Uracil adsorption

STM has also been used to examine the dynamics of potential-dependent ordering of adsorbed molecules [475-478]. For example, the reversible, charge-induced order-disorder transition of a 2-2 bipyridine mono-layer on Au(lll) has been studied [477]. At positive charges, the planar molecule stands vertically on the surface forming polymeric chains. The chains are randomly oriented at low surface charge but at higher potentials organize into a parallel array of chains, which follow the threefold symmetry of the Au(l 11) substrate as shown in Fig. 34. Similar results were found for uracil adsorption on Au(lll) and Au(lOO) [475,476]. 

In situ STM has provided detailed structural models for the adsorption of cytosine, uracil and thymine at a number of electrode surfaces.These studies have included thymine adsorbed on Au(lll), Au(lOO) and Au(210), uracil adsorption on Au(lll), Au(lOO) and Ag(lll). These pyrimidine bases show a particularly interesting phase behaviour, which can be seen from cyclic voltammograms (CV). A CV for the... 

Enhanced formation of the condensed layer observed during the adsorption of thiourea and uracil. ... 

Some attention has also been paid to the simultaneous adsorption of sulfate anions and organic compounds. Futamata [44] has detected coadsorption of water molecules and sulfate species with uracil on polycrystalline gold electrode, applying attenuated total reflection-infrared spectroscopy. The adsorbed sulfate species appeared either as S04 or HS04, depending on the pH of the electrolyte solution. Skoluda... 

Adsorption and phase formation of uracil on massive Au[ (lll)-(110)] singlecrystal and Au (111 - 20 nm) film electrodes in 0.1 M IT2SO4 has been studied in electrochemical measurements and applying ATR surface-enhanced infrared reflection absorption spectroscopy [299]. At E < 0.15 V (versus trapped hydrogen electrode), uracil molecules are disordered and planar oriented. Close to the pzc, a 2D condensed physisorbed film of planar-oriented molecules interconnected by directional hydrogen bonds, is formed. 

Adsorption of adenine and coadsorption of adenine-thymine and uracil-thymine on Au(lll) has been reported [300]. Adenine was chemisorbed in two different states. Mutual interaction between adenine and thymine was detectable only at... 

Itaya s group presented images of benzene, naphthalene and anthracene on Cudll), and naphthalene and anthracene on Rh(l 11)/ Wandlowski and coworkers monitored adsorption of uracil on gold surfaces They reported imaging chemisorbed molecules as well as physisorbed molecules and determined their adlattice structures. They also made a correlation between the structure and lateral interaction forces of adsorbed molecules. They showed that application of sufficiently positive electrode potentials results in uracil deprotonation, leading to different surface structure and geometric orientation. 

Figure 7-8. A proposed adsorption model for chemisorbed uracil and thymine. ...

Figure 9 shows the SERS spectra of the dinucleoside monophosphates adenylyl-(3 -5 )-uridine (ApU) and adenylyl-(3 -5 )-cytidine (ApC) at different adsorption potentials in the characteristic spectral range of the ring-breathing modes. The adsorbed base modes alone on the electrode surface are at 736 cm " in adenine, 798 cm in cytosine and 795 cm in uracil. The corresponding frequencies in the dinucleoside monophosphates ApC and ApU are at 734 cm for adenine, 792 cm for cytosine and 796cm for uracil. 

A higher time resolution of 28 ms was used in a rapid-scan time-resolved SEIRA study of adsorption kinetics of uracil on a quasi-Au(lll) electrode surface [15]. Since the adsorption/desorption of uracil is reversible, the S/N of the spectra were enhanced by averaging 64 consecutive repetitions. This study showed that the kinetics is represented by the first-order rate equation, and that the rate constants evaluated from the time-resolved SEIRAS are much smaller than those for overall transition determined by chronoamperometry. The result suggests that the processes observed by the two measurements are not the same. 

Sub-millisecond time-resolved SEIRAS has also been applied for other dynamic processes such as the redox reactions of heptylviologen on Ag [12], adsorption/desorption of fumaric acid [13] on Au and sulfate on Ag [16], and phase transitions in uracil adlayers on Au [15]. In the latter two studies, discrepancies between the time-resolved IR and chronoamperometry were suggested. 

Two works were devoted to the ab initio cluster calculations of the interactions between minerals of the kaolinite group with thymine (TH) and uracil (U). The key purpose of such studies was to determine (i) the equilibrium adsorption of selected nucleic acids, differing in chemical, molecular structure and functions (DNA, RNA) on specific clay mineral surfaces and (ii) the nature of the interaction between nucleic acids and clay using computational chemistry methods and modeling. An additional objective was to assess the effect of presence of water and sodium cation commonly occurring in soils on the process of adsorption. 

Table 21.4 presents the atomic charges of adsorbed and isolated thymine obtained by the fitting of the electrostatic potential. For uracil and thymine the adsorption... 

The characteristics of adsorption binding of thymine and uracil were confirmed by the maps of electrostatic potential drawn for all complexes. The isomorphic substitution and the presence of the cation in both fragments affect the electron redistribution and this influence varies based on the surface type. 

In older studies adsorption of nucleobases on clay minerals was shown to be promoted by the presence of polyvalent cations [56,122], This finding corresponds well with our results [151]. Periodic plane wave calculations based on the PBE functional [146] revealed sizeable adsorption of thymine and uracil on the external surfaces of Na-montmorillonite in the case of surface free from Na+ (from —6 to —11 kcal/mol), due to the stabilizing effect of dispersion interactions. As one can see from the comparison of these interaction energies with the Ecorr values obtained for K(3t)Na and K(3t)NaW systems with thymine and uracil (—28, —25 kcal/mol for uracil and —27, —24 for thymine as given in Table 21.6) and for D(t), D(t)W without cation (from -1 to -9 kcal/mol) [147], the addition of Na+ leads to a significant stabilization of the tetrahedral systems. The same is true for K(3o)Na systems, for which interaction energies increase (in absolute value) from —30 to —36 for uracil... 

The calculations of solvated (hydrated) complexes simulated by explicit inclusion of water molecule shows the energy loss only for the tetrahedral systems, which is due to the structural changes of the substrate induced by water adsorption [151]. It amounts to about 3 kcal/mol. In the case of octahedral systems presence of water does not increase the Ecorr value for K(3o)NaW-U but it stabilizes thymine by 1.7 kcal/mol. Isolated uracil is more stable in the water-cation environment than in the microcosmic environment with only water [157]. In all K(3o)NaW systems orientation by 02 towards Na+ remains to be the most favorable. On the other hand, in study of hydrated Li+-thymine and Li+-uracil complexes binding of (H20)Li+ to the 04 site is stabilized by 1.7- 2.9 kcal/mol over the binding to the 02 site [156],... 

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