Limitations in the description of conformational preferences of C-disaccharides: The (1 -> 3)-C-mannobiose case

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F17%3A00480867" target="_blank" >RIV/61388963:_____/17:00480867 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/60461373:22330/17:43913463

Výsledek na webu

<a href="http://dx.doi.org/10.1016/j.carres.2017.09.006" target="_blank" >http://dx.doi.org/10.1016/j.carres.2017.09.006</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.carres.2017.09.006" target="_blank" >10.1016/j.carres.2017.09.006</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Limitations in the description of conformational preferences of C-disaccharides: The (1 -> 3)-C-mannobiose case

Popis výsledku v původním jazyce

Conformational preferences of two C-glycosyl analogues of Manp-(1 -> 3)-Manp, were studied using a combined method of theoretical and experimental chemistry. Molecular dynamics was utilized to provide conformational behavior along C-glycosidic bonds of methyl 3-deoxy-3-C-[(alpha-D-mannopyranosyl) methyl]-alpha-D-and L-mannopyranosides. The OPLS2005 and Glycam06 force fields were used. Simulations were performed with explicit water (TIP3P) and methanol. Results were compared with a complete conformational scan at the MM4 level with the dielectric constant corresponding to methanol. In order to verify predicted conformational preferences, vicinal (3)J(HH) NMR coupling constants were calculated by the Karplus equation on simulated potential energy surfaces (PES). A set of new parameters for the Karplus equation was also designed. Predicted 3JHH were compared with experimental data. We also used reverse methodology, in which the (3)J(HH) coupling constants were calculated at the DFT level for each family of (phi, psi)-conformers separately and then experimental values were decomposed onto calculated (3)J(HH) couplings in order to obtain experimentally derived populations of conformers. As an alternative method of evaluation of preferred conformers, analysis of sensitive C-13 chemical shifts was introduced. We were able to thoroughly discuss several fundamental issues in predictions of preferred conformers of C-saccharides, such as the solvent effect, reliability of the force field, character of empirical Karplus equation or applicability of NMR parameters in predictions of conformational preferences in general.

Název v anglickém jazyce

Limitations in the description of conformational preferences of C-disaccharides: The (1 -> 3)-C-mannobiose case

Popis výsledku anglicky

Conformational preferences of two C-glycosyl analogues of Manp-(1 -> 3)-Manp, were studied using a combined method of theoretical and experimental chemistry. Molecular dynamics was utilized to provide conformational behavior along C-glycosidic bonds of methyl 3-deoxy-3-C-[(alpha-D-mannopyranosyl) methyl]-alpha-D-and L-mannopyranosides. The OPLS2005 and Glycam06 force fields were used. Simulations were performed with explicit water (TIP3P) and methanol. Results were compared with a complete conformational scan at the MM4 level with the dielectric constant corresponding to methanol. In order to verify predicted conformational preferences, vicinal (3)J(HH) NMR coupling constants were calculated by the Karplus equation on simulated potential energy surfaces (PES). A set of new parameters for the Karplus equation was also designed. Predicted 3JHH were compared with experimental data. We also used reverse methodology, in which the (3)J(HH) coupling constants were calculated at the DFT level for each family of (phi, psi)-conformers separately and then experimental values were decomposed onto calculated (3)J(HH) couplings in order to obtain experimentally derived populations of conformers. As an alternative method of evaluation of preferred conformers, analysis of sensitive C-13 chemical shifts was introduced. We were able to thoroughly discuss several fundamental issues in predictions of preferred conformers of C-saccharides, such as the solvent effect, reliability of the force field, character of empirical Karplus equation or applicability of NMR parameters in predictions of conformational preferences in general.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

<a href="/cs/project/GA16-00270S" target="_blank" >GA16-00270S: Objasnění struktury a interakcí glykokonjugátů a glykanů pomocí vibrační spektroskopie</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2017

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Carbohydrate Research

ISSN

0008-6215

e-ISSN

—

Svazek periodika

451

Číslo periodika v rámci svazku

Nov 8

Stát vydavatele periodika

NL - Nizozemsko

Počet stran výsledku

9

Strana od-do

42-50

Kód UT WoS článku

000413320300005

EID výsledku v databázi Scopus

2-s2.0-85029726149