A theoretical study of the interaction between DNA/RNA and the noble metal atoms of gold and silver - Ground-state properties L. A. Espinosa Leal 1, a) and O. Lopez-Acevedo 1, b) COMP Centre of Excellence, Department of Applied Physics, Aalto University, P.O. Box 11100, 00076 Aalto, Finland Here, we present results from a study of DNA/RNA bases interacting with gold and silver atoms at three charge states: neutral, cationic, and anionic. Using a real-space DFT methodology, we describe the nature of the stability, bonding, and electronic properties in each hybrid metal. After studying five isolated nucleobases, including the effect of pairing respective DNA-Watson-Crick base pairs and the sugar-backbone by studying the nucleotide guanine monophosphate, we discerned that the energetic ordering of isomers, for a given base- metal combination, follows simple electrostatic rules, and therefore can be extrapolated to more complex structures. When considering the electronic properties of the ground-state structure in every combination of base and charge, we derived several general features. First, allthough the metal localizes almost all of the extra charge in the anionic system, a donation of charge is shared almost equally by the metal and nucleobase in the cationic system. Second, the frontier orbitals of the anionic and cationic system are different, with the latter tending to have more effects from the pairing and inclusion of the backbone. Finally, the electronic gap varies greatly among all of the considered structures and is particularly sensitive to the backbone participation in the bonding. Thus, it could be further used as a fingerprint when searching Au/Ag-DNA hybrid atomic structures. I. INTRODUCTION Because of their unique optical properties, stabilized noble metal nanoclusters (MNCs) have gathered a great deal of attention in biochemistry. These nanostructures have the capacity to emit and absorb straightforward electromagnetic radiation in the visible range. This property can be tuned by changing the size (number of atoms), the electronic charge, and/or the surrounding en- vironment. Experimentally, there has been a wide range of stabilizers used, including dendrimers, DNA strands, and water-soluble polymers 1 . Yet, despite the wide in- terest received and experimental efforts underway, MNCs actual structure is unknown. In addition, cluster fluxion- ality and a non-covalent metal-organic interaction would allow that isomers close in energy can be attained by thermal agitation. A long-range ordering in the form of crystals therefore can hardly be achieved, and computa- tional support becomes of high necessity in the search for stabilized MNCs atomic structures. Among the most remarkable stabilizers the DNA/RNA polymers have emerged as a promising bottom-up technology 2 . These hybrid metallic nanostructures present high fluorescent properties upon interaction with few-atom noble metal clusters, in particular gold 3 and silver 4,5 . Recently, an experimental breakthrough has made it possible to measure the composition of DNA- stabilized fluorescent silver clusters 6 . These advances in separation techniques and optical characterization have led to the first identification of numbers of neutral silver atoms, silver ions, and DNA strands contained in fluo- rescent Ag-DNA complexes. Based on their results, the a) Electronic mail: leonardo.espinosa@aalto.fi b) Electronic mail: olga.lopez.acevedo@aalto.fi experimental group has proposed several models of highly charged rod-like structures that would follow a shell (or jellium model) for absorption and emission properties. To explore this type of shell-structure model with a superatomic electronic counting rule 7 for the metal in DNA/RNA complexes, it is necessary to define an atomic stabilizing layer, a metal core, and to have a set of well- defined electronic properties that the model can explain in a simple way. A guide for this type of exploration, us- ing only ab initio methods, has been presented for metal clusters (of gold, aluminum, and gallium) with different organo-metallic interactions (covalent, ionic, and polar- ized ionic, respectively) 8 . Previously, several computational studies mainly fo- cused on DNA/RNA-MNCs properties by fixing the charge state or considering a reduced number of nucle- obases: search of the structures of the DNA/RNA bases 9 , Watson-Crick base pairs 10 interacting with small neutral gold clusters, and single nucleobases interacting with dif- ferent noble metal atoms 11,12 , among others. In this work, we provide an overview of every possi- ble gold and silver metal atom in DNA/RNA geometries —reporting each atoms corresponding electronic proper- ties as a step towards the modeling of hybrid DNA/RNA- MNCs. We carried out this research using the simplest model of a single nucleobase —guanine (G), adenine (A), thymine (T), cytosine (C) and uracil (U) —interacting with one noble metal atom (gold and silver) at different charge states (cationic, neutral, and anionic). We studied structural and electronic properties, including ionization potential and electron affinity, Bader charge, electronic gap, and localization of frontier orbitals. For every prop- erty, the effects of pairing between bases (Watson-Crick) and the presence of the sugar backbone (guanosine nu- cleotide) were also simulated and discussed. arXiv:1403.3494v3 [cond-mat.mtrl-sci] 20 May 2014