Search results for "COMPUTATION"

1,3-Dipolar cycloadditions with meso-tetraarylchlorins – site selectivity and mixed bisadducts

2017

The 1,3-dipolar cycloaddition reaction of meso-tetraarylporphyrins with nitrones gives isoxazolidine-fused chlorins. Depending on the substitution pattern on the meso-aryl groups and the nitrone, the chlorins can be obtained in high yields (up to 91%). Bacteriochlorin-type bisadducts are also obtained, although in low yield, from the reaction of meso-tetrakis(pentafluorophenyl)porphyrin with N-methyl, N-cyclohexyl or N-benzyl nitrone. The structure of a bis(N-benzyl isoxazolidine-fused) bacteriochlorin was determined by single-crystal X-ray diffraction and rationalized by DFT calculations. To further explore the nature of site selectivity in the formation of bisadducts, isomeric mixed bacte…

Understanding the mechanism and regioselectivity of the copper(i) catalyzed [3 + 2] cycloaddition reaction between azide and alkyne: a systematic DFT…

2017

The copper(I) catalyzed azide–alkyne [3 + 2] cycloaddition (32CA) reaction and its uncatalyzed version have been studied for systematic understanding of this relevant organic transformation, using DFT calculations at the B3LYP/6-31G(d) (LANL2DZ for Cu) computational levels. In the absence of a copper(I) catalyst, two regioisomeric reaction paths were studied, indicating that the 32CA reaction takes place through an asynchronous one-step mechanism with a very low polar character. The two reactive channels leading to 1,4- and 1,5-regisomer present similar high activation energies of 18.84 and 18.51 kcal mol−1, respectively. The coordination of copper(I) to alkyne produces relevant changes in …

Host–Guest Interactions of Sodiumsulfonatomethyleneresorcinarene and Quaternary Ammonium Halides: An Experimental–Computational Analysis of the Guest…

2020

The molecular recognition of nine quaternary alkyl- and aryl-ammonium halides (Bn) by two different receptors, Calkyl-tetrasodiumsulfonatomethyleneresorcinarene (An), were studied in solution using...

Unveiling the high reactivity of benzyne in the formal [3+2] cycloaddition reactions towards thioamides through the Molecular Electron Density Theory

2020

Abstract The domino reaction of benzyne with thioamide has been studied within the Molecular Electron Density Theory (MEDT) at the MPWB1K/6-311G(d) level. This domino reaction takes place through i) a formal [3 + 2] cycloaddition (32CA) reaction affording an ammonium ylide, and ii) an extrusion of ethylene from this species yielding a dihydrothiazole. Topological analysis of the electron density of benzyne shows its pseudodiradical structure, that is, without any energy cost, changes to a carbenoid one, allowing its participation as electrophile in polar reactions. As a consequence, the formal 32CA reaction does not have an activation enthalpy. Analysis of the changes of electron density al…

The Role of Enzymes in Biomineralization Processes

2010

Analysis of pseudouridines and other RNA modifications using hydraPsiSeq protocol

2021

Detection of RNA modified nucleotides using deep sequencing can be performed by several approaches, including antibody-driven enrichment and natural or chemically induced RT signatures. However, only very few RNA modified nucleotides generate natural RT signatures and antibody-driven enrichment heavily depends on the quality of antibodies used and may be highly biased. Thus, the use of chemically-induced RT signatures is now considered as the most trusted experimental approach. In addition, the use of chemical reagents allows inclusion of simple "mock-treated" controls, to exclude spontaneous RT arrests, SNPs and other misincorporation-prone sites. Hydrazine is a well-known RNA-specific rea…

Mapping and Quantification of tRNA 2′-O-Methylation by RiboMethSeq

2018

Current development of epitranscriptomics field requires efficient experimental protocols for precise mapping and quantification of various modified nucleotides in RNA. Despite important advances in the field during the last 10 years, this task is still extremely laborious and time-consuming, even when high-throughput analytical approaches are employed. Moreover, only a very limited subset of RNA modifications can be detected and only rarely be quantified by these powerful techniques. In the past, we developed and successfully applied alkaline fragmentation-based RiboMethSeq approach for mapping and precise quantification of multiple 2'-O-methylation residues in ribosomal RNA. Here we descr…

AlkAniline-Seq: A Highly Sensitive and Specific Method for Simultaneous Mapping of 7-Methyl-guanosine (m7G) and 3-Methyl-cytosine (m3C) in RNAs by Hi…

2021

Epitranscriptomics is an emerging field where the development of high-throughput analytical technologies is essential to profile the dynamics of RNA modifications under different conditions. Despite important advances during the last 10 years, the number of RNA modifications detectable by next-generation sequencing is restricted to a very limited subset. Here, we describe a highly efficient and fast method called AlkAniline-Seq to map simultaneously two different RNA modifications: 7-methyl-guanosine (m7G) and 3-methyl-cytosine (m3C) in RNA. Our protocol is based on three subsequent chemical/enzymatic steps allowing the enrichment of RNA fragments ending at position n + 1 to the modified nu…

Application of headspace analysis to the study of aroma compounds-lipids interactions

1998

Taking into account interactions between aroma compounds and food components is necessary to better manage the flavoring of food products. These interactions occur at a molecular level and reflect changes, at a macroscopic level, in thermodynamic equilibria, such as solubility or volatility. The rate of transfer of an aroma compound from the liquid to the vapor phase can be affected as well. The behavior of aroma compounds in water and lipid solutions was studied in two complementary ways, a thermodynamic and a kinetic approach (head-space analysis). The transfer rate of volatiles at the liquid-water interface does not only depend on the hydrophobicity of the aroma compounds. Vapor-liquid p…

An analysis of the regioselectivity of 1,3-dipolar cycloaddition reactions of benzonitrile n-oxides based on global and local electrophilicity and nu…

2009

The regioselectivity of the 1,3-dipolar cycloaddition (13DC) reactions of benzonitrile N-oxides (BNOs) with electrophilic and nucleophilic alkenes has been analyzed by using global and local nucleophilicity and electrophilicity reactivity indices defined within the conceptual DFT. The BNOs react with electron-deficient and electron-rich ethylenes, but the regioselectivities of these polar reactions are different. Whereas the reactions with electron-rich ethylenes are completely regioselective, yielding 5-isoxazolines, a change in the regioselectivity is observed in the reactions with electron-deficient ethylenes, which yield a mixture of 4- and 5-isoxazolines. Analysis of the energies, geom…