| 551. |
- Monti, Susanna, et al.
(författare)
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Characterization of the adsorption dynamics of trisodium citrate on gold in water solution
- 2017
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Ingår i: RSC Advances. - : ROYAL SOC CHEMISTRY. - 2046-2069. ; 7:78, s. 49655-49663
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations (MDs) based on a reactive force field (ReaxFF) are carried out to investigate typical adsorption modes of trisodium citrate (CIT) on gold nanoparticles (AuNPs). All possible configurations of CIT on a model AuNP in solution are identified and the stabilizing role played by the adsorbate on the AuNP structure is disclosed by analyzing protonation state, dynamics and interactions of the molecules with the surrounding environment. A realistic scenario is created by sampling extensively the conformational space of citrate and by validating the simulation results against data extracted from the literature. Carboxyl moieties are found in contact with the gold substrate through one or both oxygens and Na+ ions are present in the adsorbed citrate layer. Citrate binding is relatively strong and its action as a chelator stabilizes surface reconstructions. The molecules have the tendency to self-assemble and form a stable cover, which is reinforced by adatoms. All the results are in perfect agreement with experimental observations and theoretical data.
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| 552. |
- Monti, Susanna, et al.
(författare)
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Decoration of gold nanoparticles with cysteine in solution : reactive molecular dynamics simulations
- 2016
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Ingår i: Nanoscale. - : Royal Society of Chemistry. - 2040-3364 .- 2040-3372. ; 8:26, s. 12929-12938
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 553. |
- Monti, Susanna, et al.
(författare)
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Dropping a droplet of cysteine molecules on a rutile (110) interface: Reactive versus nonreactive classical molecular dynamics simulations
- 2015
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 119:12, s. 6703-6712
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 554. |
- Monti, Susanna, et al.
(författare)
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Dynamics and self-assembly of bio-functionalized gold nanoparticles in solution : Reactive molecular dynamics simulations
- 2018
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Ingår i: Nano Reseach. - : TSINGHUA UNIV PRESS. - 1998-0124 .- 1998-0000. ; 11:4, s. 1757-1767
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Tidskriftsartikel (refereegranskat)abstract
- The self-assembling properties, stability, and dynamics of hybrid nanocarriers (gold nanoparticles (AuNPs) functionalized with cysteine-based peptides) in solution are studied through a series of classical molecular dynamics simulations based on a recently parametrized reactive force field. The results reveal, at the atomic level, all the details regarding the peptide adsorption mechanisms, nanoparticle stabilization, aggregation, and sintering. The data confirm and explain the experimental findings and disclose aspects that cannot be scrutinized by experiments. The biomolecules are both chemisorbed and physisorbed; self-interactions of the adsorbates and formation of stable networks of interconnected molecules on the AuNP surfaces limit substrate reconstructions, protect the AuNPs from the action of the solvent, and prevent direct interactions of the gold surfaces. The possibility of agglomeration of the functionalized nanoparticles, compared with the sintering of the bare supports in a water solution, is demonstrated through relatively long simulations and fast steered dynamics. The analysis of the trajectories reveals that the AuNPs were well stabilized by the peptides. This prevented particle sintering and kept the particles far apart; however, part of their chains could form interconnections (crosslinks) between neighboring gold vehicles. The excellent agreement of these results with the literature confirm the reliability of the method and its potential application to the modeling of more complex materials relevant to the biomedical sector.
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| 555. |
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| 556. |
- Monti, Susanna, et al.
(författare)
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Simulation of Gold Functionalization with Cysteine by Reactive Molecular Dynamics
- 2016
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 7:2, s. 272-276
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 557. |
- Monti, Susanna, et al.
(författare)
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Theoretical Study of the Adsorption Mechanism of Cystine on Au(110) in Aqueous Solution
- 2016
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Ingår i: Small. - : Wiley-VCH Verlagsgesellschaft. - 1613-6810 .- 1613-6829. ; 12:44, s. 6134-6143
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 558. |
- Mudedla, Sathish Kumar, et al.
(författare)
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Destabilization of amyloid fibrils on interaction with MoS2-based nanomaterials
- 2019
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Ingår i: RSC Advances. - : ROYAL SOC CHEMISTRY. - 2046-2069. ; 9:3, s. 1613-1624
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Tidskriftsartikel (refereegranskat)abstract
- The present work is motivated by the established concept that the structure and energetics of biomacromolecules can be modulated by confining their dimensions in the nanoscale. In particular, here we use force-field methods to understand the stability of amyloid fibrils at nanostructured interfaces, which can be useful for the development of new therapeutics for Alzheimer's disease. We explore the binding modes and structural properties of fibrils at the interface of molybdenum disulphide nanotubes and the nanosurface using classical molecular dynamics simulations. We find that in general the MoS2 materials induces disruptions in the structure of the amyloid fibrils where the beta sheet conformation of the fibrils changes to a turned conformation, and it is large in the case of nanotubes in comparison to the nanosurfaces. The intermolecular hydrogen bonds, hydrophilic and hydrophobic contacts between the monomer peptides in the fibril are reduced due to their adsorption onto the MoS2 materials, which results in a destabilization of the fibril. The destabilization of fibril is to some extent compensated for by the van der Waals interactions between the fibril and MoS2. Overall the results indicate that MoS2-based materials can be useful in inhibiting the aggregation of smaller protofibrils to matured fibrils and to bust the already formed fibrils. Therapeutic materials should not exhibit any cross interaction with other off-targets compounds. In order to test whether the MoS2 nanomaterial has any such effect we have studied its interaction with two additional biomacromolecules, the human serum albumin and p53 protein, and we report no significant changes in the secondary structure of these biomolecules. Through molecular docking studies we also established that the drug binding ability of HSA is not altered by its surface binding to MoS2 nanosurface.
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| 559. |
- Mudedla, Sathish Kumar, et al.
(författare)
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Effect of Familial Mutations on the Interconversion of alpha-Helix to beta-Sheet Structures in an Amyloid-Forming Peptide : Insight from Umbrella Sampling Simulations
- 2019
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Ingår i: ACS Chemical Neuroscience. - : American Chemical Society (ACS). - 1948-7193. ; 10:3, s. 1347-1354
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the initial events of aggregation of amyloid beta monomers to form beta-sheet rich fibrils is useful for the development of therapeutics for Alzheimer's disease. In this context, the changes in energetics involved in the aggregation of helical amyloid beta monomers into beta-sheet rich dimers have been investigated using umbrella sampling simulations and density functional theory calculations. The results from umbrella sampling simulations for the free energy profile for the interconversion closely agree with the results of density functional theory calculations. The results reveal that helical peptides converted to beta-sheet structures through coil-like conformations as intermediates that are mostly stabilized by intramolecular hydrogen bonds. The stabilization of intermediate structures could be a possible way to inhibit fibril formation. Mutations substantially decrease the height of the energy barrier for interconversion from alpha-helix to beta-sheet structure when compared to that of the wild type, something that is attributed to an increase in the number of intramolecular hydrogen bonds between backbone atoms in the coil structures that correspond to a maximum value on the free energy surface. The reduction of the energy barrier leads to an enhancement of the rate of aggregation of amyloid beta monomers upon introduction of various familial mutations, which is consistent with previous experimental reports.
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| 560. |
- Mudedla, S. K., et al.
(författare)
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Enhancement of Internal Motions of Lysozyme through Interaction with Gold Nanoclusters and its Optical Imaging
- 2015
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 119:1, s. 653-664
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the interaction of gold nanoclusters with proteins has important ramifications in various fields. We present a study of the interaction between gold nanoclusters and lysozyme investigated using classical molecular dynamics and center-of-mass pulling simulations. The results reveal that the gold nanoclusters induce significant structural changes in lysozyme. Because the internal motions of lysozyme are related to its function, the changes in these internal motions have been quantified using principal component analysis of the molecular dynamics trajectories. The internal motions of lysozyme that are important for its function have been altered because of the interaction with the gold nanocluster. We have also explored how these induced changes in the lysozyme structure affect specific optical properties of the gold nanocluster using the complex polarization propagator method within the time-dependent density functional theory framework, which is of relevance for studies of the optical imaging of lysozyme using gold nanoclusters as molecular probes.
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