Basis set superposition error effects, excited-state potential energy surface and photodynamics of thymine

En aquesta tesi he estudiat l'efecte de l'error de superposició de base (BSSE) en la planaritat d'algunes molècules. He observat que l'ús d'alguns mètodes de càlcul amb determinades funcions de base descriuen mínims d'energia no planars per les bases nitrogenades de l'ADN. He demostrat que aquests problemes es poden arreglar utilitzant el mètode Counterpoise per corregir el BSSE en els càlculs. En aquesta tesi també he estudiat la fotofísica de la timina i els resultats mostren que existeixen dos camins de relaxació des de l'estat excitat que permeten la regeneració de l'estructura inicial de forma ultraràpida.

Fast approximate calculation of multiply scattered lidar returns

An efficient method is described for the approximate calculation of the intensity of multiply scattered lidar returns. It divides the outgoing photons into three populations, representing those that have experienced zero, one, and more than one forward-scattering event. Each population is parameterized at each range gate by its total energy, its spatial variance, the variance of photon direction, and the covariance, of photon direction and position. The result is that for an N-point profile the calculation is O(N-2) efficient and implicitly includes up to N-order scattering, making it ideal for use in iterative retrieval algorithms for which speed is crucial. In contrast, models that explicitly consider each scattering order separately are at best O(N-m/m!) efficient for m-order scattering and often cannot be performed to more than the third or fourth order in retrieval algorithms. For typical cloud profiles and a wide range of lidar fields of view, the new algorithm is as accurate as an explicit calculation truncated at the fifth or sixth order but faster by several orders of magnitude. (C) 2006 Optical Society of America.

A 3D stochastic cloud model for investigating the radiative properties of inhomogeneous cirrus clouds

(From author). Comments: First 3D stochastic/fractal model of cirrus; first detailed analysis & explanation of power spectra of ice water content, including first observations of 50-km scale break and mixing-induced steepening of spectrum; first demonstration of the potential effect of wind shear on radiative fluxes by changing fall-streak orientation. Has spawned work on the effect of 3D photon transport on the radiative effects of cirrus clouds.

Vibrationally mediated photodissociation of nitrous acid

Hitherto unobserved overtone and combination bands of nitrous acid have been investigated by Fourier-transform infrared absorption spectroscopy and through the resonance enhancements they provide in the two-photon excition spectrum for forming OH(X) photofragments. Analysis of the band profiles associated with the second and third O—H stretching overtones of trans-HONO, and of the energy disposal into the OH(X) fragments resulting from two-photon dissociation mediated by these overtone levels, provide some clues as to the mechanism for intramolecular vibrational energy redistribution (IVR) within these vibrationally excited molecules. The work serves to highlight further the extreme sensitivity of vibrationally mediated photodissociation (VMP) as a means of revealing weak O—H stretching overtones, even in situations (as here) where the species of interest is but a minor constituent of an equilibrium mixture.

Ultrastructural alterations in mesophyll and bundle sheath chloroplasts of two maize cultivars in response to chilling at high irradiance

Maize (Zea mays L.) seedlings of two cultivars (cv. Bastion adapted to W. Europe, and cv. Batan 8686 adapted to the highlands of Mexico), raised in a glasshouse (19-25 degrees C), were transferred to 4.5 or 9 degrees C at photon flux density (PPFD) of 950 mu mol m(-2) s(-1) with 10-h photoperiod for 58 h and then allowed to recover at 22 degrees C for 16 h (14 h dark and 2 h at PPFD of 180 mu mol m(-2) s(-1)). The ultrastructural responses after 4 h or 26 h at 4.5 degrees C were the disappearance of starch grains in the bundle sheath chloroplasts and the contraction of intrathylakoid spaces in stromal thylakoids of the mesophyll chloroplasts. At this time, bundle sheath chloroplasts of cv. Batan 8686 formed peripheral reticulum. Prolonged stress at 4.5 degrees C (50 h) caused plastid swelling and the dilation of intrathylakoid spaces, mainly in mesophyll chloroplasts. Bundle sheath chloroplasts of cv. Batan 8686 seedlings appeared well preserved in shape and structure. Batan 8686 had also higher net photosynthetic rates during chilling and recovery than Bastion. Extended leaf photobleaching developed during the recovery period after chilling at 4.5 degrees C. This was associated with collapsed chloroplast envelopes, disintegrated chloroplasts and very poor staining.

Agonist-dependent internalization of D2 receptors: imaging quantification by confocal microscopy

In positron emission tomography and single photon emission computed tomography studies using D2 dopamine (DA) receptor radiotracers, a decrease in radiotracer binding potential (BP) is usually interpreted in terms of increased competition with synaptic DA. However, some data suggest that this signal may also reflect agonist (DA)-induced increases in D2 receptor (D2R) internalization, a process which would presumably also decrease the population of receptors available for binding to hydrophilic radioligands. To advance interpretation of alterations in D2 radiotracer BP, direct methods of assessment of D2R internalization are required. Here, we describe a confocal microscopy-based approach for the quantification of agonist-dependent receptor internalization. The method relies upon double-labeling of the receptors with antibodies directed against intracellular as well as extracellular epitopes. Following agonist stimulation, DA D2R internalization was quantified by differentiating, in optical cell sections, the signal due to the staining of the extracellular from intracellular epitopes of D2Rs. Receptor internalization was increased in the presence of the D2 agonists DA and bromocriptine, but not the D1 agonist SKF38393. Pretreatment with either the D2 antagonist sulpiride, or inhibitors of internalization (phenylarsine oxide and high molarity sucrose), blocked D2-agonist induced receptor internalization, thus validating this method in vitro. This approach therefore provides a direct and streamlined methodology for investigating the pharmacological and mechanistic aspects of D2R internalization, and should inform the interpretation of results from in vivo receptor imaging studies.

Experimental and theoretical study of the infrared spectra of BrHI- and BrDI-

Gas phase vibrational spectra of BrHI- and BrDI- have been measured from 6 to 17 mum (590-1666 cm-1) using tunable infrared radiation from the free electron laser for infrared experiments in order to characterize the strong hydrogen bond in these species. BrHI-.Ar and BrDI-.Ar complexes were produced and mass selected, and the depletion of their signal due to vibrational predissociation was monitored as a function of photon energy. Additionally, BrHI- and BrDI- were dissociated into HBr (DBr) and I- via resonant infrared multiphoton dissociation. The spectra show numerous transitions, which had not been observed by previous matrix studies. New ab initio calculations of the potential-energy surface and the dipole moment are presented and are used in variational ro-vibrational calculations to assign the spectral features. These calculations highlight the importance of basis set in the simulation of heavy atoms such as iodine. Further, they demonstrate extensive mode mixing between the bend and the H-atom stretch modes in BrHI- and BrDI- due to Fermi resonances. These interactions result in major deviations from simple harmonic estimates of the vibrational energies. As a result of this new analysis, previous matrix-isolation spectra assignments are reevaluated. (C) 2004 American Institute of Physics.

Improved fluorescent proteins for single-molecule research in molecular tracking and co-localization

Three promising variants of autofluorescent proteins have been analyzed photophysically for their proposed use in single-molecule microscopy studies in living cells to compare their superiority to other fluorescent proteins previously reported regarding the number of photons emitted. The first variant under investigation the F46L mutant of eYFP has a 10% greater photon emission rate and > 50% slower photobleaching rate on average than the standard eYFP fluorophore. The monomeric red fluorescent protein (mRFP) has a fivefold lower photon emission rate, likely due to the monomeric content, and also a tenfold faster photobleaching rate than the DsRed fluorescent protein. In contrast, the previously reported eqfp611 has a 50% lower emission rate yet photobleaches more than a factor 2 slowly. We conclude that the F46L YFP and the eqfp611 are superior new options for single molecule imaging and tracking studies in living cells. Studies were also performed on the effects of forced quenching of multiple fluorescent proteins in sub-micrometer regions that would show the effects of dimerization at low concentration levels of fluorescent proteins and also indicate corrections to stoichiometry patterns with fluorescent proteins previously in print. We also introduce properties at the single molecule level of new FRET pairs with combinations of fluorescent proteins and artificial fluorophores.

Agonist-dependent internalization of D2 receptors: Imaging quantification by confocal microscopy

In positron emission tomography and single photon emission computed tomography studies using D2 dopamine (DA) receptor radiotracers, a decrease in radiotracer binding potential (BP) is usually interpreted in terms of increased competition with synaptic DA. However, some data suggest that this signal may also reflect agonist (DA)-induced increases in D2 receptor (D2R) internalization, a process which would presumably also decrease the population of receptors available for binding to hydrophilic radioligands. To advance interpretation of alterations in D2 radiotracer BP, direct methods of assessment of D2R internalization are required. Here, we describe a confocal microscopy-based approach for the quantification of agonist-dependent receptor internalization. The method relies upon double-labeling of the receptors with antibodies directed against intracellular as well as extracellular epitopes. Following agonist stimulation, DA D2R internalization was quantified by differentiating, in optical cell sections, the signal due to the staining of the extracellular from intracellular epitopes of D2Rs. Receptor internalization was increased in the presence of the D2 agonists DA and bromocriptine, but not the D1 agonist SKF38393. Pretreatment with either the D2 antagonist sulpiride, or inhibitors of internalization (phenylarsine oxide and high molarity sucrose), blocked D2-agonist induced receptor internalization, thus validating this method in vitro. This approach therefore provides a direct and streamlined methodology for investigating the pharmacological and mechanistic aspects of D2R internalization, and should inform the interpretation of results from in vivo receptor imaging studies.

Adsorption of frog foam nest proteins at the air-water interface

The surfactant properties of aqueous protein mixtures ( ranaspumins) from the foam nests of the tropical frog Physalaemus pustulosus have been investigated by surface tension, two-photon excitation. uorescence microscopy, specular neutron reflection, and related biophysical techniques. Ranaspumins lower the surface tension of water more rapidly and more effectively than standard globular proteins under similar conditions. Two- photon excitation. uorescence microscopy of nest foams treated with fluorescent marker ( anilinonaphthalene sulfonic acid) shows partitioning of hydrophobic proteins into the air-water interface and allows imaging of the foam structure. The surface excess of the adsorbed protein layers, determined from measurements of neutron reflection from the surface of water utilizing H2O/D2O mixtures, shows a persistent increase of surface excess and layer thickness with bulk concentration. At the highest concentration studied ( 0.5 mg ml(-1)), the adsorbed layer is characterized by three distinct regions: a protruding top layer of similar to20 Angstrom, a middle layer of similar to30 Angstrom, and a more diffuse submerged layer projecting some 25 Angstrom into bulk solution. This suggests a model involving self-assembly of protein aggregates at the air-water interface in which initial foam formation is facilitated by specific surfactant proteins in the mixture, further stabilized by subsequent aggregation and cross-linking into a multilayer surface complex.

Experimental evidence for a partially dissociated water bilayer on Ru{0001}

Core-level photoelectron spectra, in excellent agreement with ab initio calculations, confirm that the stable wetting layer of water on Ru{0001} contains O-H and H2O in roughly 3:5 proportion, for OHx coverages between 0.25 and 0.7 ML, and T<170 K. Proton disorder explains why the wetting structure looks to low energy electron diffraction (LEED) to be an ordered p(root3xroot3)R30degrees adlayer, even though approximate to3/8 of its molecules are dissociated. Complete dissociation to atomic oxygen starts near 190 K. Low photon flux in the synchrotron experiments ensured that the diagnosis of the nature of the wetting structure quantified by LEED is free of beam-induced damage.

Retrievals of thick cloud optical depth from the Geoscience Laser Altimeter System (GLAS) by calibration of solar background signal

Laser beams emitted from the Geoscience Laser Altimeter System (GLAS), as well as other spaceborne laser instruments, can only penetrate clouds to a limit of a few optical depths. As a result, only optical depths of thinner clouds (< about 3 for GLAS) are retrieved from the reflected lidar signal. This paper presents a comprehensive study of possible retrievals of optical depth of thick clouds using solar background light and treating GLAS as a solar radiometer. To do so one must first calibrate the reflected solar radiation received by the photon-counting detectors of the GLAS 532-nm channel, the primary channel for atmospheric products. Solar background radiation is regarded as a noise to be subtracted in the retrieval process of the lidar products. However, once calibrated, it becomes a signal that can be used in studying the properties of optically thick clouds. In this paper, three calibration methods are presented: (i) calibration with coincident airborne and GLAS observations, (ii) calibration with coincident Geostationary Opera- tional Environmental Satellite (GOES) and GLAS observations of deep convective clouds, and (iii) cali- bration from first principles using optical depth of thin water clouds over ocean retrieved by GLAS active remote sensing. Results from the three methods agree well with each other. Cloud optical depth (COD) is retrieved from the calibrated solar background signal using a one-channel retrieval. Comparison with COD retrieved from GOES during GLAS overpasses shows that the average difference between the two retriev- als is 24%. As an example, the COD values retrieved from GLAS solar background are illustrated for a marine stratocumulus cloud field that is too thick to be penetrated by the GLAS laser. Based on this study, optical depths for thick clouds will be provided as a supplementary product to the existing operational GLAS cloud products in future GLAS data releases.

A study of the atmospherically relevant reaction between molecular chlorine and dimethylsulfide (DMS): establishing the reaction intermediate and measurement of absolute photoionization cross-sections

In a study using UV photoelectron spectroscopy (PES) of the atmospherically relevant reaction CH3SCH3 + Cl2 → CH3SCH2Cl + HCl bands associated with a reaction intermediate have been observed. These have been assigned to ionization of the covalently bound molecule (CH3)2SCl2 on the basis of the intensity of the observed bands as a function of reaction time, molecular orbital calculations of vertical ionization energies and evidence from infrared spectroscopy. A method has also been developed, with the flow-tube/PE spectrometer combination used, to measure photoionization cross-sections of the reagents and products at the photon energy utilized and this has allowed the photoionization cross-section of the intermediate to be estimated. This work augments an earlier study in which the rate constant of the reaction between CH3SCH3 (DMS) and Cl2 has been measured at room temperature.

Fluorescence lifetime imaging microscopy (FLIM) to demonstrate the nuclear binding of flavanols and (--epigallocatechin gallate

The use of light microscopy and DMACA staining strongly suggested that plant and animal cell nuclei act as sinks for flavanols [1, 2]. Detailed uv-vis spectroscopic titration experiments indicated that histone proteins are the likely binding sites in the nucleus [2]. Here we report the development of a multi-photon excitation microscopy technique combined with fluorescent lifetime measurements of flavanols. Using this technique, (+) catechin, (-) epicatechin and (-) epigallocatechin gallate (EGCG) showed strikingly different excited state lifetimes in solution. Interaction of histone proteins with flavanols was indicated by the appearance of a significant τ2-component of 1.7 to 4.0ns. Tryptophan interference could be circumvented in the in vivo fluorescence lifetime imaging microscopy (FLIM) experiments with 2-photon excitation at 630nm. This enabled visualisation and semi-quantitative measurements that demonstrated unequivocally the absorption of (+)catechin, (-)epicatechin and EGCG by nuclei of onion cells. 3D FLIM revealed for the first time that externally added EGCG penetrated the whole nucleus in onion cells. The relative proportions of EGCG in cytoplasm: nucleus: nucleoli were ca. 1:10:100. FLIM experiments may therefore facilitate probing the health effects of EGCG, which is the major constituent of green tea.