Synthesis, luminescence properties and energy transfer of binary and ternary rare earth complexes with aromatic acids and 1,10-phenanthroline

A series of binary and ternary rare earth (Gd, Eu, Tb) complexes with ortho hydroxyl benzoic acid, pam aminobenzoic acid, nicotinic acid and 1,10-phenanthroline were synthesized. Phosphorescence spectra and lifetimes of Gd complexes were measured and the lowest triplet state energies of gadolinium binary complexes end the intramolecular energy transfer efficiencies were determined. The luminescence properties and energy transfer process of Eu3+ and Tb3+ complexes were discussed.

The photophysical properties of binary and ternary complexes of rare earths with conjugated carboxylic acids and 1,10-phenanthroline

Results of photophysical properties of the complexes of Gd3+, Eu3+ and Tb3+ with conjugated carboxylic acids (3,4-funandicarboxylic acid and nicotinic acid) and 1,10-phenanthroline are reported. Whether between central ions and ligands or between the two ligands, it is found that the intramolecular energy efficiency is a sensitive function of the relative positions of the resonance energy levels of the central ions and the lowest triplet states of the ligands. Couplings of rare earth ions to the ligands are discussed in detail. (C) 1997 Elsevier Science S.A.

The synthesis, luminescence and energy transfer of the binary and ternary complexes of rare earth with aminobenzoic acids and 1,10-phenanthroline

Thirteen kinds of binary and ternary complexes of rare earth (Gd, Eu,Tb) with ortho (para) aminobenzoic acid and 1.10--phenanthroline were synthesized and characterized. The phosphorescence spectra and lifetimes of gadolinium complexes were measured and the lowest triplet state energies of ligands and the energy transfer efficiencies between ligands were determined. The luminescence properties and intramolecular energy transfer of these complexes were studied in details.

Probabilistic distribution of one-phase structure seminvariants for an isomorphous pair of structures: Theoretical basis and initial applications

Given a special type of triplet of reciprocal-lattice vectors in the monoclinic and orthorhombic systems, there exist eight three-phase structure seminvariants (3PSSs) for a pair of isomorphous structures. The first neighborhood of each of these 3PSSs is defined by the six magnitudes and the joint probability distribution of the corresponding six structure factors is derived according to Hauptman's neighborhood principle. This distribution leads to the conditional probability distribution of each of the 3PSSs, assuming as known the six magnitudes in its first neighborhood. The conditional probability distributions can be directly used to yield the reliable estimates (0 or pi) of the one-phase structure seminvariants (1PSSs) in the favorable case that the variances of the distributions happen to be small [Hauptman (1975). Acta Cryst. A31, 680-687]. The relevant parameters in the formulas for the monoclinic and orthorhombic systems are given in a tabular form. The applications suggest that the method is efficient for estimating the 1PSSs with values of 0 or pi.

物体朝向对场景内在参照系建立的影响

Six experiments tested how headings of objects in scenes influenced the construction for the intrinsic frame of reference under different structure and viewpoint amount conditions. In Experiment 1 and 2, participants stood at 0 degree and learned an asymmetrical scene and a symmetrical scene that were composed by balls with no apparent headings separately. In Experiment 3, 4, 5 and 6, toys with apparent headings were used and they all faced the 315 degree of the scene. In Experiment 3 and 4, participants stood at 0 degree and learned an asymmetrical scene and a symmetrical scene that were composed by toys separately. In Experiment 5 and 6, participants stood at 0 and 315 degree and learned an asymmetrical scene and a symmetrical scene that were composed by toys separately. After learning, participants needed to finish triplet recognition tasks in all the experiments. The dependent measures were response latency and accuracy. The correct response latencies to the targets were analyzed by ANOVA. Accuracy was used to filter data and analyzed in an ANOVA in some experiments as a reference. Results indicate that headings of objects in scenes influence the pattern for intrinsic frame of reference. The structure of scene affects the acting mechanism of heading, but the amount of viewpoints does not have this effect. If the objects in scenes have no apparent headings, there will be viewpoint dependent effect and the advantage of symmetry axis as intrinsic axis in triplet recognition tasks. If the objects in scenes have apparent headings, people’s spatial memory pattern will be affected by objects’ headings. If the heading of objects (315 degree) is not parallel to the viewpoint (0 degree) in an asymmetrical scene, people will be inclined to represent the scene from the heading of objects but not from the viewpoint. As a result, the viewpoint dependent effect will disappear, and there is significant advantage for the triplets presented from heading of objects. If the heading of objects is not parallel to the symmetry axis in a symmetrical scene, people will represent the scene not only according to the symmetry axis as intrinsic axis, but also according to the heading of objects. As a result, the significant advantage for symmetry axis as intrinsic axis in triplet recognition tasks will disappear but there will be still a tendency. By contrast, the effect for the headings of objects is more significant in asymmetrical scenes than that in symmetrical scenes.

Real-time investigation of the photodissociation dynamics of p-chlorotoluene and p-dichlorobenzene

De-excited dynamics of p-chlorotoluene and p-dichlorobenzene have been investigated by the femtosecond pump-probe method in a supersonic molecular beam. The yields of the parent ion and daughter ion are examined as a function of the delay time between the pump and probe laser pulses. The lifetime constants of excited p-chlorotoluene and p-dichlorobenzene are determined. Possible de-excitation mechanisms are suggested that the initially excited S-1 state is predissociative via the repulsive triplet state. The substituent effects of additional chlorine atom and methyl group are discussed. Moreover, for the first time, we observe a novel quantum beat oscillation in p-dichlorobenzene. (c) 2005 Elsevier B.V. All rights reserved.

Analysis of Sequence Periodicity in E. coli Proteins: Empirical Investigation of the ?Duplication and Divergence? Theory of Protein Evolution

Gatherer, D., and McEwan, N.R. (2003). Analysis of sequence periodicity in E. coli proteins: empirical investigation of the 'duplication and divergence' theory of protein evolution. Journal of Molecular Evolution 57, 149-158. RAE2008

Electronic spectroscopy of thiones

The phosphorescence excitation spectra of two thiones, 4-H-1-xanthione (XT) and 4-H-1-pyrane-4-thione (PT), cooled in a supersonic jet were investigated. The vibronic lineshape of the T1z origin of PT measured by cavity ring-down spectroscopy is considered and the excited state rotational constants are calculated. For XT the 3A2(nπ* ) → X1A1 phosphorescence excitation spectrum was investigated in the region 14900-17600 cm-1. The structure observed is shown to be due to the T1← S0 absorption and an assignment in terms of the vibronic structure of the band is proposed. A previous assignment of the S1 ← S0 origin is considered and the transition involved is shown to be most probably due to the absorption of a vibronic tiplet state T1z,v7. An alternative but tentative assignment of the S1,0 ←S0,0 transition is suggested. In the case of PT the phosphorescence excitation spectrum was investigated in the region of the 1A2(ππ*) ← X1A1 absorption band between 27300 and 28800 cm-1. The spectrum exhibits complex features which are typical for the strong vibronic coupling case of two adjacent electronic states. The observed intermediate level structure was attributed to the coupling with a lower lying dark electronic state 1B1(nπ*2), whose origin was estimated to be ~ 825 - 1025 cm-1 below the origin of 1A2(ππ*)0. Consequences of the vibronic coupling on the decay dynamics of 1A2(ππ*) as well as tentative assignments of vibronic transitions 1A2(ππ*)v ← X1A1 are also discussed. In the T1z ← S0 cavity ring-down absorption spectrum of PT, the vibronic lineshape of the T1z origin is analysed. As the T1z line is separated from the T1x,1y lines by a large zero-field splitting it is possible to use an Asyrot-like program to calculate the vibrational-rotational parameters determining the lineshape. It is shown that PT is non-planar in the first excited triplet state and the lineshape is composed of a mixture of A-type and C-type bandshapes. The non-planarity of PT is discussed.

Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation

Ribosome profiling (ribo-seq) is a recently developed technique that provides genomewide information on protein synthesis (GWIPS) in vivo. The high resolution of ribo-seq is one of the exciting properties of this technique. In Chapter 2, I present a computational method that utilises the sub-codon precision and triplet periodicity of ribosome profiling data to detect transitions in the translated reading frame. Application of this method to ribosome profiling data generated for human HeLa cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame. Since the initial publication of the ribosome profiling technique in 2009, there has been a proliferation of studies that have used the technique to explore various questions with respect to translation. A review of the many uses and adaptations of the technique is provided in Chapter 1. Indeed, owing to the increasing popularity of the technique and the growing number of published ribosome profiling datasets, we have developed GWIPS-viz (http://gwips.ucc.ie), a ribo-seq dedicated genome browser. Details on the development of the browser and its usage are provided in Chapter 3. One of the surprising findings of ribosome profiling of initiating ribosomes carried out in 3 independent studies, was the widespread use of non-AUG codons as translation initiation start sites in mammals. Although initiation at non-AUG codons in mammals has been documented for some time, the extent of non-AUG initiation reported by these ribo-seq studies was unexpected. In Chapter 4, I present an approach for estimating the strength of initiating codons based on the leaky scanning model of translation initiation. Application of this approach to ribo-seq data illustrates that initiation at non-AUG codons is inefficient compared to initiation at AUG codons. In addition, our approach provides a probability of initiation score for each start site that allows its strength of initiation to be evaluated.

Altered gene expression and DNA damage in peripheral blood cells from Friedreich's ataxia patients: cellular model of pathology.

The neurodegenerative disease Friedreich's ataxia (FRDA) is the most common autosomal-recessively inherited ataxia and is caused by a GAA triplet repeat expansion in the first intron of the frataxin gene. In this disease, transcription of frataxin, a mitochondrial protein involved in iron homeostasis, is impaired, resulting in a significant reduction in mRNA and protein levels. Global gene expression analysis was performed in peripheral blood samples from FRDA patients as compared to controls, which suggested altered expression patterns pertaining to genotoxic stress. We then confirmed the presence of genotoxic DNA damage by using a gene-specific quantitative PCR assay and discovered an increase in both mitochondrial and nuclear DNA damage in the blood of these patients (p<0.0001, respectively). Additionally, frataxin mRNA levels correlated with age of onset of disease and displayed unique sets of gene alterations involved in immune response, oxidative phosphorylation, and protein synthesis. Many of the key pathways observed by transcription profiling were downregulated, and we believe these data suggest that patients with prolonged frataxin deficiency undergo a systemic survival response to chronic genotoxic stress and consequent DNA damage detectable in blood. In conclusion, our results yield insight into the nature and progression of FRDA, as well as possible therapeutic approaches. Furthermore, the identification of potential biomarkers, including the DNA damage found in peripheral blood, may have predictive value in future clinical trials.

Spectroscopy and metastability of CO22+ molecular ions

The spectroscopy and metastability of the carbon dioxide doubly charged ion, the CO22+ dication, have been studied with photoionization experiments: time-of-flight photoelectron photoelectron coincidence (TOF-PEPECO), threshold photoelectrons coincidence (TPEsCO), and threshold photoelectrons and ion coincidence (TPEsCO ion coincidence) spectroscopies. Vibrational structure is observed in TOF-PEPECO and TPEsCO spectra of the ground and first two excited states. The vibrational structure is dominated by the symmetric stretch except in the TPEsCO spectrum of the ground state where an antisymmetric stretch progression is observed. All three vibrational frequencies are deduced for the ground state and symmetric stretch and bending frequencies are deduced for the first two excited states. Some vibrational structure of higher electronic states is also observed. The threshold for double ionization of carbon dioxide is reported as 37.340+/-0.010 eV. The fragmentation of energy selected CO22+ ions has been investigated with TPEsCO ion coincidence spectroscopy. A band of metastable states from similar to38.7 to similar to41 eV above the ground state of neutral CO2 has been observed in the experimental time window of similar to0.1-2.3 mus with a tendency towards shorter lifetimes at higher energies. It is proposed that the metastability is due to slow spin forbidden conversion from bound excited singlet states to unbound continuum states of the triplet ground state. Another result of this investigation is the observation of CO++O+ formation in indirect dissociative double photoionization below the threshold for formation of CO22+. The threshold for CO++O+ formation is found to be 35.56+/-0.10 eV or lower, which is more than 2 eV lower than previous measurements. (C) 2005 American Institute of Physics.

Electron impact ionization of He above the threshold

Near-threshold ionization of He has been studied by using a uniform semiclassical wavefunction for the two outgoing electrons in the final channel. The quantum mechanical transition amplitude for the direct and exchange scattering derived earlier by using the Kohn variational principle has been used to calculate the triple differential cross sections. Contributions from singlets and triplets are critically examined near the threshold for coplanar asymmetric geometry with equal energy sharing by the two outgoing electrons. It is found that in general the tripler contribution is much smaller compared to its singlet counterpart. However, at unequal scattering angles such as theta (1) = 60 degrees, theta (2) = 120 degrees the smaller peaks in the triplet contribution enhance both primary and secondary TDCS peaks. Significant improvements of the primary peak in the TDCS are obtained for the singlet results both in symmetric and asymmetric geometry indicating the need to treat the classical action variables without any approximation. Convergence of these cross sections are also achieved against the higher partial waves. Present results are compared with absolute and relative measurements of Rosel et al (1992 Phys. Rev. A 46 2539) and Selles et al (1987 J. Phys. B. At. Mel. Phys. 20 5195) respectively.

Density functional and Monte Carlo studies of sulfur. I. Structure and bonding in S-n rings and chains (n=2-18) (vol 118, pg 9257, 2003)

Density functional calculations have been performed for ring isomers of sulfur with up to 18 atoms, and for chains with up to ten atoms. There are many isomers of both types, and the calculations predict the existence of new forms. Larger rings and chains are very flexible, with numerous local energy minima. Apart from a small, but consistent overestimate in the bond lengths, the results reproduce experimental structures where known. Calculations are also performed on the energy surfaces of S8 rings, on the interaction between a pair of such rings, and the reaction between one S8 ring and the triplet diradical S8 chain. The results for potential energies, vibrational frequencies, and reaction mechanisms in sulfur rings and chains provide essential ingredients for Monte Carlo simulations of the liquid–liquid phase transition. The results of these simulations will be presented in Part II.

Molecular dynamics studies of trinucleotide repeat DNA involved in neurodegenerative disorders.

Expansion of trinucleotide repeat DNA of the classes CAG�·CTG, CGG�·CCG and GAA�·TTC are found to be associated with several neurodegenerative disorders. Different mechanisms have been attributed to the expansion of triplets, mainly involving the formation of alternate secondary structures by such repeats. This paper reports the molecular dynamics simulation of triplet repeat DNA sequences to study the basic structural features of DNA that are responsible for the formation of structures such as hairpins and slip-strand DNA leading to expansion. All the triplet repeat sequences studied were found to be more flexible compared to the control sequence unassociated with disease. Moreover, flexibility was found to be in the order CAG�·CTG > CGG�·CCG = GAA�·TTC, the highly flexible CAG�·CTG repeat being the most common cause of neurodegenerative disorders. In another simulation, a single G�·C to T�·A mutation at the 9th position of the CAG�·CTG repeat exhibited a reduction in bending compared to the pure 15-mer CAGâ�¢CTG repeat. EPM1 dodecamer repeat associated with the pathogenesis of progressive myoclonus epilepsy was also simulated and showed flexible nature suggesting a similar expansion mechanism.

Novel Porphyrin-Incorporated Hydrogels for Photoactive Intraocular Lens Biomaterials

Novel surface-modified hydrogel materials have been prepared by binding charged porphyrins TMPyP (tetrakis-(4-N-methylpyridyl)porphyrin) and TPPS (tetrakis(4-sulfonatophenyl)porphyrin) to copolymers of HEMA (2-hydroxyethyl methacrylate) with either MAA (methacrylic acid) or DEAEMA (2-(diethylamino)ethylmethacrylate). The charged hydrogels display strong electrostatic interactions with the appropriate cationic or anionic porphyrins to give materials which are intended to be used to generate cytotoxic singlet oxygen (1O2) on photoexcitation and can therefore be used to reduce postoperative infection of the intraocular hydrogel-based replacement lenses that are used in cataract surgery. The UV/vis spectra of TMPyP in MAA:HEMA copolymers showed a small shift in the Soret band and a change from single exponential (161 ���­s) triplet decay lifetime in solution to a decay that could be fitted to a biexponential fit with two approximately equal components with ���´ ) 350 and 1300 ���­s. O2 bubbling reduced the decay to a dominant (90%) component with a much reduced lifetime of 3 ���­s and a minor, longer lived (20 ���­s) component. With D2O solvent the 1O2 lifetime was measured by 1270 nm fluorescence as 35 ���­s in MAA:HEMA, compared to 67 ���­s in solution, although absorbance-matched samples showed similar yield of 1O2 in the polymers and in aqueous solution. In contrast to the minor perturbation in photophysical properties caused by binding TMPyP to MAA:HEMA, TPPS binding to DEAEMA:HEMA copolymers profoundly changed the 1O2 generating ability of the TPPS. In N2-bubbled samples, the polymer-bound TPPS behaved in a similar manner to TMPyP in its copolymer host; however, O2 bubbling had only a very small effect on the triplet lifetime and no 1O2 generation could be detected. The difference in behavior may be linked to differences in binding in the two systems. With TMPyP in MAA:HEMA, confocal fluorescence microscopy showed significant penetration of the porphyrin into the core of the polymer film samples (>150 ���­m). However, for TPPS in DEAEMA:HEMA copolymers, although the porphyrin bound much more readily to the polymer, it remained localized in the first 20 ���­m, even in heavily loaded samples. It is possible that the resulting high concentration of TPPS may have cross-linked the hydrogels to such an extent that it significantly reduced the solubility and/or diffusion rate of oxygen into the doped polymers. This effect is significant since it demonstrates that even simple electrostatic binding of charged porphyrins to hydrogels can have an unexpectedly large effect on the properties of the system as a whole. In this case it makes the apparently promising TPPS/DEAEMA:HEMA system a poor candidate for clinical application as a postoperative antibacterial treatment for intraocular lenses while the apparently equivalent cationic system TMPyP/MAA:HEMA displays all the required properties.