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Paramagnetic Perturbation of the F-19 NMR Chemical Shift in Fluorinated Cysteine by O-2: A Theoretical Study
KTH, School of Biotechnology (BIO), Theoretical Chemistry.ORCID iD: 0000-0001-6508-8355
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
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2009 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 31, 10916-10922 p.Article in journal (Refereed) Published
Abstract [en]

We present a combined molecular dynamics and density functional theory study of dioxygen-induced perturbation of the F-19 NMR chemical shifts in an aqueous solution of fluorinated cysteine under 100 atm of O-2 partial pressure. Molecular dynamics Simulations are carried out to determine the dominant structures of O-2 and the fluorinated cysteine complexes in water, and the collected structural information is exploited in computation of F-19 chemical shifts using density functional theory. The obtained results indicate that the density redistribution of the O-2 unpaired electrons between the dioxygen and fluorinated cysteine is responsible for the experimentally observed perturbation of the F-19 NMR chemical shifts, where the Fermi contact interaction plays the key role. The O-2-induced paramagnetic F-19 chemical shift, averaged over the simulation trajectory, is comparable with the reported experimental values, proving the availability of the developed strategy for modeling F-19 NMR chemical shifts in the presence of paramagnetic agents in ail aqueous solution. The applicability of the combined molecular dynamics/density functional theory approach for dioxygen NMR perturbation to all resonating nuclei including H-1, C-13, N-15, and F-19 is emphasized, and the ramification of this for investigations of membrane protein structures is discussed.

Place, publisher, year, edition, pages
2009. Vol. 113, no 31, 10916-10922 p.
Keyword [en]
correlated molecular calculations, hyperfine coupling-constants, particle mesh ewald, gaussian-basis sets, solvent exposure, liquid, water, protein-structure, functional theory, immersion depth, dynamics, method
URN: urn:nbn:se:kth:diva-18641DOI: 10.1021/jp902659sISI: 000268479000046ScopusID: 2-s2.0-68149124047OAI: diva2:336688
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2011-05-11Bibliographically approved
In thesis
1. Applications of Molecular Dynamics in Atmospheric and Solution Chemistry
Open this publication in new window or tab >>Applications of Molecular Dynamics in Atmospheric and Solution Chemistry
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. The work behind the thesis takes account of the fast development of computer hardware, which has made computationally intensive simulations become more and more popular in disciplines like pharmacy, biology and materials science. In molecular dynamics simulations using classical force fields, the atoms are represented by mass points with partial charges and the inter-atomic interactions are modeled by approximate potential functions that produce satisfactory results at an economical computational cost. The three-dimensional trajectory of a many-body system is generated by integrating Newton’s equations of motion, and subsequent statistical analysis on the trajectories provides microscopic insight into the physical properties of the system.

The applications in this thesis of molecular dynamics simulations in solution chemistry comprise four aspects: the 113Cd nuclear magnetic resonance shielding constant of aqua Cd(II) ions, paramagnetic 19F nuclear magnetic resonance shift in fluorinated cysteine, solvation free energies and structures of metal ions, and protein adsorption onto TiO2. In the studies of nuclear magnetic resonance parameters, the relativistic effect of the 113Cd nucleus and the paramagnetic shift of 19F induced by triplet O2 are well reproduced by a combined molecular dynamics and density functional theory approach. The simulation of the aqua Cd(II) ion is also extended to several other monovalent, divalent and trivalent metal ions, where careful parameterization of the metal ions ensures the reproduction of experimental solvation structures and free energies. Molecular dynamics simulations also provided insight into the mechanism of protein adsorption onto the TiO2 surface by suggesting that the interfacial water molecules play an important role of mediating the adsorption and that the hydroxylated TiO2 surface has a large affinity to the proteins.

The applications of molecular dynamics simulations in atmospheric chemistry are mainly focused on two types of organic components in aerosol droplets: humic-like compounds and amino acids. The humic-like substances, including cis-pinonic acid, pinic acid and pinonaldehyde, are surface-active organic compounds that are able to depress the surface tension of water droplets, as revealed by both experimental measurements and theoretical computations. These compounds either concentrate on the droplet surface or aggregate inside the droplet. Their effects on the surface tension can be modeled by the Langmuir-Szyszkowski equation. The amino acids are not strong surfactants and their influence on the surface tension is much smaller. Simulations show that the zwitterionic forms of serine, glycine and alanine have hydrophilic characteristics, while those of valine, methionine and phenylalanine are hydrophobic. The curvature dependence of the surface tension is also analyzed, and a slight improvement in the Köhler equation is obtained by introducing surface tension corrections for droplets containing glycine and serine.

Through several examples it is shown that molecular dynamics simulations serve as a promising tool in the study of aqueous systems. Both solute-solvent interactions and interfaces can be treated properly by choosing suitable potential functions and parameters. Specifically, molecular dynamics simulations provide a microscopic picture that evolves with time, making it possible to follow the dynamic processes such as protein adsorption or atmospheric droplet formation. Moreover, molecular dynamics simulations treat a large number of molecules and give a statistical description of the system; therefore it is convenient to compare the simulated results with experimentally measured data. The simulations can provide hints for better design of experiments, while experimental data can be fed into the refinement of the simulation model. As an important complementary to experiments, molecular dynamics simulations will continue to play significant roles in the research fields of physics, chemistry, materials science, biology and medicine.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology (KTH), 2011. viii, 54 p.
Trita-BIO-Report, ISSN 1654-2312 ; 2011:10
National Category
Theoretical Chemistry
urn:nbn:se:kth:diva-33309 (URN)978-91-7415-963-9 (ISBN)
Public defence
2011-05-26, FB52, AlbaNova, Roslagstullsbacken 21, Stockholm, 14:00 (English)
Swedish e‐Science Research Center
QC 20110511Available from: 2011-05-11 Created: 2011-05-03 Last updated: 2012-05-24Bibliographically approved

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