1,721,031 research outputs found
Quantum mechanical computations and spectroscopy: From small rigid molecules in the gas phase to large flexible molecules in solution
No full textInterpretation of structural properties and dynamic behavior of molecules in solution is of fundamental importance to understand their stability, chemical reactivity, and catalytic action. While information can be gained, in principle, by a variety of spectroscopic techniques, the interpretation of the rich indirect information that can be inferred from the analysis of experimental spectra is seldom straightforward because of the subtle interplay of several different effects, whose specific role is not easy to separate and evaluate. In such a complex scenario, theoretical studies can be very helpful at two different levels: (i) supporting and complementing experimental results to determine the structure of the target molecule starting from its spectral properties; (ii) dissecting and evaluating the role of different effects in determining the observed, spectroscopic properties. This is the reason why computational spectroscopy is rapidly evolving from a highly specialized research field into a versatile and widespread tool for the assignment of experimental spectra and their interpretation in terms of chemical physical effects. In such a situation, it becomes important that both computationally and experimentally oriented chemists are aware that new methodological advances and integrated computational strategies are available, providing reliable estimates of fundamental spectral parameters not only for relatively small molecules in the gas phase but also for large and flexible molecules in condensed phases.In this Account, we review the most significant methodological contributions from our research group in this field, and by exploiting some recent results of their application to the computation of IR, UV-vis, NMR, and EPR spectral parameters, we discuss the microscopic mechanisms underlying solvent and vibrational effects on the spectral parameters.After reporting some recent achievements for the study of excited states by first principle quantum mechanical approaches, we focus on the treatment of environmental effects by means of mixed discrete-continuum solvent models and on effective methods for computing vibronic contributions to the spectra. We then discuss some new developments, mainly based on time-dependent approaches, allowing us to go beyond the determination of spectroscopic parameters toward the simulation of line widths and shapes.Although further developments are surely needed to improve the accuracy and effectiveness of several items in the proposed approach, we try to show that the first important steps toward a direct. comparison between the results obtained in vitro and those obtained in silico have been made, making easier fruitful crossovers among experiments, computations and theoretical models, which would be decisive for a deeper understanding of the spectral behavior associated with complex systems and processes
Excited states behavior of nucleobases in solution: insights from computational studies
No full textWe review the most significant results obtained in the study of isolated nucleobases in solution by quantum mechanical methods, trying to highlight also the most relevant open issues. We concisely discuss some methodological issues relevant to the study of molecular electronic excited molecular states in condensed phases, focussing on the methods most commonly applied to the study of nucleobases, i.e. continuum models as the Polarizable Continuum Model and explicit solvation models. We analyse how the solvent changes the relative energy of the lowest energy excited states in the Franck-Condon region, their minima and the Conical Intersections among the different states, interpreting the experimental optical spectra, both steady state and time-resolved. Several methods are available for accurately including solvent effects in the Franck-Condon region, and for most of the nucleobases the solvent shift on the different excited states can be considered assessed. The study of the excited state decay, both radiative and non-radiative, in solution still poses instead significant theoretical challenges
TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids
Full text linkWe present a computational study of the magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil, thymine, and cytosine, using the B3LYP and CAM-B3LYP functionals. Solvent effects are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In general, the computed spectra are found to be in good agreement with the experimental ones, apart from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine bases are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific, but they do not in general alter the qualitative shape of the spectra. The bands are dominated by the bright π → π* transitions, and our calculations in solution nicely reproduce their energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n → π* excitations, but they are too weak to be observed in the experiment
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
Relative Stability of the La and Lb Excited States in Adenine and Guanine: Direct Evidence from TD-DFT Calculations of MCD Spectra
No full textThe relative position of La and Lb ππ* electronic states in purine
nucleobases is a much debated topic, since it can strongly affect our understanding of
their photoexcited dynamics. To assess this point, we calculated the absorption and
magnetic circular dichroism (MCD) spectra of adenine, guanine, and their nucleosides
in gas-phase and aqueous solution, exploiting recent developments in MCD
computational technology within time-dependent density functional theory. MCD
spectroscopy allows us to resolve the intense S0→ La transition from the weak S0→ Lb
transition. The spectra obtained in water solution, by using B3LYP and CAM-B3LYP
functionals and describing solvent effect by cluster models and by the polarizable
continuum model (PCM), are in very good agreement with the experimental
counterparts, thus providing direct and unambiguous evidence that the energy ordering
predicted by TD-DFT, La < Lb, is the correct one
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
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
Localized and Excimer Triplet Electronic States of Naphthalene Dimers: A Computational Study
No full text18 pages, 8 figures, 4 tables . -- This article belongs to the Section Physical ChemistryWe perform DFT calculations with different hybrid (ωB97X-D and M05-2X) and double hybrid (B2PLYP-D3 and ωB2PLYP) functionals to characterize the lowest energy triplet excited states of naphthalene monomer and dimers in different stacking arrangements and to simulate their absorption spectra. We show that both excimer and localized triplet minima exist. In the former, the spin density is delocalized over the two monomers, adopting a face-to-face arrangement with a short inter-molecular distance. In the latter, the spin density is localized on a single naphthalene molecule, and different minima or pseudo-minima are possible, the most stable one corresponding to a slipped parallel arrangement. According to B2PLYP-D3 calculations, excimer minima are the most stable, in line with the indications of ADC(2) studies. However, the relative stability of the minima is reverted when including thermal and vibrational effects. Excimer minima exhibit a very intense absorption spectrum, peaking above 500 nm. The computed absorption spectra of localized minima significantly depend on the stacking geometry and do not coincide with that of isolated naphthalene. Hybrid functionals provide very accurate vibronic absorption spectra for naphthalene monomer, both in the singlet and in the triplet state, but underestimate the stability of the excimer triplet.This research was funded by the National Center for Gene Therapy and Drugs Based
on RNA Technology, funded by the European Union—Next Generation EU, Project CN00000041,
CUP B93D21010860004; program “Progetti di Ricerca @cnr”, project UCATG4; NUTRAGE funded by
FOE-2021 DBA.AD005.225.Peer reviewe
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
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