Computational study of the rotational pathways of the amino group in 2-chloroaniline, azines and formamide: One or two rotational barriers?

Gálvez, Jesús; Sánchez, José Ignacio López; Guirado, Antonio

doi:10.1016/j.comptc.2015.06.020

Cited by 4 publications

(4 citation statements)

References 21 publications

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“…The hindered internal rotation around the C-N bond in formamide and thioformamide has been intensively studied theoretically due to its importance for understanding the conformations of peptides and proteins [24,25]. The rotational barrier in formamide is known to be lower than in its thioanalogue [26].…”

Section: This Paper Belongs To Topical Collection 8th Conference On Mmentioning

confidence: 99%

Evolution of the atomic valence observed by the reaction fragility spectra on the reaction path

2019

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The computational fragility spectra of atoms on the reaction path are presented for a selection of canonical processes represented by an amino group rotation around the (X)HC-NH(Y) bond (X = O, S; Y=H, CH 3). Calculated spectra are found to very accurately describe the variation of atomic valence. Significant linear correlation is also demonstrated between the Wiberg bond indices and the corresponding elements of the connectivity matrix, instrumental for calculation of the spectra. Demonstrated atomic fragility spectra contain rich and subtle information on the variation of the bonding status of all atoms, including the weak interacting individual hydrogens. Correlation with the atomic valences confirm the earlier finding that the spectra contain a picture of the electron density flow upon a reaction.

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Section: This Paper Belongs To Topical Collection 8th Conference On Mmentioning

confidence: 99%

Evolution of the atomic valence observed by the reaction fragility spectra on the reaction path

2019

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“…N -(2-Aminoethyl)-4-azido-tetrafluorobenzamide (ATFB-NH 2 ) was prepared and reacted with 1 under similar reaction conditions except for the temperature (0 °C) to produce disubstituted s -triazine 2 with 50% yield. Amino-substituted s -triazines often exist as mixtures of rotamers in conformational equilibrium generating multiple peaks on NMR spectra. , As expected, most of the 1 H and 13 C NMR signals of 2 were split, making assignment difficult. Nevertheless, the unambiguous characterization of 2 was achieved by mass spectrometry and NMR spectroscopy (see Supporting Information).…”

Section: Resultsmentioning

confidence: 65%

Unprecedented Affinity Labeling of Carbohydrate-Binding Proteins with s-Triazinyl Glycosides

et al. 2019

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Carbohydrate−protein interactions trigger a wide range of biological signaling pathways, the mainstays of physiological and pathological processes. However, there are an incredible number of carbohydrate-binding proteins (CBPs) that remain to be identified and characterized. This study reports for the first time the covalent labeling of CBPs by triazinyl glycosides, a new and promising class of affinitybased glycoprobes. Mono-and bis-clickable triazinyl glycosides were efficiently synthesized from unprotected oligosaccharides (chitinpentaose and 2′-fucosyl-lactose) in a single step. These molecules allow the specific covalent labeling of chitin-oligosaccharide-binding proteins (wheat germ agglutinin WGA and Bc ChiA1 D202A, an inactivated chitinase) and fucosyl-binding lectin (UEA-I), respectively.

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“…Formamide (HCONH 2 ) is a simple molecule that features hindered internal rotation of C–N bond. Its rotational barrier of 15–20 kcal/Mol has been the subject of many experimental [ 77–82 ] and theoretical studies [ 83–99 ] designed to obtain fundamental insights into the conformational flexibility of peptide chains. Herein, the efficiency of the DC‐DFTB‐MWMetaD simulation for overcoming and estimating the free energy barrier was examined.…”

Section: Computational Detailsmentioning

confidence: 99%

“…[76] Throughout this study, the integration time step was 0.5 fs. Mol has been the subject of many experimental [77][78][79][80][81][82] and theoretical studies [83][84][85][86][87][88][89][90][91][92][93][94][95][96][97][98][99] used to verify RE-based simulation techniques. [34,[100][101][102][103][104][105][106][107][108][109][110][111] The model system was a cubic box with a side length of 24. walker escapes free energy minima was adopted [26][27][28] for consistent validation of DC-DFTB-MWMetaD efficiency.…”

Section: Common Computational Detailsmentioning

confidence: 99%

Hierarchical parallelization of divide‐and‐conquer density functional tight‐binding molecular dynamics and metadynamics simulations

Nishimura

Nakai

2020

J Comput Chem

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Massively parallel divide‐and‐conquer density functional tight‐binding (DC‐DFTB) molecular dynamics and metadynamics simulations are efficient approaches for describing various chemical reactions and dynamic processes of large complex systems via quantum mechanics. In this study, DC‐DFTB simulations were combined with multi‐replica techniques. Specifically, multiple walkers metadynamics, replica exchange molecular dynamics, and parallel tempering metadynamics methods were implemented hierarchically into the in‐house Dcdftbmd program. Test simulations in an aqueous phase of the internal rotation of formamide and conformational changes of dialanine showed that the newly developed extensions increase the sampling efficiency and the exploration capabilities in DC‐DFTB configuration space.

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Computational study of the rotational pathways of the amino group in 2-chloroaniline, azines and formamide: One or two rotational barriers?

Cited by 4 publications

References 21 publications

Evolution of the atomic valence observed by the reaction fragility spectra on the reaction path

Evolution of the atomic valence observed by the reaction fragility spectra on the reaction path

Unprecedented Affinity Labeling of Carbohydrate-Binding Proteins with s-Triazinyl Glycosides

Hierarchical parallelization of divide‐and‐conquer density functional tight‐binding molecular dynamics and metadynamics simulations

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