, the role of the TNT Meisenheimer complex formation and the resulting electronic structure thereof on of the quenching mechanism of II-VI semiconductors is discussed. PMID:23432018

  13. DEMNUni: ISW, Rees-Sciama, and weak-lensing in the presence of massive neutrinos

    NASA Astrophysics Data System (ADS)

    Carbone, Carmelita; Petkova, Margarita; Dolag, Klaus

    2016-07-01

    We present, for the first time in the literature, a full reconstruction of the total (linear and non-linear) ISW/Rees-Sciama effect in the presence of massive neutrinos, together with its cross-correlations with CMB-lensing and weak-lensing signals. The present analyses make use of all-sky maps extracted via ray-tracing across the gravitational potential distribution provided by the ``Dark Energy and Massive Neutrino Universe'' (DEMNUni) project, a set of large-volume, high-resolution cosmological N-body simulations, where neutrinos are treated as separate collisionless particles. We correctly recover, at 1-2% accuracy, the linear predictions from CAMB. Concerning the CMB-lensing and weak-lensing signals, we also recover, with similar accuracy, the signal predicted by Boltzmann codes, once non-linear neutrino corrections to HALOFIT are accounted for. Interestingly, in the ISW/Rees-Sciama signal, and its cross correlation with lensing, we find an excess of power with respect to the massless case, due to free streaming neutrinos, roughly at the transition scale between the linear and non-linear regimes. The excess is ~ 5 - 10% at l ~ 100 for the ISW/Rees-Sciama auto power spectrum, depending on the total neutrino mass Mν, and becomes a factor of ~ 4 for Mν = 0.3 eV, at l ~ 600, for the ISW/Rees-Sciama cross power with CMB-lensing. This effect should be taken into account for the correct estimation of the CMB temperature bispectrum in the presence of massive neutrinos.

  14. Solvent induced channel interference in the two-photon absorption process--a theoretical study with a generalized few-state-model in three dimensions.

    PubMed

    Alam, Md Mehboob; Chattopadhyaya, Mausumi; Chakrabarti, Swapan

    2012-01-21

    For the first time, we report the effect of interference between different optical channels on the two-photon absorption (TPA) process in three dimensions. We have employed response theory as well as a sum-over-states (SOS) approach involving few intermediate states to calculate the TPA parameters like transition probabilities (δ(TP)) and TPA tensor elements. In order to use the limited SOS approach, we have derived a new formula for a generalized few-state-model (GFSM) in three dimensions. Due to the presence of additional terms related to the angle between different transition moment vectors, the channel interference associated with the TPA process in 3D is significantly different and much more complicated than that in 1D and 2D cases. The entire study has been carried out on the two simplest Reichardt's dyes, namely 2- and 4-(pyridinium-1-yl)-phenolate (ortho- and para-betain) in gas phase, THF, CH(3)CN and water solvents. We have meticulously inspected the effect of the additional angle related terms on the overall TPA transition probabilities of the two 3D isomeric molecules studied and found that the interfering terms involved in the δ(TP) expression contribute both constructively and destructively as well to the overall δ(TP) value. Moreover, the interfering term has a more conspicuous role in determining the net δ(TP) associated with charge transfer transition in comparison to that of π-π* transition of the studied systems. Interestingly, our model calculations suggest that, for o- and p-betain, the quenching of destructive interference associated with a particular two-photon process can be done with high polarity solvents while the enhancement of constructive interference will be achieved in solvents having relatively small polarity. All the one- and two-photon parameters are evaluated using a range separated CAMB3LYP functional. PMID:22127437

  15. 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.

  16. Effects of the acceptor unit in dyes with acceptor-bridge-donor architecture on the electron photo-injection mechanism and aggregation in DSSCs.

    PubMed

    Zarate, Ximena; Claveria-Cadiz, Francisca; Arias-Olivares, David; Rodriguez-Serrano, Angela; Inostroza, Natalia; Schott, Eduardo

    2016-09-21

    Dye-sensitized solar cells (DSSCs) are devices that convert light to electrical energy. Nowadays, researchers have focused on the understanding of the performance of dyes in solar cells. In this way, new efficient dyes have been obtained which can act as efficient light-harvesting compounds where the combination and the balance of acceptor(A)-bridge-donor(D) architectures confer suitable attributes and properties to the dye. Herein, we have carried out a DFT study on the optical and electronic properties of eight different A motifs and their influence on the electron photo-injection (PI) mechanisms through type I (indirect) or type II (direct) pathways in A-bridge-D dyes in DSSCs. The models consisted of thiophene as a bridge and triphenylamine as a D anchored to a TiO2 anatase cluster. All geometry optimizations were calculated using the B3LYP, CAM-B3LYP and BHandHLYP functionals combined with the 6-31G(d,p) basis set for C, H, N, O and S and the LANL2DZ pseudopotential for Ti atoms. Most of the A dyes display optoelectronic properties consistent with a type-I (indirect) mechanism except for the A5 dye where the results suggest a type-II (direct) PI pathway. In addition, molecular dynamics (MD) simulations have been carried out in order to describe the formation of dye dimers and analyze the stability of the aggregates due to intermolecular interactions. The observed trends indicate that dyes with A2 and A5 anchoring groups have less tendency to dimerize due to weaker intermolecular interactions resulting in less stable dimer complexes. Specifically, we found that the A motif influences the PI by a dye and the dimerization profiles. PMID:27530076

  17. Examination of DFT and TDDFT Methods II

    NASA Astrophysics Data System (ADS)

    Wang, Yi-Gui

    2009-09-01

    We investigated the isomerization energies for C8 alkanes (n-octane and 2,2,3,3-tetra-methyl butane) and 1-X-propenes (X = CH3, F, Cl, Br) and the excited states for tropolone. The recently implemented TDDFT gradients enabled us to optimize the adiabatic excited-state structures and to obtain wave function files for excited-state electron density analyses with 25 functionals. The dispersion interactions had been found to be important for predicting the isomerization energies for n-octane and 2,2,3,3-tetra-methyl butane and for cis- and trans-1-X-propenes (X = CH3, F, Cl, Br). B3LYP failed to predict the isomerization energies for the first case but succeeded for the latter. We noticed that the integrated electron density and the merging contour values in the electron density difference plots were related to the isomerization energies; the DFT functionals (LSDA, BHandH, VSXC, and M052X) that could correctly account for the dispersion forces produced a greater electron density response for 2,2,3,3-tetramethyl butane than n-octane. Although the faster proton transfer reaction rate in the Ã1B2 excited state relative to the X˜1A1 ground state of tropolone could be reproduced only by M052X, the three newly designed functionals (BMK, CAM-B3LYP, and M052X) apparently performed better than other DFT functionals. The C-C' bond lengths of the Cs symmetry excited state were possibly underestimated by DFT methods; the underestimation of C-C' bond lengths contributed to the high proton transfer barriers in the Ã1B2 excited state of tropolone.

  18. Vibrational relaxation as the driving force for wavelength conversion in the peridinin-chlorophyll a-protein.

    PubMed

    Götze, Jan P; Karasulu, Bora; Patil, Mahendra; Thiel, Walter

    2015-12-01

    We present a computationally derived energy transfer model for the peridinin-chlorophyll a-protein (PCP), which invokes vibrational relaxation in the two lowest singlet excited states rather than internal conversion between them. The model allows an understanding of the photoinduced processes without assuming further electronic states or a dependence of the 2Ag state character on the vibrational sub-state. We report molecular dynamics simulations (CHARMM22 force field) and quantum mechanics/molecular mechanics (QM/MM) calculations on PCP. In the latter, the QM region containing a single peridinin (Per) chromophore or a Per-Chl a (chlorophyll a) pair is treated by density functional theory (DFT, CAM-B3LYP) for geometries and by DFT-based multireference configuration interaction (DFT/MRCI) for excitation energies. The calculations show that Per has a bright, green light absorbing 2Ag state, in addition to the blue light absorbing 1Bu state found in other carotenoids. Both states undergo a strong energy lowering upon relaxation, leading to emission in the red, while absorbing in the blue or green. The orientation of their transition dipole moments indicates that both states are capable of excited-state energy transfer to Chl a, without preference for either 1Bu or 2Ag as donor state. We propose that the commonly postulated partial intramolecular charge transfer (ICT) character of a donating Per state can be assigned to the relaxed 1Bu state, which takes on ICT character. By assuming that both 1Bu and 2Ag are able to donate to the Chl a Q band, one can explain why different chlorophyll species in PCP exhibit different acceptor capabilities.

  19. Complex self-assembly of reverse poly(butylene oxide)-poly(ethylene oxide)-poly(butylene oxide) triblock copolymers with long hydrophobic and extremely lengthy hydrophilic blocks.

    PubMed

    Cambón, Adriana; Figueroa-Ochoa, Edgar; Juárez, Josué; Villar-Álvarez, Eva; Pardo, Alberto; Barbosa, Silvia; Soltero, J F Armando; Taboada, Pablo; Mosquera, Víctor

    2014-05-15

    Amphiphilic block copolymers have emerged during last years as a fascinating substrate material to develop micellar nanocontainers able to solubilize, protect, transport, and release under external or internal stimuli different classes of cargos to diseased cells or tissues. However, this class of materials can also induce biologically relevant actions, which complement the therapeutic activity of their cargo molecules through their mutual interactions with biologically relevant entities (cellular membranes, proteins, organelles...); these interactions at the same time, are regulated by the nature, conformation, and state of the copolymeric chains. For these reasons, in this paper we investigated the self-assembly process and physico-chemcial properties of two reverse triblock poly(butylene oxide)-poly(ethylene oxide)-poly(butylene oxide) block copolymers, BO14EO378BO14 and BO21EO385BO21, which have been recently found to be very useful as drug delivery nanovehicles and biological response modifiers under certain conditions (A. Cambón et al. Int. J. Pharm. 2013, 445, 47-57) in order to obtain a clear picture of the solution behavior of this class or block copolymers and to understand their biological activity. These block copolymers are characterized by possessing long BO blocks and extremely lengthy central EO ones, which provide them with a rich rheological behavior characterized by the formation of flowerlike micelles with sizes ranging from 20 to 40 nm in aqueous solution and the presence of intermicellar bridging even at low copolymers concentrations as denoted by atomic force microscopy. Bridging is also clearly observed by analyzing the rheological response of these block copolymers both storage and loss moduli upon changes on time, temperature, and or concentration. Strikingly, the relatively wide Poisson distribution of the polymeric chains make the present copolymers behave rather distinctly to conventional associative thickeners. The observed rich

  20. Assessment of density-functionals for describing the X(-) + CH3ONO2 gas-phase reactions with X = F, OH, CH2CN.

    PubMed

    Proenza, Yaicel G; de Souza, Miguel A F; Ventura, Elizete; do Monte, Silmar A; Longo, Ricardo L

    2014-12-28

    The energetics of the ECO2, SN2@C and SN2@N channels of X(-) + CH3ONO2 (X = F, OH, CH2CN) gas-phase reactions were computed using the CCSD(T)/CBS method. This benchmark extends a previous study with X = OH [M. A. F. de Souza et al., J. Am. Chem. Soc., 2012, 134, 19004] and was used to ascertain the accuracy and robustness of nineteen density-functionals for describing these potential energy profiles (PEP) as well as the kinetic product distributions obtained from RRKM calculations. Assessments were based on the mean unsigned error (MUE), the mean signed error (MSE), the #best : #worst (BW) criterion and the statistical confidence interval (CI) for the MSE. In general, double-hybrid (DH) functionals perform better than the range-separated ones, and both are better than the global-hybrid functionals. Based on the MUE and CI criteria the B2GPPLYP, B2PLYP, M08-SO, BMK, ωB97X-D, CAM-B3LYP, M06, M08-HX, ωB97X and B97-K functionals show the best performance in the description of these PEPs. Within this set, the B2GPPLYP functional is the most accurate and robust. The RRKM results indicate that the DHs are the best for describing the selectivities of these reactions. Compared to CCSD(T), the B2PLYP method has a relative error of only ca. 1% for the selectivity and the accuracy to provide the correct conclusion concerning the nonstatistical behavior of these reactions.

  1. DEMNUni: ISW, Rees-Sciama, and weak-lensing in the presence of massive neutrinos

    NASA Astrophysics Data System (ADS)

    Carbone, Carmelita; Petkova, Margarita; Dolag, Klaus

    2016-07-01

    We present, for the first time in the literature, a full reconstruction of the total (linear and non-linear) ISW/Rees-Sciama effect in the presence of massive neutrinos, together with its cross-correlations with CMB-lensing and weak-lensing signals. The present analyses make use of all-sky maps extracted via ray-tracing across the gravitational potential distribution provided by the ``Dark Energy and Massive Neutrino Universe'' (DEMNUni) project, a set of large-volume, high-resolution cosmological N-body simulations, where neutrinos are treated as separate collisionless particles. We correctly recover, at 1–2% accuracy, the linear predictions from CAMB. Concerning the CMB-lensing and weak-lensing signals, we also recover, with similar accuracy, the signal predicted by Boltzmann codes, once non-linear neutrino corrections to HALOFIT are accounted for. Interestingly, in the ISW/Rees-Sciama signal, and its cross correlation with lensing, we find an excess of power with respect to the massless case, due to free streaming neutrinos, roughly at the transition scale between the linear and non-linear regimes. The excess is ~ 5 – 10% at l ~ 100 for the ISW/Rees-Sciama auto power spectrum, depending on the total neutrino mass Mν, and becomes a factor of ~ 4 for Mν = 0.3 eV, at l ~ 600, for the ISW/Rees-Sciama cross power with CMB-lensing. This effect should be taken into account for the correct estimation of the CMB temperature bispectrum in the presence of massive neutrinos.

  2. Efficient Implementation of the Pair Atomic Resolution of the Identity Approximation for Exact Exchange for Hybrid and Range-Separated Density Functionals

    PubMed Central

    2015-01-01

    An efficient new molecular orbital (MO) basis algorithm is reported implementing the pair atomic resolution of the identity approximation (PARI) to evaluate the exact exchange contribution (K) to self-consistent field methods, such as hybrid and range-separated hybrid density functionals. The PARI approximation, in which atomic orbital (AO) basis function pairs are expanded using auxiliary basis functions centered only on their two respective atoms, was recently investigated by Merlot et al. [J. Comput. Chem.2013, 34, 1486]. Our algorithm is significantly faster than quartic scaling RI-K, with an asymptotic exchange speedup for hybrid functionals of (1 + X/N), where N and X are the AO and auxiliary basis dimensions. The asymptotic speedup is 2 + 2X/N for range separated hybrids such as CAM-B3LYP, ωB97X-D, and ωB97X-V which include short- and long-range exact exchange. The observed speedup for exchange in ωB97X-V for a C68 graphene fragment in the cc-pVTZ basis is 3.4 relative to RI-K. Like conventional RI-K, our method greatly outperforms conventional integral evaluation in large basis sets; a speedup of 19 is obtained in the cc-pVQZ basis on a C54 graphene fragment. Negligible loss of accuracy relative to exact integral evaluation is demonstrated on databases of bonded and nonbonded interactions. We also demonstrate both analytically and numerically that the PARI-K approximation is variationally stable. PMID:25691831

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

    DOE PAGES

    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 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

  4. 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.

  5. Experimental and DFT studies on the vibrational and electronic spectra of 9-p-tolyl-9H-carbazole-3-carbaldehyde.

    PubMed

    Wang, Yiwei; Zhang, Yu; Ni, Haiwei; Meng, Nana; Ma, Kuirong; Zhao, Jianying; Zhu, Dunru

    2015-01-25

    The compound 9-p-tolyl-9H-carbazole-3-carbaldehyde (HCCD) was synthesized and characterized by X-ray diffraction, FT-IR, FT-Raman and UV-Vis spectra. The X-ray diffraction study showed that HCCD has a Z-configuration. The benzene ring including methyl is twisted from the mean plane of the carbazole group by 59.7(3)°, which is comparable with the calculated result 65° for B3LYP/6-311++G(d, p) method. Vibrational spectra and electronic spectra measurements were made for the compound. Optimized geometrical structure and harmonic vibrational frequencies were computed with B-based DFT (BLYP, B3LYP and cam-B3LYP) methods, and WB-based DFT (WB97, WB97X and WB97XD) methods and ab initio RHF method using 6-311++G(d, p) basis set. Assignments of the observed spectra were proposed. The equilibrium geometries computed by all of the methods were compared with X-ray diffraction results. The absorption spectra of the title compound were computed both in gas phase and in DMF solution using TD-(cam)B3LYP/6-311++G(d, p) and PCM-(cam)B3LYP/6-311++G(d, p) approaches, respectively. The calculated results provide good descriptions of the bands maxima in the observed electronic spectrum. Temperature dependence of thermodynamic parameters in the range of 100-1000 K was determined. The natural atomic hybrids were calculated and discussed.

  6. Gas-Phase Thermal Tautomerization of Imidazole-Acetic Acid: Theoretical and Computational Investigations

    PubMed Central

    Aziz, Saadullah G.; Osman, Osman I.; Elroby, Shaaban A.; Hilal, Rifaat H.

    2015-01-01

    The gas-phase thermal tautomerization reaction between imidazole-4-acetic (I) and imidazole-5-acetic (II) acids was monitored using the traditional hybrid functional (B3LYP) and the long-range corrected functionals (CAM-B3LYP and ωB97XD) with 6-311++G** and aug-cc-pvdz basis sets. The roles of the long-range and dispersion corrections on their geometrical parameters, thermodynamic functions, kinetics, dipole moments, Highest Occupied Molecular Orbital–Lowest Unoccupied Molecular Orbital (HOMO–LUMO) energy gaps and total hyperpolarizability were investigated. All tested levels of theory predicted the preference of I over II by 0.750–0.877 kcal/mol. The origin of predilection of I is assigned to the H-bonding interaction (nN8→σ*O14–H15). This interaction stabilized I by 15.07 kcal/mol. The gas-phase interconversion between the two tautomers assumed a 1,2-proton shift mechanism, with two transition states (TS), TS1 and TS2, having energy barriers of 47.67–49.92 and 49.55–52.69 kcal/mol, respectively, and an sp3-type intermediate. A water-assisted 1,3-proton shift route brought the barrier height down to less than 20 kcal/mol in gas-phase and less than 12 kcal/mol in solution. The relatively high values of total hyperpolarizability of I compared to II were interpreted and discussed. PMID:26556336

  7. 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.

  8. Assessment of the photosensitization properties of cationic porphyrins in interaction with DNA nucleotide pairs.

    PubMed

    Cárdenas-Jirón, Gloria I; Cortez, Luis

    2013-07-01

    We present a theoretical assessment of the photosensitization properties of meso-mono(N-methylpyridyl) triphenylporphyrin (1, MmPyP(+)), which interacts with DNA nucleotide pairs [adenine (A)-thymine (T); guanine (G)-cytosine (C)] via an external binding mode. The photosensitization properties of the arrangements 1A, 1T, 1G and 1C were investigated. A set of density functionals (B3LYP, PBE0, CAM-B3LYP, M06-2X, B97D) with the 6-31G(d) basis set was used to calculate the electronic absorption spectra in solution (water) following TD-DFT methodology. In all the arrangements, with the exception of 1C, the functional PBE0 produced the lowest deviation of the Soret band (0.1-0.2 eV). Using this functional, we show that the porphyrin-nucleotide interaction is stabilized, as reflected by a larger HOMO-LUMO gap than free porphyrin. A more important effect of the interaction corresponds to the red-shift of the Soret band of MmPyP(+), which is in agreement with experimental results. This behavior could be explained by the higher symmetry found in arrangements with a lower dipole moment, and by the more symmetrical distribution of electronic density along the molecular orbitals, which provokes electronic transitions of lower energy. The structural model allowed us to show that MmPyP(+) improves the characteristics as a photosensitizer when it interacts with nucleotide pairs due to the longer wavelength required for the Soret band. Results obtained for porphyrins with larger monocationic substituents (2, MmAP+; 3, MONPP+) do not lead to the same behavior. Although the structural model is insufficient to describe porphyrin photosensitization, it suggests that improvements in this property are produced by the inclusion of a cationic charge in the pyridyl ring and a smaller size of the substituent leading to a better communication in the porphyrin-nucleotide pair.

  9. Experimental and TD-DFT study of optical absorption of six explosive molecules: RDX, HMX, PETN, TNT, TATP, and HMTD.

    PubMed

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

    2013-07-25

    Time dependent density function theory (TD-DFT) has been utilized to calculate the excitation energies and oscillator strengths of six common explosives: RDX (1,3,5-trinitroperhydro-1,3,5-triazine), β-HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), TATP (triacetone triperoxide), HMTD (hexamethylene triperoxide diamine), TNT (2,4,6-trinitrotoluene), and PETN (pentaerythritol tetranitrate). The results were compared to experimental UV-vis absorption spectra collected in acetonitrile. Four computational methods were tested including: B3LYP, CAM-B3LYP, ωB97XD, and PBE0. PBE0 outperforms the other methods tested. Basis set effects on the electronic energies and oscillator strengths were evaluated with 6-31G(d), 6-31+G(d), 6-31+G(d,p), and 6-311+G(d,p). The minimal basis set required was 6-31+G(d); however, additional calculations were performed with 6-311+G(d,p). For each molecule studied, the natural transition orbitals (NTOs) were reported for the most prominent singlet excitations. The TD-DFT results have been combined with the IPv calculated by CBS-QB3 to construct energy level diagrams for the six compounds. The results suggest optimization approaches for fluorescence based detection methods for these explosives by guiding materials selections for optimal band alignment between fluorescent probe and explosive analyte. Also, the role of the TNT Meisenheimer complex formation and the resulting electronic structure thereof on of the quenching mechanism of II-VI semiconductors is discussed.

  10. New design strategy for the two-photon active material based on push-pull substituted bisanthene molecule.

    PubMed

    Chattopadhyaya, Mausumi; Alam, Md Mehboob; Chakrabarti, Swapan

    2011-03-31

    In the present work, we have critically examined the origin of strong two-photon transition probability of a donor-acceptor substituted bisanthene molecule that imitates a small piece of edge passivated (4, 4) graphene nanoribbon. In our calculations, we have considered -OMe, and -NH(2) as donors and -NO(2) as an acceptor. The one- and two-photon absorption parameters are evaluated using state-of-the-art linear and quadratic response theory, respectively, and all these calculations are carried out within the framework of time dependent density functional theory. To give a proper judgment on our findings, we have used the long-range corrected CAMB3LYP functional for all of the time dependent calculations. The present investigation reveals that the bisanthene molecule with three pairs of donor/acceptor moiety has a lower two-photon transition probability than that of a suitably designed bisanthene with only a single pair of donor/acceptor moiety. This in silico observation is consistent for all of the donor/acceptor moieties chosen in the present work. A comprehensive analysis at the two state model level of theory clearly offers us a verdict that by placing the donor/acceptor moiety in a suitable position of bisanthene, we can create a significant asymmetry in the electron density in the first excited state, which eventually leads to a significant difference in the ground and excited state dipole moment and is attributed to the higher two-photon transition probability of a particular bisanthene with a single pair of donor/acceptor moiety than bisanthene with three pairs of donor/acceptor.

  11. 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

  12. 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

  13. 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

  14. Genetic architecture and evolution of the mating type locus in fusaria that cause soybean sudden death syndrome and bean root rot.

    PubMed

    Hughes, Teresa J; O'Donnell, Kerry; Sink, Stacy; Rooney, Alejandro P; Scandiani, María Mercedes; Luque, Alicia; Bhattacharyya, Madan K; Huang, Xiaoqiu

    2014-01-01

    Fusarium tucumaniae is the only known sexually reproducing species among the seven closely related fusaria that cause soybean sudden death syndrome (SDS) or bean root rot (BRR). In a previous study, laboratory mating of F. tucumaniae yielded recombinant ascospore progeny but required two mating-compatible strains, indicating that it is heterothallic. To assess the reproductive mode of the other SDS and BRR fusaria, and their potential for mating, whole-genome sequences of two SDS and one BRR pathogen were analyzed to characterize their mating type (MAT) loci. This bioinformatic approach identified a MAT1-1 idiomorph in F. virguliforme NRRL 22292 and MAT1-2 idiomorphs in F. tucumaniae NRRL 34546 and F. azukicola NRRL 54364. Alignments of the MAT loci were used to design PCR primers within the conserved regions of the flanking genes APN1 and SLA2, which enabled primer walking to obtain nearly complete sequences of the MAT region for six MAT1-1 and five MAT1-2 SDS/BRR fusaria. As expected, sequences of the highly divergent 4.7 kb MAT1-1 and 3.7 kb MAT1-2 idiomorphs were unalignable. However, sequences of the respective idiomorphs and those that flank MAT1-1 and MAT1-2 were highly conserved. In addition to three genes at MAT1-1 (MAT1-1-1, MAT1-1-2, MAT1-1-3) and two at MAT1-2 (MAT1-2-1, MAT1-2-3), the MAT loci of the SDS/BRR fusaria also include a putative gene predicted to encode for a 252 amino acid protein of unknown function. Alignments of the MAT1-1-3 and MAT1-2-1 sequences were used to design a multiplex PCR assay for the MAT loci. This assay was used to screen DNA from 439 SDS/BRR isolates, which revealed that each isolate possessed MAT1-1 or MAT1-2, consistent with heterothallism. Both idiomorphs were represented among isolates of F. azukicola, F. brasiliense, F. phaseoli and F. tucumaniae, whereas isolates of F. virguliforme and F. cuneirostrum were only MAT1-1 and F. crassistipitatum were only MAT1-2. Finally, nucleotide sequence data from the RPB1 and RPB2

  15. Theoretical studies on two-dimensional nonlinear optical chromophores with pyrazinyl cores and organic or ruthenium(II) ammine electron donors.

    PubMed

    Coe, Benjamin J; Pilkington, Rachel A

    2014-03-27

    Density functional theory calculations have been carried out on twelve cationic, 2D nonlinear optical chromophores with pyrazinylbis(pyridinium) electron acceptors. These species contain either 4-(methoxy/dimethylamino)phenyl or pyridyl-coordinated {Ru(II)(NH3)5}(2+)/trans-{Ru(II)(NH3)4(py)}(2+) (py = pyridine) electron donor groups. The results are compared with data obtained by using experimental techniques including hyper-Rayleigh scattering and Stark (electroabsorption) spectroscopy previously (Coe, B. J.; et al. Inorg. Chem. 2010, 49, 10718; J. Org. Chem. 2010, 75, 8550). The B3LYP/6-311G(d) level of theory models the visible absorption spectra in MeCN for the -NMe2 derivatives relatively well, whereas CAM-B3LYP/6-311G(d) gives better results for the -OMe-substituted species. These spectra are dominated by intramolecular charge-transfer (ICT) bands. Static first hyperpolarizabilities β0 are computed also at the B3LYP/6-311G(d) level. The overall extent of prediction of trends in the ICT bands and β0 responses is partial, with the main discrepancies relating to the progression from one to two electron donor groups. The experimental data show that this structural change red-shifts the ICT bands and increases β0 significantly, but only the second trend is reproduced to some extent by the calculations. The UV-vis absorption spectra of the Ru complexes in MeCN are modeled relatively well with B3LYP and the LANL2DZ/6-311G(d) mixed basis set, including 100 excited states. However, again, some degree of disagreement between theory and experiment is evident, even when a larger basis set like def2-TZVP is used for Ru. In particular, substantial red shifts are predicted on adding a third metal center, whereas the measured spectra show corresponding small blue shifts. The experimental trend of the total β0 value increasing on moving from one to two Ru centers is predicted in the gas phase, but not in MeCN. For both classes of chromophore, the β(xxx) tensor component

  16. 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

  17. 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

    2015-06-01

    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

  18. 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

  19. Hydroxyl radical (OH•) reaction with guanine in an aqueous environment: a DFT study.

    PubMed

    Kumar, Anil; Pottiboyina, Venkata; Sevilla, Michael D

    2011-12-22

    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 bonds 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 bonds. 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 C(4)═C(5) 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 H(2)O and neutral G radicals favoring G(N(1)-H)(•) with an activation barrier of ca. 5 kcal/mol. The overall process from the G(C(4))-OH(•) (adduct) to G(N(1)-H)(•) and water is found to be exothermic in nature by more than 13 kcal/mol. (G-OH(•)), (G(•+)---OH(-)), and G(N(1)-H)(•) were further characterized by the CAM-B3LYP calculations of their UV-vis spectra and good agreement between theory and experiment is achieved. Our calculations for the direct hydrogen abstraction pathway from N(1) and N(2) sites of guanine by the OH(•) show that this is also a competitive route to produce G(N(2)-H)(•), G(N(1)-H)(•) and H(2)O.

  20. 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

  1. Lifetime Occupational Physical Activity and Musculoskeletal Aging in Middle-Aged Men and Women in Denmark: Retrospective Cohort Study Protocol and Methods

    PubMed Central

    Mortensen, Ole Steen; Reventlow, Susanne; Skov, Peder Georg; Andersen, Johan Hviid; Rubak, Tine Steen; Hansen, Åse Marie; Andersen, Lars L; Lund, Rikke; Osler, Merete; Christensen, Ulla; Avlund, Kirsten

    2012-01-01

    Background Physical function is essential for performing most aspects of daily life and musculoskeletal aging leads to a decline in physical function. The onset and rate of this process vary and are influenced by environmental, genetic, and hormonal factors. Although everyone eventually experiences musculoskeletal aging, it is beneficial to study the factors that influence the aging process in order to prevent disability. The role of occupational physical activity in the musculoskeletal aging process is unclear. In the past, hard physical work was thought to strengthen the worker, but current studies in this field fail to find a training effect in jobs with a high level of occupational physical activity. Objective The aim of this study is to examine the influence of lifetime occupational physical activity on physical function in midlife. The study follows the “occupational life-course perspective,” emphasizing the importance of occupational exposures accumulated throughout life on the musculoskeletal aging process taking socioeconomic and lifestyle factors into consideration. Methods This study is a retrospective cohort study including a cross-sectional measurement of physical function in 5000 middle-aged Danes. Data was obtained from the Copenhagen Aging and Midlife Biobank (CAMB) which is based on three existing Danish cohorts. Using questionnaire information about the five longest-held occupations, the job history was coded from the Danish version of the International Standard Classification of Occupations (D-ISCO 88) and a job exposure matrix containing information about occupational physical activity in Danish jobs was applied to the dataset. The primary outcomes are three tests of physical function: handgrip strength, balance, and chair rise. In the analyses, we will compare physical function in midlife according to accumulated exposure to high levels of occupational physical activity. Conclusions We have a unique opportunity to study the influence of

  2. Theoretical study on absorption and emission spectra of size-expanded Janus-type AT nucleobases and effect of base pairing.

    PubMed

    Liu, Hongxia; Song, Qixia; Liu, Jianhua; Li, Yan; Wang, Haijun

    2014-01-01

    Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we design benzo- and naphtha-expanded Janus AT base analogues, using DFT, TDDFT, and CIS methods to investigate the structural and optical properties of the Janus AT base analogues (termed as J-AT, xJ-AT, yyJ-AT, BF, xBF and yyBF), and also consider the effect of base pairing. The results show that the Janus AT base analogues can pair with T and A simultaneously to form stable H-bonded WC base pairs. The ground state structure of J-AT is similar to BF, the size expansion is 2.42Å for the x-Janus AT bases and 4.86Å for the yy-Janus AT bases. The excited state geometries of J-AT and BF change dramatically, while the other bases are similar to the ground state geometries. The lowest excited singlet transitions of the Janus AT base analogues are predicted to be of ππ(*) character and mainly dominated by the configuration HOMO-LUMO. The maximum absorption wavelengths of size expansion Janus AT base analogues are greatly red shifted compared with J-AT (or BF). BF, xBF and yyJ-AT have larger oscillator strengths than J-AT, xJ-AT and yyBF. The emission wavelengths of the Janus AT base analogues also exhibit red shifts from x-Janus AT bases to yy-Janus AT bases. However, the emission wavelengths of J-AT and BF change greatly, which are coincident with the structures observed in the excited state geometries. With regard to the WC base pairs, the B3LYP functional reveals that the lowest energy transitions of some base pairs are charge transfer excitation, while the other base pairs are local excitation. The CAM-B3LYP functional predicts that all the lowest transitions are localized on the Janus AT bases, and show good agreement with the results of the M062X functional. PMID:24368287

  3. Theoretical study on absorption and emission spectra of size-expanded Janus-type AT nucleobases and effect of base pairing

    NASA Astrophysics Data System (ADS)

    Liu, Hongxia; Song, Qixia; Liu, Jianhua; Li, Yan; Wang, Haijun

    2014-03-01

    Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we design benzo- and naphtha-expanded Janus AT base analogues, using DFT, TDDFT, and CIS methods to investigate the structural and optical properties of the Janus AT base analogues (termed as J-AT, xJ-AT, yyJ-AT, BF, xBF and yyBF), and also consider the effect of base pairing. The results show that the Janus AT base analogues can pair with T and A simultaneously to form stable H-bonded WC base pairs. The ground state structure of J-AT is similar to BF, the size expansion is 2.42 Å for the x-Janus AT bases and 4.86 Å for the yy-Janus AT bases. The excited state geometries of J-AT and BF change dramatically, while the other bases are similar to the ground state geometries. The lowest excited singlet transitions of the Janus AT base analogues are predicted to be of ππ* character and mainly dominated by the configuration HOMO-LUMO. The maximum absorption wavelengths of size expansion Janus AT base analogues are greatly red shifted compared with J-AT (or BF). BF, xBF and yyJ-AT have larger oscillator strengths than J-AT, xJ-AT and yyBF. The emission wavelengths of the Janus AT base analogues also exhibit red shifts from x-Janus AT bases to yy-Janus AT bases. However, the emission wavelengths of J-AT and BF change greatly, which are coincident with the structures observed in the excited state geometries. With regard to the WC base pairs, the B3LYP functional reveals that the lowest energy transitions of some base pairs are charge transfer excitation, while the other base pairs are local excitation. The CAM-B3LYP functional predicts that all the lowest transitions are localized on the Janus AT bases, and show good agreement with the results of the M062X functional.

  4. Tuning the push-pull configuration for efficient second-order nonlinear optical properties in some chalcone derivatives.

    PubMed

    Muhammad, Shabbir; Al-Sehemi, Abdullah G; Irfan, Ahmad; Chaudhry, Aijaz R

    2016-07-01

    Using the density functional theory methods, we effectively tune the second-order nonlinear optical (NLO) properties in some chalcone derivatives. Various unique push-pull configurations are used to efficiently enhance the intramolecular charge transfer process over the designed derivatives, which result in significantly larger amplitudes of the first hyperpolarizability as compared to their parent molecule. The ground state molecular geometries have been optimized using B3LYP/6-311G** level of theory. A variety of methods including B3LYP, CAM-B3LYP, PBE0, M06, BHandHLYP and MP2 are tested with 6-311G** basis set to calculate the first hyperpolarizability of parent system 1. The results of M06 are found closer to highly correlated MP2 method, which has been selected to calculate static and frequency dependent first hyperpolarizability amplitudes of all selected systems. At M06/6-311G** level of theory, the permanent electronic dipole moment (μtot), polarizability (α0) and static first hyperpolarizability (βtot) amplitudes for parent system 1 are found to be 5.139 Debye, 274a. u. and 24.22×10(-30)esu, respectively. These amplitudes have been significantly enhanced in designed derivatives 2 and 3. More importantly, the (βtot) amplitudes of systems 2 and 3 mount to 75.78×10(-30) and 128.51×10(-30)esu, respectively, which are about 3 times and 5 times larger than that of their parent system 1. Additionally, we have extended the structure-NLO property relationship to several newly synthesized chalcone derivatives. Interestingly, the amplitudes of dynamic frequency dependent hyperpolarizability μβω (SHG) are also significantly larger having values of 366.72×10(-48), 856.32×10(-48) and 1913.46×10(-48)esu for systems 1-3, respectively, at 1400nm of incident laser wavelength. The dispersion behavior over a wide range of change in wavelength has also been studied adopting a range of wavelength from 1907 to 544nm. Thus, the present work realizes the potential of

  5. 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.

  6. 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

  7. 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.

  8. 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)