A comparison of the binding of DNA bases (adenine, cytosine, guanine, and thymine) and nucleosides (2'deoxyadenosine, 2'deoxycytidine, 2'deoxyguanosine, and thymidine) to gold thin films is presented. Desorption of monolayer/submonolayer and multilayer films of the adsorbates on gold studied via temperature-programmed desorption (TPD) and reflection-absorption infrared (RAIR) spectroscopy reveals that there are major differences in the binding affinities of the different bases to gold, for example, thymine DeltaHdes = 111 +/- 2 kJ/mol compared to guanine DeltaHdes = 146 +/- 2 kJ/mol. The differences can be rationalized by molecular structures of the bases and their binding modes to gold surfaces deduced from IR data. Similar trends in desorption energies, shifted to lower desorption energy by more than 10 kJ/mol, are observed for deoxynucleoside layers on gold thin films.

The structure and desorption dynamics of mono- and multilayer samples of adenine, cytosine, guanine, and thymine on polycrystalline gold thin films are studied using temperature-programmed desorption-infrared reflection absorption spectroscopy (TPD-IRAS) and temperature-programmed desorption-mass spectroscopy (TPD-MS). It is shown that the pyrimidines, adenine and guanine, adsorb to gold in a complex manner and that both adhesive (adenine) and cohesive (guanine) interactions contribute the apparent binding energies to the substrate surface. Adenine displays at least two adsorption sites, including a high-energy site (210 degrees C, approximately 136 kJ/mol), wherein the molecule coordinates to the gold substrate via the NH2 group in an sp3-like, strongly perturbed, nonplanar configuration. The purines, cytosine and thymine, display a less complicated adsorption/desorption behavior. The desorption energy for cytosine (160 degrees C, approximately 122 kJ/mol) is similar to those obtained for adenine and guanine, but desorption occurs from a single site of dispersed, nonaggregated cytosine. Thymine desorbs also from a single site but at a significantly lower energy (100 degrees C, approximately 104 kJ/mol). Infrared data reveal that the monolayer architectures discussed herein are structurally very different from those observed for the bases in the bulk crystalline state. It is also evident that both pyrimidines and purines adsorb on gold with the plane of the molecule in a nonparallel orientation with respect to the substrate surface. The results of this work are discussed in the context of improving the understanding of the design of capturing oligonucleotides or DNA strands for bioanalytical applications, in particular, for gold nanoparticle-based assays.

A comparative study of the self-assembly and phase behavior of seven different oligo(ethylene glycol) (OEG)terminated alkanethiols on polycrystalline gold surfaces is presented. The general structure of the compounds is HS(CH 2 ) m -X-EG n , where m ) 11, 15; n ) 2, 4, 6, and the linkages X are amide (-CONH-), ester (-COO-), or ether (-O-) groups. The amide and ester groups give rise to the intermolecular hydrogen bonding and dipole-dipole interactions, respectively, whereas the ether lacks specific interactions. The results from contact angle goniometry, null ellipsometry, and infrared reflection-absorption spectroscopy (IRAS) indicate that the intermolecular interactions can be partly used to control the conformation and order of the OEG portion of the self-assembled monolayers (SAMs). It is shown that the lateral hydrogen bonding stabilizes the all-trans conformation of the EG 4 tails in the SAMs. Further on, the mechanism behind the thermal phase behavior of the OEG SAMs is investigated using temperature-programmed IRAS in ultrahigh vacuum. In the present study we show that the earlier reported helix-to-all-trans conformational transition at 60 °C in the

Temperature-programmed desorption (TPD) of self-assembled monolayers (SAMs) on gold is investigated by using in parallel mass spectrometry (MS) and infrared reflection−absorption spectroscopy (IRAS). Monolayers formed by HS(CH2) n −OH (n = 18, 22) and HS(CH2)15−CONH−(CH2CH2O)−H (EG1) are compared to reveal the influence of specifically introduced hydrogen-bonding groups on their thermal stability. The overall desorption process of the above molecules is found to occur in two main steps; a disordering of the alkyl chains followed by a complex series of decomposition/desorption reactions. The final step of the process involves desorption of sulfur from different chemisorption states. The amide-group-containing SAM, which is stabilized by lateral hydrogen bonds, displays a substantial delay of the alkyl chain disordering by about 50 K, as compared to the linear chain alcohols HS(CH2) n −OH. Moreover, the decomposition of the alkyls and the onset of sulfur desorption occur at a temperature that is higher by approximately 25 K as compared to the HS(CH2)18−OH SAM. The desorption process is also studied for two oligo(ethylene glycol)-terminated SAMs, HS(CH2)15−X−(CH2CH2O)4−H (EG4-SAMs), where X is −CONH− and −COO− linking groups. In addition to the molecular chain disordering, the decomposition/desorption process of the EG4-SAMs occurs in two steps. The first is associated with the loss of the oligomer portion and the second with the desorption of the alkylthiolate part of the molecule. Our study points out that lateral hydrogen bonding, introduced via amide groups, is a convenient way to improve the thermal stability of alkanthiolate SAMs.