Copper-catalyzed Eglinton oxidative homocoupling of terminal alkynes: a computational study

The copper(II) acetate mediated oxidative homocoupling of terminal alkynes, namely the Eglinton coupling, has been studied with DFT methods. The mechanism of the whole reaction has been modeled using phenylacetylene as substrate. The obtained results indicate that, in contrast to some classical proposals, the reaction does not involve the formation of free alkynyl radicals and proceeds by the dimerization of copper(II) alkynyl complexes followed by a bimetallic reductive elimination. The calculations demonstrate that the rate limiting-step of the reaction is the alkyne deprotonation and that more acidic substrates provide faster reactions, in agreement with the experimental observations

Nickel-catalyzed aryl trifluoromethyl sulfides synthesis: A DFT study

The Ni-catalyzed trifluoromethylthiolation of aryl halides with [NMe4][SCF3] has been studied with DFT methodology to find out the mechanism governing the reaction. Two different cross-coupling pathways have been explored; the first one, involving the classical Ni(0)/Ni(II) catalytic cycle, does not provide a good explanation for the experimental outcomes. In contrast, an alternative Ni(I)/Ni(III) catalytic cycle affords a much better agreement with what is observed experimentally: a low reaction barrier that allows the reaction to work at room temperature for aryl iodides, and an interpretation of the reactivity for other aryl halides and substituted iodobenzenes. The active Ni(I) catalyst is generated through a two-step process consisting of a singlet to triplet transformation of the initial nickel species followed by a subsequent halogen atom transfer from the aryl halide

From Simple Alkenes and CO2 to Fluorinated Carboxylic Acids: Computational Studies and Predictions

Fluorinated carboxylic acids may soon become a relevant class of compounds for new materials development and as synthons in medicinal chemistry. In this report, a potential method based on a hydroboration/copper-catalyzed carboxylation reaction sequence has been computationally explored to check whether these moieties could be synthetically accessible. DFT calculations fully support the possibility of obtaining fluorinated carboxylic acids from simple fluorinated alkenes and gaseous carbon dioxide, paving the way to future preparation of this class of chemicals

Computational assessment on the Tolman cone angles for P-ligands

The Tolman cone angle (θ), the par excellence descriptor of the steric measure of a phosphine, has been recomputed for a set of 119 P-ligands, including simple phosphines and phosphites, as well as bulky biaryl species often employed in catalytic processes. The computed cone angles have been obtained from three different transition metal coordination environments: linear [AuCl(P)] (θL), tetrahedral [Ni(CO)3(P)] (θT) and octahedral [IrCl3(CO)2(P)] (θO), allowing us to observe the steric behavior of the ligand when increasing the steric hindrance around the metal center. The computed cone angles have been extracted from the lowest-energy conformer geometry obtained with a combined MM/DFT methodology. A conformational screening has been done using MM, which allows us to identify the lowest energy structure of each ligand in each coordination environment. These low energy conformers have been subsequently reoptimized at the DFT theory level, from which the cone angle value can be extracted. The computed cone angles have been compared with the original Tolman cone angles, and with other steric parameters such as solid angles (Θ), percent buried volumes (%Vbur), and angular symmetric deformation coordinate (S′4). This new set of values correlates with phosphine ligand dissociation enthalpies in titanocene complexes of the general formula [Ti(2,4-C7H11)2(PR3)], and with reaction barriers in the Suzuki-Miyaura reaction between [Pd-PR3] and bromobenzene, proving that this newly proposed set of cone angles can be employed to establish linear correlations between different experimental and calculated properties for systems in which phosphine ligands play a significant role

Zn(II) Byproduct Enhances the Cu-Catalyzed Cross-Coupling of Bromozinc Difluorophosphonate with Iodobenzoates: A DFT Study

The copper-catalyzed cross-coupling of bromozinc difluorophosphonate with iodobenzoates has been studied with the DFT methodology in order to understand the experimentally observed reactivity. The directing carboxylate group promotes the reaction for methyl 2-iodobenzoate and, unexpectedly, also for methyl 4-iodobenzoate, although to a lesser extent. DFT calculations show that the Zn(II) byproduct, formed in the initial stages of the reaction, remains attached to the catalyst and serves as an anchoring point for the benzoate moiety, allowing in turn the reaction for both ortho- and para-substituted iodobenzoates. The computationally derived reaction mechanism has also been applied to study whether other substrates may engage in a similar cross-coupling process with bromozinc difluorophosphonate. The calculations carried out on substrates bearing nitrogen-directing groups, such as triazene and pyridine, indicate that their reactions should be possible and that the latter should produce a much faster reaction in comparison to iodobenzoates

Quantitative DFT modeling of product concentration in organometallic reactions: Cu-mediated pentafluoroethylation of benzoic acid chlorides as a case study

DFT calculations are widely used for computing properties, reaction mechanisms and energy profiles in organometallic reactions. A qualitative agreement between the experimental and the calculated results seems to usually be enough to validate a computational methodology but recent advances in computation indicate that a nearly quantitative agreement should be possible if an appropriate DFT study is carried out. Final percent product concentrations, often reported as yields, are by far the most commonly reported properties in experimental metal-mediated synthesis studies but reported DFT studies have not focused on predicting absolute product amounts. The recently reported stoichiometric pentafluoroethylation of benzoic acid chlorides (R-C6H4COCl) with [(phen) Cu(PPh3)C2F5] (phen = 1,10-phenanthroline, PPh3 = triphenylphosphine) has been used as a case study to check whether the experimental product concentrations can be reproduced by any of the most popular DFT approaches with high enough accuracy. To this end, the Gibbs energy profile for the pentafluoroethylation of benzoic acid chloride has been computed using 14 different DFT methods. These computed Gibbs energy profiles have been employed to build kinetic models predicting the final product concentration in solution. The best results are obtained with the D3-dispersion corrected B3LYP functional, which has been successfully used afterwards to model the reaction outcomes of other simple (R = o-Me, p-Me, p-Cl, p-F, etc.) benzoic acid chlorides. The product concentrations of more complex reaction networks in which more than one position of the substrate may be activated by the copper catalyst (R = o-Br and p-I) are also predicted appropriately

Aplicació de la metodologia QSPR al càlcul de propietats de compostos inorgànics i de sistemes multicomponents

[spa] En esta tesis se ha utilizado la metodología QSPR para calcular las propiedades de diferentes compuestos y sistemas complejos que no habían estudiados anteriormente. En concreto, se han establecido modelos que permiten el cálculo de la viscosidad y la tensión superficial, en estado líquido, y la entalpía de formación en fase gas para conjuntos de compuestos organometálicos de fórmula general MRnXm, en la que M puede ser un metal, semimetal o no metal de los grupos 12 al 16 de la tabla periódica; los grupos R corresponden a sustituyentes orgánicos alquílicos, arílicos, etc.; y los ligandos terminales X pueden ser cloro, bromo, yodo e hidrógeno. Se ha estudiado también la basicidad catiónica de un conjunto de compuestos orgánicos, de naturaleza química muy diversa, frente al catión Li+. En general, esta propiedad puede asociarse a la energía del proceso de formación de los complejos [Li-Ligando]+. Los sistemas complejos estudiados, que reciben el nombre de multicomponentes, son aquellos en los que la propiedad estudiada depende, a la vez, de dos o más elementos constituyentes del sistema. Las propiedades estudiadas en esta tesis son: las afinidades y basicidades catiónicas de los aminoácidos habituales frente a los cationes monovalentes de litio, sodio, potasio, cobre y plata; y las constantes de acidez (pKa) de familias de ácidos orgánicos en diferentes solventes, en este caso las familias de ácidos orgánicos estudiadas son fenoles, ácidos benzoicos, ácidos carboxílicos alifáticos y anilinas. En el tratamiento de estos sistemas multicomponentes se han utilizado descriptores externos para caracterizar a los cationes metálicos y los solventes. En el primer caso se han utilizado propiedades físicas, como potenciales de ionización, afinidades electrónicas, escalas de electronegatividad, etc.; para los diferentes solventes se han usado también propiedades físicas, como el momento dipolar, la constante dieléctrica, la polarizabilidad, etc.; y parámetros derivados de las diferentes escalas de polaridad más habituales, como los parámetros de Kamlet y Taft, los de Koppel y Palm, los de Drago, Gutmann, etc. Los modelos, lineales y no lineales, desarrollados para todas las propiedades proporcionan resultados excelentes para todas ellas, con valores de R2 mayores que 0.95, errores muy bajos y capacidad predictiva elevada, comprobada mediante la utilización de conjuntos de valores externos. Además de proporcionar una manera de calcular las propiedades, los modelos establecidos contienen descriptores que permiten realizar, en todos los casos, una interpretación razonable de las propiedades en términos fisicoquímicos

Aplicació de la metodologia QSPR al càlcul de propietats de compostos inorgànics i de sistemes multicomponents

En esta tesis se ha utilizado la metodología QSPR para calcular las propiedades de diferentes compuestos y sistemas complejos que no habían estudiados anteriormente. En concreto, se han establecido modelos que permiten el cálculo de la viscosidad y la tensión superficial, en estado líquido, y la entalpía de formación en fase gas para conjuntos de compuestos organometálicos de fórmula general MRnXm, en la que M puede ser un metal, semimetal o no metal de los grupos 12 al 16 de la tabla periódica; los grupos R corresponden a sustituyentes orgánicos alquílicos, arílicos, etc.; y los ligandos terminales X pueden ser cloro, bromo, yodo e hidrógeno. Se ha estudiado también la basicidad catiónica de un conjunto de compuestos orgánicos, de naturaleza química muy diversa, frente al catión Li+. En general, esta propiedad puede asociarse a la energía del proceso de formación de los complejos [Li-Ligando]+. Los sistemas complejos estudiados, que reciben el nombre de multicomponentes, son aquellos en los que la propiedad estudiada depende, a la vez, de dos o más elementos constituyentes del sistema. Las propiedades estudiadas en esta tesis son: las afinidades y basicidades catiónicas de los aminoácidos habituales frente a los cationes monovalentes de litio, sodio, potasio, cobre y plata; y las constantes de acidez (pKa) de familias de ácidos orgánicos en diferentes solventes, en este caso las familias de ácidos orgánicos estudiadas son fenoles, ácidos benzoicos, ácidos carboxílicos alifáticos y anilinas. En el tratamiento de estos sistemas multicomponentes se han utilizado descriptores externos para caracterizar a los cationes metálicos y los solventes. En el primer caso se han utilizado propiedades físicas, como potenciales de ionización, afinidades electrónicas, escalas de electronegatividad, etc.; para los diferentes solventes se han usado también propiedades físicas, como el momento dipolar, la constante dieléctrica, la polarizabilidad, etc.; y parámetros derivados de las diferentes escalas de polaridad más habituales, como los parámetros de Kamlet y Taft, los de Koppel y Palm, los de Drago, Gutmann, etc. Los modelos, lineales y no lineales, desarrollados para todas las propiedades proporcionan resultados excelentes para todas ellas, con valores de R2 mayores que 0.95, errores muy bajos y capacidad predictiva elevada, comprobada mediante la utilización de conjuntos de valores externos. Además de proporcionar una manera de calcular las propiedades, los modelos establecidos contienen descriptores que permiten realizar, en todos los casos, una interpretación razonable de las propiedades en términos fisicoquímicos

Supported -Complexes of LiC Bonds from Coordination of Monomeric Molecules of LiCH3, LiCH2CH3 and LiC6H5 to MoMo Bonds

LiCH3 and LiCH2CH3 react with the complex [Mo2(H)2(μ-AdDipp2)2(thf)2] (1⋅thf) with coordination of two molecules of LiCH2R (R=H, CH3) and formation of complexes [Mo2{μ-HLi(thf)CH2R}2(AdDipp2)2], 5⋅LiCH3 and 5⋅LiCH2CH3, respectively (AdDipp2=HC(NDipp)2; Dipp=2,6-iPr2C6H3; thf=C4H8O). Due to steric hindrance, only one molecule of LiC6H5 adds to 1⋅thf generating the complex [Mo2(H){μ-HLi(thf)C6H5}(μ-AdDipp2)2], (4⋅LiC6H5). Computational studies disclose the existence of five-center six-electron bonding within the H−Mo≣Mo−C−Li metallacycles, with a mostly covalent H−Mo≣Mo−C group and predominantly ionic Li−C and Li−H interactions. However, the latter bonds exhibit non-negligible covalency, as indicated by X-ray, computational data and the large one-bond 6,7Li,1H and 6,7Li,13C NMR coupling constants found for the three-atom H−Li−C chains. By contrast, the phenyl group in 4⋅LiC6H5 coordinates in an η2 fashion to the lithium atom through the ipso and one of the ortho carbon atoms

The chloroplast protein HCF164 is predicted to be associated with Coffea SH 9 resistance factor against Hemileia vastatrix

This work was funded by Portuguese national funds through FCT—Fundação para a Ciência e Tecnologia, I.P., under the Projects: UID/AGR/04129/2020 of LEAF; UIDP/04378/2020 and UIDB/04378/2020 of UCIBIO; and LA/P/0140/2020 of i4HB and FCT and FEDER funds through PORNorte under the projects: HDT-Coffee (PTDC/ASP-PLA/32429/2017) and CoffeeRES (PTDC/ASP-PLA/29779/2017). H.A. was supported by Portuguese national funds through FCT within the scope of the Stimulus of Scientific Employment—Individual Support (CEECIND/00399/2017/CP1423/CT0004). A.O. was supported at the University of Bristol by Oracle for Research and the Biological and Biotechnological Sciences Research Council ([BB/X009831/1] and [BBW003449/1]). All molecular modelling work was carried out using the computational facilities of the Advanced Computing Research Centre, University of Bristol (http://www.bris.ac.uk/acrc).To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid “Híbrido de Timor”. Individual reads were also aligned on the C. arabica reference genome to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.CoffeeRES CEECIND/00399/2017/CP1423/CT0004, PTDC/ASP-PLA/29779/2017University of Bristol by Oracle for ResearchBiotechnology and Biological Sciences Research Council BB/X009831/1, BBW003449/1 BBSRCUniversity of BristolFundação para a Ciência e a Tecnologia LA/P/0140/2020, UID/AGR/04129/2020, UIDB/04378/2020, UIDP/04378/2020 FCTEuropean Regional Development Fund PTDC/ASP-PLA/32429/2017 ERD