Surface-Altered Protonation Studied by Photoelectron Spectroscopy and Reactive Dynamics Simulations

Silva, Áderson Miranda da; Mocellin, Alexandra; Monti, Susanna; Cui, Li; Marinho, Ricardo R. T.; Medina, Aline; Ågren, Hans; Carravetta, Vincenzo; Brito, A. Naves de

doi:10.1021/acs.jpclett.5b00131

Cited by 13 publications

(24 citation statements)

References 23 publications

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“…Stimulated by these findings and by the satisfactory results obtained in our previous theoretical investigations regarding motion and reactivity of cysteine in water, on TiO 2 , and on gold supports we have extended our studies to describe the behavior of cystine in close contact with a gold substrate. The appearance of this molecule in our molecular dynamics (MD) simulations is not new.…”

Section: Introductionsupporting

confidence: 58%

“…The computational procedure we have used for studying adsorption modes and behavior in solution of the cysteine dimer was already employed successfully in the case of the monomer . The reactive force field parameters were carefully determined in an earlier work by choosing appropriate descriptors to render the interaction of the molecule with the metal support.…”

Section: Computational Detailsmentioning

confidence: 99%

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Theoretical Study of the Adsorption Mechanism of Cystine on Au(110) in Aqueous Solution

Monti

Carravetta

Ågren

2016

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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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Section: Introductionsupporting

confidence: 58%

Section: Computational Detailsmentioning

confidence: 99%

Theoretical Study of the Adsorption Mechanism of Cystine on Au(110) in Aqueous Solution

Monti

Carravetta

Ågren

2016

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“…Apreviousstudy [24] has suggested that species at the surface of al iquid jet might differ from those observed in the bulk because of the surface effect. In our study on glycine nanoparti- Table 1.…”

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confidence: 99%

Guanidinium Group Remains Protonated in a Strongly Basic Arginine Solution

Jacobs

Kostko

et al. 2017

ChemPhysChem

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Knowledge of the acid dissociation constant of an amino acid has very important ramifications in the biochemistry of proteins and lipid bilayers in aqueous environments because charge and proton transfer depend on its value. The acid dissociation constant for the guanidinium group in arginine has historically been posited as 12.5, but there is substantial variation in published values over the years. Recent experiments suggest that the dissociation constant for arginine is much higher than 12.5, which explains why the arginine guanidinium group retains its positive charge under all physiological conditions. In this work, we use X-ray photoelectron spectroscopy to study unsupported, aqueous arginine nanoparticles. By varying the pH of the constituent solution, we provide evidence that the guanidinium group is protonated even in a very basic solution. By analyzing the energy shifts in the C and N X-ray photoelectron spectra, we establish a molecular level picture of how charge and proton transport in aqueous solutions of arginine occur.

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“…Suitable reactive force field (FF) parameters were identified through the optimization procedure included in the original program (serial ReaxFF), starting from the conjunction of the protein FF , and force fields developed by van Duin and co-workers − for gold. These data were combined with other quantum chemistry (QC) data describing the interaction of the different atom types with Au (see Supporting Information).…”

mentioning

confidence: 99%

Simulation of Gold Functionalization with Cysteine by Reactive Molecular Dynamics

Monti

Carravetta

Ågren

2016

J. Phys. Chem. Lett.

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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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Surface-Altered Protonation Studied by Photoelectron Spectroscopy and Reactive Dynamics Simulations

Cited by 13 publications

References 23 publications

Theoretical Study of the Adsorption Mechanism of Cystine on Au(110) in Aqueous Solution

Theoretical Study of the Adsorption Mechanism of Cystine on Au(110) in Aqueous Solution

Guanidinium Group Remains Protonated in a Strongly Basic Arginine Solution

Simulation of Gold Functionalization with Cysteine by Reactive Molecular Dynamics

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