Estudi teòric de l'activitat enzimàtica de l'anhidrasa carbònica

Consultable des del TDXTítol obtingut de la portada digitalitzadaEn aquesta Tesi s'ha fet un estudi teòric complet del mecanisme de reacció de l'enzim Anhidrasa Carbònica fent servir el mètode Hartree-Fock i mètodes correlacionats MP2. S'han analitzat dos possibles mecanismes de reacció per la hidratació del CO2: el mecanisme de Lipscomb i el de Lindskog. Les barreres energètiques obtingudes per a les reaccions directa i inversa de formació del (NH3)3ZnII(HCO3-) segons els mecanismes de Lipscomb i Lindskog, quan s'hi ha considerat els efectes de correlació electrònica i del medi, són ambdues petites i del mateix ordre. Els millors valors, de 5.5 kcal/mol pel mecanisme de Lindskog i de 6.7 kcal/mol per al de Lipscomb, són compatibles amb el valor màxim permès des d'un punt de vista experimental, que és de 10 kcal/mol. Això fa pensar que la reacció d'hidratació del CO2 en l'Anhidrasa Carbònica es pot donar perfectament per les dues vies. Finalment s'ha analitzat el bescanvi de HCO3- per H2O en l'Anhidrasa Carbònica que porta a recuperar l'enzim en la seva forma inicial. S'ha vist que aquest bescanvi té lloc per coordinació directa d'una molècula d'aigua i posterior sortida de la molècula de bicarbonat facilitada per l'entrada de la molècula d'aigua.In this Thesis, we have carried out a complete theoretical study of the reaction mechanism of the Cabonic Anhydrase enzyme using the Hartree-Fock method and including correlation energy at the MP2 level. We have studied two possible reaction mechanisms for the hydration of CO2: the Lipscomb and Lindskog mechanisms. The energetic barriers obtained for the direct and inverse formation of the (NH3)3ZnII(HCO3-) species are both small and of the same order for the two reaction mechanisms when including the effects of the environment and the correlation corrections. The best values of 5.5 kcal/mol for the Lindskog mechanism and of 6.7 kcal/mol for the Lipscomb mechanism both match the maximum value permitted from an experimental point of view (10 kcal/mol). Therefore, we conclude that the hydration of CO2 by Carbonic Anhydrase can follow any of the two studied reaction mechanisms. Finally, we have analyzed the HCO3- /H2O exchange in the Carbonic Anhydrase that leads to the recovery of the catalytic form of the enzyme. We have found that this exchange takes place after the direct coordination of water to the (NH3)3ZnII(HCO3-) species followed by the HCO3- dissociation, which is favored by the presence of water in the coordination sphere of the metal

Relations among several nuclear and electronic density functional reactivity indexes

A set of connections among several nuclear and electronic indexes of reactivity in the framework of the conceptual Density Functional Theory by using an expansion ofthe energy functional in terms of the total number of electrons and the normal coordinates within a canonical ensemble was derived. The relations obtained provided explicit links between important quantities related to the chemical reactivity of a system. This paper particularly demonstrates that the derivative of the electronic energy with respect to the external potential of a system in its equilibrium geometry was equal to the negative of the nuclear repulsion derivative with respect to the external potentia

2D carbon nitride as a support with single Cu, Ag, and Au atoms for carbon dioxide reduction reaction

Altres ajuts: Red Española de Supercomputación (QHS-2022-1-0017 and QHS-2022-2-0012)The electrochemical conversion of CO into value-added chemicals is an important approach to recycling CO. In this work, we have combined the most efficient metal catalysts for this reaction, namely Cu, Ag, and Au, as single-atom particles dispersed on a two-dimensional carbon nitride support, with the aim of exploring their performance in the CO reduction reaction. Here, we report density functional theory computations showing the effect of single metal-atom particles on the support. We found that bare carbon nitride needed a high overpotential to overcome the energy barrier for the first proton-electron transfer, while the second transfer was exergonic. The deposition of single metal atoms enhances the catalytic activity of the system as the first proton-electron transfer is favored in terms of energy, although strong binding energies were found for CO adsorption on Cu and Au single atoms. Our theoretical interpretations are consistent with the experimental evidence that the competitive H generation is favored due to the strong CO binding energies. Our computational study paves the road to finding suitable metals that catalyze the first proton-electron transfer in the carbon dioxide reduction reaction and produce reaction intermediates with moderate binding energies, promoting a spillover to the carbon nitride support and thereby serving as bifunctional electrocatalysts. Single metal atoms supported on 2D carbon nitride are promising electrocatalysts for carbon dioxide reduction reaction and produce reaction intermediates with moderate binding energies, promoting a spillover to the carbon nitride support and thereby serving as bifunctional electrocatalysts

Structural preferences in phosphanylthiolato platinum(II) complexes

The transition-metal complexes of heterotopic phosphanylthiolato ligands are useful in various reactions which depend on the stereochemistry of the complexes. Bis-chelate complex [Pt(SCH₂CH₂PPh₂-κ²P,S₂)] (1) was obtained in good yields by direct base-free substitution reaction of the corresponding phosphanylthiol (HSCH₂CH₂PPh₂) with K₂PtCl₄ or by oxidative addition of the same phosphanylthiol to Pt(PPh₃)₄. In agreement with the antisymbiosis rule, complex 1 shows a cis -P,P arrangement in solid state crystallizing in the monoclinic system (C2 /c). Density functional theory (DFT) calculations on 1 reveal the right characteristics for the preferred cis -P,P arrangement, rationalizing its formation. Direct base-free reaction of [PtCl₂(1,5-cyclooctadiene)] with one equivalent of the same phosphanylthiol produce the trinuclear complex [PtCl(μ-SCH₂CH₂PPh₂-κ²P,S)]₃ (2) instead of the binuclear structure common in palladium and nickel derivatives. Crystals of 2 are triclinic (P ) showing a sulfur-bridging edge-sharing cyclic trinuclear complex with square-planar coordination geometry around the platinum atoms and a Pt₃S₃ cycle in skew-boat conformation. This preference for the trinuclear structure was rationalized mechanistically and through conceptual DFT

Estudi teòric de l'activitat enzimàtica de l'Anhidrasa Carbònica

En aquesta Tesi s'ha fet un estudi teòric complet del mecanisme de reacció de l'enzim Anhidrasa Carbònica fent servir el mètode Hartree-Fock i mètodes correlacionats MP2. S'han analitzat dos possibles mecanismes de reacció per la hidratació del CO2: el mecanisme de Lipscomb i el de Lindskog. Les barreres energètiques obtingudes per a les reaccions directa i inversa de formació del (NH3)3ZnII(HCO3-) segons els mecanismes de Lipscomb i Lindskog, quan s'hi ha considerat els efectes de correlació electrònica i del medi, són ambdues petites i del mateix ordre. Els millors valors, de 5.5 kcal/mol pel mecanisme de Lindskog i de 6.7 kcal/mol per al de Lipscomb, són compatibles amb el valor màxim permès des d'un punt de vista experimental, que és de 10 kcal/mol. Això fa pensar que la reacció d'hidratació del CO2 en l'Anhidrasa Carbònica es pot donar perfectament per les dues vies. Finalment s'ha analitzat el bescanvi de HCO3- per H2O en l'Anhidrasa Carbònica que porta a recuperar l'enzim en la seva forma inicial. S'ha vist que aquest bescanvi té lloc per coordinació directa d'una molècula d'aigua i posterior sortida de la molècula de bicarbonat facilitada per l'entrada de la molècula d'aigua.In this Thesis, we have carried out a complete theoretical study of the reaction mechanism of the Cabonic Anhydrase enzyme using the Hartree-Fock method and including correlation energy at the MP2 level. We have studied two possible reaction mechanisms for the hydration of CO2: the Lipscomb and Lindskog mechanisms. The energetic barriers obtained for the direct and inverse formation of the (NH3)3ZnII(HCO3-) species are both small and of the same order for the two reaction mechanisms when including the effects of the environment and the correlation corrections. The best values of 5.5 kcal/mol for the Lindskog mechanism and of 6.7 kcal/mol for the Lipscomb mechanism both match the maximum value permitted from an experimental point of view (10 kcal/mol). Therefore, we conclude that the hydration of CO2 by Carbonic Anhydrase can follow any of the two studied reaction mechanisms. Finally, we have analyzed the HCO3- /H2O exchange in the Carbonic Anhydrase that leads to the recovery of the catalytic form of the enzyme. We have found that this exchange takes place after the direct coordination of water to the (NH3)3ZnII(HCO3-) species followed by the HCO3- dissociation, which is favored by the presence of water in the coordination sphere of the metal

Why Aromaticity Is a Suspicious Concept? Why?

From time to time I have the opportunity to give lectures on topics related to aromaticity. Quite often in these occasions I get comments from the audience complaining about the fact that aromaticity is not a well-defined concept. My usual answer is that the most fruitful concepts in chemistry share the same lack of strict definition (Grunenberg, 2017). In one of these occasions, the comment was formulated by someone who give a talk the day before justifying all the results he/she obtained using the concept of hyperconjugation. His/her comment was a little bit irritating to me because, in a way, he/she was saying I am a serious scientist because I am working with rigorous concepts like hyperconjugation whereas you are a kind of pseudoscientist playing with floppy concepts like aromaticity. Was he/she right? I do not think so. Conjugation involves interactions (electron delocalization) between π-orbitals, although its definition can also be extended to p-orbitals to cover lone pair interactions with the π-system. Hyperconjugation accounts for the interaction between two orbitals with π-symmetry where one or both of them come from a saturated moiety (Mulliken, 1939; Mulliken et al., 1941). It can also be defined as the interaction between the orbitals involved in a σ-bond (usually C–H or C–C) with those related with an adjacent π-bond (usually C=C) or another σ-bond. Aromaticity is conjugation (and in some cases hyperconjugation) that generates closed two- and three-dimensional electronic circuits. Conjugation, hyperconjugation, and aromaticity lead to stabilizing interactions that influence the geometry, electron density, dissociation energies or nuclear magnetic resonance properties among many other physicochemical observables. Despite their importance and widespread use, neither hyperconjugation nor aromaticity have a strict physical definition and, therefore, these properties cannot be experimentally directly measured. These two properties share the same origin that is stabilization due to electron delocalization. Indeed, differences between these two concepts are minor as compared to similarities. Thus, the claim that one property is more rigorous than the other is totally unfounded. The above-mentioned anecdote together with the existence of a series of papers (Balaban, 1980; Lloyd, 1996; Hoffmann, 2015) discussing the concept of aromaticity point out that aromaticity for some chemists is a controversial concept, while parent concepts like conjugation or hyperconjugation are not. Why? In the next paragraphs, I pointed out possible explanations to this fact and I propose ways of action to improve the prestige of this concep

Forty years of Clar's aromatic π-sextet rule

In 1972 Erich Clar formulated his aromatic π-sextet rule that allows discussing qualitatively the aromatic character of benzenoid species. Now, 40 years later, Clar's aromatic π-sextet rule is still a source of inspiration for many chemists. This simple rule has been validated both experimentally and theoretically. In this review, we select some particular examples to highlight the achievement of Clar's aromatic π-sextet rule in many situations and we discuss two recent successful cases of its applicationThe following organizations are thanked for financial support: the Ministerio de Ciencia e Innovación (MICINN, project number CTQ2011-23156/BQU), the Generalitat de Catalunya (project number 2009SGR637, Xarxa de Referència en Química Teòrica i Computacional, and ICREA Academia 2009 prize), and the FEDER fund (European Fund for Regional Development) for the grant UNGI08-4E-00

Does the endohedral borospherene supersalt FLi2@B39 maintain the “super” properties of its subunits?

The behavior of the entirely unique system represented by superalkaline species incorporated into a superhalogen cage has been studied using density functional theory with hybrid functionals and the triple-ξ quality basis set level of theory. The singlet ground state and triplet excited state of an FLi2@B39 borospherene complex as well as its cationic and anionic doublet ground states have been investigated. Only the encapsulation of FLi2+ into B39 in FLi2@B39+ is a thermodynamically unfavorable process. All other systems are stabilized during encapsulation most likely via an unpaired electron delocalization process and electrostatic interaction. The calculations revealed that superhalogen and superalkaline properties inherent in the separated fragments are lost in FLi2@B39 complexes. The applicability of vertically estimated ionization potentials and electron affinities instead of adiabatic ones for description of such systems has been demonstratedThe authors acknowledge the support of the Ministerio de Economía y Competitividad of Spain (Project CTQ2014-54306-P), Generalitat de Catalunya (project number 2014SGR931, Xarxa de Referència en Química Teòrica i Computacional, and ICREA Academia prize 2014 for MS), and the European Fund for Regional Development (FEDER grant UNGI10-4E-801

Complete σ* intramolecular aromatic hydroxylation mechanism through O2 activation by a Schiff base macrocyclic dicopper (I) complex

In this work we analyze the whole molecular mechanism for intramolecular aromatic hydroxylation through O2 activation by a Schiff hexaazamacrocyclic dicopper(I) complex, [CuI2(bsH2m)]2+. Assisted by DFT calculations, we unravel the reaction pathway for the overall intramolecular aromatic hydroxylation, i.e., from the initial O2 reaction with the dicopper(I) species to first form aCuICuII-superoxo species, the subsequent reaction with the second CuI center to form a μ-η2:η2-peroxo-CuII 2 intermediate, theconcerted peroxide O–O bond cleavage and C–O bond formation, followed finally by a proton transfer to an alpha aromatic carbon that immediately yields the product [CuII 2(bsH2m-O)(μ-OH)]2

Prediction of the ground state for indenofluorene-type systems with Clar\u27s π-sextet model

This study introduces the Ground State Stability (GSS) rule that allows predicting the nature of the ground state of indenofluorene (IF)-type systems from the simple counting of the Clar pi-sextets in the closed- and open-shell configurations. The IF-type system exhibits a triplet ground state when acquiring double or more the number of Clar pi-sextet in the open-shell form relative to the closed-shell form; otherwise, it assumes an open-shell singlet ground state. Performed state-of-the-art DFT calculations and analysis of aromaticity for the systems of interest validate the effectiveness of the proposed rule. We demonstrate that aromaticity plays the most crucial role in determining the ground electronic state for such polycyclic hydrocarbons. The simplicity of the GSS rule makes it a robust strategy for identifying promising systems in the development of indenofluorene-type materials