Unraveling the Self-Assembly of the ( S )-Glutamic Acid “Flower” Structure on Ag(100) (original) (raw)
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Self-Assembly of ( S )-Glutamic Acid on Ag(100): A Combined LT-STM and Ab Initio Investigation
Langmuir, 2010
Self-assembly of organic molecules at metal surfaces is of greatest importance in nanoscience; in fact, it opens new perspectives in the field of molecular electronics and in the study of biocompatible materials. Combining an experimental low-temperature scanning tunneling microscopy investigation with ab initio calculations, we succeeded to describe in detail (S)-glutamic acid adsorption on Ag(100) at T = 350 K. We find that (S)-glutamic acid organizes in a squared structure and, at variance with the majority of cases reported in literature, it adsorbs in the neutral form, 4.6 Å above the surface plane. The interaction with the poorly reactive Ag substrate is only due to weak van der Waals forces, while H-bonds between carboxyl groups and the formation of a OCOH-OCOH-OCOH-OCOH cycle at the vertex of the squares are the main responsible for the self-assembly.
Density functional theory study of the interaction of monomeric water with the Ag(111) surface
Ab initio density-functional theory has been used to investigate the adsorption of a single H 2 O molecule on the Ag͕111͖ surface. A series of geometry optimizations on a slab model has allowed us to identify a preferred energy minimum and several stationary points in the potential-energy surface of this system. The most stable adsorption position for water corresponds to the atop site, with the dipole moment of the molecule oriented nearly parallel to the surface. The electronic structure of several H 2 O-Ag clusters has been compared to results obtained by the extended slab calculations. The agreement found for several properties ͑binding energy, tilt angle of the dipole moment of water, and interatomic distances͒ provides evidence for the local nature of the water-metal atop interaction. The covalent contribution to the weak H 2 O-Ag bond is found to be an important one.
Molecular Ordering and Adsorbate Induced Faceting in the Ag{110}−(S)-Glutamic Acid System
Langmuir, 2005
The adsorption of the amino acid, (S)-glutamic acid, was investigated on Ag{110} as a function of coverage and adsorption temperature using the techniques of scanning tunneling microscopy, low energy electron diffraction, and reflection absorption infrared spectroscopy. In the monolayer, (S)-glutamic acid was found to adsorb predominantly in the anionic glutamate form. Several discrete ordered adlayer structures were observed depending on preparation conditions. In addition, (S)-glutamic acid was found to induce both oneand two-dimensional faceting of the Ag{110} surface. In some cases, evidence was found that the 2-D faceting involved the creation of a chiral facet distribution. A comparison is made of the Ag/(S)-glutamic acid system with analogous studies of amino acids on Cu.
Oxygen adsorption on Ag(111): A density-functional theory investigation
Physical Review B, 2002
The oxygen/silver system exhibits unique catalytic behavior for several large-scale oxidation ͑and partial oxidation͒ industrial processes. In spite of its importance, very little is known on the microscopic level concerning the atomic geometry and chemical nature of the various O species that form. Using densityfunctional theory within the generalized gradient approximation, the interaction between atomic oxygen and the Ag͑111͒ surface is investigated. We consider, for a wide range of coverages, on-surface adsorption as well as surface-substitutional adsorption. The on-surface fcc-hollow site is energetically preferred for the whole coverage range considered. A significant repulsive interaction between adatoms is identified, and on-surface adsorption becomes energetically unstable for coverages greater than about 0.5 monolayer ͑ML͒ with respect to gas-phase O 2 . The notable repulsion even at these lower coverages causes O to adsorb in subsurface sites for coverages greater than about 0.25 ML. The O-Ag interaction results in the formation of bonding and antibonding states between Ag 4d and O 2p orbitals where the antibonding states are largely occupied, explaining the found relatively weak adsorption energy. Surface-substitutional adsorption initially exhibits a repulsive interaction between O atoms, but for higher coverages switches to attractive, towards a (ͱ3ϫͱ3)R30°structure. Scanning tunneling microscopy simulations for this latter structure show good agreement with those obtained from experiment after high-temperature and high-O 2 -gas-pressure treatments. We also discuss the effect of strain and the found marked dependence of the adsorption energy on it, which is different for different kinds of sites.
Modern first principles modeling techniques using appropriate parallel algorithms and supercomputing platforms can give novel insight in the molecular self-assembly on surfaces. After a brief description the Car-Parrinello method and its parallel implementation, we consider two systems, 1-nitronaphtalene (NN) on the reconstructed Au(111) surface and 4-[pyrid-4-yl-ethynyl] benzoic acid (PEBA) adsorbed on the Ag(111) surface. Both systems have been studied also by scanning tunnelling microscopy (STM). We show how ab initio calculations allow us to explain the shape of the observed superstructures, to elucidate the role of molecular hydrogen bonding and to reveal details of the atomic structures not yet experimentally accessible.
Density functional theory (DFT)-based molecular dynamics (DFTMD) simulations in combination with a Fourier transform of dipole moment autocorrelation function are performed to investigate the adsorption dynamics and the reaction mechanisms of self-coupling reactions of both acetylide (H3C–C(β)≡C(α) (ads)) and ethyl (H3C(β)–C(α)H2(ads)) with I(ads) coadsorbed on the Ag(111) surface at various temperatures. In addition, the calculated infrared spectra of H3C–C(β)≡C(α)(ads) and I coadsorbed on the Ag(111) surface indicate that the active peaks of –C(β)≡C(α)– stretching are gradually merged into one peak as a result of the dominant motion of the stand-up – C–C(β)≡C(α)– axis as the temperature increases from 200 K to 400 K. However, the calculated infrared spectra of H3C(β)–C(α)H2(ads) and I coadsorbed on the Ag(111) surface indicate that all the active peaks are not altered as the temperature increases from 100 K to 150 K because only one orientation of H3C(β)–C(α)H2(ads) adsorbed on the Ag(111) surface has been observed. These calculated IR spectra are in a good agreement with experimental reflection absorption infrared spectroscopy results. Furthermore, the dynamics behaviors of H3C–C(β)≡C(α)(ads) and I coadsorbed on the Ag(111) surface point out the less diffusive ability of H3C–C(β)≡C(α)(ads) due to the increasing s-character of Cα leading to the stronger Ag–Cα bond in comparison with that of H3C(β)–C(α)H2(ads) and I coadsorbed on the same surface. Finally, these DFTMD simulation results allow us to predict the energetically more favourable reaction pathways for self-coupling of both H3C–C(β)≡C(α)(ads) and H3C(β)–C(α)H2(ads) adsorbed on the Ag(111) surface to form 2,4- hexadiyne (H3C–C≡C–C≡C–CH3(g)) and butane (CH3–CH2–CH2–CH3(g)), respectively. The calculated reaction energy barriers for both H3C–C≡C–C≡C–CH3(g) (1.34 eV) and CH3–CH2–CH2– CH3(g) (0.60 eV) are further employed with the Redhead analysis to estimate the desorption temperatures approximately at 510 K and 230 K, respectively, which are in a good agreement with the experimental low-coverage temperature programmed reaction spectroscopy measurements.
Structure and dynamics of oxygen adsorbed on Ag(100) vicinal surfaces
Physical Review B, 2004
The structure and dynamics of atomic oxygen adsorbed on Ag(410) and Ag(210) surfaces has been investigated using density functional theory. Our results show that the adsorption configuration in which O adatoms decorate the upper side of the (110) steps forming O-Ag-O rows is particularly stable for both surfaces. On Ag , this arrangement is more stable than other configurations at all the investigated coverages. On Ag(410), adsorption on the terrace and at the step edge are almost degenerate, the former being slightly preferred at low coverage while the latter is stabilized by increasing the coverage. These findings are substantiated by a comparison between the vibrational modes, calculated within density-functional perturbation theory, and the HREEL spectrum which has been recently measured in these systems.
Van der Waals interactions at the molecule-metal interface: PTCDA on Ag (111)
2008
A thorough understanding of the adsorption of molecules on metallic surfaces is a crucial prerequisite for the development and improvement of functionalized materials. A prominent representative within the class of π-conjugated molecules is 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) which, adsorbed on the Ag(111), Au(111) or Cu(111) surfaces, shows characteristic trends for work-function modification, alignment of molecular levels with the substrate Fermi energy and binding distances. We carried out density functional theory (DFT) calculations to investigate to what extent these trends can be rationalized on a theoretical basis. We used different density functionals (DF) including a fully non-local van der Waals (vdW) DF capable of describing dispersion interactions. We show that, rather independent of the DF, the calculations yield level alignments and work-function modifications consistent with ultra-violet photoelectron spectroscopy when the monolayer is placed onto the surfaces at the experimental distances (as determined from xray standing wave experiments). The lowest unoccupied molecular orbital is occupied on the Ag and Cu surfaces, whereas it remains unoccupied on the Au surface. Simultaneously, the work function increases for Ag but decreases for Cu and Au. Adsorption distances and energies, on the other hand, depend very sensitively on the choice of the DF. While calculations in the local density approximation bind the monolayer consistently with the experimental trends, the generalized gradient approximation in several flavors fails to reproduce 2 realistic distances and energies. Calculations employing the vdW-DF reveal that substantial bonding contributions arise from dispersive interactions. They yield reasonable binding energies but larger binding distances than the experiments.
Oxygen molecules on Ag(0 0 1): superstructure, binding site and molecular orientation
Chemical Physics Letters, 2000
Oxygen molecules on Ag(0 0 1), adsorbed at about 60 K, are found to form two-dimensional c2 Â 4 compact islands. We determine binding site and orientation of the molecules within the superstructure by comparing experimental and calculated scanning tunneling images in combination with molecular dynamics simulations. The molecule adsorbs in the thermodynamically stable fourfold hollow site with its molecular axis in the direction of short periodicity of the superstructure. Rehybridization of 1p and 2p orbitals on adsorption is at the origin of the observed image contrast. Ó
Physical Review B, 2004
Density functional theory calculations of adsorption of chlorine at the perfect and defective silver ͑111͒ surface have shown that the energies of adsorption of chlorine atoms show little variation ͑less than 30 kJ mol Ϫ1) between the different sites, from Ϫ136 kJ mol Ϫ1 next to a silver adatom, through Ϫ159 kJ mol Ϫ1 at the perfect surface to Ϫ166 kJ mol Ϫ1 next to a silver vacancy at the surface. Molecular chlorine adsorbs in a series of energetically similar overlayers, which are in good agreement with experimentally found structures. The lowest energy configuration is a planar hexagonal honeycomb structure of chlorine atoms adsorbed in fcc and hcp hollow sites on the silver surface. An energetically similar structure is geometrically nonplanar, but has a planar electronic structure. Although the chlorine molecules are virtually dissociated ͑Cl-Cl distanceϭ3.40 Å), significant electron density is distributed along the Cl-Cl axes, leading to a network of electronic interactions between the adsorbed chlorine atoms. The adsorption energy for Cl 2 is calculated at Ϫ231 kJ mol Ϫ1 , in good agreement with experiment. Calculated Ag-Cl bond lengths of 2.69, 2.47, and 2.33 Å agree with several experimental studies and show that the different bond lengths found experimentally are not anomalous, but due to the formation of geometrically different but energetically almost identical chlorine overlayer structures.