Modelling water adsorption on Au(210) surfaces. I. A force field for water–Au interactions by DFT

Neves, Rodrigo S.; Motheo, Artur J.; Fartaria, Rui P. S.; Fernandes, Fernando M. S. Silva

doi:10.1016/j.jelechem.2007.06.020

Cited by 20 publications

(20 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, for the adsorption of biomolecules with considerable dipole moments, including some peptides and proteins, the surface polarization contributes to the binding energy and influences the binding mode. Although studies have shown that, for water-metal surface systems, the energy due to polarization is less than 10% of the total binding energy (Feng et al 2011;Neves et al 2007;Siepmann & Sprik, 1995;Vila Verde et al 2009, for proteins, in particular, on Au (111) surfaces, the contribution from polarization has been estimated to be about 10-20% of the total binding energy . Further, on surfaces such as Au(100), where the van der Waals attraction is weaker, polarization was found to tune the adsorption of proteins ) and act as a major contributor to the adsorption of highly charged peptides .…”

Section: Polarizationmentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

197

199

View full text Add to dashboard Cite

Abstract. Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time-and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

show abstract

Section: Polarizationmentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

197

199

View full text Add to dashboard Cite

show abstract

“…The interactions between the water molecules and the Au(210) were modelled by the DFT force field recently proposed by us, whose full details are described elsewhere [34], submitted to a cut off radius of 25 Å. As this force field is somewhat elaborated we recall here its main components.…”

Section: Interaction Force Fieldsmentioning

confidence: 99%

“…As such, adsorption is a crucial subject for various technologic research fields, ranging from surface modification [17][18][19] to heterogeneous catalysis applied to fuel cells [20][21][22]. In the last decades, ab initio quantum calculations, especially those using density functional theory (DFT) [23][24][25][26][27][28][29][30][31][32][33][34][35][36], and molecular simulation techniques, namely Monte Carlo (MC) [37][38][39][40][41][42][43][44][45] and molecular dynamics (MD) [46][47][48][49][50][51][52][53][54][55], have become powerful tools to study molecular and ionic adsorption on metallic surfaces. The ab initio/DFT calculations of the interactions between different molecules and ions with a broad variety of metallic clusters, representing different crystallographic orientations of noble metals, mainly platinum [29,32,35], gold [25, 31, 34-36, 56, 57], copper [24,...…”

Section: Introductionmentioning

confidence: 99%

“…The results of such calculations have pointed, for example, to the occurrence of preferential site adsorption and the influence of the site geometry on the orientation of adsorbed molecules. These calculations are also the basis of the development of analytical potential functions to be used in MD and MC simulations of adsorption processes, such as halides on copper [39], water on platinum [55,62] and gold [34], and ethanol on gold [31]. MD and MC simulations have provided invaluable information on the structure of the adsorbed layers, assessing the preferential orientation of adsorbed molecules in the presence of the solvent, the preferential sites for adsorption and the changes on the interface properties in the direction normal to the surface.…”

Section: Introductionmentioning

confidence: 99%

“…Nonetheless, since this study used a flat surface, the influence of the surface corrugation on the preferential adsorption and on the local properties of the solvent layer has not been assessed. In this context, the objective of the present work is to calculate, by canonical MC simulations, the solvent contribution to the PMF for the adsorption of phenol, from a dilute aqueous solution, now on a corrugated Au(210) electrode, over different surface sites and molecular orientations under conditions similar to pzc, from a DFT force field recently proposed by us [34]. The Au(210) surface is a suitable choice, since it is experimentally accessible as a single crystal surface that does not undergoes potential induced surface reconstruction, and has electrochemical characteristics resembling those of gold polycrystalline surfaces due to its high heterogeneity [66,67].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Monte Carlo Simulation of the Solvent Contribution to the Potential of Mean Force for the Phenol Adsorption on Au(210) Electrodes

Neves

Motheo

Fartaria

et al. 2009

Port. Electrochim. Acta

View full text Add to dashboard Cite

This paper reviews some recent canonical Monte Carlo simulations of the Au(210)/H 2 O interface using a DFT force field developed by us. New results are reported on the solvent contribution to the potential of mean force (PMF) for the phenol adsorption, from a dilute aqueous solution, onto the Au(210) surface. The Monte Carlo simulations show the common features normally observed in the simulation of water in contact with metallic surfaces, where the water molecules adsorb forming bilayers. The molecules adsorbed over the Top gold sites form hydrogen bonds between the first and second solvent layers. The PMF calculations indicate that the phenol molecule penetrates the solvent layers with the aromatic ring in a perpendicular configuration and the oxygen atom pointing to the surface. The PMF results also suggest the existence of hydrogen bonds between the phenol molecule and the first solvent layer of the water molecules adsorbed onto the Top sites.

show abstract

Models for the adsorption and self‐assembly of ethanol and 1‐decanethiol on Au(111) surfaces. A comparative study by computer simulation

Fartaria

Freitas

Fernandes

2009

Int J of Quantum Chemistry

View full text Add to dashboard Cite

Results from computer simulations, based on different models to study theadsorption and self-assembly of the ethanol and 1-decanethiol on gold surfaces, Au(111), are presented. Canonical ensemble Monte Carlo simulations were performed at 298 K using two different force fields. One from DFT calculations, where the gold electrode has an explicit structure (corrugated electrode), and the other representing an electrode, in which the structure is taken into account on an average way (flat electrode). The behavior of the ethanol adsorption on gold surfaces, with and without the 1-decanethiol presence, is analyzed. The introduction of molecular flexibility is also discussed. The relative surface density for the ethanol oxygen, adsorbed on gold, and the density profiles, in different conditions, show that the structure of the surface has a fundamental role on the way the adsorption takes place, not only on the preferential adsorption sites of the surface but also on the ethanol distribution over the electrodes. Potentials of mean force have also been calculated for the two surface models, giving the free energy barriers to the 1-decanethiol crossing of the solvent adsorption layers. The average tilt angle, obtained with a single thiol molecule in the simulation box, presents the values: ∼ 26 • for the rigid molecule model and 74 • ± 18 • for the flexible one. These differences are analyzed.

show abstract

Modelling water adsorption on Au(210) surfaces. I. A force field for water–Au interactions by DFT

Cited by 20 publications

References 54 publications

Modeling and simulation of protein–surface interactions: achievements and challenges

Modeling and simulation of protein–surface interactions: achievements and challenges

Monte Carlo Simulation of the Solvent Contribution to the Potential of Mean Force for the Phenol Adsorption on Au(210) Electrodes

Models for the adsorption and self‐assembly of ethanol and 1‐decanethiol on Au(111) surfaces. A comparative study by computer simulation

Contact Info

Product

Resources

About