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Applications of Molecular Dynamics in Atmospheric and Solution Chemistry
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0001-6508-8355
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.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2011:10
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-33309ISBN: 978-91-7415-963-9OAI: oai:DiVA.org:kth-33309DiVA: diva2:414439
Public defence
2011-05-26, FB52, AlbaNova, Roslagstullsbacken 21, Stockholm, 14:00 (English)
Opponent
Supervisors
Funder
Swedish e‐Science Research Center
Note
QC 20110511Available from: 2011-05-11 Created: 2011-05-03 Last updated: 2012-05-24Bibliographically approved
List of papers
1. Nuclear magnetic shielding of the Cd-113(II) ion in aqua solution: A combined molecular dynamics/density functional theory study
Open this publication in new window or tab >>Nuclear magnetic shielding of the Cd-113(II) ion in aqua solution: A combined molecular dynamics/density functional theory study
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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.

Keyword
quadrupole coupling-constant, initio scf calculations, chemical-shift, tensor, particle mesh ewald, single-crystal, liquid water, cadmium, compounds, solid-state, resonance spectroscopy, acetate dihydrate
Identifiers
urn:nbn:se:kth:diva-17803 (URN)10.1021/jp802238f (DOI)000258979800024 ()2-s2.0-52349102051 (ScopusID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2011-05-11Bibliographically approved
2. Paramagnetic Perturbation of the F-19 NMR Chemical Shift in Fluorinated Cysteine by O-2: A Theoretical Study
Open this publication in new window or tab >>Paramagnetic Perturbation of the F-19 NMR Chemical Shift in Fluorinated Cysteine by O-2: A Theoretical Study
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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.

Keyword
correlated molecular calculations, hyperfine coupling-constants, particle mesh ewald, gaussian-basis sets, solvent exposure, liquid, water, protein-structure, functional theory, immersion depth, dynamics, method
Identifiers
urn:nbn:se:kth:diva-18641 (URN)10.1021/jp902659s (DOI)000268479000046 ()2-s2.0-68149124047 (ScopusID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2011-05-11Bibliographically approved
3. Computer simulations of aqua metal ions for accurate reproduction of hydration free energies and structures
Open this publication in new window or tab >>Computer simulations of aqua metal ions for accurate reproduction of hydration free energies and structures
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.

Keyword
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
Identifiers
urn:nbn:se:kth:diva-28432 (URN)10.1063/1.3352567 (DOI)000275589700030 ()2-s2.0-77953644518 (ScopusID)
Note
QC 20110117Available from: 2011-01-17 Created: 2011-01-14 Last updated: 2011-05-11Bibliographically approved
4. On the Mechanism of Protein Adsorption onto Hydroxylated and Nonhydroxylated TiO2 Surfaces
Open this publication in new window or tab >>On the Mechanism of Protein Adsorption onto Hydroxylated and Nonhydroxylated TiO2 Surfaces
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2010 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 114, no 34, 14496-14502 p.Article in journal (Refereed) Published
Abstract [en]

Protein adsorption onto implant surfaces is of great importance for the regulation of implant bioactivity. Surface modification of implants is a promising way in the molecular design of biocompatible materials against nonspecific adsorption of proteins. On the basis of these fundamental facts, we focus in this work on the different behavior of protein adsorption on hydroxylated and nonhydroxylated rutile TiO2 (110) surfaces through molecular dynamics simulations. Our investigation indicates that the distribution of the water molecules at the interface induced by the surface modification plays an important role in the protein adsorption. The surface with modified hydroxyl groups was observed to have much greater affinity to the protein, as reflected by the larger protein-surface electrostatic interaction and by the larger amount of adsorbed residues. The highly ordered structure of the modified hydroxyl groups on the hydroxylated surface diminishes the possibility of hydrogen bond formation between the surface and the water molecules above it, which in turn makes it easier for the protein to move closer to the surface with hydroxyl modification.

National Category
Chemical Sciences Physical Sciences
Identifiers
urn:nbn:se:kth:diva-26852 (URN)10.1021/jp1037156 (DOI)000281129100026 ()2-s2.0-77956149715 (ScopusID)
Note
QC 20101201Available from: 2010-12-01 Created: 2010-11-29 Last updated: 2012-03-21Bibliographically approved
5. Surface-Active cis-Pinonic Acid in Atmospheric Droplets: A Molecular Dynamics Study
Open this publication in new window or tab >>Surface-Active cis-Pinonic Acid in Atmospheric Droplets: A Molecular Dynamics Study
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2010 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, Vol. 1, no 4, 769-773 p.Article in journal (Refereed) Published
Abstract [en]

Water vapor in the atmosphere can condensate and form cloud droplets when there is a certain amount of humidity and a presence of cloud condensation nuclei, and organic solutes called surfactants can significantly lower the surface tension of water-one of the parameters determining cloud droplet population. We here present a molecular dynamics study of the behavior of cis-pinonic acid, a commonly found organic compound in cloud condensation nuclei, and its effect on the surface tension of water clusters. Specifically, the decrease in surface tension is found to depend on not only the concentration of the organic compound but also the droplet size due to the spontaneous assembly of the surfactant molecules on the droplet surface. This leads to the conclusion that the partitioning of the surfactant between the bulk and surface plays an important role in the behavior of atmospheric aerosol particles and thus in their availability for cloud formation.

Keyword
LINEAR CONSTRAINT SOLVER, PARTICLE MESH EWALD, COATED NANOAEROSOLS, AQUEOUS-SOLUTIONS, ORGANIC-COMPOUNDS, TENSION, SIMULATIONS, NUCLEUS, LINCS
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-28253 (URN)10.1021/jz9004784 (DOI)000277040600018 ()2-s2.0-77749264304 (ScopusID)
Note
QC 20110118Available from: 2011-01-18 Created: 2011-01-12 Last updated: 2011-05-11Bibliographically approved
6. HULIS in Nanoaerosol Clusters; Investigations of Surface Tension and Aggregate Formation using Molecular Dynamics Simulations
Open this publication in new window or tab >>HULIS in Nanoaerosol Clusters; Investigations of Surface Tension and Aggregate Formation using Molecular Dynamics Simulations
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2011 (English)In: Atmospheric Chemistry and Physics Discussions, ISSN 1680-7367, E-ISSN 1680-7375Article in journal (Other academic) Published
Abstract [en]

Cloud condensation nuclei act as cores for water vapor condensation, and their composition and chemical properties may enhance or depress the ability for droplet growth. In this study we use molecular dynamics simulations to show that humic-like substances of larger systems (8.6 nm in diameter) mimic experimental data well referring to reduction of surface tension. The structural properties examined show the ability for the humic-like substances to aggregate inside the nanoaerosol clusters.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-33308 (URN)10.5194/acpd-11-6957-2011 (DOI)
Note

QC 20110511

Available from: 2011-05-03 Created: 2011-05-03 Last updated: 2016-12-06Bibliographically approved
7. Glycine in aerosol water droplets: a critical assessment of Köhler theory by predicting surface tension from molecular dynamics simulations
Open this publication in new window or tab >>Glycine in aerosol water droplets: a critical assessment of Köhler theory by predicting surface tension from molecular dynamics simulations
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2011 (English)In: Atmospheric Chemistry And Physics, ISSN 1680-7316, Vol. 11, no 2, 519-527 p.Article in journal (Refereed) Published
Abstract [en]

Aerosol particles in the atmosphere are important participants in the formation of cloud droplets and have significant impact on cloud albedo and global climate. According to the Kohler theory which describes the nucleation and the equilibrium growth of cloud droplets, the surface tension of an aerosol droplet is one of the most important factors that determine the critical supersaturation of droplet activation. In this paper, with specific interest to remote marine aerosol, we predict the surface tension of aerosol droplets by performing molecular dynamics simulations on two model systems, the pure water droplets and glycine in water droplets. The curvature dependence of the surface tension is interpolated by a quadratic polynomial over the nano-sized droplets and the limiting case of a planar interface, so that the so-called Aitken mode particles which are critical for droplet formation could be covered and the Kohler equation could be improved by incorporating surface tension corrections.

National Category
Theoretical Chemistry Meteorology and Atmospheric Sciences
Identifiers
urn:nbn:se:kth:diva-31645 (URN)10.5194/acp-11-519-2011 (DOI)000286722300008 ()2-s2.0-78751504505 (ScopusID)
Funder
Swedish Research Council, 2009-3614Swedish e‐Science Research Center
Note
QC 20110321Available from: 2011-03-21 Created: 2011-03-21 Last updated: 2012-05-23Bibliographically approved
8. Molecular Dynamics Study on the Surface Tension of Atmospheric Water Droplets Containing Amino Acids
Open this publication in new window or tab >>Molecular Dynamics Study on the Surface Tension of Atmospheric Water Droplets Containing Amino Acids
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Atmospheric amino acids constitute an important fraction of the water-soluble organic nitrogen compounds in both marine and continental aerosols, and have been confirmed as effective cloud condensation nuclei materials in laboratory tests. We here present molecular dynamics study of six types of amino acids in atmospheric water droplets, in order to investigate molecular distributions, orientations and induced changes in surface tension, and to evaluate their indirect effects on optical properties of clouds. These amino acids, including serine, glycine, alanine, valine, methionine and phenylalanine, are categorized into hydrophilic and hydrophobic species according to their affinities to water. Different amino acids show distinct effects on the surface tension; even the same amino acid has different influence on the surface tension of planar and spherical interfaces. Finally the curvature dependence of the surface tension is modeled by a quadratic polynomial function of the inverse of droplet radius, and such relationship is used to improve the Köhler equation in predicting the critical supersaturation of droplet activation.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-33307 (URN)
Note
QS 2011Available from: 2011-05-03 Created: 2011-05-03 Last updated: 2011-05-11Bibliographically approved

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