Effect of Conformational Symmetry upon the Formation of Cysteine Clusters on the Au(110)-(1 × 1) Surface: A First-Principles Study

Buimaga-Iarinca, Luiza; Morari, Cristian

doi:10.1021/jp4072857

Cited by 17 publications

(16 citation statements)

References 41 publications

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“…Attempts based on DFT calculations were reported by Kühnle and associates. [33][34][35][36] A stable double row of cyclic Cys molecular dimers on Au(110) in UHV was found, supported by UHV STM data. 33 Cys molecules were also found to diffuse freely along the Au(111) surface by combining experimental techniques (XPS, ultraviolet photoelectron spectroscopy, low energy electron diffraction, and STM) with density functional theory (DFT), resembling a 2Dmolecular gas.…”

Section: Introductionsupporting

confidence: 64%

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Chemistry of cysteine assembly on Au(100): electrochemistry, in situ STM and molecular modeling

et al. 2019

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Section: Introductionsupporting

confidence: 64%

“…26 No stable cyclic dimers were observed, and formation of single molecular rows was concluded to be more likely. Different types of Cys-Cys dimers (radical forms) on Au(110) were also investigated 35 . Some dimers could be considered as nucleation centers for the SAM formation.…”

Section: Introductionmentioning

confidence: 99%

Chemistry of cysteine assembly on Au(100): electrochemistry, in situ STM and molecular modeling

et al. 2019

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“…If barriers to the diffusion of Au atoms along the surface can be overcome, the four-atom vacancy structures proposed by Kühnle et al [188] (See Figure 38) provide reactive kink sites, ideally spaced for binding homochiral cysteinate dimers, with highly stable COOH-based hydrogen bonding (See Figure 40). [125] Also Cys dimers on Au(110)-(1×1) were studied by periodic DFT [126]. Three types of rotational conformers (rotamers) of a cysteine dimer (See Figure 41 and Figure 42) were investigated in the protonated and unprotonated forms.…”

Section: Ii)mentioning

confidence: 99%

“…Three types of rotational conformers (rotamers) of a cysteine dimer (See Figure 41 and Figure 42) were investigated in the protonated and unprotonated forms. With this model, Morari et al [126] were able to describe the formation of new nucleation centres formed by Cys pairs on the surface as well as the properties of long chains of cysteine molecules adsorbed on the Au (110) The PC conformer is found to be the most stable structure as well as the one having the most convenient shape of the potential energy surface. Interestingly, in this conformers the NH 2 group is located at a high position relative to the surface (i.e., about 5 Å), which reduces significantly its interaction with it.…”

Section: Ii)mentioning

confidence: 99%

Adsorption and self-assembly of bio-organic molecules at model surfaces: A route towards increased complexity

Costa

Pradier

Tielens

et al. 2015

Surface Science Reports

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Understanding the bio-physical-chemical interactions at nanostructured biointerfaces and the assembling mechanisms of so-called hybrid nano-composites is nowadays a keyissue for nanoscience in view of the many possible applications foreseen. The contribution of surface science in this field is noteworthy since, using a bottom-up approach, it allows the investigation of the fundamental processes at the basis of complex interfacial phenomena and thus it helps to unravelthe elementary mechanisms governing them. Nowadays it is well demonstrated that a wide variety of different molecular assemblies can form upon adsorption of small biomolecules at surfaces. The geometry of such self-organized structures can often be tuned by a careful control of the experimental conditions during the deposition process. Indeed an impressive number of studies exist (both experimental and -to a lesser extendtheoretical), which demonstrate the ability of molecular self-assembly to create different structural motifs in a more or less predictable manner, by tuning the molecular building blocks as well as the metallic substrate. In this frame, amino acidsand small peptides at surfaces are key, basic, systems to be studied. The amino acidsstructure is simple enough to serve as a model for the chemisorption of biofunctional molecules, but their adsorption at surfaces has applications in surface functionalization, in enantiospecific catalysis, biosensing, nanoparticles shape control or in emerging fields such as "green" corrosion inhibition. In this paper we review the most recent advancements in this field. We will start from amino acids adsorption at metal surfaces and we will evolve then in the direction of more complex systems, in thelight of the latest improvements of surface science techniques and of computational methods. On one side, we will focus on amino acids adsorption at oxide surfaces, on the other on peptide adsorption both at metal and oxide substrates. Particular attention will be drawn to the added value provided by the combination of several experimental surface science techniques and to the precious contribution of advanced complementary computational methods to resolve the details of systems of increased complexity. Finally, some hints into experiments performed in the presence of water and then characterized in UHV and in the related theoretical work will be presented. This is a further step towards abetter approximation of real biological systems. However, since the methods employed are often not typical of surface science, this topic is not developed in details.2

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“…Molecule–surface charge transfer occurs through a whole range of effects, from chemical bonds to Pauli push-back of electrons from the close shells and from the surface [ 69 – 71 ]. The accumulation of charge in the region between the molecule and the surface indicates the formation of a chemical bond while a depletion is connected to molecule–surface repulsion.…”

Section: Resultsmentioning

confidence: 99%

The effect of translation on the binding energy for transition-metal porphyrines adsorbed on Ag(111) surface

Buimaga-Iarinca

Morari

2019

Beilstein J. Nanotechnol.

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The characteristics of interaction between six transition-metal porphyrines and the Ag(111) surface are detailed here as resulted from DFT calculations. Van der Waals interactions as well as the strong correlation in 3d orbitals of transition metals were taken into account in all calculations, including the structural relaxation. For each system we investigate four relative positions of the metallic atom on top the surface. We show that the interaction between the transition metal and silver is the result of a combination between the dispersion interaction, charge transfer and weak chemical interaction. The detailed analysis of the physical properties, such as dipolar and magnetic moments and the molecule–surface charge transfer, analyzed for different geometric configurations allows us to propose qualitative models, relevant for the understanding of the self-assembly processes and related phenomena.

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Effect of Conformational Symmetry upon the Formation of Cysteine Clusters on the Au(110)-(1 × 1) Surface: A First-Principles Study

Cited by 17 publications

References 41 publications

Chemistry of cysteine assembly on Au(100): electrochemistry, in situ STM and molecular modeling

Chemistry of cysteine assembly on Au(100): electrochemistry, in situ STM and molecular modeling

Adsorption and self-assembly of bio-organic molecules at model surfaces: A route towards increased complexity

The effect of translation on the binding energy for transition-metal porphyrines adsorbed on Ag(111) surface

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