Search results for "Dft"

Experimental and theoretical NMR and IR studies of the side‐chain orientation effects on the backbone conformation of dehydrophenylalanine residue

2011

Conformation of N‐acetyl‐(E)‐dehydrophenylalanine N′, N′‐dimethylamide (Ac‐(E)‐ΔPhe‐NMe2) in solution, a member of (E)‐α, β‐dehydroamino acids, was studied by NMR and infrared spectroscopy and the results were compared with those obtained for (Z) isomer. To support the spectroscopic interpretation, the ϕ, ψ potential energy surfaces were calculated at the MP2/6‐31 + G(d,p) level of theory in chloroform solution modeled by the self‐consistent reaction field‐polarizable continuum model method. All minima were fully optimized by the MP2 method and their relative stabilities were analyzed in terms of π‐conjugation, internal H‐bonds and dipole interactions between carbonyl groups. The obtained N…

Mpro-SARS-CoV-2 Inhibitors and Various Chemical Reactivity of 1-Bromo- and 1-Chloro-4-vinylbenzene in [3 + 2] Cycloaddition Reactions

2021

The regioselectvity and the mechanism of the (32CA) cycloadditions reactions of 1-bromo-4-vinylbenzene 1 and 1-chloro-4-vinylbenzene 2 with benzonitrile oxide 3 were investigated under the molecular electron density theory (MEDT) at the B3LYP/6-311++G(d,p) computational level. Evaluation of the ELF reveals that these zwitterionic type (zw-type) 32CA reactions take place in a two-stage one-step mechanism. This MEDT study shows that the meta isoxazolines are kinetically and thermodynamically favored over the ortho ones, these 32CA reactions being completely regioselective, in agreement with experimental outcomes. In addition, the efficiency of isoxazolines against SARS-CoV-2 have been also in…

A Universal Length-Dependent Vibrational Mode in Graphene Nanoribbons

2019

Graphene nanoribbons (GNRs) have attracted considerable interest as their atomically tunable structure makes them promising candidates for future electronic devices. However, obtaining detailed information about the length of GNRs has been challenging and typically relies on low-temperature scanning tunneling microscopy. Such methods are ill-suited for practical device application and characterization. In contrast, Raman spectroscopy is a sensitive method for the characterization of GNRs, in particular for investigating their width and structure. Here, we report on a length-dependent, Raman active low-energy vibrational mode that is present in atomically precise, bottom-up synthesized armch…

Exploration of the Activation Mechanism of the Epigenetic Regulator MLL3: A QM/MM Study

2021

The mixed lineage leukemia 3 or MLL3 is the enzyme in charge of the writing of an epigenetic mark through the methylation of lysine 4 from the N-terminal domain of histone 3 and its deregulation has been related to several cancer lines. An interesting feature of this enzyme comes from its regulation mechanism, which involves its binding to an activating dimer before it can be catalytically functional. Once the trimer is formed, the reaction mechanism proceeds through the deprotonation of the lysine followed by the methyl-transfer reaction. Here we present a detailed exploration of the activation mechanism through a QM/MM approach focusing on both steps of the reaction, aiming to provide new…

Hydrogenolysis of hydroxymatairesinol on Y derived catalysts: a computational study

2010

Hydrogenolysis of 7-hydroxymatairesinol (HMR) to matairesinol (MAT) occurs on palladium supported acidic catalysts. HMR has three stereochemical centres and naturally exists as a mixture of two diastereoisomers, namely RRR-HMR and SRR-HMR. The latter is significantly more reactive than the former, in the reaction above. In order to elucidate the hydrogenolysis mechanism, simple surface events involving HMR derivatives on aluminated faujasite (H-Y) fragments were simulated by quantum chemical calculations. The metallic function of a Pd/H-Y acidic catalyst was also mimicked by a minimal palladium cluster. Stereochemical evidences pointed already out that water β-elimination on the epimeric ce…

A computational approach to study Aqueous Phase Reforming

2014

Interactions of amino acids with aluminum octacarboxyphthalocyanine hydroxide. Experimental and DFT studies

2017

The influence of albumin and amino acids (l-serine, glycine, l-histidine, l-tryptophan, l-cysteine) on the properties of aluminum octacarboxyphthalocyanine hydroxide (Al(OH)PcOC) was investigated in a phosphate buffer (pH 8.0). Particular attention was paid to the spectroscopic properties and photostability of Al(OH)PcOC. The effect of albumin or amino acids on the photodegradation of Al(OH)PcOC was examined in water using red light: 685 nm and daylight irradiation. Analysis of kinetic curves indicated that interaction with those molecules increases the photostability of Al(OH)PcOC. The molecular structure of Al(OH)PcOC complexes (in vacuum and in water) with axially or equatorially coordin…

Role of Electrical Charges on the Adsorption of Hydrogen: Something Old, Something New.

2022

The adsorption of H2 in zeolites by molecular simulations use, in many applications, single sphere model. Although this representation provides coherent results with ex- periments above 77K, below this temperature the usual hydrogen representation fails to reproduce experimental results. The disagreement can be associated to the interplay of the atomistic heterogeneity and the electric field produced by the zeolite faujasite. These aspects are generally excluded in classical force fields. For elucidating the influ- ence of these issues, we performed DFT simulations for the faujasite Na86X at 40K with and without guest hydrogen molecules for determining the electrical field generated by the …

Selective Introduction of Acid Sites in Different Confined Positions in ZSM-5 and Its Catalytic Implications

2018

Controlling the location of acid sites in zeolites can have a great effect on catalysis. In this work we face the objective of directing the location of Al into the 10R channels of ZSM-5 by taking advantage of the structural preference of B to occupy certain positions at the channel intersections, as suggested by theoretical calculations. The synthesis of B-Al-ZSM-5 zeolites with variable Si/Al and Si/B ratios, followed by B removal in a postsynthesis treatment, produces ZSM-5 samples enriched in Al occupying positions at 10R channels. The location of the acid sites is determined on the basis of the product distribution of 1-hexene cracking as a test reaction. The higher selectivity to prop…

DFT study of N–H···O hydrogen bond between model dehydropeptides and water molecule

2013

The strength of the hydrogen bond formed between a water molecule and two α,β-dehydroalanine derivatives including Ac-ΔAla-NMe2 (1) and Ac-ΔAla-NHMe (2) in comparison with standard amino acid Ac-Ala-NMe2 (3) is studied by density functional theory (with M06-2X and B3LYP functionals). Calculations were conducted for two different conformations of the peptides: extended (C5) and bent (β) with polyproline II backbone dihedral angles. The obtained results show that both dehydro and standard peptides in bent conformation form stronger hydrogen bonds with water than in the extended ones. Moreover, due to higher polarity of the N–H group of α,β-dehydroalanine residues, the H-bond in their complexe…