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Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation: 2. Interpretation of Complex Dynamics in Linear Oligosaccharides
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Charles University Prague .
Stockholm University, Faculty of Science, Department of Organic Chemistry.
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2012 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 50, 14541-14555 p.Article in journal (Refereed) Published
Abstract [en]

A computational stochastic approach is applied to the description of flexible molecules. By combining (i) molecular dynamics simulations, (ii) hydrodynamics approaches, and (iii) a multidimensional diffusive description for internal and global dynamics, it is possible to build an efficient integrated approach to the interpretation of relaxation processes in flexible systems. In particular, the model is applied to the interpretation of nuclear magnetic relaxation measurements of linear oligosaccharides, namely a mannose-containing trisaccharide and the pentasaccharide LNF-1. Experimental data are reproduced with sufficient accuracy without free model parameters.

Place, publisher, year, edition, pages
2012. Vol. 116, no 50, 14541-14555 p.
National Category
Physical Chemistry Organic Chemistry
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-85935DOI: 10.1021/jp306627qISI: 000312519900004OAI: oai:DiVA.org:su-85935DiVA: diva2:585548
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

Author count: 8;

Available from: 2013-01-10 Created: 2013-01-10 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Fast Dynamic Processes in Solution Studied by NMR Spectroscopy
Open this publication in new window or tab >>Fast Dynamic Processes in Solution Studied by NMR Spectroscopy
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Nuclear magnetic resonance (NMR) spectroscopy is capable to deliver a detailed information about the dynamics on molecular level in a wide range of time scales, especially if accompanied by suitably chosen theoretical tools. In this work, we employed a set of high-resolution NMR techniques to investigate dynamics processes in several weakly interacting molecular systems in solution.

Van der Waals interactions play an important role in inclusion complexes of cryptophane-C with chloroform or dichloromethane. The complex formation was thoroughly investigated by means of 1H and 13C NMR experiments along with the quantum-chemical density functional theory (DFT) calculations. We characterized kinetics, thermodynamics, as well as fine details of structural rearrangements of the complex formation.

Internal dynamics of oligo- and polysaccharides presents a considerable challenge due to possible coupling of internal and global molecular motions. Two small oligosaccharides were investigated as test cases for a newly developed integrated approach for interpreting the dynamics of the molecules with non-trivial internal flexibility. The approach comprised advanced theoretical tools, including stochastic modeling, molecular dynamics (MD) simulations, and hydrodynamic simulations.

A biologically important bacterial O-antigenic polysaccharide from E. Coli O91 was addressed employing selective isotope labeling and multiple-field 13C relaxation experiments. The complex dynamics of the polysaccharide is characterized by the conformational motion of the exocyclic groups of the sugars, superimposed to the breathing motion of the polymeric chain.

Hydrogen bonding is another major non-covalent interaction. Dilute solutions of ethanol were chosen as a model of liquid systems containing extensive hydrogen-bonded networks. We developed a new methodology consisting of NMR diffusion measurements, DFT calculations, and hydrodynamic modeling and utilized it to determine average size of the molecular clusters of ethanol at given conditions.

Abstract [cs]

Nukleární magnetická rezonance (NMR) dokáže poskytnout detailní informace o dynamice na molekulární úrovni v širokém oboru časových škál, zejména pokud je doplněna vhodnými teoretickými nástroji. V této práci byla použita sada technik NMR spektroskopie vysokého rozlišení pro výzkum dynamických procesů slabě interagujících molekulárních struktur v roztoku.

Van der Waalsovy interakce hrají důležitou roli v inkluzních komplexech kryptofanu-C s chloroformem nebo dichlormethanem. Tvorba komplexu byla podrobně zkoumána za použití 1H a13C NMR experimentů spolu s kvantově-chemickými výpočty. Byla charakterizována kinetika, termodynamika, jakož i detaily strukturních změn při tvorbě komplexu.

Vnitřní dynamika oligo- a polysacharidů představuje velkou výzvu  kvůli možnému provázání lokálního a globálního molekulárního pohybu. Dva modelové oligosacharidy byly použity pro testování nově vyvinuté integrované metody pro popis dynamiky molekul s netriviální vnitřní flexibilitou. Tato metoda spojuje pokročilé teoretické výpočty včetně stochastického modelování, simulací molekulové dynamiky a hydrodynamiky.

Antigenní bakteriální polysacharid z E. Coli O91, důležitý z biologického hlediska, byl studován za pomoci selektivního izotopového značení a NMR relaxačních experimentů ve více magnetických polích. Komplexní dynamika polysacharidu je charakterizována konformačními změnami exocyklických skupin cukerných reziduí a omezenou interní flexibilitou polymerního řetězce.

Vodíkové vazby jsou další z důležitých nekovalentních interakcí. Zředěné roztoky ethanolu byly vybrány jako model kapalného systému obsahujícího rozsáhlou síť vodíkových vazeb. Vyvinuli jsme novou metodologii, složenou z NMR difúzních měření, kvantově-chemických výpočtů a hydrodynamického modelování a aplikovali ji pro zjištění průměrné velikosti molekulových klastrů ethanolu za specifických podmínek.

Place, publisher, year, edition, pages
Stockholm: Department of Materials and Environmental Chemistry, Stockholm University, 2013. 52 p.
Keyword
Nuclear magnetic resonance, Dynamics, Ethanol, Cryptophanes, Saccharides, Nukleární magnetická rezonance, dynamika, ethanol, kryptofan, sacharidy
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-92881 (URN)978-91-7447-741-2 (ISBN)
Public defence
2013-09-25, Magnéli Hall, Arrhenius Laboratory, Svante Arrhenius väg 16 B, Stockholm, 13:00 (English)
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Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Accepted. Paper 5: Manuscript.

Available from: 2013-09-03 Created: 2013-08-23 Last updated: 2013-08-26Bibliographically approved

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