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| 2. |
- Bushnell, Eric A. C., et al.
(author)
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The first branching point in porphyrin biosynthesis : a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase
- 2011
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In: Journal of Computational Chemistry. - New York : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 32:5, s. 822-834
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Journal article (peer-reviewed)abstract
- In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.
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| 3. |
- Carraminana, Albert, et al.
(author)
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Rationale and Study Design for an Individualized Perioperative Open Lung Ventilatory Strategy in Patients on One-Lung Ventilation (iPROVE-OLV)
- 2019
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In: Journal of Cardiothoracic and Vascular Anesthesia. - : W B SAUNDERS CO-ELSEVIER INC. - 1053-0770 .- 1532-8422. ; 33:9, s. 2492-2502
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Journal article (peer-reviewed)abstract
- Objective: The aim of this clinical trial is to examine whether it is possible to reduce postoperative complications using an individualized perioperative ventilatory strategy versus using a standard lung-protective ventilation strategy in patients scheduled for thoracic surgery requiring one-lung ventilation. Design: International, multicenter, prospective, randomized controlled clinical trial. Setting: A network of university hospitals. Participants: The study comprises 1,380 patients scheduled for thoracic surgery. Interventions: The individualized group will receive intraoperative recruitment maneuvers followed by individualized positive end-expiratory pressure (open lung approach) during the intraoperative period plus postoperative ventilatory support with high-flow nasal cannula, whereas the control group will be managed with conventional lung-protective ventilation. Measurements and Main Results: Individual and total number of postoperative complications, including atelectasis, pneumothorax, pleural effusion, pneumonia, acute lung injury; unplanned readmission and reintubation; length of stay and death in the critical care unit and in the hospital will be analyzed for both groups. The authors hypothesize that the intraoperative application of an open lung approach followed by an individual indication of high-flow nasal cannula in the postoperative period will reduce pulmonary complications and length of hospital stay in high-risk surgical patients. (C) 2019 Published by Elsevier Inc.
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| 4. |
- Lipfert, Jan, et al.
(author)
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Radiation Induced Damage in Serine Phosphate : Insights into a Mechanism for Direct DNA Strand Breakage
- 2004
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 108:23, s. 8036-8042
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Journal article (peer-reviewed)abstract
- The radiation-induced decomposition mechanisms of l-O-serine phosphate and the properties of the resulting radicals are explored at the hybrid Hartree−Fock−density functional theory level B3LYP, incorporating a polarized continuum model (IEF-PCM). Three different radical products were identified in earlier experimental studies, formed through deamination (radical I), decarboxylation plus radical exchange (radical II), or dephosphorylation (radical III) reactions, respectively. The calculated hyperfine coupling constants of the resulting radicals agree well with experimental data. The computed energetics for the two competing mechanisms resulting from electron capture, radicals I and III, show that the deamination reaction is barrierless, whereas the dephosphorylation reaction requires an initial electronic redistribution and formation of a phosphoranyl radical with trigonal bipyramidal geometry. From this, the dephosphorylation reaction has to overcome a barrier of approximately 26 kcal/mol, which explains the predominance of radical I over radical III in the experimental measurements. For radical II, the initial decarboxylation step resulting from electron loss was explored and found to proceed without barriers. The results of the current study have implications for radiation-induced damage of amino acids. In addition, serine phosphate is a model of a DNA sugar−phosphate fragment, and thus we may obtain new insights into a possible mechanism for cleavage of the phosphate ester bond of the DNA backbone leading to strand break.
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| 5. |
- Llano, Jorge, et al.
(author)
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First Principles Electrochemical Study of Redox Events in DNA Bases and Chemical Repair in Aqueous Solution
- 2004
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In: Physical Chemistry, Chemical Physics - PCCP. - 1463-9076 .- 1463-9084. ; 6, s. 2426-2433
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Journal article (peer-reviewed)abstract
- Primary and secondary radiation-induced damage to DNA, and chemical repair of the lesions on the nucleobases in solution involve a cascade of proton transfer (PT), electron transfer (ET), and proton-coupled electron transfer (PT-ET) reactions. The rate constants of these reactions depend on the standard Gibbs energy changes that can be derived from experiment. We here apply a first principles approach to calculate standard Gibbs energy changes of proton, electron, and proton-coupled electron transfer reactions in solution, wherein electrons and protons participate as independent ions; data that is fully compatible with that experimentally derived. Hence, the thermodynamic feasibility of ET and PT-ET pathways for these reactions depending on the effective concentration of hydrogen ions can be directly rationalized from first principles. The focus of this study is the primary and secondary ionization events in nucleobases in the presence of hydrogen atoms, solvated electrons and protons in aqueous solution, leading to the formation of nucleobase radical anions B˙−, radical cations B˙+ and their major deprotonated radical forms B(–H)˙. We also examine the chemical repair reaction by thiols, B(–H)˙(aq)+RSH(aq)=B(aq)+RS˙(aq), where B=A,G,C,T. Our results for the chemical repair of B(–H)˙ suggest that a PT-ET pathway should be favored for A and C at any pH, whereas for G and T, a PT-ET pathway is preferred at acidic and near neutral pH, but in the pH range 9-11, the ET pathway would dominate.
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| 6. |
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| 7. |
- Llano, Jorge, et al.
(author)
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Mechanism of Hydroxyl Radical Addition to Imidazole and Subsequent Water Elimination
- 1999
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 103:26, s. 5598-5607
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Journal article (peer-reviewed)abstract
- The addition reaction of the hydroxyl radical to imidazole and subsequent elimination of water to form the 1-dehydroimidazolyl radical is investigated using MP2 and B3LYP methods, including large basis sets and SCI-PCM modeling of solvent effects. It is found that the barrier to addition of the hydroxyl radical at the 5-position is energetically favored over addition to the 2- or 4-positions by 2−3 kcal/mol at the SCI-PCM/MP2/6-311G(2df,p)//MP2/6-31G(d,p) level, whereas the corresponding B3LYP calculations yield a barrier-free addition at the 5-position. The lower barrier and NBO analysis explain the experimentally observed specificity for the 5-hydroxylation of imidazole and histidine, albeit the 2-adduct is about 4 kcal/mol more stable than the 5-adduct. The NBO energetic analysis shows that the exoanomeric effect stabilizes the transition state at the 5-position about 0.3 kcal/mol more than that at the 2-position. Moreover, the π-interaction between the attacking nonbonding spin orbital of the hydroxyl radical and the π-cloud of imidazole is the least for the transition state at the 5-position, favoring the σC5-O bond formation. The 5-hydroxyimidazolyl radical undergoes a slow elimination of water (the added OH group and the hydrogen at the N1 position) to yield the 1-dehydroimidazolyl radical. The base-catalyzed dehydration profile was modeled in two steps at the B3LYP/6-311G(2df,p)//6-31G(d,p) level. The PES for the dehydration reaction seems rather flat. The first step is a barrier-free loss of the proton at N1 induced by the hydroxide ion to yield the 1-dehydro-5-hydroxyimidazolyl radical anion. In the second step, the hydroxide ion is regenerated from the intermediate to yield the final product with a barrier of 2.7 kcal/mol. The calculated hyperfine structures in the presence of the continuum solvent model for the 5-hydroxyimidazolyl and 1-dehydroimidazolyl radicals are in close agreement with the experimental ones recorded in aqueous solution.
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| 8. |
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| 9. |
- Llano, Jorge, 1968-
(author)
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Modern Computational Physical Chemistry : An Introduction to Biomolecular Radiation Damage and Phototoxicity
- 2004
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Doctoral thesis (other academic/artistic)abstract
- The realm of molecular physical chemistry ranges from the structure of matter and the fundamental atomic and molecular interactions to the macroscopic properties and processes arising from the average microscopic behaviour.Herein, the conventional electrodic problem is recast into the simpler molecular problem of finding the electrochemical, real chemical, and chemical potentials of the species involved in redox half-reactions. This molecular approach is followed to define the three types of absolute chemical potentials of species in solution and to estimate their standard values. This is achieved by applying the scaling laws of statistical mechanics to the collective behaviour of atoms and molecules, whose motion, interactions, and properties are described by first principles quantum chemistry. For atomic and molecular species, calculation of these quantities is within the computational implementations of wave function, density functional, and self-consistent reaction field theories. Since electrons and nuclei are the elementary particles in the realm of chemistry, an internally consistent set of absolute standard values within chemical accuracy is supplied for all three chemical potentials of electrons and protons in aqueous solution. As a result, problems in referencing chemical data are circumvented, and a uniform thermochemical treatment of electron, proton, and proton-coupled electron transfer reactions in solution is enabled.The formalism is applied to the primary and secondary radiation damage to DNA bases, e.g., absorption of UV light to yield electronically excited states, formation of radical ions, and transformation of nucleobases into mutagenic lesions as OH radical adducts and 8-oxoguanine. Based on serine phosphate as a model compound, some insight into the direct DNA strand break mechanism is given.Psoralens, also called furocoumarins, are a family of sensitizers exhibiting cytostatic and photodynamic actions, and hence, they are used in photochemotherapy. Molecular design of more efficient photosensitizers can contribute to enhance the photophysical and photochemical properties of psoralens and to reduce the phototoxic reactions. The mechanisms of photosensitization of furocoumarins connected to their dark toxicity are examined quantum chemically.
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| 10. |
- Llano, Jorge, et al.
(author)
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Oxidation Pathways in Adenine and Guanine in Aqueous Solution from First Principles Electrochemistry
- 2004
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In: Physical Chemistry, Chemical Physics - PCCP. - 1463-9076 .- 1463-9084. ; 6, s. 4707-4713
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Journal article (peer-reviewed)abstract
- The 8-oxo-7,8-dehydropurine tautomers (8-oxoA and 8-oxoG) are mutagenic lesions found in DNA. Two experimental pathways have been proposed for the formation of 8-oxoG: one initiated by deprotonation of the OH˙ radical adduct at the 8-position of guanine (G8OH˙) and the other initiated by a proton-coupled one-electron oxidation of G8OH˙. We here report standard Gibbs energies of the above processes involving proton transfer (PT), electron transfer (ET), and proton-coupled electron transfer (PT–ET) reactions calculated from first principles using DFT (B3LYP) and a continuum solvent model (IEF-PCM). The computed data show that the former pathway is unlikely to occur for A8OH˙ and G8OH˙ in neutral aqueous solution, because of the very low acidity of the hydrogen at the 8-position. In contrast, the latter route involving proton-coupled one-electron oxidations of A8OH˙ and G8OH˙ are exergonic by about 25 kcal mol−1 in aqueous solution. Energetically, adenine and guanine behave similarly toward oxidation to yield 8-oxoA and 8-oxoG. However, the calculated standard Gibbs energetics confirms that the ease of ionization of the native and oxidized forms of nucleobases B to yield the radical cations B˙+ or their deprotonation products B(–H)˙ is 8-oxoG > G > 8-oxoA > A > C > T in aqueous solution. Consequently, 8-oxoG will most readily trap radical cations and neutral radicals in DNA, since it can reduce any nucleobase radical cation B˙+ (via ET) or its deprotonation product B(–H)˙ (via PT–ET) back to the native form of the nucleobase.
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