Change search
ReferencesLink to record
Permanent link

Direct link
Nuclear magnetic shielding of the Cd-113(II) ion in aqua solution: A combined molecular dynamics/density functional theory study
KTH, School of Biotechnology (BIO), Theoretical Chemistry.ORCID iD: 0000-0001-6508-8355
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
Show others and affiliations
2008 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 36, 11347-11352 p.Article in journal (Refereed) Published
Abstract [en]

We present a combined molecular dynamics simulation and density functional theory investigation of the nuclear magnetic shielding constant of the Cd-113(II) ion solvated in aqueous solution. Molecular dynamics simulations are carried out for the cadmium-water system in order to produce instantaneous geometries for subsequent determination of the nuclear magnetic shielding constant at the density functional theory level. The nuclear magnetic shielding constant is computed using a perturbation theory formalism, which includes nonrelativistic and leading order relativistic contributions to the nuclear magnetic Shielding tensor. Although the NMR shielding constant varies significantly with respect to simulation time, the value averaged over increasing number of snapshots remains almost constant. The paramagnetic nonrelativistic contribution is found to be most sensitive to dynamical changes in the system and is mainly responsible for the thermal and solvent effects in solution. The relativistic correction features very little sensitivity to the chemical environment, and can be disregarded in theoretical calculations when a Cd complex is used as reference compound in Cd-113 NMR experiments, due to the mutual cancelation between individual relativistic corrections.

Place, publisher, year, edition, pages
2008. Vol. 112, no 36, 11347-11352 p.
Keyword [en]
quadrupole coupling-constant, initio scf calculations, chemical-shift, tensor, particle mesh ewald, single-crystal, liquid water, cadmium, compounds, solid-state, resonance spectroscopy, acetate dihydrate
URN: urn:nbn:se:kth:diva-17803DOI: 10.1021/jp802238fISI: 000258979800024ScopusID: 2-s2.0-52349102051OAI: diva2:335848
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

Open Access in DiVA

No full text

Other links

Publisher's full textScopus

Search in DiVA

By author/editor
Li, XinRinkevicius, ZilvinasÅgren, Hans
By organisation
Theoretical Chemistry
In the same journal
Journal of Physical Chemistry B

Search outside of DiVA

GoogleGoogle Scholar
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

Altmetric score

Total: 31 hits
ReferencesLink to record
Permanent link

Direct link