The effect of solvent upon molecularly thin rotaxane film formation Alan A. Farrell a, * , Euan R. Kay b , Giovanni Bottari b , David A. Leigh b , Suzanne P. Jarvis a a Nanoscale Function Group, Centre for Research on Adaptive Nanostructures and Nanodevices, University of Dublin, Trinity College, Dublin 2, Ireland b School of Chemistry, University of Edinburgh, The King’s Buildings, West Mains Road, Edinburgh EH9 3 JJ, UK Received 15 November 2006; received in revised form 7 January 2007; accepted 9 January 2007 Available online 14 January 2007 Abstract We have investigated variations in molecularly thin rotaxane films deposited by solvent evaporation, using atomic force microscopy (AFM). Small changes in rotaxane structure result in significant differences in film morphology. The addition of exo-pyridyl moietes to the rotaxane macrocycle results in uniform domains having orientations corresponding to the underlying substrate lattice, while a larger, less symmetric molecule results in a greater lattice mismatch and smaller domain sizes. We have measured differences in film heights both as a function of the solvent of deposition and as a function of surface coverage of rotaxanes. Based on these observations we describe how the use of solvents with higher hydrogen-bond basicity results in films which are more likely to favour sub-molecular motion. # 2007 Elsevier B.V. All rights reserved. PACS : 81.10.Dn; 68.55.Àa; 81.16.Dn; 68.37.Ps Keywords: Thin-films; Rotaxane; Atomic force microscopy; Conformation; Solvent; Hydrogen bond 1. Introduction Rotaxanes, commonly included in the ‘molecular machines’ family, are interlocked molecules, consisting of macrocycles trapped onto a linear unit (the ‘thread’) by two bulky substituents (stoppers) and are interesting because their components are connected by a mechanical rather than a chemical bond. As such the relative motion of the sub- molecular components, in terms of either their rotational or translational degrees of freedom, can be controlled through local environmental or external stimuli [1–3]. The switching process in rotaxanes known as ‘shuttling’ occurs when the macrocycle moves between stable recognition sites (stations) on the thread. Such multistability allows for a switching behaviour, as translational or positional isomers of the same molecule will have different properties. These properties may allow exploitation of these ‘molecular machines’ as devices and sensors [4,5]. While rotaxanes are known to be switchable in solution phase [1–3,6] the breadth of possible applications is extended greatly if these molecules can also function at a solid interface. It is important to understand how the functionality of such interlocked molecules will be altered or inhibited by the interaction with the surface. Efforts have previously been made to characterise the interactions of rotaxanes, their component parts, and other interlocked molecules with surfaces [7–11]. The assembly of rotaxanes and thiol-functionalised rotaxanes on gold have been studied [12], as well as their incorporation into alkanethiol monolayers [13]. In some studies, the method of deposition is from a solvent [7,8], patterning of surfaces with rotaxanes from the solvent has been investigated [14], as well as the manipulation of rotaxanes with probe microscopy [15]. In many studies there has been evidence of switchability at surfaces [10,16–19]. Solvent-dependent co-conformational changes at surfaces have also been observed, illustrating the importance of the environment during deposition [8]. To the best of out knowledge there have been no studies on controlling the morphology of molecularly thin rotaxane films. In a functional surface of such hydrogen-bonded rotaxanes, the molecules should be assembled in a controlled manner. Any surface attachment should preferably be via the macrocycle, www.elsevier.com/locate/apsusc Applied Surface Science 253 (2007) 6090–6095 * Corresponding author. Tel.: +353 1 896 3032; fax: +353 1 896 3027. E-mail address: farrelaa@tcd.ie (A.A. Farrell). 0169-4332/$ – see front matter # 2007 Elsevier B.V. All rights reserved. doi:10.1016/j.apsusc.2007.01.006