1,720,972 research outputs found
VIBRATIONAL ACTIVITY AND PHOTOISOMERIZATION PATHS OF THE GREEN FLUORESCENT PROTEIN CHROMOPHORE: VACUO AND SOLVENT EFFECTS BY QM-COMPUTATIONS
No full textThe Green Fluorescent Protein (GFP) from the jellyfish Aequorea victoria has become a useful tool in molecular biology and biochemistry. Most of these applications take advantage of the highly fluorescent chromophore generated auto-catalytically via post-translational internal cyclization, dehydration and oxidation of the Ser65-Tyr66-Gly67 tri-peptide unit. Vibrational spectroscopy (infrared, Raman and resonance Raman spectra) of GFP and model chromophores in several protonation states has been extensively studied to achieve information about its molecular structure and activity. However, these spectroscopic data have not yet been satisfactorily reproduced and interpreted on the basis of quantum-chemical calculations, and a convincing well supported model for the lack of fluorescence in solution vs. the fluorescence observed in the protein is still lacking. For this reason, the objective of this work is to simulate the vibrational structure and the photochemical reaction paths of a realistic GFP chromophore model, the 4’-hydroxybenzylidene-2,3-dimethyl-imidazolinone (HBDI), which includes the complete conjugate system of the real chromophore and has been investigated in several studies in solution.
In this work vibrational activities in the infrared, Raman and resonance Raman spectra of the cationic, neutral and anionic forms of HBDI have been obtained from quantum-chemical calculations in vacuo and with the inclusion of solvent effects through the polarizable continuum model (PCM) at different levels of theory (HF, CIS and CASSCF, in conjunction with the 6-31G* and 6-31+G* basis sets). It is found that inclusion of solvent effects improves the agreement with experimental data for all the species considered, but it is crucial to reproduce correctly the vibrational activities of the anionic form and its photochemical reaction paths. Photoisomerization routes for the anionic form in solution have been computed, which account for the ultrafast radiationless decay and lack of fluorescence observed for the chromophore in solution. Finally, a model for the photochemical behaviour of the chromophore in the protein is presented which explains its fluorescence and biological activity
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Light driven molecular switches: exploring and tuning their photophysical and photochemical properties
No full textIn recent years, computational photochemistry has become a valid tool for the investigation of photophysical properties and photochemical reaction mechanisms in organic chromophores. Theoretical chemists can now adapt their tools to the subject under investigation and to the type and accuracy of the desired information. Different computational strategies can now be adopted to characterize different aspects of the photoinduced molecular reactivity of a given chromophore and to provide, in principle, a quite detailed description of the reactive process from energy absorption to photoproducts formation. A basic aim is to establish a correlation between the structure of the molecule and its photochemical outcome, and, in particular, to assess the effect of modifications of the chromophore and of the molecular environment.
In this perspective recent advances and applications of photoinduced cistrans isomerizations involving some organic chromophores active in biologically or technologically relevant problems is reviewed here and discussed in the light of new results. In particular, the photochemistry of azobenzene, retinals and of the green fluorescent protein chromophore is considered, taking into account structural changes and environment effects. The results presented in this work are intended to be a first step toward the design of chromophores that can act as molecular photoswitches
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
A tunable QM/MM approach to chemical reactivity, structure and physico-chemical properties prediction
No full textThis contribution describes a new implementation of a general hybrid approach with a modular structure (called COBRAMM: Computations at Bologna Relating Ab‐initio and Molecular Mechanic Methods) that is able to integrate some specialized programs and acts as a flexible computational environment, thus increasing the flexibility/efficiency of both QM, and MM, and QM/MM calculations. Specifically, QM/MM ground and excited states geometry optimizations, frequency calculations, conical intersection searches and adiabatic/non‐adiabatic molecular dynamics can be performed on a large molecular system, that can be split up to three different layers corresponding to different levels of accuracy
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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