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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. 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

  3. Unequivocal NMR assignments: O-methoxy-methyl esters derivatives of acid chromanones from Calophyllum brasiliense CAMB. (Guanandi).

    PubMed

    Caneppele, D; Vieira, P C; Dall'Oglio, E L; da Silva, L E; Sousa, P T

    2008-01-01

    The present work describes the fractionation of the crude hexane extract (EBHEX) from Calophyllum brasiliense (Clusiaceae) stem bark. Derivatization of DCM(2-9) fraction with diazomethane afforded the chromanones inophylloidic acid, isobrasiliensic acid, as well as, a mixture containing isobrasiliensic and brasiliensic acids, in the form of their more stable O-methoxy-methyl esters derivatives 1, 2, and 3, respectively. The isolation of 1 from C. brasiliense is described for the first time herein. The use of two-dimensional NMR methods ((1)H-COSY, HMQC, and HMBC) allowed the precise determination of (13)C and (1)H chemical shifts of compounds 1, 2, and 3. PMID:18626818

  4. MGCAMB: Modification of Growth with CAMB

    NASA Astrophysics Data System (ADS)

    Hojjati, A.; Zhao, G.-B.; Pogosian, L.; Silvestri, A.

    2011-06-01

    CAMB is a public Fortran 90 code written by Antony Lewis and Anthony Challinor for evaluating cosmological observables. MGCAMB is a modified version of CAMB in which the linearized Einstein equations of General Relativity (GR) are modified. MGCAMB can also be used in CosmoMC to fit different modified-gravity (MG) models to data.

  5. Colonization patterns of an mCherry-tagged Pectobacterium carotovorum subsp. brasiliense strain in potato plants.

    PubMed

    Kubheka, Gugulethu C; Coutinho, Teresa A; Moleleki, Ntsane; Moleleki, Lucy N

    2013-12-01

    Pectobacterium carotovorum subsp. brasiliense is a newly identified member of the potato soft rot enterobacteriaceae. The pathogenesis of this pathogen is still poorly understood. In this study, an mCherry-P. carotovorum subsp. brasiliense-tagged strain was generated to study P. carotovorum subsp. brasiliense-potato plant interactions. Prior to use, the tagged strain was evaluated for in vitro growth, plasmid stability, and virulence on potato tubers and shown to be similar to the wild type. Four potato cultivars were evaluated for stem-based resistance against P. carotovorum subsp. brasiliense. Confocal laser-scanning microscopy and in vitro viable cell counts showed that P. carotovorum subsp. brasiliense is able to penetrate roots of a susceptible potato cultivar as early as 12 h postinoculation and migrate upward into aerial stem parts. Due to the phenotypic differences observed between tolerant and susceptible cultivars, a comparison of P. carotovorum subsp. brasiliense colonization patterns in these cultivars was undertaken. In the susceptible cultivar, P. carotovorum subsp. brasiliense cells colonized the xylem tissue, forming "biofilm-like" aggregates that led to occlusion of some of the vessels. In contrast, in the tolerant cultivar, P. carotovorum subsp. brasiliense appeared as free-swimming planktonic cells with no specific tissue localization. This suggests that there are resistance mechanisms in the tolerant cultivar that limit aggregation of P. carotovorum subsp. brasiliense in planta and, hence, the lack of symptom development in this cultivar. PMID:23758294

  6. Draft Genome Sequence of a Virulent Pectobacterium carotovorum subsp. brasiliense Isolate Causing Soft Rot of Cucumber.

    PubMed

    Onkendi, Edward M; Ramesh, Aadi Moolam; Kwenda, Stanford; Naidoo, Sanushka; Moleleki, Lucy

    2016-01-01

    Pectobacterium carotovorum subsp. brasiliense causes soft rot and blackleg diseases on potatoes, ornamentals, and other crops of economic importance. Here, we report a draft genome sequence of a highly virulent P. carotovorum subsp. brasiliense strain, PcbHPI01, isolated from a cucumber in South Africa. PMID:26744374

  7. New Bergamotane Sesquiterpenoids from the Plant Endophytic Fungus Paraconiothyrium brasiliense.

    PubMed

    Guo, Zhe; Ren, Fengxia; Che, Yongsheng; Liu, Gang; Liu, Ling

    2015-01-01

    Brasilamides K-N (1-4), four new bergamotane sesquiterpenoids; with 4-oxatricyclo (3.3.1.0 (2,7))nonane (1)and 9-oxatricyclo(4.3.0.0 (4,7))nonane (2-4) skeletons; were isolated from the scale-up fermentation cultures of the plant endophytic fungus Paraconiothynium brasiliense Verkley. The previously identified sesquiterpenoids brasilamides A and C (5 and 6) were also reisolated in the current work. The structures of 1-4 were elucidated primarily by interpretation of NMR spectroscopic data. The absolute configurations of 1-3 were deduced by analogy to the co-isolated metabolites 5 and 6; whereas that of C-12 in 4 was assigned using the modified Mosher method. The cytotoxicity of all compounds against a panel of eight human tumor cell lines were assayed. PMID:26274948

  8. 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

  9. 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

  10. 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

  11. An antifungal gamma-pyrone and xanthones with monoamine oxidase inhibitory activity from Hypericum brasiliense.

    PubMed

    Rocha, L; Marston, A; Kaplan, M A; Stoeckli-Evans, H; Thull, U; Testa, B; Hostettmann, K

    1994-08-01

    A new gamma-pyrone (hyperbrasilone), three known xanthones (1,5-dihydroxyxanthone, 5-hydroxy-1-methoxyxanthone and 6-deoxyjacareubin) and betulinic acid have been isolated from a dichloromethane extract of stems and roots of Hypericum brasiliense. Their structures were established by spectroscopic methods (UV, EI-MS, 1H and 13C NMR) and that of the gamma-pyrone was confirmed by X-ray crystallography. Hyperbrasilone and the xanthones were all antifungal against Cladosporium cucumerinum, while the three xanthones showed differing degrees of inhibition of monoamine oxidase A and B. PMID:7765428

  12. Pharmacological and phytochemical investigations of different parts of Calophyllum brasiliense (Clusiaceae).

    PubMed

    Isaias, D E B; Niero, R; Noldin, V F; de Campos-Buzzi, F; Yunes, R A; Delle-Monache, F; Cechinel-Filho, V

    2004-11-01

    Continuing our search for antinociceptive agents from natural sources, this study analyzed the antinociceptive effects of some fractions obtained from different parts (roots, flowers and fruits) of Calophyllum brasiliense, a Brazilian medicinal plant used to treat several diseases, including inflammation and pain. For this purpose, the writhing and formalin induced-pain models in mice were used. We also analyzed the chemical composition of these different parts and tested two pure compounds isolated from chloroform fraction (roots) identified as friedelin (1) and 1,5-dihydroxyxanthone (3), by direct comparison with authentic samples. The results showed that some fractions and both compounds exhibited considerable antinociception properties, particularly against the writhing test, and that these are more potent than acetyl salicylic acid and acetaminophen, two reference drugs used here for comparison. PMID:15587592

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  16. 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

  17. 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. PMID:26177258

  18. 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

  19. 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

  20. 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.

  1. 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. PMID:19875147

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

    PubMed

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

    2016-05-01

    Calophyllum brasiliense (Calophyllaceae) is a tropical rain forest tree distributed in Central and South America. It is an important source of tetracyclic dipyrano coumarins (Soulatrolide) and Mammea type coumarins. Soulatrolide is a potent inhibitor of HIV-1 reverse transcriptase and displays activity against Mycobacterium tuberculosis. Meanwhile, Mammea A/BA and A/BB, pure or as a mixture, are highly active against several human leukemia cell lines, Trypanosoma cruzi and Leishmania amazonensis. Nevertheless, there are few studies evaluating their safety profile. In the present work we performed toxicogenomic and toxicological analysis for both type of compounds. Soulatrolide, and the Mammea A/BA + A/BB mixture (2.1) were slightly toxic accordingly to Lorke assay classification (DL50 > 3000 mg/kg). After a short-term administration (100 mg/kg/daily, orally, 1 week) liver toxicogenomic analysis revealed 46 up and 72 downregulated genes for Mammea coumarins, and 665 up and 1077 downregulated genes for Soulatrolide. Gene enrichment analysis identified transcripts involved in drug metabolism for both compounds. In addition, network analysis through protein-protein interactions, tissue evaluation by TUNEL assay, and histological examination revealed no tissue damage on liver, kidney and spleen after treatments. Our results indicate that both type of coumarins displayed a safety profile, supporting their use in further preclinical studies to determine its therapeutic potential. PMID:26995226

  3. 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

  4. 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

  5. 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

  6. 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...

  7. Chemical and agronomic development of Kalanchoe brasiliensis Camb. and Kalanchoe pinnata Pers under light and temperature levels.

    PubMed

    Cruz, Bruna P; Chedier, Luciana M; Fabri, Rodrigo L; Pimenta, Daniel S

    2011-12-01

    This study compares the development of Kalanchoe brasiliensis and Kalanchoe pinnata, which are medicinal species known as "saião" and "folha da fortuna" that are used interchangeably by the population for medicinal purposes. The experiment consisted of 20 plots/species planted in plastic bags with homogeneous substrate in a randomized design, which grown under light levels (25%, 50%, 70%, full sunlight) at environment temperature, and a treatment under a plastic with greater temperature range than the external environment. It was obtained for K. pinnata a greater plant height, total length of sprouts, stems, production and dry matter content of leaves than that obtained for K. brasiliensis, which achieved higher averages only for the length of lateral branches. The species showed increases in height, which varied in inverse proportion to the light, and it was observed the influence of temperature in K. pinnata. The production and dry matter content of leaves were proportional to the luminosity; the same occurred in the thickness of leaves for K. brasiliensis. In the swelling index and Brix degree, K. brasiliensis showed higher averages than K. pinnata. In relation to the total content of flavonoids it was not observed significant differences for both species. The analyzed parameters showed the main differences in the agronomic development of the two species. PMID:22146966

  8. [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

  9. 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

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

    PubMed

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

    2015-11-18

    Pequi is an oleaginous fruit whose edible oil is composed mainly by saturated and monounsaturated fatty acids. The biological and nutritional properties of pequi oil are dependent on its composition, which can change according to the oil source (pulp or kernel). There is little data in the scientific literature concerning the differences between the compositions of pequi kernel and pulp oils. Therefore, in this study, different pequi genotypes were evaluated to determine the fatty acid composition of pulp and kernel oils. PCA and PLS-DA were applied to develop a model to distinguish these oils. For all evaluated genotypes, the major fatty acids of both pulp and kernel oils were oleic and palmitic acids. Despite the apparent similarity between the analyzed samples, it was possible to discriminate pulp and kernel oils by means of their fatty acid composition using chemometrics, as well as the unique pequi genotype without endocarp spines (CPAC-PQ-SE-06). PMID:26506457

  11. 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.

  12. 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

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

    PubMed Central

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

    2015-01-01

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

  14. 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...

  15. 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.

  16. LRG DR7 Likelihood Software

    NASA Astrophysics Data System (ADS)

    Reid, Beth A.

    2013-06-01

    This software computes likelihoods for the Luminous Red Galaxies (LRG) data from the Sloan Digital Sky Survey (SDSS). It includes a patch to the existing CAMB software (the February 2009 release) to calculate the theoretical LRG halo power spectrum for various models. The code is written in Fortran 90 and has been tested with the Intel Fortran 90 and GFortran compilers.

  17. "Escola Familia": A Proposal

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  18. Computational methodology study of the optical and thermochemical properties of a molecular photoswitch.

    PubMed

    Olsen, Stine T; Elm, Jonas; Storm, Freja Eilsø; Gejl, Aske Nørskov; Hansen, Anne S; Hansen, Mia Harring; Nikolajsen, Jens Rix; Nielsen, Mogens Brøndsted; Kjaergaard, Henrik G; Mikkelsen, Kurt V

    2015-02-01

    We assess how the utilization of different DFT functionals for obtaining the equilibrium geometries and vibrational frequencies affect the description of the thermochemistry and subsequent calculation of the optical properties of a dihydroazulene-vinylheptafulvene photoswitch. The assessment covers nine popular DFT functionals (BLYP, B3LYP, CAM-B3LYP, M06-L, M06, M06-2X, PBE, PBE0, and ωB97X-D) in conjugation with five different Pople style basis sets (6-31+G(d), 6-31++G(d,p), 6-311+G(d), 6-311++G(d,p), and 6-311++G(3df,3pd)). It is identified that only CAM-B3LYP, M06-2X, and PBE0 are able to quantitatively describe the correct trends in the thermochemical properties. The subsequent calculation of the optical properties using the CAM-B3LYP functional shows that there is little difference in whether the CAM-B3LYP, M06-2X, or PBE0 functionals have been used to calculate the equilibrium geometries. Utilizing the identified functionals, we investigate how the number of electron withdrawing cyano substituents influence the thermochemistry and optical properties of the molecular photoswitch. PMID:25569127

  19. Angiotensin-converting enzyme inhibition by Brazilian plants.

    PubMed

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

    2007-07-01

    The potential antihypertensive activity of Brazilian plants was evaluated in vitro by its ability to inhibit the angiotensin-converting enzyme (ACE). Forty-four plants belonging to 30 families were investigated. Plants were selected based on their popular use as antihypertensive and/or diuretics. The following plants presented significant ACE inhibition rates: Calophyllum brasiliense, Combretum fruticosum, Leea rubra, Phoenix roebelinii and Terminalia catappa. PMID:17513067

  20. 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. PMID:18797754

  1. 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

  2. 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

  3. Mechanism of the cysteine sulfenic acid O-sulfenylation of 1,3-cyclohexanedione.

    PubMed

    Freeman, Fillmore

    2014-04-21

    The density functionals B3LYP, B3PW91, M062X, and CAM-B3LYP with the 6-311+G(d,p) basis set predict the cysteine sulfenic acid O-sulfenylation of the s-cis-ketoenol tautomer of 1,3-cyclohexanedione proceeds through a cyclic 14-membered transition state structure containing three water molecules. PMID:24619216

  4. 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.

  5. CMB power spectrum parameter degeneracies in the era of precision cosmology

    SciTech Connect

    Howlett, Cullan; Lewis, Antony; Hall, Alex; Challinor, Anthony E-mail: antony@cosmologist.info E-mail: adc1000@ast.cam.ac.uk

    2012-04-01

    Cosmological parameter constraints from the CMB power spectra alone suffer several well-known degeneracies. These degeneracies can be broken by numerical artefacts and also a variety of physical effects that become quantitatively important with high-accuracy data e.g. from the Planck satellite. We study degeneracies in models with flat and non-flat spatial sections, non-trivial dark energy and massive neutrinos, and investigate the importance of various physical degeneracy-breaking effects. We test the CAMB power spectrum code for numerical accuracy, and demonstrate that the numerical calculations are accurate enough for degeneracies to be broken mainly by true physical effects (the integrated Sachs-Wolfe effect, CMB lensing and geometrical and other effects through recombination) rather than numerical artefacts. We quantify the impact of CMB lensing on the power spectra, which inevitably provides degeneracy-breaking information even without using information in the non-Gaussianity. Finally we check the numerical accuracy of sample-based parameter constraints using CAMB and COSMOMC. In an appendix we document recent changes to CAMB's numerical treatment of massive neutrino perturbations, which are tested along with other recent improvements by our degeneracy exploration results.

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

    PubMed

    Krawczyk, Przemysław

    2010-04-01

    A theoretical analysis of the linear and nonlinear optical properties of six push-pull pi-conjugated molecules with stilbene, azobenzene and benzilideneaniline as a backbone is presented. The photophysical properties of the investigated systems were determined by using response functions combined with density functional theory (DFT). Several different exchange-correlation potentials were applied in order to determine parameters describing the one- and two-photon spectra of the studied molecules. In particular, the recently proposed Coulomb-attenuated model (CAM-B3LYP) was used to describe charge-transfer (CT) excited states. In order to compare theoretical predictions with available experimental data, calculations with inclusion of solvent effects were performed. The BLYP and the CAM-B3LYP functionals were found to yield values of two-photon absorption (TPA) probabilities closer to experimental values than the B3LYP functional or the HF wavefunction. Moreover, molecular static hyperpolarisabilities were determined using both DFT and second-order Møller-Plesset perturbation (MP2) theory. Likewise, the CAM-B3LYP functional was found to outperform other applied exchange-correlation potentials in determining first hyperpolarisability (beta). Moreover, it was confirmed on a purely theoretical basis that the presence of a -C=C- bridge between the phenyl rings leads to a much larger nonlinear optical response in comparison with a -N=N- bridge. PMID:19957196

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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

  13. Assessment of the efficiency of long-range corrected functionals for some properties of large compounds

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

    Using the long-range correction (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 a series of properties that are known to be poorly reproduced by standard functionals: Bond length alternation of π-conjugated polymers, polarizabilities of delocalized chains, and electronic spectra of extended dyes. For each of these properties, we present cases in which traditional hybrid functionals do provide accurate results and cases in which they fail to reproduce the correct trends. The quality of the results is assessed with regard to experimental values and/or data arising from electron-correlated wave function approaches. It turns out that (i) both LC-DFT and CAM-B3LYP provide an accurate bond length alternation for polyacetylene and polymethineimine, although for the latter they decrease slightly too rapidly with chain length. (ii) The LC generalized gradient approximation and MP2 polarizabilities of long polyphosphazene and polymethineimine oligomers agree almost perfectly. In the same way, CAM-B3LYP corrects the major part of the B3LYP faults. (iii) LC and CAM techniques do not help in correcting the nonrealistic evolution with chain length of the absorption wavelengths of cyanine derivatives. In addition, though both schemes significantly overestimate the ground to excited state transition energy of substituted anthraquinone dyes, they provide a more consistent picture once a statistical treatment is performed than do traditional hybrid functionals.

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

    NASA Astrophysics Data System (ADS)

    Piattella, O. F.; Casarini, L.; Fabris, J. C.; de Freitas Pacheco, J. A.

    2016-02-01

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

  15. Explicit calculation of the excited electronic states of the photosystem II reaction centre.

    PubMed

    Frankcombe, Terry J

    2015-02-01

    The excited states of sets of the cofactors found in the photosystem II reaction centre have been calculated directly as a multi-monomer supermolecule for the first time. Time-dependent density functional theory was used with the CAM-B3LYP functional. Multiple excited states for each cofactor were found at lower energies than the lowest energy state corresponding to charge transfer states (in which an electron is shifted from one cofactor to another). The electrostatic environment was found to have a dramatic impact on the excited state energies, with the effect of a surrounding dielectric medium being less significant. PMID:25523136

  16. POLYCHORD: nested sampling for cosmology

    NASA Astrophysics Data System (ADS)

    Handley, W. J.; Hobson, M. P.; Lasenby, A. N.

    2015-06-01

    POLYCHORD is a novel nested sampling algorithm tailored for high-dimensional parameter spaces. In addition, it can fully exploit a hierarchy of parameter speeds such as is found in COSMOMC and CAMB. It utilizes slice sampling at each iteration to sample within the hard likelihood constraint of nested sampling. It can identify and evolve separate modes of a posterior semi-independently and is parallelized using OPENMPI. POLYCHORD is available for download at http://ccpforge.cse.rl.ac.uk/gf/project/polychord/.

  17. Dynamically defined measures and equilibrium states

    NASA Astrophysics Data System (ADS)

    Werner, Ivan

    2011-12-01

    A technique of dynamically defined measures is developed and its relation to the theory of equilibrium states is shown. The technique uses Carathéodory's method and the outer measure introduced in a previous work by I. Werner [Math. Proc. Camb. Phil. Soc. 140(2), 333-347 (2006), 10.1017/S0305004105009072]. As an application, equilibrium states for contractive Markov systems [I. Werner, J. London Math. Soc. 71(1), 236-258 (2005), 10.1112/S0024610704006088] are obtained.

  18. Structure and absorption of Co(III) azo complex dyes based on pyrrolinone esters: DFT and TD DFT study

    NASA Astrophysics Data System (ADS)

    Luňák, Stanislav; Aysha, Tarek; Lyčka, Antonín; Machalický, Oldřich; Hrdina, Radim

    2014-07-01

    The relation between structure and absorption of three symmetrical 2:1 octahedral Co(III) azo complexes was studied. Quantum chemical calculations based on density functional theory (DFT) relate well with E-azo configuration of ligands with coordinated nitrogen atoms coming solely from phenolic residues. DFT calculations estimate the mer stereoisomer as remarkably preferred with respect to any fac arrangement. Time dependent DFT calculations using B3LYP and CAM-B3LYP functionals were successfully used to interpret the absorption spectra in a visible range.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  20. 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

  1. Azobenzene-functionalized cage silsesquioxanes as inorganic-organic hybrid, photoresponsive, nanoscale, building blocks.

    PubMed

    Liu, Yun; Yang, Wenyan; Liu, Hongzhi

    2015-03-16

    Mono- and octa-azobenzene-functionalized cage silsesquioxanes were easily synthesized by the reaction of 4-bromoazobenzene with monovinyl-substituted octasilsesquioxane and cubic octavinylsilsesquioxane through the Heck coupling reaction. Excited-state energies obtained from time-dependent density functional theory (TDDFT) and the CAM-B3LYP functional correlate very well with experimental trans-cis photoisomerization results from UV/Vis spectroscopy. These azobenzene-functionalized cages exhibit good thermal stability and are fluorescent with maximum emission at approximately 400 nm, making them potential materials for blue-light emission. PMID:25663005

  2. 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.

  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. 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. PMID:24437874

  5. π-Delocalization and the vibrational spectroscopy of conjugated materials: computational insights on Raman frequency dispersion in thiophene, furan, and pyrrole oligomers.

    PubMed

    Donohoo-Vallett, Paul J; Bragg, Arthur E

    2015-02-26

    The symmetric C═C stretching frequency (ν(Я)) of conjugated polymers and oligomers is a sensitive spectroscopic reporter of molecular structure and material morphologies; however, thorough understanding of how structure affects this frequency is lacking because computational investigations of this relationship have been undertaken with limited approaches. We present a comprehensive computational investigation of the structure-dependent Raman spectroscopy of oligothiophenes, oligofurans, and oligopyrroles in their ground electronic states using density functional theory. We assessed how various functionals (BLYP, B3LYP, BHLYP, and CAM-B3LYP) impact predictions of length-dependent trends in ν(Я). The amount of Hartree-Fock exchange in a functional is critical for accurately treating π-delocalization and polarizability and hence the structure-dependent Raman behavior. BLYP and B3LYP fail to accurately predict trends in ν(Я) with oligomer length because they over-represent delocalization; in contrast, the range-corrected CAM-B3LYP functional produces the same trends observed experimentally for oligomers in solution and in the solid phase. Through comparisons with a simple mechanical model, we demonstrate that the length- and conformation-dependent spectroscopy of oligothiophenes results from a delicate balance between delocalization-induced softening of ν(Я) and the coupling of oscillators that increase ν(Я). These findings are used to address how variations in inter- and intramolecular order impact the Raman spectroscopy of polythiophenes. PMID:25625486

  6. 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

  7. 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.

  8. Fast cosmological parameter estimation using neural networks

    NASA Astrophysics Data System (ADS)

    Auld, T.; Bridges, M.; Hobson, M. P.; Gull, S. F.

    2007-03-01

    We present a method for accelerating the calculation of cosmic microwave background (CMB) power spectra, matter power spectra and likelihood functions for use in cosmological parameter estimation. The algorithm, called COSMONET, is based on training a multilayer perceptron neural network and shares all the advantages of the recently released PICO algorithm of Fendt & Wandelt, but has several additional benefits in terms of simplicity, computational speed, memory requirements and ease of training. We demonstrate the capabilities of COSMONET by computing CMB power spectra over a box in the parameter space of flat Λ cold dark matter (ΛCDM) models containing the 3σ WMAP1-year confidence region. We also use COSMONET to compute the WMAP3-year (WMAP3) likelihood for flat ΛCDM models and show that marginalized posteriors on parameters derived are very similar to those obtained using CAMB and the WMAP3 code. We find that the average error in the power spectra is typically 2-3 per cent of cosmic variance, and that COSMONET is ~7 × 104 faster than CAMB (for flat models) and ~6 × 106 times faster than the official WMAP3 likelihood code. COSMONET and an interface to COSMOMC are publically available at http://www.mrao.cam.ac.uk/software/cosmonet.

  9. 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. PMID:23605138

  10. 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

  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. 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

  13. 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.

  14. 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

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

    PubMed

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

    2014-06-14

    Ab initio calculations and molecular dynamic simulation were employed to study the interaction of molecular hydrogen with the borazine-melamine polymer (BMP) in order to explore its potential for hydrogen storage applications. The calculations were performed using the long range corrected version of density functional theory, the Coulomb-attenuating method (CAM-B3LYP) and the second order Møller-Plesset perturbation theory (MP2). The results showed that the average adsorption energy per hydrogen is about -0.7 and -0.3 kcal mol(-1) at the MP2/6-311+G(d,p) and CAMB3LYP/6-311+G(d,p) levels of theory, respectively. The adsorption energies were corrected for the basis set superposition error (BSSE) by the counterpoise method. It was found that the hydrogen storage capacity of the BMP is about 6.49 wt%, which is close to the values reported for the other selected materials for the hydrogen storage in the literature. The maximum number of hydrogen molecules, which were adsorbed by the BMP building block, is about ten. Molecular dynamic simulation was performed to assess the potential of BMP for hydrogen storage. PMID:24736673

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Wu, Feng-Quan; Qiang, Li-E.; Wang, Xin; Chen, Xuelei

    2010-10-01

    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).

  18. Evaluation of the nonlinear optical properties for an expanded porphyrin Hückel-Möbius aromaticity switch

    NASA Astrophysics Data System (ADS)

    Torrent-Sucarrat, Miquel; Anglada, Josep M.; Luis, Josep M.

    2012-11-01

    The conformational flexibility of the expanded porphyrins allows them to achieve different topologies with distinct aromaticities and nonlinear optical properties (NLOP). For instance, it is possible to switch between Möbius and Hückel topologies applying only small changes in the external conditions or in the structure of the ring. In this work, we evaluate the electronic and vibrational contributions to static and dynamic NLOP of the Hückel and Möbius conformers of A,D-di-p-benzi[28]hexaphyrin(1.1.1.1.1.1) synthesized by Latos-Grażyński and co-workers [Angew. Chem., Int. Ed. 46, 7869 (2007), 10.1002/anie.200700555]. Calculations are performed at the HF, M052X, and CAM-B3LYP levels using the 6-31G, 6-311G(d), and 6-31+G(d) basis sets. Our results conclude that M052X/6-31G and CAM-B3LYP/6-31G methods provide a correct qualitative description of the electronic and vibrational contributions for the NLOP of expanded porphyrins. The studied systems show high NLOP with large differences between the Möbius and Hückel conformations (around 1 × 106 a.u. for bar γ). The obtained results indicate that the expanded porphyrins are promising systems to manufacture Hückel-to-Möbius topological switches.

  19. 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

  20. 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

  1. 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

  2. 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. PMID:25166327

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

    PubMed

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

    2009-07-01

    Information about predation risks is critical for herbivorous insects, and natural selection favors their ability to detect predators before oviposition and to select enemy-free foliage when offspring mortality risk is high. Food plants are selected by ovipositing butterflies, and offspring survival frequently varies among plants because of variation in the presence of predators. Eunica bechina butterflies oviposit on Caryocar brasiliense, an ant-defended plant. Experiments with dried Camponotus and Cephalotes ants pinned to leaves revealed that butterflies use ant size and form as visual cues to avoid ovipositing on plant parts occupied by ants more likely to kill larval offspring. Presence of sap-sucking bugs did not affect butterfly oviposition. This is the first demonstration that visual recognition of predators can mediate egg-laying decisions by an insect herbivore and that an insect will discriminate among different species of potential predators. This unusual behavioral capability permits specialization on a risky, ant-defended food plant. PMID:19456265

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. POLYCHORD: next-generation nested sampling

    NASA Astrophysics Data System (ADS)

    Handley, W. J.; Hobson, M. P.; Lasenby, A. N.

    2015-11-01

    POLYCHORD is a novel nested sampling algorithm tailored for high-dimensional parameter spaces. This paper coincides with the release of POLYCHORD v1.6, and provides an extensive account of the algorithm. POLYCHORD utilizes slice sampling at each iteration to sample within the hard likelihood constraint of nested sampling. It can identify and evolve separate modes of a posterior semi-independently, and is parallelized using OPENMPI. It is capable of exploiting a hierarchy of parameter speeds such as those present in COSMOMC and CAMB, and is now in use in the COSMOCHORD and MODECHORD codes. POLYCHORD is available for download from http://ccpforge.cse.rl.ac.uk/gf/project/polychord/.

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

    DOEpatents

    Lu, Yi; Xiang, Yu

    2015-01-13

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

  10. Experimental and DFT studies on the vibrational and electronic spectra of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Zhang, Fang; Ma, Kuirong; Tang, Guodong

    2013-03-01

    Vibrational and electronic spectral measurements were made for 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ). Optimized geometrical structure and harmonic vibrational frequencies were computed by DFT(B3LYP, CAMB3LYP, B3P86, M062X, mPW3PBE and PBE1PBE) using 6-311++G(d,p) basis set. Complete assignments of the observed spectra were proposed. The absorption spectra of the compound were computed both in gas-phase and in CH2Cl2 solution using TDCAMB3LYP/6-311++G(d,p) and PCM-TDCAMB3LYP/6-311++G(d,p) approaches, respectively, the calculated results provide a good description of positions of the bands maxima in the observed electronic spectrum.

  11. 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

  12. Prediction of ROA and ECD Related to Conformational Changes of Astaxanthin Enantiomers.

    PubMed

    Zajac, Grzegorz; Kaczor, Agnieszka; Buda, Szymon; Młynarski, Jacek; Frelek, Jadwiga; Dobrowolski, Jan Cz; Baranska, Małgorzata

    2015-09-17

    ECD, ROA, and VCD were used to characterize astaxanthin conformers that differ in their arrangements of the β-ionone ring in respect to the chain. We obtained ECD spectra experimentally, and the ECD, ROA, and VCD spectra of both individual conformers and conformation-averaged mixtures were predicted using quantum-chemical calculations at the CAM-B3LYP level of theory using the PCM solvation model. The chiroptical methods employed (particularly ECD and ROA) were considerably more sensitive to conformational changes of astaxanthin compared to "mono-signed" conventional Raman spectroscopy. Strikingly, conformers that are the same optical isomers (e.g., of 3S,3'S-astxanthin), while geometrically nearly mirror images, exhibited sign-inversed ECD and ROA spectra. The conformational sensitivity of these chiroptical methods makes them a promising tool in the study of carotenoids in the natural environment (for instance, in de novo algal or yeast astaxanthin sources). PMID:26305416

  13. 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.

  14. B-mode polarization in Einstein-aether theory

    SciTech Connect

    Nakashima, Masahiro; Kobayashi, Tsutomu

    2011-10-15

    We study how the dynamical vector degree of freedom in modified gravity affects the CMB B-mode polarization in terms of the Einstein-aether theory. In this theory, vector perturbations can be generated from inflation, which can grow on superhorizon scales in the subsequent epochs and thereby leaves imprints on the CMB B-mode polarization. We derive the linear perturbation equations in a covariant formalism, and compute the CMB B-mode polarization using the CAMB code modified so as to incorporate the effect of the aether vector field. We find that the amplitude of the B-mode signal from the aether field can be larger than the contribution from the inflationary gravitational waves for reasonable initial conditions and for a viable range of model parameters, in which perturbation modes propagate superluminally. We also give an analytic argument explaining the shape of the spectrum based on the tight coupling approximation.

  15. CosmoSIS: Modular cosmological parameter estimation

    DOE PAGESBeta

    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

  16. Critical assessment of density functional theory for computing vibrational (hyper)polarizabilities

    NASA Astrophysics Data System (ADS)

    Zaleśny, R.; Bulik, I. W.; Mikołajczyk, M.; Bartkowiak, W.; Luis, J. M.; Kirtman, B.; Avramopoulos, A.; Papadopoulos, M. G.

    2012-12-01

    Despite undisputed success of the density functional theory (DFT) in various branches of chemistry and physics, an application of the DFT for reliable predictions of nonlinear optical properties of molecules has been questioned a decade ago. As it was shown by Champagne, et al. [1, 2, 3] most conventional DFT schemes were unable to qualitatively predict the response of conjugated oligomers to a static electric field. Long-range corrected (LRC) functionals, like LC-BLYP or CAM-B3LYP, have been proposed to alleviate this deficiency. The reliability of LRC functionals for evaluating molecular (hyper)polarizabilities is studied for various groups of organic systems, with a special focus on vibrational corrections to the electric properties.

  17. FalconIC: Initial conditions generator for cosmological N-body simulations in Newtonian, Relativistic and Modified theories

    NASA Astrophysics Data System (ADS)

    Valkenburg, Wessel; Hu, Bin

    2015-09-01

    FalconIC generates discrete particle positions, velocities, masses and pressures based on linear Boltzmann solutions that are computed by libraries such as CLASS and CAMB. FalconIC generates these initial conditions for any species included in the selection, including Baryons, Cold Dark Matter and Dark Energy fluids. Any species can be set in Eulerian (on a fixed grid) or Lagrangian (particle motion) representation, depending on the gauge and reality chosen. That is, for relativistic initial conditions in the synchronous comoving gauge, Dark Matter can only be described in an Eulerian representation. For all other choices (Relativistic in Longitudinal gauge, Newtonian with relativistic expansion rates, Newtonian without any notion of radiation), all species can be treated in all representations. The code also computes spectra. FalconIC is useful for comparative studies on initial conditions.

  18. 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.

  19. DFT investigation of endohedral boron oxide nanocapsules: Encapsulation of He, Ne, Ar, H, N, and Cl atoms

    NASA Astrophysics Data System (ADS)

    Dabbagh, Hossein A.; Zamani, Mehdi; Farrokhpour, Hossein

    2012-01-01

    The electronic structure and stabilization energy of spherical and pyramidal shapes of boron oxide nanocapsules (X@B 20O 30, X = He, Ne, Ar, H, N, Cl) were investigated by long-range and dispersion corrected density functional theory (DFT + Disp) including CAM-B3LYP, B3LYP-D3, ωB97X-D and B2PLYP-D methods. Based on these calculations, the formation of nanocapsules is an exothermic process (except for Cl@B 20O 30). The spherical boron oxide nanocapsules are mainly stabilized by dispersion, while the stability of pyramidal complexes is mainly due to monomer relaxation energy. The theoretical results obtained in this work show that the boron oxide capsule is a good potential candidate for gas storage.

  20. 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.

  1. 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.

  2. 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

  3. Computational engineering of low bandgap copolymers

    PubMed Central

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

    2013-01-01

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

  4. 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}.

  5. Switchable nonlinear optical properties of η5-monocyclopentadienylmetal complexes: a DFT approach.

    PubMed

    Mendes, Paulo J; Silva, Tiago J L; Garcia, M Helena; Ramalho, J P Prates; Carvalho, A J Palace

    2012-08-27

    Density functional theory (DFT) calculations have been carried out to investigate the switching of the second-order nonlinear optical (NLO) properties of η(5)-monocyclopentadienyliron(II) and ruthenium(II) model complexes presenting 5-(3-(thiophen-2-yl)benzo[c]thiophen-1-yl)thiophene-2-carbonitrile as a ligand. The switching properties were induced by redox means. Both oxidation and reduction stimulus have been considered, and calculations have been performed both for the complexes and for the free benzo[c]thiophene derivative ligand in order to elucidate the role played by the organometallic fragment on the second-order NLO properties of these complexes. B3LYP, CAM-B3LYP, and M06 functionals were used for our calculations. The results show some important structural changes upon oxidation/reduction that are accompanied by significant differences on the corresponding second-order NLO properties. TD-DFT calculations show that these differences on the second-order NLO response upon oxidation/reduction are due to a change in the charge transfer pattern, in which the organometallic iron and ruthenium moieties play an important role. The calculated static hyperpolarizabilities were found to be strongly functional dependent. CAM-B3LYP, however, seems to predict more reliable structural and optical data as well as hyperpolarizabilities when compared to experimental data. The use of this functional predicts that the studied complexes can be viewed as acting as redox second-order NLO switches, in particular using oxidation stimulus. The β(tot) value of one-electron oxidized species is at least ~8.3 times (for Ru complex) and ~5.5 times (for Fe complex) as large as that of its nonoxidized counterparts. PMID:22830563

  6. 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.

  7. 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

  8. Density functional theory based generalized effective fragment potential method.

    PubMed

    Nguyen, Kiet A; Pachter, Ruth; 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. PMID:24985612

  9. 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

  10. 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

  11. Dietary carotenoid-rich pequi oil reduces plasma lipid peroxidation and DNA damage in runners and evidence for an association with MnSOD genetic variant -Val9Ala.

    PubMed

    Miranda-Vilela, A L; Akimoto, A K; Alves, P C Z; Pereira, L C S; Gonçalves, C A; Klautau-Guimarães, M N; Grisolia, C K

    2009-01-01

    Physical training induces beneficial adaptations; however, exhausting exercise increases reactive oxygen species generation, resulting in damage to DNA and tissues. Pequi (Caryocar brasiliense), a fruit of the Brazilian Cerrado, contains a carotenoid-rich oil. We investigated whether pequi oil had antioxidant effects in runners. Evaluations were made after outdoor races before and after ingestion of 400 mg pequi-oil capsules for 14 days. Blood samples were taken after races and submitted to comet and TBARS assays and biochemical analyses of creatine kinase (CK), aspartate aminotransferase (AST) and alanine aminotransferase (ALT). To determine if the protective effects of pequi-oil were influenced by antioxidant enzyme genotypes, MnSOD (-Val9Ala), CAT (-21A/T) and GPX1 (Pro198Leu) gene polymorphisms were also investigated. Pequi oil was efficient in reducing tissue injuries evaluated for AST and ALT, particularly in women, and in reducing DNA damages in both sexes. Except for CK levels, the results were influenced by MnSOD genotypes; heterozygous excess was related to less DNA damage, tissue injury and lipid peroxidation, besides presenting a better response to pequi oil against exercise-induced damage. PMID:20082261

  12. Naturally occurring compounds affect glutamatergic neurotransmission in rat brain.

    PubMed

    Martini, Lucia Helena; Jung, Fernanda; Soares, Felix Antunes; Rotta, Liane Nanci; Vendite, Deusa Aparecida; Frizzo, Marcos Emilio dos Santos; Yunes, Rosendo A; Calixto, João Batista; Wofchuk, Susana; Souza, Diogo O

    2007-11-01

    Natural products, including those derived from plants, have largely contributed to the development of therapeutic drugs. Glutamate is the main excitatory neurotransmitter in the central nervous system and it is also considered a nociceptive neurotransmitter, by acting on peripheral nervous system. For this reason, in this study we investigated the effects of the hydroalcoholic extracts from Drymis winteri (polygodial and drimanial), Phyllanthus (rutin and quercetine), Jathopha elliptica (jatrophone), Hedyosmum brasiliense (13HDS), Ocotea suaveolens (Tormentic acid), Protium kleinii (alphabeta-amyrin), Citrus paradise (naringin), soybean (genistein) and Crataeva nurvala (lupeol), described as having antinociceptive effects, on glutamatergic transmission parameters, such as [(3)H]glutamate binding, [(3)H]glutamate uptake by synaptic vesicles and astrocyte cultures, and synaptosomal [(3)H]glutamate release. All the glutamatergic parameters were affected by one or more of these compounds. Specifically, drimanial and polygodial presented more broad and profound effects, requiring more investigation on their mechanisms. The putative central side effects of these compounds, via the glutamatergic system, are discussed. PMID:17577666

  13. 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

  14. The bacterial signal transduction protein GlnB regulates the committed step in fatty acid biosynthesis by acting as a dissociable regulatory subunit of acetyl-CoA carboxylase.

    PubMed

    Gerhardt, Edileusa C M; Rodrigues, Thiago E; Müller-Santos, Marcelo; Pedrosa, Fabio O; Souza, Emanuel M; Forchhammer, Karl; Huergo, Luciano F

    2015-03-01

    Biosynthesis of fatty acids is one of the most fundamental biochemical pathways in nature. In bacteria and plant chloroplasts, the committed and rate-limiting step in fatty acid biosynthesis is catalyzed by a multi-subunit form of the acetyl-CoA carboxylase enzyme (ACC). This enzyme carboxylates acetyl-CoA to produce malonyl-CoA, which in turn acts as the building block for fatty acid elongation. In Escherichia coli, ACC is comprised of three functional modules: the biotin carboxylase (BC), the biotin carboxyl carrier protein (BCCP) and the carboxyl transferase (CT). Previous data showed that both bacterial and plant BCCP interact with signal transduction proteins belonging to the PII family. Here we show that the GlnB paralogues of the PII proteins from E. coli and Azospirillum brasiliense, but not the GlnK paralogues, can specifically form a ternary complex with the BC-BCCP components of ACC. This interaction results in ACC inhibition by decreasing the enzyme turnover number. Both the BC-BCCP-GlnB interaction and ACC inhibition were relieved by 2-oxoglutarate and by GlnB uridylylation. We propose that the GlnB protein acts as a 2-oxoglutarate-sensitive dissociable regulatory subunit of ACC in Bacteria. PMID:25557370

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

    PubMed Central

    Cohn, E.; Sher, S. A.

    1972-01-01

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

  16. 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

  17. Taxonomic key to nymphs of the genus Amblyomma (Acari: Ixodidae) in Argentina, with description and redescription of the nymphal stage of four Amblyomma species.

    PubMed

    Martins, Thiago F; Labruna, Marcelo B; Mangold, Atilio J; Cafrune, M Mercedes; Guglielmone, Alberto A; Nava, Santiago

    2014-10-01

    In the present study, we provide morphological descriptions of the nymph of Amblyomma parvitarsum, A. tonelliae, and redescriptions of A. argentinae and A. sculptum. A taxonomic key, with relevant morphological characters illustrated by scanning electron micrographs, is provided for nymphs of the 24 species of the genus Amblyomma occurring in Argentina. Species included are A. argentinae, A. aureolatum, A. auricularium, A. boeroi, A. brasiliense, A. calcaratum, A. coelebs, A. dissimile, A. dubitatum, A. incisum, A. longirostre, A. neumanni, A. nodosum, A. ovale, A. parvitarsum, A. parvum, A. pseudoconcolor, A. pseudoparvum, A. rotundatum, A. sculptum, A. tigrinum, A. tonelliae, A. triste and A. varium. Principal morphological characters used for discrimination among species are presence/absence of auriculae, cornua and festoons with tubercles, size and shape of spurs of coxa I, margin and punctations of scutum, shape of basis capituli and length of cervical grooves. The geographical distribution of each tick species included in this work is presented and the importance of an accurate determination to species level of the Amblyomma nymphs to make epidemiological inferences is also discussed. PMID:25113984

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

    PubMed

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

    2010-06-01

    Together with the larval stage, the nymphal stage of ticks of the genus Amblyomma are the most aggressive ticks for humans entering areas inhabited by wildlife and some domestic animals in Brazil. However, due to the absence of morphological descriptions of the nymphal stage of most Brazilian Amblyomma species, plus the lack of an identification key, little or nothing is known about the life history of Amblyomma spp. nymphs in the country. In the present study, morphological description of the nymphal stage, illustrating important external characters through scanning electron microscopy, is provided for nymphs of 15 Amblyomma species that occur in Brazil, for which the nymphal stage had never been described: A. aureolatum, A. auricularium, A. calcaratum, A. coelebs, A. fuscum, A. humerale, A. incisum, A. latepunctatum, A. naponense, A. nodosum, A. ovale, A. pacae, A. pseudoconcolor, A. scalpturatum, A. varium. In addition, the nymphal stage of 12 Amblyomma species, which had been previously described, are redescribed: A. brasiliense, A. cajennense, A. dissimile, A. dubitatum, A. longirostre, A. oblongoguttatum, A. parkeri, A. parvum, A. romitii, A. rotundatum, A. tigrinum, A. triste. The descriptions and redescriptions totalized 27 species. Only 2 species (A. geayi, A. goeldii) out of the 29 Amblyomma species established in Brazil are not included in the present study. A dichotomous identification key is included to support taxonomic identification of the nymphal stage of 27 Amblyomma species established in Brazil. PMID:21771514

  19. 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

  20. 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

  1. 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

  2. From protest to programs: neighborhood associations in a Brazilian municipality.

    PubMed

    Ferguson, B W

    1992-01-01

    The examples of community participation and organization in Brazil reflect the benefits to health and education programs and land entitlement. The community and government were working together toward self-improvement. An alliance was formed between neighborhood groups and a reform mayor. The result was an end to clientelism, stronger community organization, and local participation in designing and implementing development programs. The neighborhood groups were located in Cambe, which is a region located within the metropolitan area of Londrina, the 3rd largest city in southern Brazil. Mechanization of agriculture and extensive cattle ranching had caused migration into the area. Population increased 60% during the 1980s. The poorest neighborhoods were Jardim Tupy, Santo Amaro, and Novo Bandeirantes. Jardim Tupy was the poorest, and in 1980 a neighborhood association was formed to demand infrastructure and public services. The clientelism mayor and national government refused aid. When the association sued over a motor vehicle accident involving farm workers living in the community and won, there was momentum to change city hall. Support was given to the reform mayor who won and agreed to community demands for a community garden. The garden became a model for 14 others in Cambe and led to a strong neighborhood association which learned the strength of unity. The mayor rewarded good neighborhood organization with increases in public goods and services. The Catholic Church became involved in Jardim Tupy with a Pastoral of the Child program to reduce infant and child mortality rates. Health improvements in the community are attributed to the neighborhood association, the Pastoral of the Child, the local Catholic parish, and a thaw in the relationship with local government. The residents learned the limits of local government and the lessons of self-help. Santo Amaro, while not as well organized as Jardim Tupy, was successful at overcoming the lack of resources. novo

  3. 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

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

    PubMed

    Muhammad, Shabbir

    2015-06-01

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

  5. 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

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

    PubMed

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

    2014-02-11

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

  7. 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

  8. [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

  9. Photodetachment spectroscopy of fluorenone radical anions microsolvated with methanol: rationalizing the anomalous solvatochromic behavior due to hydrogen bonding.

    PubMed

    Maeyama, Toshihiko; Yagi, Izumi; Yoshida, Keiji; Fujii, Asuka; Mikami, Naohiko

    2015-04-23

    The attribution of the extraordinary blue shift for the intramolecular charge-transfer absorption band of fluorenone radical anion solvated in protic media was investigated by means of photodetachment spectroscopy of the gas-phase anions microsolvated with methanol, in conjunction with quantum chemical calculations based on density functional theory. Sequential shifts of the vertical detachment energy as a function of the cluster size are consistent with theoretical predictions, where up to two methanol molecules can directly attach to the carbonyl group. In the photodetachment excitation spectra as alternatives to the photoabsorption spectra, with increasing cluster size, a new absorption band grows in the higher-energy region, which coincides with the blue-shifted band in protic media. Spectral simulations using time-dependent density functional theory with the CAM-B3LYP functional reproduced the feature of the phenomenon. Analyses on the electronic configuration elucidated that the extraordinarily blue shifts originate from energy-level repulsion due to solvation-induced resonant coupling with another electronic state. The orbital transition for the counterpart state corresponds to the first absorption band of the neutral fluorenone molecule, which has small oscillator strength from the ground state. It was found that correction of long-range electron exchange correlation is important for the spectral simulation involving the electronic-state coupling. PMID:25825951

  10. 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

  11. 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

  12. Evolution Under Environmental Stress at Macro- and Microscales

    PubMed Central

    Nevo, Eviatar

    2011-01-01

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

  13. 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)].

  14. Origin-independent two-photon circular dichroism calculations in coupled cluster theory.

    PubMed

    Friese, Daniel H; Hättig, Christof; Rizzo, Antonio

    2016-05-21

    We present the first origin-independent approach for the treatment of two-photon circular dichroism (TPCD) using coupled cluster methods. The approach is assessed concerning its behavior on the choice of the basis set and different coupled cluster methods. We also provide a comparison of results from CC2 with those from density functional theory using the CAM-B3LYP functional. Concerning the basis set we note that in most cases an augmented triple zeta basis or a doubly augmented double zeta basis is needed for reasonably converged results. In the comparison of different coupled cluster methods results from CCSD, CC3 and CC2 have been found to be quite similar in most cases, while CCS results differ remarkably from the results at the higher levels. However, this proof-of-principle study also shows that further benchmarking of DFT and CC2 against accurate coupled cluster reference values (e.g. CCSD or CC3) is needed. PMID:27140590

  15. 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.

  16. 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

  17. Fullerene C70 characterization by 13C NMR and the importance of the solvent and dynamics in spectral simulations.

    PubMed

    Kaminský, Jakub; Buděšínský, Miloš; Taubert, Stefan; Bouř, Petr; Straka, Michal

    2013-06-21

    The nuclear magnetic resonance (NMR) spectroscopy combined with theoretical calculations is an important tool for fullerene identification. However, the accuracy of available theoretical methods is often not adequate. Therefore, in this work, different computational aspects needed to simulate realistically chemical shifts in the C70 molecule are investigated by density functional theory (DFT) calculations. The importance of the functional choice, basis set, solvent, and molecular motions was assessed. The solvent was simulated using the implicit conductor-like polarized continuum model. The molecular motions were included via anharmonic corrections and averaging of snapshots obtained from classical and first-principles molecular dynamics (MD) simulations. Comparison to experiment revealed that density functional calculations typically overestimate the (13)C NMR chemical shifts. Hybrid functionals, such as BHandH and BHandHLYP, and long-range corrected functionals, such as wB97xd and CAM-B3LYP, give the best results. While the solvent has a minor effect (chemical shift changes by ~1 ppm), the vibrational and dynamical effects are surprisingly large, causing changes up to 9 ppm. Consideration of the latter was also necessary to explain the observed temperature dependence. While the dynamical corrections for MD performed in vacuum were overestimated, inclusion of the solvent in simulations provided more realistic results. The study thus points out the importance of an appropriate solvent model and a complex approach to the modelling, balancing the static, dynamic and environmental factors. PMID:23653057

  18. 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.

  19. 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

  20. 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.

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

    PubMed

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

    2016-02-24

    A systematic computational investigation on the optical properties of a group of novel benzofulvene derivatives (Martinelli 2014 Org. Lett. 16 3424-7), proposed as possible donor materials in small molecule organic photovoltaic (smOPV) devices, is presented. A benchmark evaluation against experimental results on the accuracy of different exchange and correlation functionals and semi-empirical methods in predicting both reliable ground state equilibrium geometries and electronic absorption spectra is carried out. The benchmark of the geometry optimization level indicated that the best agreement with x-ray data is achieved by using the B3LYP functional. Concerning the optical gap prediction, we found that, among the employed functionals, MPW1K provides the most accurate excitation energies over the entire set of benzofulvenes. Similarly reliable results were also obtained for range-separated hybrid functionals (CAM-B3LYP and wB97XD) and for global hybrid methods incorporating a large amount of non-local exchange (M06-2X and M06-HF). Density functional theory (DFT) hybrids with a moderate (about 20-30%) extent of Hartree-Fock exchange (HFexc) (PBE0, B3LYP and M06) were also found to deliver HOMO-LUMO energy gaps which compare well with the experimental absorption maxima, thus representing a valuable alternative for a prompt and predictive estimation of the optical gap. The possibility of using completely semi-empirical approaches (AM1/ZINDO) is also discussed. PMID:26808717

  2. TDDFT studies on the electronic structures and chiroptical properties of mono-tin-substituted Wells-Dawson polyoxotungstates.

    PubMed

    Sang, Yuan-Mei; Yan, Li-Kai; Wang, Jian-Ping; Su, Zhong-Min

    2012-04-26

    The UV/CD spectra of tin-bearing acetonyl-substituted Wells-Dawson polyoxotungstates α(1)- and α(2)-[P(2)W(17)O(61){SnCH(2)CH(2)C(═O)}](6-) were systematically investigated using the time-dependent density functional theory (TDDFT) method. The electronic circular dichroism (ECD) spectra were produced over the range of 3.3-5.8 eV. The calculated ECD spectra of the α(1)-R isomer were generally in agreement with the experimental spectra. The CAM-B3LYP hybrid functional was found to predict the excitation energies of tin-containing polyoxotungstates well. The fact that the UV/ECD spectra of α(1)-isomers are different from those of α(2)-isomers demonstrates the effect of the tin substitution site on the chiroptical properties of the studied isomers. The origins of the ECD bands are mainly ascribed to charge-transfer (CT) transitions from oxygen atoms to W atoms, from organic fragments to W atoms, or from the combination of two CT transitions. The results suggest that the organic fragment and polyoxometalate (POM) cage are chiroptical chromophores. PMID:22443144

  3. Theoretical assessment of the electro-optical features of the group III nitrides (B12N12, Al12N12 and Ga12N12) and group IV carbides (C24, Si12C12 and Ge12C12) nanoclusters encapsulated with alkali metals (Li, Na and K)

    NASA Astrophysics Data System (ADS)

    Tahmasebi, Elham; Shakerzadeh, Ehsan; Biglari, Zeinab

    2016-02-01

    Density functional theory (DFT) calculations have been carried out to study the influence of alkali metals (Li, Na and K) encapsulation within the group III nitrides (B12N12, Al12N12 and Ga12N12) and the group IV carbides (C24, Si12C12and Ge12C12) nanoclusters. The encapsulation of Li, Na and K atoms is found to narrow the HOMO-LUMO gaps of the considered clusters. The electronic properties of these clusters, especially the group III nitrides nanoclusters, are strongly sensitive to interaction with the alkali metals. Moreover it is observed that the encapsulation of alkali metals enhances the first hyperpolarizabilities of B12N12 nanocluster. Surprisingly, due to the alkali metals encapsulation within B12N12 nanocluster, the first hyperpolarizability values are remarkably increased to 8505.49 and 122,503.76 a.u. for Na@B12N12 and K@B12N12, respectively. Also the TD-DFT calculations at both CAM-B3LYP/6-311+G(d) and PBE0/6-311+G(d) levels of theory are also performed to investigate the origin of first hyperpolarizabilities.

  4. 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. PMID:23832222

  5. 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.

  6. 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

  7. 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

    NASA Astrophysics Data System (ADS)

    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 1H and 13C NMR chemical shifts have been calculated by gauge-indepedent atomic orbital (GIAO) method with B3LYP/6-311++G(d, p) approach.

  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. PMID:26438128

  9. 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

  10. 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.

  11. 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.

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

    PubMed

    Sun, Shuai; Brown, Alex

    2015-04-30

    The resonance Raman spectra of the 5-halogenated (F, Cl, and Br) uracils are simulated via the Herzberg-Teller (HT) short-time dynamics formalism. The gradient of the S1 excited state is computed at the CAMB3LYP/aug-cc-pVTZ level of theory in the conductor-like polarizable continuum model for water (C-PCM, H2O), based on the equilibrium geometry determined using PBE0/aug-cc-pVTZ in H2O (C-PCM). The simulated resonance Raman spectra show good agreement with the experimental spectra in terms of both peak positions and intensities. The differences between the resonance Raman spectra of the three 5-halogenated uracils, caused by the effect of halogen substitution, are examined in terms of ground-state normal-mode eigenvectors and excited-state Cartesian gradients, according to the HT formalism. The differences in the normal-mode eigenvectors and excited-state Cartesian gradients between 5-fluorouracil and 5-chlorouracil are used to interpret the dissimilarity between their resonance Raman spectra. Meanwhile, the similarity between the spectra of 5-chlorouracil and 5-bromouracil is explained by the correspondence between their normal modes and excited-state gradients. PMID:25856119

  13. 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.

  14. Theoretical studies of organotin(IV) complexes derived from ONO-donor type schiff base ligands.

    PubMed

    Şirikci, Gökhan; Ancın, Nilgün Ataünal; Öztaş, Selma Gül

    2015-09-01

    In this work a molecular modeling study was carried out based on a series of organotin(IV) derivatives which were complexed with ONO-Donor type Schiff base ligands to build up a statistical data pool for researchers. For this purpose, various properties of the selected complexes such as energies, band gaps, chemical reactivity descriptors, polarizabilities, geometric parameters, (1)H-NMR, (13)C-NMR chemical shifting values were obtained through density functional theory using B3LYP, CAM-B3LYP, TPSSTPSS, TPSSh, HCTH, wB97XD, and MN12SX functionals. Empirical dispersion corrections were incorporated for some functionals and solvent effects were also taken into account through applying polarizable continuum model (PCM). (1)H-NMR, (13)C-NMR chemical shifts were calculated via linear regression analysis using either gauge invariant atomic orbital (GIAO) or continuous set of gauge transformations (CSGT) methods. While structural properties were being explored, quantitative effects of utilized functionals and empirical dispersion corrections over calculated properties were shown in detail. PMID:26245450

  15. 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. PMID:27392135

  16. 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.

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

    PubMed

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

    2015-07-14

    A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment. PMID:26575733

  18. 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.

  19. Between a reactant rock and a solvent hard place--molecular corrals guide aromatic substitutions.

    PubMed

    Chen, Yan-Mei; Chass, Gregory Adam; Fang, De-Cai

    2014-01-21

    A novel reaction mechanism is presented for an ortho-magnesium carboxylate driven aromatic nucleophilic substitution in naphthoic acids, supported by high-level density functional theory. Results show that the rate-determining aspects involve an R-group transfer from a Grignard reagent Mg-atom to the C1-atom on a naphthalene ring. This transfer is moderated by a molecular corral comprised of two solvent THF molecules and the naphthoic acid, which collectively marshal the R-group into position. The CAM-B3LYP method was employed together with the all-electron DZVP basis set. Solvent was treated using an implicit dielectric continuum (PCM method) and IDSCRF atomic-radii. Further evolved solvent models were also investigated, consisting of explicit solvating particles forming a primary solvation layer framing the reaction center. Reaction barriers obtained are in close agreement with experimental trends, with R-group substituent-identity tempering repulsion with the molecular corral, in-turn modulating the free-energy barriers. Partitioning of the dynamic bases of entropy contribution to free-energy was central to the successful experimental-theoretical synergy. PMID:24287966

  20. 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.

  1. Density functional theory study on the influence of pyrrolidine substituent of C60 bisadduct on its supramolecular interaction with porphine

    NASA Astrophysics Data System (ADS)

    Zhao, Li-Hong; Weng, Jun-Ying; Zhao, Wei; Ruan, Wen-Juan; Xin, Fei; Zhang, Ying-Hui

    2013-09-01

    Calculation using three kinds of density functional theory (DFT) methods revealed that the nonbonded interaction of pyrrolidine-functionalized C60 bisadducts with porphine derivatives (MP: M = Zn, 2H) was significantly affected by pyrrolidine substituents. Several types of the stable interaction configurations of trans-3 C60 bisadduct/ZnP complex (abbreviated as tran-3/ZnP) were compared. The association energy predicted by the wB97XD method was larger than that predicted by CAM-B3LYP and BHandH functionals. The results showed that the closer approach of porphine ring to the two pyrrolidine substituents, the larger the association energy of the complex. This trend was ascribed to the additional C-H⋯π interaction between the pyrrolidine and porphine rings. The natural bond orbital analysis proved the existence of an additional charge transfer process between the porphine and pyrrolidine rings for the t-I type of trans-3/porphine complexes. The red shift of absorption peaks of porphine were predicted in consistent with general experimental results.

  2. Optical Rotation Calculated with Time-Dependent Density Functional Theory: The OR45 Benchmark

    SciTech Connect

    Srebro, Monika; Govind, Niranjan; De Jong, Wibe A.; Autschbach, Jochen

    2011-10-13

    Time-dependent density functional theory (TDDFT) computations are performed for 42 organic molecules and 3 transition metal complexes, with experimental molar optical rotations ranging from 2 to 2 x 10{sup 4} deg cm{sup 2} dmol{sup -1}. The performance of the global hybrid functionals B3LYP, PBE0, and BHLYP, and of the range-separated functionals CAM-B3LYP and LR-PBE0 (the latter being fully long-range corrected), are investigated. The performance of different basis sets is studied. When compared to liquid-phase experimental data, the range-separated functionals do, on average, not perform better than B3LYP and PBE0. Median relative deviations between calculations and experiment range from 25 to 29%. A basis set recently proposed for optical rotation calculations (LPol-ds) on average does not give improved results compared to aug-cc-pVDZ in TDDFT calculations with B3LYP. Individual cases are discussed in some detail, among them norbornenone for which the LR-PBE0 functional produced an optical rotation that is close to available data from coupled-cluster calculations, but significantly smaller in magnitude than the liquid-phase experimental value. Range-separated functionals and BHLYP perform well for helicenes and helicene derivatives. Metal complexes pose a challenge to first-principles calculations of optical rotation.

  3. 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

  4. Understanding the absorption and emission spectra of borondipyrromethene dye and its substituted analogues

    NASA Astrophysics Data System (ADS)

    Nithya, R.; Kolandaivel, P.; Senthilkumar, K.

    2012-04-01

    Borondipyrromethene (BODIPY) dye possesses a bright and long wavelength emitting fluorescent character with a wide spectral range from visible to near infrared region. In the present work, the spectral properties of BODIPY dyes were analyzed using ab intio and density functional theory methods. The ground and excited state geometries of BODIPY and its substituted analogues in chloroform medium, were optimized using the density functional theory (DFT) and singly excited configuration interaction (CIS) methods. Based on the ground and excited state geometries, the absorption and emission spectra have been calculated using time-dependent density functional theory (TDDFT) method. The TDDFT calculations have been performed using hybrid exchange correlation functionals B3LYP and M06-HF and long-range separated functionals LC-BLYP, LC-BOP, LC-PBE, LC-PBE0 and CAM-B3LYP. The solvent phase calculations were carried out using polarizable continuum model (PCM). The TDDFT investigation reveals that the substitution of acceptor, donor-donor, donor-acceptor-donor and phenyl group in BODIPY dye influence the absorption and emission spectra significantly.

  5. 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].

  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. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

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

    SciTech Connect

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

    2013-12-10

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

  15. 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

  16. 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.

  17. 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.

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

    PubMed

    Hochheim, Manuel; Bredow, Thomas

    2015-09-15

    Structural and optical properties of isolated perylene-3,4,9,10-tetracarboxylic acid dianhydride molecules adsorbed on (100) oriented NaCl and KCl surfaces were studied theoretically to analyze the recently observed red-shift of the optical excitation spectrum after adsorption (Müller et al., Phys. Rev. B, 2011, 83, 241203; Paulheim et al. Phys. Chem. Chem. Phys., 2013, 15, 4906). The ground-state structures were obtained by periodic dispersion-corrected density functional theory (DFT) calculations. For the excited-state calculations, nonperiodic time-dependent DFT methods were applied for a cluster model embedded in point charges. The range-separated hybrid functional CAM-B3LYP was used. Correlation-consistent basis sets were used and the calculated excitation energies were extrapolated to the complete basis set limit. The shift of the first optical excitation energy was analyzed in terms of electronic and geometric contributions. It was found that both the distortion of the molecule due to the interaction with the surface and the electrostatic potential of the surface play an important role. PMID:26152591

  19. 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.

  20. Photoactivity of Molecule-TiO2 Clusters with Time-Dependent Density-Functional Theory.

    PubMed

    Luppi, E; Urdaneta, I; Calatayud, M

    2016-07-14

    The interaction of molecules with titanium oxide substrates may lead to substantial modifications of their optical properties, in particular a red shift of the absorption spectrum compared to that of bare titania. In the present paper we discuss the role of the interface between two molecules, catechol and dopamine, with gas-phase (TiO2)N clusters (N = 2, 4, 6). We studied, for the interface, the bidentate modes (the molecule bonded to two Ti sites via its two oxygen sites), which was the most energetically favorable, followed by the chelated modes (the molecule bonded to one Ti site via its two oxygen sites), and the monodentate mode (the molecule bonded to one Ti site via one oxygen site). The absorption spectra were calculated with time-dependent functional-theory with CAM-B3LYP for the description of charge-transfer excitations. We observe a red shift of the molecule/cluster systems with respect to the molecules and clusters alone. Moreover, the chelated mode was found to present bands at lower energies than the other modes, making it the most interesting mode to tune the absorption edge of these systems. PMID:27082739

  1. New trans-stilbene derivatives with large two-photon absorption cross-section and non-linear optical susceptibility values--a theoretical investigation.

    PubMed

    Kundi, Varun; Thankachan, Pompozhi Protasis

    2015-05-14

    A detailed theoretical study of linear and non-linear optical susceptibilities (NLOS), one- and two-photon absorption (OPA and TPA) properties for a series of push-pull trans-stilbene (TSB) derivatives with introduction of different electron donor (D) and acceptor (A) groups on either side of the TSB ring system is presented. The objective of the work is to design new TSB derivatives with large TPA cross-section values and to explore their linear and non-linear optical susceptibilities, OPA and TPA properties. We have used linear and quadratic response theory methods and CAM-B3LYP functional in conjunction with the 6-31+G* basis set for all property calculations. We have explained the results of the first hyperpolarizability and TP transition probability using two-state model (2SM) calculations, the results of which are in excellent agreement with the response theory methods. The TP tensor elements have been analysed to explain the large TP activity of molecules. Orbitals involved in the transition processes have been studied both qualitatively (molecular orbital pictures) and quantitatively (Λ-values) in order to explain the nature of charge transfer in different TSB derivatives. The study reveals that the novel derivatives TSBD-10, TSBD-11, TSBD-12 and TSBD-13 have large non-linear optical susceptibilities and TPA cross-section values, the largest being found for TSBD-13 (5560 G.M.). PMID:25894609

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  3. Vibronic bandshape of the absorption spectra of dibenzoylmethanatoboron difluoride derivatives: analysis based on ab initio calculations.

    PubMed

    Rukin, Pavel S; Freidzon, Alexandra Ya; Scherbinin, Andrei V; Sazhnikov, Vyacheslav A; Bagaturyants, Alexander A; Alfimov, Michael V

    2015-07-14

    The nature of absorption bandshapes of dibenzoylmethanatoboron difluoride (DBMBF2) dye substituted in ortho-, meta-, and para-positions of the phenyl ring is investigated using DFT and TDDFT with the range-separated hybrid CAM-B3LYP functional and the 6-311G(d,p) basis set. The solvent effects are taken into account within the polarized continuum model. The vibronic bandshape is simulated using a time-dependent linear coupling model with a vertical gradient approach through an original code. For flexible chromophores, the spectra of individual conformers are summed up with Boltzmann factors. It is shown that the long-wavelength absorption bandshape of DBMBF2 derivatives is determined by three factors: the relative statistical weights of conformers with different electronic absorption patterns, the relative position and intensity of the second low-energy electronic transition, and the vibronic structure of individual electronic peaks. The latter is governed by the relationship between the hard vibrational modes, which contribute to vibronic progression, and soft modes, which provide broadening of the peaks. The simulated spectra of the dyes in the study are generally consistent with the available experimental data and explain the observed spectral features. PMID:26062782

  4. 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.

  5. DFT and TD-DFT assessment of the structural and optoelectronic properties of an organic-Ag14 nanocluster.

    PubMed

    Muniz-Miranda, Francesco; Menziani, Maria Cristina; Pedone, Alfonso

    2015-05-28

    An extensive benchmark of exchange-correlation functionals on the structure of the X-ray resolved phosphine and thiolate-protected Ag14-based nanocluster, named XMC1, is reported. Calculations were performed both on simplified model systems, with the complexity of the ligands greatly reduced, and on the complete XMC1 particle. Most of the density functionals that yielded good relaxed structures on analogous calculations on gold nanoclusters (viz. those employing the generalized gradient approximation) significantly deform the structure of XMC1. On the contrary, some of the exchange-correlation functionals including part of the exact Hartree-Fock exchange (hybrid functionals) reproduce the experimental geometry with minimal errors. In particular, the widely adopted B3LYP yields fairly accurate structures for XMC1, whereas it is outperformed by many other functionals (both hybrids and generalized gradient corrected) in similar calculations on analogous gold-based systems. Time-dependent density functional calculations have been employed to recover the experimental UV-vis spectrum. The present investigation shows that to correctly reproduce the optical feature of XMC1 the ligands cannot be omitted, because they interact with the metal core at energies much closer to the optical gap than in the case of gold-based nanoclusters of similar sizes. Due to this fact, a functional that accurately describes charge-transfer electronic transitions (such as the long-range corrected CAM-B3LYP) has to be adopted. PMID:25248052

  6. 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).

  7. 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. PMID:23891797

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

    PubMed Central

    Coccia, Emanuele; Varsano, Daniele; Guidoni, Leonardo

    2016-01-01

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

  9. TD-DFT investigation of D-π-A organic dyes with thiophene moieties as π-spacers for use as sensitizers in DSSCs.

    PubMed

    Hasanein, Ahmed A; Elmarassi, Yasser R; Kassem, Eman N

    2016-05-01

    The geometrical, conformational, and electronic properties of a series of D-π-A metal-free dyes designed for use as sensitizers in DSSCs were studied using DFT and TD-DFT methods. A substituted triphenylamine moiety was used as the donor group and 2-cyanoacrylic acid as the acceptor group in these dyes. They also contained conjugated bridging π-linker groups containing two or more thiophene rings to enhance the intramolecular charge transfer. The B3LYP, M06-HF, ωB97XD and CAM-B3LYP functionals were utilized in combination with the 6-31G(d,p) basis set for the calculations. The dye solvation process was taken into account via the polarizable continuum model. To rationalize the relationships between dye structure and the photochemical properties of the dyes when used as sensitizers in DSSCs, the vertical excitation energies, the light-harvesting efficiencies, the free-energy changes during the process of injecting an electron into the surface of a TiO2 nanocrystalline semiconductor, and the open-circuit potentials were calculated for all of the dyes in the solvent THF using the above methods. The results of these computations are discussed and compared with the available corresponding experimental data. PMID:27126050

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  11. 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.

  12. 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.

  13. Synthesis, spectral analysis (FT-IR, 1H NMR, 13C NMR and UV-visible) and quantum chemical studies on molecular geometry, NBO, NLO, chemical reactivity and thermodynamic properties of novel 2-amino-4-(4-(dimethylamino)phenyl)-5-oxo-6-phenyl-5,6-dihydro-4H-pyrano[3,2-c]quinoline-3-carbonitrile

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    In the present study novel 2-amino-4-(4-(dimethylamino)phenyl)-5-oxo-6-phenyl-5,6-dihydro-4H-pyrano[3,2-c]quinoline-3-carbonitrile was synthesized and characterized by FT-IR, 1H NMR, 13C NMR, UV-visible spectroscopy and mass spectral analysis. The chemical calculations were done by DFT level of theory using Becke3-Lee-Yang-Parr (B3LYP) and Coulomb Attenuating Method (CAM-B3LYP)/6-31G(d,p) basis set. 1H, 13C chemical shifts and vibrational wavenumbers were calculated and good correlation with the experimental data has been accomplished. UV-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 (TDDFT) method. Hyperconjugative interactions were studied with the help of natural bond orbital analysis. Electric dipole moment, polarizability and first static hyperpolarizability values have been calculated. The results show that the title compound possesses nonlinear optical behavior with non-zero values. The thermodynamic properties of the compound were calculated at different temperatures. The local reactivity descriptors show that C(7) is most reactive site for nucleophilic attack.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  15. Molecular structure, linear and nonlinear optical properties of some cyclic phosphazenes: A theoretical investigation

    NASA Astrophysics Data System (ADS)

    Hadji, Djebar; Rahmouni, Ali

    2016-02-01

    We report ab initio and density functional theory calculations of structural data, dipole moment, diagonal vibrational and electronic contributions to polarizability, vibrational and electronic contributions to first hyperpolarizability of some cyclic phosphazenes. The electronic structure of substituted cyclic phosphazenes has been investigated using Hartree-Fock and density functional theory. The vibrational and electronic contributions to polarizabilities and first hyperpolarizability of these molecules were calculated with HF method, and different DFT levels used the traditional B3LYP and PBE functional and the long-range corrected functional like Coulomb-attenuating method CAM-B3LYP, LC-BLYP and wB97XD used different basis sets. These cyclic phosphazenes adopts a planar structure. The chosen level of theory was found to describe satisfactory the molecular structure (r. m. s. of the relative deviations). The study reveals that the cyclic phosphazenes derivatives have large vibrational contribution to static first hyperpolarizability values. The results obtained from this work will provide into the electronic properties of this important class of inorganic polymers.

  16. Simulated evolution of fluorophores for light emitting diodes

    NASA Astrophysics Data System (ADS)

    Shu, Yinan; Levine, Benjamin G.

    2015-03-01

    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 × 106 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.

  17. 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. PMID:25778905

  18. Loophole-free Quantum Steering

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  19. 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

  20. 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.

  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. PMID:26593432

  2. [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

  3. Physiology of Lichtheimia ramosa obtained by solid-state bioprocess using fruit wastes as substrate.

    PubMed

    de Andrade Silva, Cinthia Aparecida; Lacerda, Maria Priscila Franco; Leite, Rodrigo Simões Ribeiro; Fonseca, Gustavo Graciano

    2014-04-01

    Due to the amount of nutrients available in the agroindustrial wastes, these can be converted into high added-value products by the action of microorganisms in solid-state bioprocesses. The aim of this work was to evaluate the growth physiology and lipase production of the fungus Lichtheimia ramosa using the following Brazilian savannah fruit wastes as substrates: bocaiuva (Acrocomia aculeata), pequi (Caryocar brasiliense), guavira (Campomanesia pubescens), araticum (Annona crassiflora) and seriguela (Spondias purpurea). These residues were triturated, homogenized, adjusted to pH 5.0 and 60 % moisture, sterilized and packaged in plastic tray-type bioreactors before inoculation with 10 % (w/v) of L. ramosa pre-culture medium. The cultivations were conducted in a bacteriological incubator at 30 °C for 40 days. Samples were taken every 5 days and fungi and bacteria contents, proximate composition and lipase activity were evaluated. The maximum fungal counting was observed between 25 and 35 days. L. ramosa reached the stationary phase next to 40 days in all substrates. Mesophilic and psicrophilic aerobic bacteria were not detected. Protein enrichment was obtained for all media, being superior in seriguela residues (391.66 %), followed by pequi (160.04 %), araticum (143.31 %), guavira (102.42 %), and bocaiuva (67.88 %). Lipase production was observed in all cultivated media, except in pequi residues that showed decreasing lipase activity. The higher production was observed in guavira (1.12 U/g) followed by araticum (0.58 U/g), seriguela (0.41 U/g) and bocaiuva (0.21 U/g) waste substrates. It was concluded that the studied fruit wastes have been successfully utilized as substrates for protein enrichment and lipase production with L. ramosa. PMID:24013442

  4. Survey of ticks (Acari: Ixodidae) and their rickettsia in an Atlantic rain forest reserve in the State of São Paulo, Brazil.

    PubMed

    Sabatini, Guilherme S; Pinter, Adriano; Nieri-Bastos, Fernanda A; Marcili, Arlei; Labruna, Marcelo B

    2010-09-01

    The current study investigated the occurrence of ticks and their rickettsiae in the Serra do Mar State Park, which encompasses one of the largest Atlantic rain forest reserves of Brazil. From July 2008 to June 2009, a total of 2439 ticks (2,196 free living and 243 collected on hosts) was collected, encompassing the following 13 species: Amblyomma aureolatum (Pallas), Amblyomma brasiliense AragAo, Amblyomma dubitatum Neumann, Amblyomma fuscum Neumann, Amblyomma incisum Neumann, Amblyomma longirostre (Koch), Amblyomma naponense (Packard), Amblyomma nodosum Neumann, Amblyomma ovale Koch, Haemaphysalis juxtakochi Cooley, Ixodes aragaoi Fonseca, Ixodes loricatus Neumann, and Rhipicephalus sanguineus (Latreille). Ticks were submitted to polymerase chain reaction assays targeting portions of the rickettsial genes gltA and ompA. Polymerase chain reaction products were DNA sequenced and compared with corresponding sequences available in GenBank. Rickettsia bellii, a rickettsia of unknown pathogenicity, was detected in one A. aureolatum, one A. ovale, and three A. incisum specimens. At least 8.8% (3/34) of the free-living A. ovale ticks, 13.6% (8/59) of the A. ovale ticks collected from dogs, and 1.9% (1/54) of the R. sanguineus (Latreille) ticks were found to be infected by Rickettsia sp strain Atlantic rain forest, a novel strain that has been shown to cause an eschar-associated spotted fever in the state of Sho Paulo. Our results suggest that A. ovale is the vector of Rickettsia sp strain Atlantic rain forest in the state of São Paulo. PMID:20939390

  5. Induction of Reduced Photorespiratory Activity in Submersed and Amphibious Aquatic Macrophytes 1

    PubMed Central

    Salvucci, Michael E.; Bowes, George

    1981-01-01

    Incubation under water in a 30 C/14-hour or 12 C/10-hour photoperiod caused the CO2 compensation points of 10 aquatic macrophytes to decrease below 25 or increase above 50 microliters CO2 per liter, respectively. Submerged and aerial leaves of two amphibious angiosperms (Myriophyllum brasiliense and Proserpinaca palustris) maintained high compensation points when incubated in air but, when the submerged or aerial leaves of Proserpinaca were incubated under water, the compensation points dropped as low as 10. This suggests that, in addition to temperature and photoperiod, some factor associated with submergence regulates the compensation point of aquatic plants. In the high-compensation point plants, photorespiration, as a percentage of net photosynthesis, was equivalent to that in terrestrial C3 plants. For Hydrilla verticillata, the decreasing CO2 compensation points (110, 40, and 10) were associated with reduced photorespiration, as indicated by decreased O2 inhibition, decreased rates of CO2 evolution into CO2-free air, and increased net photosynthetic rates. The decrease in the CO2 compensation points of Hydrilla, Egeria densa, and Cabomba caroliniana was accompanied by an increase in the activity of phosphoenolpyruvate, but not of ribulose bisphosphate, carboxylase. In Hydrilla, several C4 enzymes also increased in activity to the following levels (micromoles per gram fresh weight per hour): pyruvate Pi dikinase (35), pyrophosphatase (716), adenylate kinase (525), NAD and NADP malate dehydrogenase (6565 and 30), NAD and NADP malic enzymes (239 and 44), and aspartate and alanine aminotransferases (357 and 85), whereas glycolate oxidase (6) and phosphoglycolate and phosphoglycerate phosphatases (76 and 32) showed no change. Glycolate dehydrogenase and phosphoenolpyruvate carboxykinase were undetectable. The reduced photorespiration in these plants may be due to increased CO2 fixation via a C4 acid pathway. However, for three Myriophyllum species, some other

  6. 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

  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. [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

  9. 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

  10. 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. PMID:26588300

  11. Highly accurate incremental CCSD(T) calculations on aqua- and amine-complexes

    NASA Astrophysics Data System (ADS)

    Anacker, Tony; Friedrich, Joachim

    2013-07-01

    In this work, the accuracy of the second-order incremental expansion using the domain-specific basis set approach is tested for 20 cationic metal-aqua and 25 cationic metal-amine complexes. The accuracy of the approach is analysed by the statistical measures range, arithmetic mean, mean absolute deviation, root mean square deviation and standard deviation. Using these measures we find that the error due to the local approximations decreases with increasing basis set. Next we construct a local virtual space using projected atomic orbitals (PAOs). The accuracy of the incremental series in combination with a distance-based truncation of the PAO space is analysed and compared to the convergence of the incremental series within the domain-specific basis set approach. Furthermore, we establish the recently proposed incremental CCSD(T)|MP2 method as a benchmark method to obtain highly accurate CCSD(T) energies. In combination with a basis set of quintuple-ζ quality we establish benchmarks for the binding energies of the investigated complexes. Finally, we use the inc-CCSD(T)|MP2/aV5Z' binding energies of 45 complexes and 34 dissociation reactions to compute the accuracy of several state of the art density functional theory (DFT) functionals like BP86, B3LYP, CAM-B3LYP, M06, PBE0 and TPSSh. With our implementation of the incremental scheme it was possible to compute the inc-CCSD(T)|MP2/aV5Z' energy for Al(H2O)3+ 25 (6106 AOs).

  12. 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. PMID:25848730

  13. 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.

  14. 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

  15. 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

  16. Application of the Englert-Schwinger model to the equation of state and the fullerene molecule

    NASA Astrophysics Data System (ADS)

    Sai Venkata Ramana, A.; Menon, S. V. G.

    2011-05-01

    The Englert-Schwinger model (ESM) is applied to two problems. One is the calculation of zero-temperature equation of state (EOS) of elements within the spherically symmetric Wigner-Sietz cell approximation. The other is to obtain the equilibrium radius of fullerene molecule using March’s approach [N. H. March, Proc. Camb. Philos. Soc. 48, 665 (1952)]. In each case, the results of the ESM are compared with those of Thomas-Fermi-Dirac (TFD) and Thomas-Fermi-Dirac-Weizsacker (TFDW) models. Zero-temperature equation of state calculations are done for Al and Cu. The results of the ESM show an enormous improvement over those of the TFD model. Also, the ESM is in good agreement with the TFDW model for compressions greater than 2. In the regime of validity of TFDW theory, i.e., compressions greater than 20 and 10 for Al and Cu, respectively, the deviations between the results of the two models are negligible. Hence, the ESM may be used in lieu of the TFDW model for EOS calculations. In the fullerene case, we have obtained the cohesive energy using the models assuming the radius obtained from accurate calculations of the fullerene molecule. We have also obtained the equilibrium radius predicted by each model. The results obtained show that the ESM results are not much of an improvement over the TFD results. This shows that the ESM cannot always improve the results of the TFD model and be a replacement for the TFDW model. However, as in the EOS case, it would give results in good agreement with TFDW results for properties that are dependent on the electron density at the outer reaches of the atom.

  17. Properties of noncovalent tetraphenylporphine···C60 dyads as studied by different long-range and dispersion-corrected DFT functionals.

    PubMed

    Amelines-Sarria, Oscar; Basiuk, Vladimir A; Duarte-Alaniz, Víctor; Rivera, Margarita

    2015-11-01

    The noncovalent dyad of tetraphenylporphine and C60 fullerene (H2TPP···C60) and the tetraphenylporphine dimer (H2TPP···H2TPP) were studied by density functional theory (DFT), using functionals that incorporate empirical dispersion correction (DFT-D), functionals that use a long-range correction (LC) scheme, a hybrid functional (B3LYP) and a highly parametrized empirical exchange-correlation functional (M05-2X). The results were compared to X-ray structures and interaction energies reported in previous experimental and theoretical studies. It was found that B3LYP and CAM-B3LYP functionals fail to reproduce the X-ray structures and binding energies of the TPP···C60 system. DFT-D functionals overestimated the π···π energy interactions for both systems, however, the optimized structures agree well with those observed experimentally. The LC-BLYP functional predicts geometries similar to X-ray structures; nevertheless, due to the lack of correction in the dispersion energy, the predicted energies for both model systems are low. On the other hand, the M05-2X functional exhibited the best performance. Both the structures and binding energies calculated with M05-2X are consistent with experimental and theoretical evidence reported by other authors, as well as with our experimental results obtained by means of atomic force microscopy on H2TPP thin films grown on the HOPG/C60 substrate by physical vapor deposition. PMID:26422808

  18. Connection between Hybrid Functionals and Importance of the Local Density Approximation.

    PubMed

    Mosquera, Martín A; Borca, Carlos H; Ratner, Mark A; Schatz, George C

    2016-03-10

    The exchange-correlation (XC) local density approximation (LDA) is the original density functional used to investigate the electronic structure of molecules and solids within the formulation of Kohn and Sham. The LDA is fundamental for the development of density-functional approximations. In this work we consider the generalized Kohn-Sham (GKS) theory of hybrid functionals. The GKS formalism is an extension of the Kohn-Sham theory for electronic ground states and leads to a vast set of alternative density functionals, which can be estimated by the LDA and related methods. Herein we study auxiliary electronic systems with parametrized interactions and derive (i) a set of exact equations relating the GKS XC energies in the parameter space and (ii) a formal relation between the parameters and the standard XC derivative discontinuity. In view of the new results and previously reported findings, we discuss why the inclusion of Fock exchange, and its long-range-corrected form (in the ground-state calculations and in linear-response Kohn-Sham equations), dominate over the generalized gradient corrections to enhance the quality of the fundamental gap and to enhance excitation-energy estimations. As an example, we show that the adiabatic CAM-LDA0 (a functional with 1/4 global and 1/2 long-range Hartree-Fock interaction, respectively, a range separation factor of 1/3, and pure LDA exchange and correlation) works for electronic excitations as well as the adiabatic CAM-B3LYP functional. PMID:26901359

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

    PubMed

    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 (222) plane. SEM and AFM studies revealed that, the film with 0.1M 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. PMID:25827760

  20. 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. PMID:24954054

  1. 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.

  2. Structure of a Ca2+/CaM:Kv7.4 (KCNQ4) B helix complex provides insight into M-current modulation

    PubMed Central

    Xu, Qiang; Chang, Aram; Tolia, Alexandra; Minor, Daniel L.

    2012-01-01

    Calmodulin (CaM) is an important regulator of Kv7.x (KCNQx) voltage-gated potassium channels. Channels from this family produce neuronal M-currents and cardiac and auditory IKS currents, and harbor mutations that cause arrhythmias, epilepsy, and deafness. Despite extensive functional characterization, biochemical and structural details of the interaction between CaM and the channel have remained elusive. Here, we show that both apo-CaM and Ca2+/CaM bind to the C-terminal tail of the neuronal channel Kv7.4 (KCNQ4), which is involved both hearing and mechanosensation. Interactions between apo-CaM and the Kv7.4 tail involve two C-terminal tail segments, known as the A and B segments, whereas the interaction between Ca2+/CaM and the Kv7.4 C-terminal tail requires only the B segment. Biochemical studies show that the calcium dependence of the CaM:B segment interaction is conserved in all Kv7 subtypes. X-ray crystallographic determination of the structure of the Ca2+/CaM:Kv7.4 B segment complex shows that Ca2+/CaM wraps around the Kv7.4 B segment, which forms an α-helix, in an antiparallel orientation that embodies a variation of the classic 1-14 Ca2+/CaM interaction motif. Taken together with the context of prior studies, our data suggest a model for modulation of neuronal Kv7 channels involving a calcium-dependent conformational switch from an apo-CaM form that bridges the A and B segments to a Ca2+/CaM form bound to the B-helix. The structure presented here also provides a context for a number of disease causing mutations and for further dissection of the mechanisms by which CaM controls Kv7 function. PMID:23178170

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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. PMID:26231454

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    PubMed

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

    2016-05-26

    The SN2 reactions at N center, denoted as SN2@N, has been recognized to play a significant role in carcinogenesis, although they are less studied and less understood. The potential energy profile for the model reaction of SN2@N, chloramine (NH2Cl) with fluorine anion (F(-)), has been characterized by extensive electronic structure calculations. The back-side SN2 channel dominates the reaction with the front-side SN2 channel becoming feasible at higher energies. The minimum energy pathway shows a resemblance to the well-known double-well potential model for SN2 reactions at carbon. However, the complexes involving nitrogen on both sides of the reaction barrier are characterized by NH---X (X = F or Cl) hydrogen bond and possess C1 symmetry, in contrast to the more symmetric ion-dipole carbon analogues. In the F(-) + NH2Cl system, the proton transfer pathway is found to become more competitive with the SN2 pathway than in the F(-) + CH3Cl system. The calculations reported here indicate that stationary point properties on the F(-) + NH2Cl potential energy surface are slightly perturbed by the theories employed. The MP2 and CAM-B3LYP, as well as M06-2X and MPW1K functionals give overall best agreement with the benchmark CCSD(T)/CBS energies for the major SN2 reaction channel, and are recommended as the preferred methods for the direct dynamics simulations to uncover the dynamic behaviors of the title reaction. PMID:27144809

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Trombetti, T.; Burigana, C.

    2014-01-01

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

  12. 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. PMID:25078462

  13. Protein substrates for cGMP-dependent protein phosphorylation in cilia of wild type and atalanta mutants of Paramecium.

    PubMed

    Ann, K S; Nelson, D L

    1995-01-01

    In the ciliated protozoan Paramecium, swimming direction is regulated by voltage-gated Ca2+ channels in the ciliary membrane. In response to depolarizing stimuli, intraciliary Ca2+ rises, triggering reversal of the ciliary power stroke and backward swimming. One class of Ca(2+)-unresponsive behavioral mutants of Paramecium, atalanta mutants, cannot swim backward even though they have functional Ca2+ channels in their ciliary membrane. Several atalanta mutants were characterized with regard to several Ca(2+)-dependent activities, but no significant difference between wild type and the mutants was detected. However, one allelic group, atalanta A (initially characterized by Hinrichsen and Kung [1984: Genet. Res. Camb. 43:11-20]), showed a helical swimming path of opposite handedness from that of wild-type cells when detergent-permeabilized cells ("models") were reactivated with MgATP. When cGMP-dependent protein kinase purified from wild-type cells was added to atalanta A models, the handedness of the swimming path was reversed. Cyclic GMP stimulated in vitro phosphorylation of several proteins in isolated cilia, and the pattern of phosphoproteins was very similar for wild type and atalanta mutants, with one exception: a protein of 59 kDa was phosphorylated much less in the mutant ata A. When ciliary proteins were separated by gel electrophoresis and then phosphorylated "on blot" by purified cGMP-dependent protein kinase, phosphoprotein patterns were similar in wild type and ata mutants except that a 48 kDa protein (p48) from ata A3 was more heavily phosphorylated. This difference in p48 phosphorylation was also observed with cGMP-dependent protein kinase purified from ata A3 mutant cells.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7796456

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

    PubMed

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

    2015-08-01

    A new carboxylate rich asymmetric tripodal ligand, N-[2-carboxybenzomethyl]-N-[carboxymethyl]-β-alanine (H3camb), and its di-copper(II), (NH4)2[1]2, and di-zinc(II), ((CH3)4N)2[2]2, complexes have been synthesized as carbohydrate binding models in aqueous solutions. The ligand and complexes have been fully characterized using several techniques, including single crystal X-ray diffraction. The interactions of (NH4)2[1]2 and ((CH3)4N)2[2]2 with D-glucose, D-mannose, D-xylose and xylitol in aqueous alkaline media were investigated using UV-Vis and (13)C-NMR spectroscopic techniques, respectively. The molar conductance, NMR and ESI-MS studies indicate that the complexes dissociate in solution to produce the respective complex anions, 1(-) and 2(-). Complexes 1(-) and 2(-) showed chelating ability towards the naturally abundant and biologically relevant sugars, D-glucose, D-mannose, D-xylose, and xylitol. The complex ions bind to one molar equivalent of the sugars, even in the presence of stoichiometric excess of the substrates, in solution. Experimentally obtained spectroscopic data and computational results suggest that the substrates bind to the metal center in a bidentate fashion. Apparent binding constant values, pK(app), between the complexes and the substrates were determined and a specific mode of substrate binding is proposed. The pK(app) and relativistic density functional theory (DFT) calculated Gibbs free energy values indicate that D-mannose displayed the strongest interaction with the complexes. Syntheses, characterizations, detailed substrate binding studies using spectroscopic techniques, single crystal X-ray diffraction and geometry optimizations of the complex-substrates with DFT calculations are also reported. PMID:25969174

  15. 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

  16. 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. PMID:25528509

  17. 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

  18. 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

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

    PubMed

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

    2016-04-01

    Activated carbons (ACs) are widely used in the purification of drinking water without almost any knowledge about the adsorption mechanisms of the persistent organic pollutants. Chlordecone (CLD, Kepone) is an organochlorinated synthetic compound that has been used mainly as agricultural insecticide. CLD has been identified and listed as a persistent organic pollutant by the Stockholm Convention. The selection of the best suited AC for this type of contaminants is mainly an empirical and costly process. A theoretical study of the influence of AC surface groups (SGs) on CLD adsorption is done in order to help understanding the process. This may provide a first selection criteria for the preparation of AC with suitable surface properties. A model of AC consisting of a seven membered ring graphene sheet (coronene) with a functional group on the edge was used to evaluate the influence of the SGs over the adsorption. Multiple Minima Hypersurface methodology (MMH) coupled with PM7 semiempirical Hamiltonian was employed in order to study the interactions of the chlordecone with SGs (hydroxyl and carboxyl) at acidic and neutral pH and different hydration conditions. Selected structures were re-optimized using CAM-B3LYP to achieve a well-defined electron density to characterize the interactions by the Quantum Theory of Atoms in Molecules approach. The deprotonated form of surface carboxyl and hydroxyl groups of AC models show the strongest interactions, suggesting a chemical adsorption. An increase in carboxylic SGs content is proposed to enhance CLD adsorption onto AC at neutral pH conditions. PMID:26945637

  20. 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.

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

    DOE PAGESBeta

    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

  2. Photoinduced intramolecular charge transfer in an electronically modified flavin derivative: roseoflavin.

    PubMed

    Karasulu, Bora; Thiel, Walter

    2015-01-22

    The photophysical properties of a push-pull flavin derivative, roseoflavin (RoF), are investigated in different surroundings at the molecular level, with focus on intramolecular charge transfer (ICT). Time-dependent density functional theory (TD-DFT, CAM-B3LYP functional) and DFT-based multireference configuration interaction (DFT/MRCI) are used to compute excited-state energies and one-electron properties of a truncated RoF model, roseolumiflavin (RoLF). Solvent effects are taken into account implicitly by the conductor-like polarizable continuum model and explicitly through a microsolvation scheme. In the gas phase, the calculations predict no crossing between the lowest locally excited (LE) and charge-transfer (CT) states upon twisting the dimethylamine donor group relative to the plane of the isoalloxazine acceptor moiety, whereas this crossing is found to be facile in solution (i.e., in water or benzene). Crossing of the LE and CT states facilitates ICT, which is the main cause of the fluorescence quenching and dual fluorescence character experimentally observed for roseoflavin in solution. The barrier for the ICT process is computed to be lower in water than in benzene, consistent with the enhanced ICT rates observed in more polar solvents. We present a detailed study of the molecular mechanism of the photoinduced ICT process in RoLF. For a typical donor-acceptor chromophore, three such mechanisms are discussed in the literature, which differ in the alignment of the donor and acceptor planes, namely, planar ICT (PICT), perpendicular-twisted ICT (TICT), and wagging ICT (WICT). Our theoretical results suggest that the TICT mechanism is favored in RoLF. PMID:25214319

  3. 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

  4. 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

  5. Assessment of charge-transfer excitations with time-dependent, range-separated density functional theory based on long-range MP2 and multiconfigurational self-consistent field wave functions

    NASA Astrophysics Data System (ADS)

    Hedegârd, Erik Donovan; Heiden, Frank; Knecht, Stefan; Fromager, Emmanuel; Jensen, Hans Jørgen Aagaard

    2013-11-01

    Charge transfer excitations can be described within Time-Dependent Density Functional Theory (TD-DFT), not only by means of the Coulomb Attenuated Method (CAM) but also with a combination of wave function theory and TD-DFT based on range separation. The latter approach enables a rigorous formulation of multi-determinantal TD-DFT schemes where excitation classes, which are absent in conventional TD-DFT spectra (like for example double excitations), can be addressed. This paper investigates the combination of both the long-range Multi-Configuration Self-Consistent Field (MCSCF) and Second Order Polarization Propagator Approximation (SOPPA) ansätze with a short-range DFT (srDFT) description. We find that the combinations of SOPPA or MCSCF with TD-DFT yield better results than could be expected from the pure wave function schemes. For the Time-Dependent MCSCF short-range DFT ansatz (TD-MC-srDFT) excitation energies calculated over a larger benchmark set of molecules with predominantly single reference character yield good agreement with their reference values, and are in general comparable to the CAM-B3LYP functional. The SOPPA-srDFT scheme is tested for a subset of molecules used for benchmarking TD-MC-srDFT and performs slightly better against the reference data for this small subset. Beyond the proof-of-principle calculations comprising the first part of this contribution, we additionally studied the low-lying singlet excited states (S1 and S2) of the retinal chromophore. The chromophore displays multireference character in the ground state and both excited states exhibit considerable double excitation character, which in turn cannot be described within standard TD-DFT, due to the adiabatic approximation. However, a TD-MC-srDFT approach can account for the multireference character, and excitation energies are obtained with accuracy comparable to CASPT2, although using a much smaller active space.

  6. 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

  7. Assessment of charge-transfer excitations with time-dependent, range-separated density functional theory based on long-range MP2 and multiconfigurational self-consistent field wave functions.

    PubMed

    Hedegård, Erik Donovan; Heiden, Frank; Knecht, Stefan; Fromager, Emmanuel; Jensen, Hans Jørgen Aagaard

    2013-11-14

    Charge transfer excitations can be described within Time-Dependent Density Functional Theory (TD-DFT), not only by means of the Coulomb Attenuated Method (CAM) but also with a combination of wave function theory and TD-DFT based on range separation. The latter approach enables a rigorous formulation of multi-determinantal TD-DFT schemes where excitation classes, which are absent in conventional TD-DFT spectra (like for example double excitations), can be addressed. This paper investigates the combination of both the long-range Multi-Configuration Self-Consistent Field (MCSCF) and Second Order Polarization Propagator Approximation (SOPPA) ansätze with a short-range DFT (srDFT) description. We find that the combinations of SOPPA or MCSCF with TD-DFT yield better results than could be expected from the pure wave function schemes. For the Time-Dependent MCSCF short-range DFT ansatz (TD-MC-srDFT) excitation energies calculated over a larger benchmark set of molecules with predominantly single reference character yield good agreement with their reference values, and are in general comparable to the CAM-B3LYP functional. The SOPPA-srDFT scheme is tested for a subset of molecules used for benchmarking TD-MC-srDFT and performs slightly better against the reference data for this small subset. Beyond the proof-of-principle calculations comprising the first part of this contribution, we additionally studied the low-lying singlet excited states (S1 and S2) of the retinal chromophore. The chromophore displays multireference character in the ground state and both excited states exhibit considerable double excitation character, which in turn cannot be described within standard TD-DFT, due to the adiabatic approximation. However, a TD-MC-srDFT approach can account for the multireference character, and excitation energies are obtained with accuracy comparable to CASPT2, although using a much smaller active space. PMID:24320275

  8. 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.

  9. Towards the computations of accurate spectroscopic parameters and vibrational spectra for organic compounds

    NASA Astrophysics Data System (ADS)

    Hochlaf, M.; Puzzarini, C.; Senent, M. L.

    2015-07-01

    We present multi-component computations for rotational constants, vibrational and torsional levels of medium-sized molecules. Through the treatment of two organic sulphur molecules, ethyl mercaptan and dimethyl sulphide, which are relevant for atmospheric and astrophysical media, we point out the outstanding capabilities of explicitly correlated coupled clusters (CCSD(T)-F12) method in conjunction with the cc-pVTZ-F12 basis set for the accurate predictions of such quantities. Indeed, we show that the CCSD(T)-F12/cc-pVTZ-F12 equilibrium rotational constants are in good agreement with those obtained by means of a composite scheme based on CCSD(T) calculations that accounts for the extrapolation to the complete basis set (CBS) limit and core-correlation effects [CCSD(T)/CBS+CV], thus leading to values of ground-state rotational constants rather close to the corresponding experimental data. For vibrational and torsional levels, our analysis reveals that the anharmonic frequencies derived from CCSD(T)-F12/cc-pVTZ-F12 harmonic frequencies and anharmonic corrections (Δν = ω - ν) at the CCSD/cc-pVTZ level closely agree with experimental results. The pattern of the torsional transitions and the shape of the potential energy surfaces along the torsional modes are also well reproduced using the CCSD(T)-F12/cc-pVTZ-F12 energies. Interestingly, this good accuracy is accompanied with a strong reduction of the computational costs. This makes the procedures proposed here as schemes of choice for effective and accurate prediction of spectroscopic properties of organic compounds. Finally, popular density functional approaches are compared with the coupled cluster (CC) methodologies in torsional studies. The long-range CAM-B3LYP functional of Handy and co-workers is recommended for large systems.

  10. 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

  11. 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

  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. 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

  14. 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. PMID:22050033

  15. 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

  16. Theoretical study of relationships between structural, optical, energetic, and magnetic properties and reactivity parameters of benzidine and its oxidized forms.

    PubMed

    Bondarchuk, Sergey V; Minaev, Boris F

    2014-09-25

    Structural, topological, optical, energetic, and magnetic properties and reactivity parameters of benzidine, its radical cation, and its dication as well as molecular complexes of the benzidine dication with the F(-), Cl(-), Br(-), I(-), NO3(-), HSO4(-), and H2PO4(-) anions were calculated at the B3LYP/6-311++G(2d,2p) level of theory in the CH2Cl2 medium. The CAM-B3LYP functional (as the most reliable one) and the 6-311++G(3df,3pd) basis set were used for the UV-vis absorption spectra prediction. The obtained spectral results are in a good agreement with available experimental data. A number of the calculated global and local molecular properties, including several recently developed ones, (in general, more than 20 parameters), namely, λmax, the bond lengths and orders (l and LA,B), adiabatic ionization energy (IEad), global electrophilicity index (ω), condensed electrophilic Fukui functions (f(+)) and dual descriptor (ΔfA), van der Waals molecular volume, nuclear independent chemical shifts (NICS) and QTAIM topological parameters were estimated in the critical points of the C(1)-C(1'), C(2)-C(3), and C(4)-N bonds as well as at the ring critical point. These quantities were found to be in a strong linear dependence (R(2) > 0.99 in most cases) with the number of detached electrons (Nel) from the benzidine molecule up to formation of the dication (Nel = 2). On one hand, a position of the long-wave absorption band (λCT) corresponding to the anion-to-cation charge transfer in the neutral complexes of the benzidine dication with anions, correlates with the Mulliken electronegativity of the anion (R(2) = 0.8646) and its adiabatic ionization energy (R(2) = 0.8054). On the other hand, the correlations with the anion charge in the complexes and the anion isotropic polarizability are rather poor (R(2) = 0.6392 and 0.3470, respectively). On the ground of the obtained strong relationships, one may recommend the calculated molecular properties as potentially preferable

  17. 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

  18. 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

  19. Packing of Large Two- and Three-Photon Activity Into Smallest Possible Unsymmetrical Fluorene Chromophores.

    PubMed

    Kundi, Varun; Thankachan, Pompozhi Protasis

    2016-05-01

    The quantum chemical study of one-, two-, and three-photon absorption (1PA, 2PA, and 3PA) properties for a set of compact fluorene derivatives (FD) with combination of different donor and acceptor moieties on both sides of fluorene ring system is presented. The main goal of the study is to pack large two-photon (2P) and three-photon (3P) activity into smallest possible chromophore. Linear, quadratic, and cubic response time-dependent density functional theory was used to calculate 1PA, 2PA, and 3PA properties, respectively. We used CAMB3LYP/cc-pVDZ level of theory for all the property calculations. The 2P and 3P transition probabilities were recalculated using two-state model approach and found to be in good agreement with the response theory results for first excited state. To include the contributions from higher states, the three-state model was also employed to recalculate the 2P transition probabilities and found to be in excellent agreement with response theory. The 2P/3P tensor elements were also analyzed to find reasons behind large 2P/3P activities. All the orbitals involved in transition processes were studied in detail by both molecular orbital pictures (qualitatively) and overlap diagnostic Λ-values (quantitatively). The study reveals that the novel fluorene derivatives FD-12 and FD-13 have shown large 2PA cross-section values of 1100 G.M. and 1030 G.M.; and 3PA transition probabilities of 6.10 × 10(10) a.u. and 4.85 × 10(10) a.u., respectively, for transition S0 → S1. The largest 3PA transition probability of 4.04 × 10(11) a.u. was found with FD-12 for S0 → S2 excitation. The linear relationship between Λ-values and 2PA cross-section values was also studied. PMID:27054876

  20. 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

  1. 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

  2. Reliable Quantum Chemical Prediction of the Localized/Delocalized Character of Organic Mixed-Valence Radical Anions. From Continuum Solvent Models to Direct-COSMO-RS.

    PubMed

    Renz, Manuel; Kess, Martin; Diedenhofen, Michael; Klamt, Andreas; Kaupp, Martin

    2012-11-13

    A recently proposed quantum-chemical protocol for the description of the character of organic mixed-valence (MV) compounds, close from both sides to the localized/delocalized borderline, is evaluated and extended for a series of dinitroaryl radical anions 1-6. A combination of global hybrid functionals with exact-exchange admixtures of 35% (BLYP35) or 42% (BMK) with appropriate solvent modeling allows an essentially quantitative treatment of, for example, structural symmetry-breaking in Robin/Day class II systems, thermal electron transfer (ET) barriers, and intervalence charge-transfer (IV-CT) excitation energies, while covering also the delocalized class III cases. Global hybrid functionals with lower exact-exchange admixtures (e.g., B3LYP, M05, or M06) provide a too delocalized description, while functionals with higher exact-exchange admixtures (M05-2X, M06-2X) provide a too localized one. The B2PLYP double hybrid gives reasonable structures but far too small barriers in class II cases. The CAM-B3LYP range hybrid gives somewhat too high ET barriers and IV-CT energies, while the range hybrids ωB97X and LC-BLYP clearly exhibit too much exact exchange. Continuum solvent models describe the situation well in most aprotic solvents studied. The transition of 1,4-dinitrobenzene anion 1 from a class III behavior in aprotic solvents to a class II behavior in alcohols is not recovered by continuum solvent models. In contrast, it is treated faithfully by the novel direct conductor-like screening model for real solvents (D-COSMO-RS). The D-COSMO-RS approach, the TURBOMOLE implementation of which is reported, also describes accurately the increased ET barriers of class II systems 2 and 3 in alcohols as compared to aprotic solvents and can distinguish at least qualitatively between different aprotic solvents with identical or similar dielectric constants. The dominant role of the solvent environment for the ET character of these MV radical anions is emphasized, as in

  3. 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

  4. Nickel(II) Complex of a Hexadentate Ligand with Two o-Iminosemiquinonato(1-) π-Radical Units and Its Monocation and Dication.

    PubMed

    Ali, Akram; Dhar, Debanjan; Barman, Suman K; Lloret, Francesc; Mukherjee, Rabindranath

    2016-06-20

    Aerobic reaction of a hexadentate redox-active o-aminophenol-based ligand, H4L(3) = N,N'-bis(2-hydroxy-3,5-di-tert-butylphenyl)-2,2'-diamino(diphenyldithio)-ethane, in CH3OH with Ni(II)(O2CCH3)2·4H2O and Et3N afforded isolation of a reddish-brown crystalline solid [Ni(L(3))] 1. Cyclic voltammetry (CV) experiment exhibits two oxidative responses at E1/2 = 0.09 and 0.53 V vs SCE (saturated calomel electrode). Chemical oxidation of 1 in air by [Fe(III)(η(5)-C5H5)2][PF6] and AgBF4 in CH2Cl2 led to the isolation of one-electron oxidized species [1](1+) as purple [1][PF6]·CH2Cl2 and two-electron oxidized species [1](2+) as dark purple [1][BF4]2·CH2Cl2, respectively. X-ray crystallographic analysis at 100(2) K unambiguously established that the ligand is present in [Ni(II){(L(ISQ)O,N)(•-)}{(L(ISQ)O,N)(•-)}{(LS,S)(0)}] 1, [Ni(II){(L(IBQ)O,N)(0)}{(L(ISQ)O,N)(•-)}{(LS,S)(0)}][PF6]·CH2Cl2, and [Ni(II){(L(IBQ)O,N)(0)}{(L(IBQ)O,N)(0)}{(LS,S)(0)}][BF4]2·CH2Cl2, as monoanionic o-iminosemiquinonate(1-) π-radical (Srad = 1/2) (L(ISQ))(•-) and neutral o-iminoquinone (L(IBQ))(0) redox-levels. Complexes 1, [1][PF6]·CH2Cl2, and [1][BF4]2·CH2Cl2 possess an S = 2, 3/2, and 1 ground-state, respectively, established by temperature-dependent (2-300 K) magnetic behavior of 1 and [1][PF6]·CH2Cl2, and a μeff value of [1][BF4]2·CH2Cl2 at 300 K. Both 1 and [1][PF6]·CH2Cl2 exhibit ferromagnetic exchange-coupling between the two electrons of Ni(II) and two/one ligand π-radicals, respectively. The redox processes are shown to be ligand-based. Spectroscopic and redox properties, and density functional theory (DFT) calculations at the CAM-B3LYP-level of theory adequately describe the electronic structure of 1, [1](1+), and [1](2+). The observed UV-vis-NIR absorptions for 1, [1][PF6]·CH2Cl2, and [1][BF4]2·CH2Cl2 have been assigned, based on time-dependent (TD)-DFT calculations. PMID:27232547

  5. Meteorites and projectiles in terrestrial impact craters: implications for the composition of the asteroid belt.

    NASA Astrophysics Data System (ADS)

    Tagle, R.; Claeys, Ph.

    material from the inner part of the asteroid belt at the v6, 3:1 and 5:2 resonances, where OC were most likely formed. Interestingly, the second group of common projectiles consists of NMI meteorites, which represent up to ~20% of all iron meteorites and are responsible for the majority of the impact craters <1.5km of diameter, including the Barringer crater in Arizona [e.g. 3, 6]. NMI meteorites are very special as they may well contain up to 90% of silicate inclusion. Interestingly space weathering is assumed to cause a reduction of Fe2+ into metallic iron on the surfaces exposed to cosmic ray, resulting in a "stone+metal" spectra. Therefore an abundance of NMI asteroids within the asteroid belt, as suggested by the study of terrestrial impactors, could be an alternative type of asteroid that could 1 explain at least some of the discrepancies between the observations in meteorites and asteroids. Ref. [1] Ivezic et al. 2001 Astron. J. 122:2749-2784; [2] Burbine et al. 2002 Asteroids III, pp. 653-667; [3] Grady 2000 Camb. Uni. Press; [4] Meibom & Clark 1999 MAPS 34:7-24;[5] Jedicke et al. 2004 Nature 429:275-277; [6] Koeberl 1998 GSA 140:133-153. Acknowledgments: Thanks to the Deutsche Akademie der Naturforscher Leopoldina for financial support (BMBF-LPD 9901/8-130). 2

  6. 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.

  7. 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)