Aromatic self-assembled monolayers (SAMs) on gold show high potential for applications in nanobiotechnology [1]. Although the SAMs are typically prepared by immersing gold substrates in a solvent, their growth by vapor deposition in vacuum has various advantages both for the technological applications and fundamental studies [2, 3]. Thus, it is possible to characterize in detail the monolayer growth by various UHV compatible surface science techniques such as, e.g., electron spectroscopy. Here, we employ a new endstation of the HESGM beamline at BESSY II to study the in situ growth of 4´-nitro-1,1´-biphenyl-4-thiol (NBPT) SAMs on gold/mica substrates by X-ray photoelectron spectroscopy (XPS) and near edge X-ray absorption fine structure spectroscopy (NEXAFS). XPS C1s, N1s, O1s and S2p spectra as well as NEXAFS CK-, NK- and OK-absorption edge spectra were analyzed. These results demonstrate the formation of NBPT SAMs by vapor deposition in UHV with a similar packing density and molecular orientation as usually obtained in solvents. Moreover, we analyze the electron-radiation-induced modification of NBPT SAMs, that is widely employed in chemical nanolithography [4]. By varying the dose of electron irradiation we study two effects: (i) mechanisms of the electron-induced cross-linking [5] and (ii) conversion of the nitro groups into amino groups [6]. We analyze these transformations and compare the experimental NEXAFS data with calculations made by the StoBe software package.

Study of organic thiols adsorption on noble metals continues to be a subject of many research papers within the last three decades. Such steady interest arises mainly from the possibility to design metal surfaces with predefined chemical and physical properties that makes them suitable for a whole range of theoretical and applied studies.

Here we propose and investigate an idea that thiols with rigid or spherical hydrocarbon moieties should self-assemble on Au-surface much quicker than those with long-chain moieties. To support this idea we have investigated adsorption dynamics and monolayer structure for 1-adamantanethiol¹ (AdSH) and [1,1’:4’,1’’-terphenyl]-4-thiol (TPT) molecules self-assembled on Au(111)-surface at 393K. We have demonstrated that both thiols form defect free and uniform SAMs almost instantly at elevated temperature. It takes ~1sec for AdSH to self-assemble on gold. In case of TPT ~90% of the monolayer forms within the first ~10 seconds of adsorption, and then it takes ~60 seconds to develop into a well-ordered structure. Both SAMs on Au were characterized with ambient STM up to a single-molecule level, X-ray photoelectron spectroscopy and spectroscopic ellipsometry. We were able to obtain near atomic resolved STM images for AdSH SAM on Au. They clearly showed that all AdSH molecules adsorbed in the same conformation with the molecular tilt and the twist angles being 114⁰ and 0⁰ correspondingly. We have also demonstrated that most AdSH molecules are arranged in a head-to-tail orientation, with some molecules having a head-to-head orientation without forming a disulfide bond.

Molecular resolved STM images of TPT SAM/Au clearly demonstrated that within first seconds of adsorption the Au-surface is equally covered with two different phases (α- and β-). β-phase dominates on the Au-surface from ~10 sec of exposure and onwards. A closer inspection of the β-phase on a single molecule level allowed us to propose an upright conformation for TPT molecule on Au with the tilt angle of 0±5^o. We also estimated the tilt angle for the α-phase to be within 10-20^o. For both systems STM and XPS analysis suggest a high chemical and structural quality of the monolayers.

Overall we have proposed a simple and straightforward protocol for ultrafast fabrication of AdSH and TPT SAMs on Au-surface, which we believe can be readily extended for other similar molecular systems.

¹Korolkov et al. J. Phys. Chem. C, Vol. 114, No. 45, 2010

The physisorption of 1,4 diaminebenzene (BDA) molecule on Au(111) surface is studied within the generalized gradient approximation of the density functional theory with the PBE [1], vdW-DF [2], and vdW‑DF2 [3] exchange correlation functionals. The binding energy of an isolated BDA adsorbed on Au(111) surface calculated from vdW-DF (vdW‑DF2) is 0.78 eV (0.84 eV) in better agreement with the experimental value (1.0 eV) [4] than that from PBE (0.37 eV), while the alignment of the molecule along the surface obtained from PBE (20^o) is closer to the experimental value of 24^o [4] than that of about 5^o derived from vdW-DF (or vdW‑DF2). On the other hand, when interactions between the BDA molecules is included in the calculations, as would be the case if the molecules were to self-assemble, say in the form of a linear line structure on Au(111), inclusion of vdW interactions gives excellent agreement with experimental observations. In particular vdW‑DF and vdW‑DF2 predict the BDA tilt angles to be 23^o and 21^o, respectively. The binding energy of a BDA on Au(111) in this case is 0.70 eV and 0.71 eV, respectively. As is to be expected, PBE does not account for intermolecular interactions and does not give good agreement with the data. We suggest the presence of such alignment of molecules along the surface in the experiments, and that they are governed by hydrogen bonding between N and H atoms of neighboring BDA molecules. We compare our results also with unpublished STM data for the system.

[1] J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996).

[2] M. Dion, H. Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist,Phys. Rev. Lett. 92, 246401 (2004)

[3] K. Lee, É. D. Murray, L. Kong, B. I. Lundqvist, and D. C. Langreth,Rev. B82, 081101 (2010).

[4] M. Dell’Angela , G. Kladnik, A. Cossaro, A. Verdini, M. Kamenetska, I. Tamblyn, S. Y. Quek, J. B. Neaton, D. Cvetko, A. Morgante, and L. Venkataraman, Nano Lett. 10, 2470–2474 (2010)

*Work supported by DOE Grant DE-FG02-07ER15842.

Chiral self-assembled structures formed from organic molecules have been subject to intense investigation, motivated both by applications such as enantiospecific heterogeneous catalysis as well as by fundamental interest e.g. in relation to the origin of biomolecular homochirality. Chirality on surfaces may arise both for intrinsically chiral molecules and for prochiral molecules that become chiral due to reduced symmetry upon adsorption. However, chiral effects originating from conformational degrees of freedom have received relatively little attention.

Here we use a combination of organic synthesis and UHV-STM experiments to address how rational design of molecular building blocks allows transfer of chirality from the molecular to the supra-molecular level. We investigate a class of custom-designed molecules based on a linear oligo-phenylene-ethynylene backbone and characterize their adsorption structures on the Au(111) surface. Most of these compounds are prochiral and display conformational chirality in the sense that they can adsorb in different chiral conformations distinguished by the positions of two tert-butyl side-groups. A novel chiral switching mechanism, involving a conformational change where the terminal groups rotate around the molecular axis, is directly revealed from time-resolved STM. We demonstrate that it is possible through control of the terminal group functionalization to steer the molecular backbones into surface assemblies that are either mirror symmetric or display pronounced organizational chirality in the form of a characteristic windmill motif. We furthermore achieve control over the absolute chirality of windmill assemblies by synthesizing an intrinsically chiral variant where the tert-butyl side pendant is replaced by a chiral (S)-sec-butyl group. This intrinsically chiral compound is finally used in co-deposition experiments as an induction seed to control the chirality of assemblies formed from the original prochiral compound.

Chiral switching by spontaneous conformational change in adsorbed organic molecules

S. Weigelt, C. Busse, L. Petersen, E. Rauls, B. Hammer, K.V. Gothelf, F.Besenbacher, and T.R. Linderoth, Nature Materials, 5 11 (2006)

Steering organizational and conformational surface chirality by controlling molecular

chemical functionality

C. Bombis, S. Weigelt, M. M. Knudsen, M. Nørgaard, C. Busse, E.Lægsgaard, F. Besenbacher,

K. V. Gothelf, and T. R. Linderoth, ACS NANO 4, 297 (2010).

Controlling chiral organization of molecular rods on Au(111) by molecular design

M. Knudsen, N. Kalashnyk, F. Masini, J. Cramer, E. Lægsgaard, F. Besenbacher, T. R. Linderoth, K. Gothelf, Journ. Am. Chem. Soc. 133 4896 (2011).