Role of Hydrogen Bonding in the Formation of Adenine Chains on Cu(110) Surfaces.

Lanxia Cheng

doi:10.3390/ma9121016

Abstract

Understanding the adsorption properties of DNA bases on metal surfaces is fundamental for the rational control of surface functionalization leading to the realisation of biocompatible devices for biosensing applications, such as monitoring of particular parameters within bio-organic environments and drug delivery. In this study, the effects of deposition rate and substrate temperature on the adsorption behavior of adenine on Cu(110) surfaces have been investigated using scanning tunneling microscopy (STM) and density functional theory (DFT) modeling, with a focus on the characterization of the morphology of the adsorbed layers. STM results revealed the formation of one-dimensional linear chains and ladder-like chains parallel to the [110] direction, when dosing at a low deposition rate at room temperature, followed by annealing to 490 K. Two mirror related, well-ordered chiral domains oriented at ±55° with respect to the [110] direction are formed upon deposition on a substrate kept at 490 K. The molecular structures observed via STM are rationalized and qualitatively described on the basis of the DFT modeling. The observation of a variety of ad-layer structures influenced by deposition rate and substrate temperature indicates that dynamic processes and hydrogen bonding play an important role in the self-assembly of adenine on the Cu(110) surface.

Highlights

Molecular self-assembly on solid surfaces is a research topic of extensive experimental [1,2,3,4,5,6,7,8,9]and theoretical studies [10,11], owing to the promising applications in future organic-based nanoelectronics [1,12,13]
Unlike other DNA base molecules, such as guanine, thymine, and cytosine, the adenine molecular structure consists of only one functional group, i.e., an amino (–NH2 ) group, and a larger aromatic ring, which are favorable for flat-lying molecular orientation when interacting with substrates [5]
The formation of aggregated adenine islands is in contrast with the observation of some smaller distributed adenine clusters formed at the higher deposition rate of ~0.04 ML/min (Figure S1a), which re-organized into chiral chains upon annealing to 490 K, similar to the structures previously reported [5]

Summary

Introduction

Molecular self-assembly on solid surfaces is a research topic of extensive experimental [1,2,3,4,5,6,7,8,9]and theoretical studies [10,11], owing to the promising applications in future organic-based nanoelectronics [1,12,13]. Organic molecules, including DNA and RNA bases, are capable of forming a range of nanostructures from well-ordered, two-dimensional (2D) molecular networks to one-dimensional rows upon deposition on a surface [1,2]. Investigations of molecule-molecule and molecule-surface interactions that govern the structural and electronic properties of the molecular nanostructures formed upon adsorption are relevant, to control surface functionalization for biocompatible and biosensor applications [12,13], and to understand the complex biomolecule-surface interactions in general [14]. Unlike other DNA base molecules, such as guanine, thymine, and cytosine, the adenine molecular structure consists of only one functional group, i.e., an amino (–NH2 ) group, and a larger aromatic ring, which are favorable for flat-lying molecular orientation when interacting with substrates [5]. Experimental measurements [18,20,22] and DFT calculations [23] both show that adenine adopts a flat-lying orientation in these supramolecular structures and the interaction with the substrate

Methods

Results

Conclusion