Puckering Coordinates of Monocyclic Rings by Triangular Decomposition.

Hill, Arthur V.; Reilly, Peter J.

doi:10.1002/chin.200733226

Cited by 15 publications

(23 citation statements)

References 8 publications

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“…Geometrical features of the N‐acetyl group were calculated using in‐house python scripts, the calculation of the Cremer and Pople angle being implemented as proposed by Hill and Reilly 23 . Real‐space correlation coefficients (RSCCs) of the β‐D‐GlcNAc units were calculated with Privateer, 24 the electron density maps coming from PDB‐redo.…”

Section: Methodsmentioning

confidence: 99%

Numerous severely twisted N‐acetylglucosamine conformations found in the protein databank

2020

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Taking advantage of the known planarity of the N‐acetyl group of N‐acetylglucosamine, an analysis of the quality of carbohydrate structures found in the protein databank was performed. Few obvious defects of the local geometry of the carbonyl group were observed. However, the N‐acetyl group was often found in the less favorable cis conformation (12% of the cases). It was also found severely twisted in numerous instances, especially in structures with a resolution poorer than 1.9 Å determined between 2000 and 2015. Though the automated PDB‐REDO procedure has proved able to improve nearly 85% of the structural models deposited to the PDB, and does prove able to cure most severely twisted conformations of the N‐acetyl group, it fails to correct its high rate of cis conformations. More generally, for structures with a resolution poorer than 1.6 Å, it produces N‐acetylglucosamine models in slightly poorer agreement with experimental data, as measured using real‐space correlation coefficients. Significant improvements are thus still needed, at least as far as this carbohydrate structure is concerned.

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Section: Methodsmentioning

confidence: 99%

Numerous severely twisted N‐acetylglucosamine conformations found in the protein databank

2020

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“…Cremer−Pople coordinates were used to assign ring puckers. 22,23 Energetics, ring puckers, and coordinates of the reoptimized structures can be found in the Supporting Information.…”

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confidence: 99%

Direct Experimental Characterization of the Ferrier Glycosyl Cation in the Gas Phase

et al. 2020

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The Ferrier rearrangement reaction is crucial for the synthesis of pharmaceuticals. Although its mechanism was described more than 50 years ago, the structure of the intermediate remains elusive. Two structures have been proposed for this Ferrier glycosyl cation: a 1,2-unsaturated cation that is resonance-stabilized within the pyranose ring or a cation that is stabilized by the anchimeric assistance of a neighboring acetyl group. Using a combination of gas-phase cryogenic infrared spectroscopy in helium nanodroplets and first-principles density functional theory, we provide the first direct structural characterization of Ferrier cations. The data show that both acetylated glucal and galactal lead to glycosyl cations of the dioxolenium type.

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“…This is because glycoside chemistry is largely the chemistry of the oxocarbenium ion formed in the transition state (TS) that displays an enormous range of conformational ring deformation [52]. Numerous descriptions of ring puckering have been proposed [53] and are in popular use [54], we found the triangular decomposition [55] to be particularly amenable to the FEARCF method [16,56]. The ring puckering for a 6-membered ring can be described in terms of the relative orientation of planes made up of three atoms each.…”

Section: Application To Ring Puckeringmentioning

confidence: 98%

FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms

Naidoo

2011

Sci. China Chem.

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The development and implementation of a computational method able to produce free energies in multiple dimensions, descriptively named the free energies from adaptive reaction coordinate forces (FEARCF) method is described in this paper. While the method can be used to calculate free energies of association, conformation and reactivity here it is shown in the context of chemical reaction landscapes. A reaction free energy surface for the Claisen rearrangement of chorismate to prephenate is used as an illustration of the method's efficient convergence. FEARCF simulations are shown to achieve flat histograms for complex multidimensional free energy volumes. The sampling efficiency by which it produces multidimensional free energies is demonstrated on the complex puckering of a pyranose ring, that is described by a three dimensional W( 1 ,  2 ,  3 ) potential of mean force. free energy calculations, reaction dynamics, reaction surfaces, multidimensional free energy surfaces

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Puckering Coordinates of Monocyclic Rings by Triangular Decomposition.

Cited by 15 publications

References 8 publications

Numerous severely twisted N‐acetylglucosamine conformations found in the protein databank

Numerous severely twisted N‐acetylglucosamine conformations found in the protein databank

Direct Experimental Characterization of the Ferrier Glycosyl Cation in the Gas Phase

FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms

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