Coulombic Amino Group-Metal Bonding: Adsorption of Adenine on Cu(110) (original) (raw)
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Self-assembly of adenine on Cu (110) surfaces
Langmuir, 2002
The adsorption of the nucleic acid base, adenine, on Cu(110) surface has been studied with low-energy electron diffraction, scanning tunneling microscopy (STM), electron energy loss spectroscopy (EELS), and ab initio calculations. STM shows at low coverage an ordered one-dimensional molecular chain growing along ((1, 2) directions. At higher coverages, on annealing to 430 K, the chains order into chiral domains of ( 6 1 0 2 ) periodicity. High-resolution STM images reveal the details of molecular structure within the unit cell. EELS shows that the molecular plane is parallel to the substrate with a tilted C-NH2 bond. Ab initio calculations confirm the molecular orientation and show an sp 3 hybridization on the N (amino) atom, which is directly bonded to the substrate. The origin of the chains lies in the formation of homochiral rows of molecules, linked by two types of H-bonding interactions, commensurate with the substrate.
Toward Understanding Amino Acid Adsorption at Metallic Interfaces: A Density Functional Theory Study
ACS Applied Materials & Interfaces, 2009
In examining adsorption of a few selected single amino acids on Au and Pd cluster models by density functional theory calculations, we have shown that specific side-chain binding affinity to the surface may occur because of a combination of effects, including charge transfer. Larger binding was calculated at the Pd interface. In addition, the interplay between amino acid solvation and adsorption at the interface was considered from first principles. This analysis serves as the first step toward gaining a more accurate understanding of specific interactions at the interface of biological-metal nanostructures than has been attempted in the past.
SERS, XPS, and DFT Study of Adenine Adsorption on Silver and Gold Surfaces
The Journal of Physical Chemistry Letters, 2012
The adsorption of adenine on silver and gold surfaces has been investigated combining density functional theory calculations with surface-enhanced Raman scattering and angle-resolved X-ray photoelectron spectroscopy measurements, obtaining useful insight into the orientation and interaction of the nucleobase with the metal surfaces.
The electronic structure and surface chemistry of glycine adsorbed on Cu(110)
The Journal of Chemical Physics, 2000
We present a combined density functional theory and x-ray emission spectroscopy study of the bonding and chemistry of glycine (NH 2 CH 2 COOH) chemisorbed on Cu͑110͒. The amino acid deprotonates upon adsorption. The adsorbate exhibits a rich surface chemistry leading to several intermediate adsorption structures. The most stable geometry is found to involve both the carboxylic and amino functional end groups in the bond. This structure appears only after annealing to 400 K, which in the present work is attributed to a removal of surface or subsurface hydrogen from the metal. Comparison with experimental x-ray emission and near edge x-ray absorption fine structure ͑NEXAFS͒ spectra provide a detailed picture of the electronic structure for the most stable structure. This allows conclusions to be drawn regarding the covalent interaction of the adsorbate system. When combined with theoretical calculations addressing, e.g., the electrostatic adsorbate-substrate interaction, a complete picture of the surface chemical bond is obtained.
l-Methionine adsorption on Cu(110), binding and geometry of the amino acid as a function of coverage
Surface Science, 2015
The adsorption of L--methionine on Cu(110) has been characterized by combining in--situ Polarization Modulation Infrared Reflection Absorption Spectroscopy (PM--IRRAS) and X--ray Photoelectron Spectroscopy (XPS). Both the chemical state of the molecule, and its anchoring points were determined at various coverage values. Adsorbed methionine is anionic and first interacts with the copper surface via weak interactions of sulfur and oxygen atoms, likely in a random geometry; at higher coverage, a stronger interaction of oxygen and nitrogen atoms with copper, evidenced by slight shifts of the XPS peaks, together with an angular dependence of the peak ratios, suggest that the molecule stands up on the surface, interacting with the surface via the N and O atoms but not anymore via its S atom. Last but not least, no multilayers were evidenced, and this was explained by the geometry of the molecules which leaves no groups accessible for intermolecular interactions.
van der Waals DFT ONIOM study of the adsorption of DNA bases on the Cu(111) nanosurface
Applied Surface Science, 2017
In this work, the adsorption of DNA bases on the Cu(111) nanosurface was studied to investigate the electronic structure of the bases on the Cu surface and to find the effect of van der Waals interactions on the adsorption mode of the bases. The calculations were performed in the ONIOM scheme using two DFT functionals (PW91PW91 and wB97XD). It was found that using the long-range corrected DFT functional such as wB97XD (which considers the vdW interactions) decreases the tilt angle of the bases on the surface. The main molecular orbitals responsible for the interaction and charge transfer between each base and Cu surface were determined. The HOMO-4, (HOMO, HOMO-2, and HOMO-3), (LUMO, HOMO-3, HOMO-4, and HOMO-6), and (LUMO and HOMO-4) are responsible for the interaction and charge transfer with the surface for adenine, cytosine, guanine, and thymine, respectively. The quantum theory of atoms in molecule (QTAIM) was used for better characterization of the interaction of the bases with the surface by a topological analysis of the electron density. The results showed that the most interacting atom of adenine with the Cu surface is the N atom of the NH 2 group, whereas the most interacting atom of cytosine and guanine were the O atoms of the carbonyl groups. The QTAIM analysis also showed that the interaction of the O atom of cytosine with the Cu surface is stronger than that of guanine. For TY, the O and N atoms have higher interaction with the Cu surface compared to other atoms. Based on the calculated values of the electron density (BCP) and the positive sign of the Laplacian of the electron density (∇ 2 BCP) at the bond critical points of the atom-atom interactions, it was concluded that the interaction between the bases and the surface can be categorized as closed-shell interactions.
Soft Matter, 2011
In addition to the CHARMM22 32-METAL 22 force field (Figure 1), we employed the CVFF 33-METAL 22 force field for further validation of computed adsorption energies (Figure S1). The biomolecular force field CHARMM has been thoroughly validated with respect to molecular conformations and cohesive energies, 32 whereas the biomolecular force field CVFF 33 is a decade older and the quality of parameters is not as high, in part related to the availability of much less powerful computational resources at the time of development. The two combined biomolecular-metal force fields yield very similar results after some important differences are explained (Figure S1). These are: (1) The CVFF force field overestimates cohesive energies for aromatic molecules by 80% compared to experiment which results in overestimates of adsorption energies of
Theoretical study of Di-Amino-Triazine adsorption on Cu ( 110 ) and Au ( 111 ) surfaces
2016
The diffusion of adatoms or molecules on metal surfaces is the lifeblood of many phenomena as growth. Various microscopic experiences realized by STM (Scanning Tunneling Microscopy) or by AFM (Atomic Force Microscopy) techniques at CEMES center show that the determination of some variables is very necessary to overcome many experimental difficulties. In this paper, MM4 (Molecular Mechanics (2003)) method and ASED+ codes have been used to determine the position of the Lander molecule equipped with dual Di-Amino-Triazine (DAT, C64H68N10), 1,4-bis(4-(2,4-diaminotriazine)phenyl)-2,3,5,6-tetrakis(4-tert-butyl phenyl) benzene on the Cu(110) and Au(111) surfaces. The same tools have estimated the rotation and the diffusion barriers on the substrates. The ESQC (Elastic Scattering Quantum Chemistry) program has been developed to calculate the image and to describe the adsorbed molecule form. The adsorption of energies, geometries, diffusion and rotation barriers are very well described by th...
Electronic Structure Studies of the Interaction of Water with a Cu(100) Surface
American Chemical Society eBooks, 2001
The results of a density functional study of the chemisorption of water on a Cu(100) surface are presented. Both atomic cluster and periodic supercell models of the surface were used in the investigation. From the cluster studies a single water molecule is bound by about 0.6 eV to the surface and is in an on-top site. The addition of a second water molecule in a site adjacent to the first one is not favorable due to polarization of the electron density near the surface. The periodic density functional calculations give results consistent with the cluster studies. The nature of the interaction of water with noble metal surfaces is of great importance in electrochemistry, corrosion, and heterogeneous catalysis. There is evidence that intermolecular interactions between water molecules can compete with water-surface interactions, although little is known about the role that hydrogen bonding between water molecules plays in determining the structure of the metal/water interface. Very little is known experimentally about the nature of the interaction of a single water molecule with noble metal surfaces because it is difficult to separate out the water/water effects from the water/surface interactions. In a study of water on a Au(lll) surface, Kay et al.(i) have reported that the temperature programmed desorption (TPD) spectrum does not display a well-resolved submonolayer peak indicating that H 2 0 binds more strongly to itself than to the Au substrate. Arrhenius analysis of the TPD peak gave a binding energy of about 0.4 eV. In an electronenergy-loss spectroscopic (EELS) study of water on a Cu(100) surface , Andersson et al. (2) found that it adsorbs with the oxygen end towards the surface and its molecular axis significantly tilted relative to the surface normal.