PhotochemCAD‡: A Computer‐Aided Design and Research Tool in Photochemistry

Du, Hai; Fuh, Ru-Chun Amy; Li, Junzhong; Corkan, L. Andrew; Lindsey, Jonathan S.

doi:10.1111/j.1751-1097.1998.tb02480.x

Cited by 522 publications

(638 citation statements)

References 5 publications

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“…The emission loadings are similar to the pure emission spectrum of tryptophan. 40 This fact corroborates the mechanism presented in Figure 2, in which tryptophan is the precursor in the violacein biosynthesis. The second fluorophore has an emission peak at 423 nm when excited at 280 and 308 nm (see Figure 6a, sample-20 h).…”

Section: Parafac Modelingsupporting

confidence: 76%

The violacein biosynthesis monitored by multi-wavelength fluorescence spectroscopy and by the PARAFAC method

Dantas¹,

Volpe²,

Durán³

et al. 2012

J. Braz. Chem. Soc.

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A obtenção de informações sobre uma rota biossintética é um procedimento complexo e trabalhoso. Neste sentido, o presente trabalho apresenta uma nova abordagem para a análise inicial da biossíntese de produtos naturais fluorescentes usando a biossíntese da violaceína como exemplo. Para tanto, uma cultura da Chromobacterium violaceum foi inoculada em um biorreator de onde alíquotas eram retiradas a cada 2 h para posterior análise por espectroscopia de fluorescência 2D. As matrizes de emissão-excitação obtidas demonstraram o comportamento dinâmico dos sinais de fluoróforos que são consumidos e produzidos pela bactéria. Estes sinais foram resolvidos pelo método PARAFAC (análise paralela de fatores) perfazendo um total de seis espécies químicas. O triptofano e a violaceína foram identificados por comparação espectral. A identificação dos outros fluoróforos mostrou-se a etapa crítica devido à falta de banco de dados de produtos naturais fluorescentes para comparação. Por fim, esta metodologia apresenta um grande potencial para fornecer informações da biossíntese de produtos naturais.Obtaining information about a biosynthetic pathway is a complex and laborious procedure. In this sense, this work presents a new approach for the initial analysis of the biosynthesis of fluorescent natural products using as example the violacein biosynthesis. For this, a culture of Chromobacterium violaceum was grown in a bioreactor from which aliquots were collected every 2 h for subsequent analysis by multi-wavelength fluorescence spectroscopy. The excitation-emission matrices demonstrated the dynamic behavior of the fluorophores signal that are consumed and produced by the bacterium. These signals were resolved by PARAFAC (parallel factor analysis) method totalizing six pure components. Tryptophan and violacein were identified by comparison to spectra available in the literature. The identification of other fluorophores was critical step due to the lack of a database of fluorescent natural products to compare spectra. Finally, this methodology has great potential to achieve a deeper insight into the biosynthesis of natural products.

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Section: Parafac Modelingsupporting

confidence: 76%

The violacein biosynthesis monitored by multi-wavelength fluorescence spectroscopy and by the PARAFAC method

Dantas¹,

Volpe²,

Durán³

et al. 2012

J. Braz. Chem. Soc.

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“…83 The light emission from fluorescent molecules such as fluorescein ( ) 9.23 × 10 4 M -1 cm -1 with a quantum yield ∼0.98 at 483 nm), 82 also commonly used in imaging is 5 orders of magnitude lower than the light scattering from the 80-nm gold nanospheres (C sca ) 1.23 × 10 -14 m 2 corresponding to a molar scattering coefficient of 3.22 × 10 10 M -1 cm -1 ). The superior scattering properties of gold nanospheres have already been exploited for the selective imaging of cancer cells by using simple dark field microscopy 17 and confocal microscopy.…”

Section: Resultsmentioning

confidence: 99%

Calculated Absorption and Scattering Properties of Gold Nanoparticles of Different Size, Shape, and Composition: Applications in Biological Imaging and Biomedicine

et al. 2006

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The selection of nanoparticles for achieving efficient contrast for biological and cell imaging applications, as well as for photothermal therapeutic applications, is based on the optical properties of the nanoparticles. We use Mie theory and discrete dipole approximation method to calculate absorption and scattering efficiencies and optical resonance wavelengths for three commonly used classes of nanoparticles: gold nanospheres, silica-gold nanoshells, and gold nanorods. The calculated spectra clearly reflect the well-known dependence of nanoparticle optical properties viz. the resonance wavelength, the extinction cross-section, and the ratio of scattering to absorption, on the nanoparticle dimensions. A systematic quantitative study of the various trends is presented. By increasing the size of gold nanospheres from 20 to 80 nm, the magnitude of extinction as well as the relative contribution of scattering to the extinction rapidly increases. Gold nanospheres in the size range commonly employed (∼40 nm) show an absorption cross-section 5 orders higher than conventional absorbing dyes, while the magnitude of light scattering by 80-nm gold nanospheres is 5 orders higher than the light emission from strongly fluorescing dyes. The variation in the plasmon wavelength maximum of nanospheres, i.e., from ∼520 to 550 nm, is however too limited to be useful for in vivo applications. Gold nanoshells are found to have optical cross-sections comparable to and even higher than the nanospheres. Additionally, their optical resonances lie favorably in the near-infrared region. The resonance wavelength can be rapidly increased by either increasing the total nanoshell size or increasing the ratio of the core-toshell radius. The total extinction of nanoshells shows a linear dependence on their total size, however, it is independent of the core/shell radius ratio. The relative scattering contribution to the extinction can be rapidly increased by increasing the nanoshell size or decreasing the ratio of the core/shell radius. Gold nanorods show optical cross-sections comparable to nanospheres and nanoshells, however, at much smaller effective size. Their optical resonance can be linearly tuned across the near-infrared region by changing either the effective size or the aspect ratio of the nanorods. The total extinction as well as the relative scattering contribution increases rapidly with the effective size, however, they are independent of the aspect ratio. To compare the effectiveness of nanoparticles of different sizes for real biomedical applications, size-normalized optical cross-sections or per micron coefficients are calculated. Gold nanorods show per micron absorption and scattering coefficients that are an order of magnitude higher than those for nanoshells and nanospheres. While nanorods with a higher aspect ratio along with a smaller effective radius are the best photoabsorbing nanoparticles, the highest scattering contrast for imaging applications is obtained from nanorods of high aspect ratio with a larger effective radi...

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“…This is provided by very efficient pumping with pulsed laser excitation of an electronic transition having a huge extinction coefficient-e = 162 000 cm À1 /M at 698.5 nm for H 2 Pc in chloronaphthalene. 20 For indirect excitation via the Q Y state (Level 2 0 ) an efficient relaxation to Level 2 is required. This is indeed the case, because the only emission that has been observed with Q Y is relaxed, originating from v 0 = 0 in the Q X state.…”

Section: Discussionmentioning

confidence: 99%

Amplified emission of phthalocyanine isolated in cryogenic matrices

Dozova

Murray

McCaffrey

et al. 2008

Phys. Chem. Chem. Phys.

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Laser induced fluorescence spectroscopy of free-base (H 2 Pc) and zinc (ZnPc) phthalocyanines trapped in rare gas and nitrogen matrices reveals a quite unexpected phenomenon with a moderate increase in the laser intensity. In all matrices except Xe, a huge increase occurs in the intensity of an emission band near 755 nm when pumping the S 1 ' S 0 transition. The band involves a vibrational mode of the ground state, located at 1550 and 1525 cm À1 for H 2 Pc and ZnPc, respectively. Many of the characteristics of amplified emission (AE) are exhibited by this vibronic transition. Excitation scans recorded for the AE band yield greatly enhanced site selectivity compared to what is obtained in normal fluorescence excitation scans.

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PhotochemCAD‡: A Computer‐Aided Design and Research Tool in Photochemistry

Cited by 522 publications

References 5 publications

The violacein biosynthesis monitored by multi-wavelength fluorescence spectroscopy and by the PARAFAC method

The violacein biosynthesis monitored by multi-wavelength fluorescence spectroscopy and by the PARAFAC method

Calculated Absorption and Scattering Properties of Gold Nanoparticles of Different Size, Shape, and Composition: Applications in Biological Imaging and Biomedicine

Amplified emission of phthalocyanine isolated in cryogenic matrices

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