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Molecular Dynamics Studies of the Adsorption of Biomolecular Systems on Metal and Metal Oxide Surfaces
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Place, publisher, year, edition, pages
KTH Royal Institute of Technology, 2016. , p. 74
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2016:19
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
URN: urn:nbn:se:kth:diva-198489ISBN: 978-91-7729-180-0 (print)OAI: oai:DiVA.org:kth-198489DiVA, id: diva2:1056760
Public defence
2016-12-16, FP41, Roslagstullsbacken 33, Stockholm, 09:15 (English)
Opponent
Supervisors
Note

QC 20161220

Available from: 2016-12-20 Created: 2016-12-15 Last updated: 2016-12-21Bibliographically approved
List of papers
1. Dropping a droplet of cysteine molecules on a rutile (110) interface: Reactive versus nonreactive classical molecular dynamics simulations
Open this publication in new window or tab >>Dropping a droplet of cysteine molecules on a rutile (110) interface: Reactive versus nonreactive classical molecular dynamics simulations
2015 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, no 12, p. 6703-6712Article in journal (Refereed) Published
Abstract [en]

Two different types of classical molecular dynamics approaches, based on reactive and nonreactive force-field parametrizations, are used to investigate the adsorption process of a nanodroplet of cysteine molecules onto a perfect and a defective rutile (110) surface in the gas phase. Three molecular samples made of different cysteine species, namely, one neutral and two zwitterionic models, are tested in order to check how much the starting configurations can bias the description of the deposition onto the surface and if the initial composition of the droplet can influence the final mixture and adsorption arrangements. The present comparison between the two classical computational strategies is useful to identify and suggest the most appropriate approach to depict the behavior of hybrid materials, which cannot be treated at the quantum dynamical level because of the prohibitive computational cost. The complex interaction mechanisms between the molecules of the isolated droplet far from the slab and when it is spread on the inorganic interface are represented reliably and effectively by the reactive dynamics, which is revealed to be a powerful and more appropriate methodology, in comparison with standard molecular dynamics, to disclose all the aspects connected with the process of adsorption. Indeed, differently from the usual nonreactive molecular dynamics, simulations based on reactive force fields do not require any arbitrary assumption on the nature of the adsorbed units and include chemical reactivity. This is often fundamental to identify the most relevant biomolecular species interacting with the inorganic supports and the proton exchange mechanisms acting at the interface.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2015
Keywords
Adsorption, Amino acids, Drops, Hybrid materials, Molecules, Oxide minerals, Classical molecular dynamics, Classical molecular dynamics approaches, Computational strategy, Initial composition, Inorganic interfaces, Interaction mechanisms, Proton exchange mechanisms, Reactive force field
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-198476 (URN)10.1021/acs.jpcc.5b00932 (DOI)000351970800026 ()2-s2.0-84925936961 (Scopus ID)
Note

QC 20161216

Available from: 2016-12-15 Created: 2016-12-15 Last updated: 2017-11-29Bibliographically approved
2. Cysteine on TiO2(110): A Theoretical Study by Reactive Dynamics and Photoemission Spectra Simulation
Open this publication in new window or tab >>Cysteine on TiO2(110): A Theoretical Study by Reactive Dynamics and Photoemission Spectra Simulation
2014 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 30, no 29, p. 8819-8828Article in journal (Refereed) Published
Abstract [en]

A coherent account of adsorption modes, dynamics, self aggregation, and spectroscopic properties of an indoline organic dye adsorbed on TiO2 anatase (101) substrates is reported. The study is performed by combining reactive molecular dynamics (reaxFF) simulations with time-dependent density functional theory calculations, and the reliability of the results is assessed through comparison with theoretical and experimental data available in the literature. The use of a theoretical multilevel approach has proven to be crucial to gain a deep understanding, at an atomistic level, of the morphology and electronic properties of dye-sensitized heterogeneous interfaces. A realistic description of the functionalized anatase (101) interface, where a variety of binding modes are present, has been achieved by means of extensive molecular dynamics simulations of the adsorption of dye clusters made of different molecular units on medium/large size TiO2 anatase slabs. Our results disclose that the main driving forces toward formation of ordered surface aggregates are pi stacking and T-shaped interactions between the aromatic rings of the donor moiety of the molecules, as well as the tendency to maximize the anchoring points with the surface. The dye aggregates were found to be organized in domains, characterized by a different orientation of the packing units, and, in the high coverage limit, presenting a certain degree of short-to-medium range order.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2014
Keywords
Adsorbates, Biocompatibility, Computer simulation, Molecular dynamics, Photoemission, Titanium dioxide, Adsorbate structures, Bio-inorganic interfaces, Photoemission spectra, Reactive force field, Reactive molecular dynamics, Structure property relation, Technological applications, Theoretical study
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-198483 (URN)10.1021/la5014973 (DOI)000339686700023 ()25020148 (PubMedID)2-s2.0-84905015438 (Scopus ID)
Note

QC 20161216

Available from: 2016-12-15 Created: 2016-12-15 Last updated: 2017-11-29Bibliographically approved
3. Simulation of Gold Functionalization with Cysteine by Reactive Molecular Dynamics
Open this publication in new window or tab >>Simulation of Gold Functionalization with Cysteine by Reactive Molecular Dynamics
2016 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 7, no 2, p. 272-276Article in journal (Refereed) Published
Abstract [en]

The anchoring mechanism of cysteine to gold in water solution is characterized in detail by means of a combination of quantum chemistry (QC) and reactive classical molecular dynamics (RC-MD) calculations. A possible adsorption-reaction route is proposed, through RC-MD simulations based on a modified version of the protein reactive force field (ReaxFF), in which gold-protein interactions have been included after accurate parametrization at the QC level. The computational results confirm recent experimental findings regarding the mechanism as a two-step binding, namely, a slow physisorption followed by a fast chemisorption. The reaction barriers are estimated through the nudged elastic band approach and checked by QC calculations. Surface reconstructions, induced by the strong adsorption of the molecule, are identified, and their role, as further adsorbate stabilizers, is properly disclosed. The satisfactory agreement with QC data and experiments confirm the reliability of the simulations and the unique opportunity they provide to follow locally molecule adsorption on selected materials.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2016
Keywords
Adsorption, Amino acids, Gold, Molecules, Proteins, Quantum chemistry, Reaction kinetics, Adsorption reaction, Anchoring mechanism, Computational results, Molecule adsorptions, Nudged elastic band, Reactive classical molecular dynamics, Reactive force field, Reactive molecular dynamics
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-198477 (URN)10.1021/acs.jpclett.5b02769 (DOI)000368652700010 ()26731127 (PubMedID)2-s2.0-84955501883 (Scopus ID)
Note

QC 20161216

Available from: 2016-12-15 Created: 2016-12-15 Last updated: 2017-11-29Bibliographically approved
4. Decoration of gold nanoparticles with cysteine in solution: reactive molecular dynamics simulations
Open this publication in new window or tab >>Decoration of gold nanoparticles with cysteine in solution: reactive molecular dynamics simulations
2016 (English)In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 8, no 26, p. 12929-12938Article in journal (Refereed) Published
Abstract [en]

The dynamics of gold nanoparticle functionalization by means of adsorption of cysteine molecules in water solution is simulated through classical reactive molecular dynamics simulations based on an accurately parametrized force field. The adsorption modes of the molecules are characterized in detail disclosing the nature of the cysteine-gold interactions and the stability of the final material. The simulation results agree satisfactorily with recent experimental and theoretical data and confirm previous findings for a similar system. The covalent attachments of the molecules to the gold support are all slow physisorptions followed by fast chemisorptions. However, a great variety of binding arrangements can be observed. Interactions with the adsorbate caused surface modulations in terms of adatoms and dislocations which contributed to strengthen the cysteine adsorption.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2016
Keywords
Adsorption, Amino acids, Gold, Metal nanoparticles, Molecules, Nanoparticles, Adsorption modes, Covalent attachment, Force fields, Gold Nanoparticles, Gold support, Reactive molecular dynamics, Surface modulations, Water solutions
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-198481 (URN)10.1039/c6nr03181a (DOI)000379490600012 ()27305447 (PubMedID)2-s2.0-84977080775 (Scopus ID)
Note

QC 20161216

Available from: 2016-12-15 Created: 2016-12-15 Last updated: 2017-11-29Bibliographically approved
5. Theoretical Study of the Adsorption Mechanism of Cystine on Au(110) in Aqueous Solution
Open this publication in new window or tab >>Theoretical Study of the Adsorption Mechanism of Cystine on Au(110) in Aqueous Solution
2016 (English)In: Small, ISSN 1613-6810, E-ISSN 1613-6829, Vol. 12, no 44, p. 6134-6143Article in journal (Refereed) Published
Abstract [en]

The adsorption and dynamics of cystine, which is the oxidized dimer of cysteine where the monomers are connected through a disulfide bond, on the Au(110) surface, in water solution, is characterized by means of classical molecular dynamics simulations based on a recently developed reactive force field (ReaxFF). The adopted computational procedure and the force field description are able to give a complete and reliable picture, in line with experiments, of the molecule behavior in solution and in close contact with the metal support. Many different aspects, which have never been explored computationally at this level of theory, are disclosed, namely, physisorption, chemisorption, disulfide bridge breaking/creation, and formation of staples. It is demonstrated that all these events are connected with the specific orientation and location of cystine on the substrate. Simulations in pure water reveal that the disulfide bridge is stable, whereas dissociation is observed on gold. This is favored at low coverage, whereas at high coverage both intact and dissociated forms can be observed depending on local arrangements. The computed photoemission spectra at different K-edges for the predicted adsorbate structures satisfactorily agree with the experimental measurements extracted from literature.

Place, publisher, year, edition, pages
Wiley-VCH Verlagsgesellschaft, 2016
Keywords
biocompatibility, gold nanoparticle stabilization, hybrid materials, peptide–metal binding
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-198482 (URN)10.1002/smll.201602275 (DOI)000389407000009 ()2-s2.0-84989221395 (Scopus ID)
Note

QC 20161216

Available from: 2016-12-15 Created: 2016-12-15 Last updated: 2017-11-29Bibliographically approved
6. Theoretical Investigation of Adsorption, Dynamics, Self-Aggregation, and Spectroscopic Properties of the D102 Indoline Dye on an Anatase (101) Substrate
Open this publication in new window or tab >>Theoretical Investigation of Adsorption, Dynamics, Self-Aggregation, and Spectroscopic Properties of the D102 Indoline Dye on an Anatase (101) Substrate
Show others...
2016 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 5, p. 2787-2796Article in journal (Refereed) Published
Abstract [en]

A coherent account of adsorption modes, dynamics, self aggregation, and spectroscopic properties of an indoline organic dye adsorbed on TiO2 anatase (101) substrates is reported. The study is performed by combining reactive molecular dynamics (reaxFF) simulations with time-dependent density functional theory calculations, and the reliability of the results is assessed through comparison with theoretical and experimental data available in the literature. The use of a theoretical multilevel approach has proven to be crucial to gain a deep understanding, at an atomistic level, of the morphology and electronic properties of dye-sensitized heterogeneous interfaces. A realistic description of the functionalized anatase (101) interface, where a variety of binding modes are present, has been achieved by means of extensive molecular dynamics simulations of the adsorption of dye clusters made of different molecular units on medium/large size TiO2 anatase slabs. Our results disclose that the main driving forces toward formation of ordered surface aggregates are pi stacking and T-shaped interactions between the aromatic rings of the donor moiety of the molecules, as well as the tendency to maximize the anchoring points with the surface. The dye aggregates were found to be organized in domains, characterized by a different orientation of the packing units, and, in the high coverage limit, presenting a certain degree of short-to-medium range order.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2016
Keywords
Adsorption, Aggregates, Binding energy, Dyes, Electronic properties, Molecular dynamics, Reliability theory, Substrates, Titanium dioxide, Heterogeneous interfaces, Medium range order, Molecular dynamics simulations, Multilevel approach, Reactive molecular dynamics, Spectroscopic property, Theoretical investigations, Time dependent density functional theory calculations
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-198484 (URN)10.1021/acs.jpcc.5b11332 (DOI)000370210400034 ()2-s2.0-84958063771 (Scopus ID)
Note

QC 20161216

Available from: 2016-12-15 Created: 2016-12-15 Last updated: 2017-11-29Bibliographically approved

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