Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Fast Dynamic Processes in Solution Studied by NMR Spectroscopy
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Charles University in Prague, Department of low temperature physics.
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 [en]
Nuclear magnetic resonance, Dynamics, Ethanol, Cryptophanes, Saccharides
Keyword [cs]
Nukleární magnetická rezonance, dynamika, ethanol, kryptofan, sacharidy
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-92881ISBN: 978-91-7447-741-2 (print)OAI: oai:DiVA.org:su-92881DiVA: diva2:642913
Public defence
2013-09-25, Magnéli Hall, Arrhenius Laboratory, Svante Arrhenius väg 16 B, Stockholm, 13:00 (English)
Opponent
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
List of papers
1. NMR Investigation of Guest–Host Complex between Chloroform and Cryptophane C
Open this publication in new window or tab >>NMR Investigation of Guest–Host Complex between Chloroform and Cryptophane C
Show others...
2010 (English)In: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 48, no 8, 623-629 p.Article in journal (Refereed) Published
Abstract [en]

Guest–host complex between cryptophane C, possessing two non-equivalent caps, and chloroform is investigated by NMR spectroscopy. The kinetics of the chloroform exchange between the bound and free sites is determined by 1H exchange spectroscopy. Moreover, the preferential orientation of chloroform molecule with respect to the cryptophane C frame is examined by the NOESY and ROESY experiments. The experimental findings are compared to the results of quantum chemical calculations.

Keyword
proton NMR, inclusion complexes, complexation kinetics, cross-relaxation
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-81422 (URN)10.1002/mrc.2637 (DOI)000280218800008 ()
Available from: 2012-10-19 Created: 2012-10-19 Last updated: 2017-12-07Bibliographically approved
2. Host-Guest Complexes between Cryptophane-C and Chloromethanes Revisited
Open this publication in new window or tab >>Host-Guest Complexes between Cryptophane-C and Chloromethanes Revisited
2013 (English)In: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 51, no 1, 19-31 p.Article in journal (Refereed) Published
Abstract [en]

Cryptophane-C is composed of two nonequivalent cyclotribenzylene caps, one of which contains methoxy group substituents on the phenyl rings. The two caps are connected by three OCH2CH2O linkers in an anti arrangement. Host-guest complexes of cryptophane-C with dichloromethane and chloroform in solution were investigated in detail by nuclear magnetic resonance techniques and density functional theory (DFT) calculations. Variable temperature proton and carbon-13 spectra show a variety of dynamic processes, such as guest exchange and host conformational transitions. The guest exchange was studied quantitatively by exchange spectroscopy measurements or by line-shape analysis. The conformational preferences of the guest-containing host were interpreted through cross-relaxation measurements, providing evidence of the gauche+2 and gauche-2 conformations of the linkers. In addition, the mobility of the chloroform guest inside the cavity was studied by carbon-13 relaxation experiments. Combining different types of evidence led to a detailed picture of molecular recognition, interpreted in terms of conformational selection.

Keyword
inclusion complexes, complexation kinetics, cross relaxation
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-92050 (URN)10.1002/mrc.3898 (DOI)000319965700005 ()
Funder
Swedish Research Council, 613-2011-3311Knut and Alice Wallenberg Foundation
Note

AuthorCount:6;

Available from: 2013-07-15 Created: 2013-07-15 Last updated: 2017-12-06Bibliographically approved
3. Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation: 2. Interpretation of Complex Dynamics in Linear Oligosaccharides
Open this publication in new window or tab >>Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation: 2. Interpretation of Complex Dynamics in Linear Oligosaccharides
Show others...
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.

National Category
Physical Chemistry Organic Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-85935 (URN)10.1021/jp306627q (DOI)000312519900004 ()
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
4. Dynamics of exocyclic groups in the Escherichia coli O91 O-antigen polysaccharide in solution studied by carbon-13 NMR relaxation
Open this publication in new window or tab >>Dynamics of exocyclic groups in the Escherichia coli O91 O-antigen polysaccharide in solution studied by carbon-13 NMR relaxation
2013 (English)In: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 57, no 1, 37-45 p.Article in journal (Refereed) Published
Abstract [en]

Carbon-13 relaxation data are reported for exocyclic groups of hexopyranosyl sugar residues in the repeating unit within the Escherichia coli O91 O-antigen polysaccharide in a dilute D2O solution. The measurements of T 1, T 2 and heteronuclear nuclear Overhauser enhancements were carried out at 310 K at two magnetic fields (16.4 T, 21.1 T). The data were analyzed using the standard and extended Lipari–Szabo models, as well as a conformational jump model. The extended version of the Lipari–Szabo and the two-site jump models were most successful for the hydroxymethyl groups of Gal and GlcNAc sugar residues. Different dynamics was found for the hydroxymethyl groups associated with different configurations (d-gluco, d-galacto) of the sugar residues, the latter being faster than the former.

Place, publisher, year, edition, pages
Springer Netherlands, 2013
Keyword
Carbohydrates, Polysaccharide, Biopolymer, NMR spectroscopy, Model free approach, Two-site jump model
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-92898 (URN)10.1007/s10858-013-9763-5 (DOI)000323673800005 ()
Funder
Swedish Research Council, 613-2011-3311Swedish Research Council, 621-2010-4960Knut and Alice Wallenberg Foundation
Available from: 2013-08-26 Created: 2013-08-26 Last updated: 2017-12-06Bibliographically approved
5. Determination of size of molecular clusters of ethanol by means of diffusion NMR and hydrodynamic calculations
Open this publication in new window or tab >>Determination of size of molecular clusters of ethanol by means of diffusion NMR and hydrodynamic calculations
Show others...
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Microscopic structure of ethanol in liquid state is characterized as dynamic equilibrium of hydrogen bonded clusters of different sizes and topologies. We have developed a novel method for determination of average size of the clusters that combines measurement of diffusion coefficient by means of PFG NMR technique and hydrodynamic simulations. The approach includes the use of HydroNMR [de la Torre 2000] for small molecules, which is attained here by the calibration procedure using dilute solution of tetramethylsilane. It is thus possible to correlate the experimentally determined apparent hydrodynamic radius of ethanol with calculated hydrodynamic radii of the modeled clusters of different sizes. We found that average size of the clusters in 0.16 M solution of ethanol in hexane ranges from monomer above 300 K to hexamer below 200 K. The clusters in the case of 0.44 M are generally slightly larger – from average size of dimer at 320 K to heptamer below 210 K.

Keyword
ethanol, hydrogen bond, NMR, hydrodynamic simulation, density functional theory, diffusion coefficient, hydrodynamic radius
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-92899 (URN)
Available from: 2013-08-26 Created: 2013-08-26 Last updated: 2013-08-26Bibliographically approved

Open Access in DiVA

fulltext(1396 kB)495 downloads
File information
File name FULLTEXT01.pdfFile size 1396 kBChecksum SHA-512
ab0367a5f2024bd26310e55104765933aa8dce51a539b4df4af64117a3f862f5d27711f5a8253948348e2e592a025a380747091bb69e5c09988c4b56ae130a67
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Šoltésová, Mária
By organisation
Department of Materials and Environmental Chemistry (MMK)
Physical Chemistry

Search outside of DiVA

GoogleGoogle Scholar
Total: 495 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 343 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf