| 1. |
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| 2. |
- Gonzalez-Ramirez, Israel, et al.
(författare)
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On the photoproduction of DNA/RNA cyclobutane pyrimidine dimers
- 2011
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 128:4-6, s. 705-711
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Tidskriftsartikel (refereegranskat)abstract
- The UV photoreactivity of different pyrimidine DNA/RNA nucleobases along the singlet manifold leading to the formation of cyclobutane pyrimidine dimers has been studied by using the CASPT2 level of theory. The initially irradiated singlet state promotes the formation of excimers between pairs of properly oriented nucleobases through the overlap between the pi structures of two stacked nucleobases. The system evolves then to the formation of cyclobutane pyrimidine dimers via a shearing-type conical intersection activating a [2 + 2] photocycloaddition mechanism. The relative location of stable excimer conformations or alternative decay channels with respect to the reactive degeneracy region explains the differences in the photoproduction efficiency observed in the experiments for different nucleobases sequences. A comparative analysis of the main structural parameters and energetic profiles in the singlet manifold is carried out for thymine, uracil, cytosine, and 5-methylcytosine homodimers. Thymine and uracil dimers display the most favorable paths, in contrast to cytosine. Methylation of the nucleobases seems to increase the probability for dimerization.
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| 3. |
- Idelfonso-García, Osiris Germán, et al.
(författare)
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Nucleoredoxin Redox Interactions Are Sensitized by Aging and Potentiated by Chronic Alcohol Consumption in the Mouse Liver
- 2024
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Ingår i: Antioxidants. - 2076-3921. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- Aging is characterized by increased reactive species, leading to redox imbalance, oxidative damage, and senescence. The adverse effects of alcohol consumption potentiate aging-associated alterations, promoting several diseases, including liver diseases. Nucleoredoxin (NXN) is a redox-sensitive enzyme that targets reactive oxygen species and regulates key cellular processes through redox protein–protein interactions. Here, we determine the effect of chronic alcohol consumption on NXN-dependent redox interactions in the liver of aged mice. We found that chronic alcohol consumption preferentially promotes the localization of NXN either into or alongside senescent cells, declines its interacting capability, and worsens the altered interaction ratio of NXN with FLII, MYD88, CAMK2A, and PFK1 proteins induced by aging. In addition, carbonylated protein and cell proliferation increased, and the ratios of collagen I and collagen III were inverted. Thus, we demonstrate an emerging phenomenon associated with altered redox homeostasis during aging, as shown by the declining capability of NXN to interact with partner proteins, which is enhanced by chronic alcohol consumption in the mouse liver. This evidence opens an attractive window to elucidate the consequences of both aging and chronic alcohol consumption on the downstream signaling pathways regulated by NXN-dependent redox-sensitive interactions.
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| 4. |
- Sauri, Vicenta, et al.
(författare)
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Proton/Hydrogen Transfer Mechanisms in the Guanine-€“Cytosine Base Pair : Photostability and Tautomerism
- 2013
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:1, s. 481-496
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Tidskriftsartikel (refereegranskat)abstract
- Proton/hydrogen-transfer processes have been broadly studied in the past 50 years to explain the photostability and the spontaneous tautomerism in the DNA base pairs. In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine–cytosine (GC) base pair. Concerted and stepwise pathways are explored initially in vacuo, and three mechanisms are studied: the stepwise double proton transfer, the stepwise double hydrogen transfer, and the concerted double proton transfer. The results are consistent with previous findings related to the photostability of the GC base pair, and a new contribution to tautomerism is provided. The C-based imino-oxo and imino-enol GC tautomers, which can be generated during the UV irradiation of the Watson–Crick base pair, have analogous radiationless energy-decay channels to those of the canonical base pair. In addition, the C-based imino-enol GC tautomer is thermally less stable. A study of the GC base pair is carried out subsequently taking into account the DNA surroundings in the biological environment. The most important stationary points are computed using the quantum mechanics/molecular mechanics (QM/MM) approach, suggesting a similar scenario for the proton/hydrogen-transfer phenomena in vacuo and in DNA. Finally, the static model is complemented by ab initio dynamic simulations, which show that vibrations at the hydrogen bonds can indeed originate hydrogen-transfer processes in the GC base pair. The relevance of the present findings for the rationalization of the preservation of the genetic code and mutagenesis is discussed.
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| 5. |
- Andres-Martin, Miguel, et al.
(författare)
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Uncertainty in surface wind speed projections over the Iberian Peninsula: CMIP6 GCMs versus a WRF-RCM
- 2023
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Ingår i: Annals of the New York Academy of Sciences. - 0077-8923 .- 1749-6632. ; 1529:1, s. 101-108
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Tidskriftsartikel (refereegranskat)abstract
- This study assessed the projected near-surface wind speed (SWS) changes and variability over the Iberian Peninsula for the 21st century. Here, we compared Coupled Model Intercomparison Project Phase 6 global climate models (GCMs) with a higher spatial resolution regional climate model (RCM; ∼20km), known as WRF-CESM2, which was created by a dynamic downscaling of the Community Earth System Model version 2 (CESM2) using the Weather Research and Forecasting (WRF) model. Our analysis found that the GCMs tended to overestimate observed SWS for 1985–2014, while the higher spatial resolution of the WRF-CESM2 did not improve the accuracy and underestimated the SWS magnitude. GCMs project a decline of SWS under highshared socioeconomic pathways (SSPs) greenhouse concentrations, such as SSP370 and SSP585, while an interdecadal oscillation appears in SSP126 and SSP245 for the end of the century. The WRF-CESM2 under SSP585 predicts the opposite increasing SWS. Our results suggest that 21st-century projections of SWS are uncertain even for regionalized products and should be taken with caution.
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| 6. |
- Aquilante, Francesco, et al.
(författare)
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Software news and update MOLCAS 7 : The Next Generation
- 2010
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 31:1, s. 224-247
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Forskningsöversikt (refereegranskat)abstract
- Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two-electron integrals and in the generation of so-called auxiliary basis sets. The article describes how the method is implemented for most known wave functions models: self-consistent field, density functional theory, 2nd order perturbation theory, complete-active space self-consistent field multiconfigurational reference 2nd order perturbation theory, and coupled-cluster methods. The report further elaborates on the implementation of a restricted-active space self-consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas-Kroll-Hess transformation for one-component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so-called picture-change-free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies.
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| 7. |
- Borg, Anders, 1978-
(författare)
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Theoretical Photochemistry : Halogenated Arenes, Phytochromobilin, Ru(II)polypyridyl complexes and 6-4 photoadducts
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis presents Quantum Chemical calculations on the Photochemistry of Halogenated benzenes, Phytochromobilin, Ruthenium Polypyridyl complexes and 6-4 photoadducts in DNA. The work is focused on improving the understanding of a number of experimentally observed photochemical processes in these systems. New results regarding the mechanism of photodissociation of halogenated arenes, photointerconversion of phytochromobilin are presented, as well as of the photoprocesses of Ruthenium Polypyridyl complexes and new mechanistic insights in the repair of 6-4 photoadducts in DNA.
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| 8. |
- Boström, Jonas, et al.
(författare)
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Calibration of Cholesky Auxiliary Basis Sets for Multiconfigurational Perturbation Theory Calculations of Excitation Energies
- 2010
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 6:3, s. 747-754
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Tidskriftsartikel (refereegranskat)abstract
- The accuracy of auxiliary basis sets derived from Cholesky decomposition of two-electron integrals is assessed for excitation energies calculated at the state-average complete active space self-consistent field (CASSCF) and multiconfigurational second order perturbation theory (CASPT2) levels of theory using segmented as well as generally contracted atomic orbital basis sets. Based on 196 valence excitations in 26 organic molecules and 72 Rydberg excitations in 3 organic molecules, the results show that Cholesky auxiliary basis sets can be used without compromising the accuracy of the multiconfigurational methods. Specifically, with a decomposition threshold of 10(-4) au, the mean error due to the Cholesky auxiliary basis set is 0.001 eV, or smaller, decreasing with increasing atomic orbital basis set quality.
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| 9. |
- Giussani, Angelo, et al.
(författare)
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Photoinduced Formation Mechanism of the Thymine-Thymine (6-4) Adduct
- 2013
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:7, s. 1999-2004
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Tidskriftsartikel (refereegranskat)abstract
- The photoinduced mechanism leading to the formation of the thymine-thymine (6-4) photolesion has been studied by using the CASPT2//CASSCF approach over a dinucleotide model in vacuo. Following light absorption, localization of the excitation on a single thymine leads to fast singlet-triplet crossing that populates the triplet 3(n pi*) state of thymine. This state, displaying an elongated C-4=O bond, triggers (6-4) dimer formation by reaction with the C-5=C-6 double bond of the adjacent thymine, followed by a second intersystem crossing, which acts as a gate between the excited state of the reactant and the ground state of the photoproduct. The requirement of localized excitation on just one thymine, whose main decay channel (by radiationless repopulation of its ground state) is nonphotochemical, can rationalize the experimentally observed low quantum yield of formation for the thymine-thymine (6-4) adduct.
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| 10. |
- Gobbo, Joao Paulo, et al.
(författare)
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On the Deactivation Mechanisms of Adenine-Thymine Base Pair
- 2012
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 116:13, s. 4089-4097
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Tidskriftsartikel (refereegranskat)abstract
- In this contribution, the multiconfigurational second-order perturbation theory method based on a complete active space reference wave function (CASSCF/CASPT2) is applied to study all possible single and double proton/hydrogen transfers between the nucleobases in the adenine-thymine (AT) base pair, analyzing the role of excited states with different nature [localized (LE) and charge transfer (CT)] and considering concerted as well as step-wise mechanisms. According to the findings, once the lowest excited states, localized in adenine, are populated during UV irradiation of the Watson-Crick base pair, the proton transfer in the N-O bridge does not require high energy in order to populate a CT state. The latter state will immediately relax toward a crossing with the ground state, which will funnel the system to either the canonical structure or the imino-enol tautomer. The base pair is also capable of repairing itself easily since the imino-enol species is unstable to thermal conversion.
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