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Computer simulations of aqua metal ions for accurate reproduction of hydration free energies and structures
KTH, School of Biotechnology (BIO), Theoretical Chemistry.ORCID iD: 0000-0001-6508-8355
KTH, School of Biotechnology (BIO), Theoretical Chemistry.ORCID iD: 0000-0002-1763-9383
2010 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 132, no 10, 104505- p.Article in journal (Refereed) Published
Abstract [en]

Metal ions play essential roles in biological processes and have attracted much attention in both experimental and theoretical fields. By using the molecular dynamics simulation technology, we here present a fitting-refining procedure for deriving Lennard-Jones parameters of aqua metal ions toward the ultimate goal of accurately reproducing the experimentally observed hydration free energies and structures. The polarizable SWM4-DP water model {proposed by Lamoureux [J. Chem. Phys. 119, 5185 (2003)]} is used to properly describe the polarization effects of water molecules that interact with the ions. The Lennard-Jones parameters of the metal ions are first obtained by fitting the quantum mechanical potential energies of the hexahydrated complex and are subsequently refined through comparison between the calculated and experimentally measured hydration free energies and structures. In general, the derived Lennard-Jones parameters for the metal ions are found to reproduce hydration free energies accurately and to predict hydration structures that are in good agreement with experimental observations. Dynamical properties are also well reproduced by the derived Lennard-Jones parameters.

Place, publisher, year, edition, pages
2010. Vol. 132, no 10, 104505- p.
Keyword [en]
free energy, Lennard-Jones potential, molecular dynamics method, polarisability, solvation, water
National Category
Atom and Molecular Physics and Optics Atom and Molecular Physics and Optics
URN: urn:nbn:se:kth:diva-28432DOI: 10.1063/1.3352567ISI: 000275589700030ScopusID: 2-s2.0-77953644518OAI: diva2:388376
QC 20110117Available from: 2011-01-17 Created: 2011-01-14 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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