J 2011

Three-Dimensional Potential Energy Surface of Selected Carbohydrates' CH/p Dispersion Interactions Calculated by High-Level Quantum Mechanical Methods

KOZMON, Stanislav; Radek MATUŠKA; Vojtech SPIWOK and Jaroslav KOČA

Basic information

Original name

Three-Dimensional Potential Energy Surface of Selected Carbohydrates' CH/p Dispersion Interactions Calculated by High-Level Quantum Mechanical Methods

Authors

KOZMON, Stanislav (703 Slovakia, belonging to the institution); Radek MATUŠKA (203 Czech Republic, belonging to the institution); Vojtech SPIWOK (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic, guarantor, belonging to the institution)

Edition

Chemistry - A European Journal, Weinheim, WILEY-VCH Verlag, 2011, 0947-6539

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

is not subject to a state or trade secret

Impact factor

Impact factor: 5.925

RIV identification code

RIV/00216224:14740/11:00049962

Organization unit

Central European Institute of Technology

DOI

UT WoS

000290216000024

Keywords in English

carbohydrates; CH/pi interactions; DFT calculations; dispersion interactions; molecular recognition

Tags

Changed: 27/1/2017 21:01, prof. RNDr. Jaroslav Koča, DrSc.

Abstract

In the original language

In this study we present the first systematic computational three-dimensional scan of carbohydrate hydrophobic patches for the ability to interact through CH/pi dispersion interactions. The carbohydrates beta-D-glucopyranose, beta-D-mannopyranose and alpha-l-fucopyranose were studied in a complex with a benzene molecule, which served as a model of the CH/pi interaction in carbohydrate/protein complexes. The 3D relaxed scans were performed at the SCC-DFTB-D level with 3 757 grid points for both carbohydrate hydrophobic sides. The interaction energy of all grid points was recalculated at the DFT-D BP/def2-TZVPP level. The results obtained clearly show highly delimited and separated areas around each CH group, with an interaction energy up to -5.40 kcal mol(-1). The results also show that with increasing H center dot center dot center dot pi distance these delimited areas merge and form one larger region, which covers all hydrogen atoms on that specific carbohydrate side.

Links

GD301/09/H004, research and development project
Name: Molekulární a strukturní biologie vybraných cytostatik. Od mechanistických studií k chemoterapii rakoviny
Investor: Czech Science Foundation
LC06030, research and development project
Name: Biomolekulární centrum
Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular centre
MSM0021622413, plan (intention)
Name: Proteiny v metabolismu a při interakci organismů s prostředím
Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment
205872, interní kód MU
Name: Program developing interdisciplinary research POtential for the STudies of BIOMolecular INteractions (Acronym: POSTBIOMIN)
Investor: European Union, Program developing interdisciplinary research POtential for the STudies of BIOMolecular INteractions, Capacities