ORIGINAL PAPER Self-assembled monolayers of oligosilane on the silicon (001) surface: molecular dynamics simulations Li Zhao & Xue-Mei Duan & Xiang-Gui Xue & Ming-Hui Li & Ze-Sheng Li Received: 6 March 2010 / Accepted: 28 May 2010 / Published online: 10 June 2010 # Springer-Verlag 2010 Abstract Atomistic molecular dynamics simulations have been used to investigate the adsorption of permethyldeca- silane (MS10) on the silicon (001) surface. The condition under which the self-assembled monolayer forms is examined. The properties of the well-ordered structures, including the packing patterns, the equilibrium distances between two neighboring chains, and the tilt angles, are calculated to characterize the structure of the self-assembled monolayer. The results are comparable with those obtained experimentally. Keywords Self-assembled monolayer . Oligosilane . Molecular dynamics simulations Introduction Conjugated molecules have received considerable attention in recent years due to their wide range of possible applications. They can be used in active electronic and optoelectronic organic materials such as light-emitting diodes, polymer lasers, photovoltaic cells, field-effect tran- sistors, photoconductors, and electroluminescent devices. Si-based polymers and oligomers that possess σ-conjugated electrons that are delocalized along the silicon main chains have attracted much interest among the wide range of conjugated polymer systems available because of their unusual photophysical and electronic properties [1–11], especially their relatively high hole mobilities [12–17]. Compared with polysilanes, oligosilanes have definite silicon chain lengths and hence well-defined σ-conjugated lengths, and thus the relationship between the structures and the interesting properties of these polymers should be studied [16, 17]. Most properties of conjugated molecules are anisotropic with respect to the main chain axis, so the molecular conformation and the intermolecular packing are important for understanding their interesting properties and for effectively utilizing those properties to design optical and electronic devices. Many oligosilane systems with well- ordered structures have been prepared and studied by different experimental techniques. Kaito and co-workers prepared highly oriented films of permethyloligosilanes by the vacuum-deposition method and studied their properties by X-ray diffraction, low-wavenumber Raman scattering, infrared spectroscopy and ultraviolet absorption spectros- copy [18, 19]. They also reported that the films showed liquid-crystalline properties [20, 21]. Tamao and Tsuji showed a powerful way to control the conformation along a linear oligosilane chain unambiguously in their recent papers [22–26]. Krempner and co-workers studied well- defined oligosilane dendrimers in the nanometer regime, which was useful for understanding the photophysical properties of silicon nanostructures [27–30]. Although many experimental studies have been performed to explore the structures of oligosilanes and their unique properties, there are still some problems to solve, such as the detailed packing structure of the molecules. Take the linear permethyldecasilane (Me(SiMe 2 ) 10 Me) prepared by vacuum- deposition for example [31]: two types of highly ordered structures, one with its molecules oriented normal to the substrate and the other with an oblique orientation, were found in Me(SiMe 2 ) 10 Me films deposited at room tempera- ture using X-ray diffractometry and absorption spectroscopy L. Zhao : X.-M. Duan : X.-G. Xue : M.-H. Li : Z.-S. Li (*) State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China e-mail: zeshengli@mail.jlu.edu.cn J Mol Model (2011) 17:721–726 DOI 10.1007/s00894-010-0774-9