Research paper Accessing the structural and thermodynamic properties of ultra-thin layers of C32 adsorbed on a SiO 2 surface Sebastian E. Gutierrez-Maldonado a,b , Jose Antonio Garate a,b , Maria Jose Retamal c,d , Marcelo A. Cisternas c,d , Ulrich G. Volkmann c,d , Tomas Perez-Acle a,b,⇑ a Computational Biology Lab (DLab), Fundacion Ciencia & Vida, Av. Zañartu 1482, Ñuñoa, Santiago, Chile b Centro Interdisciplinario de Neurociencias de Valparaíso (CINV), Pasaje Harrington 287, Playa Ancha, Valparaíso, Chile c Laboratorio de Superficies (SurfLab), Instituto de Física, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile d Centro de Investigación en Nanotecnología y Materiales Avanzados (CIEN-UC), Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile article info Article history: Received 19 October 2016 In final form 29 January 2017 Available online 1 February 2017 abstract Medium-chain alkanes are important molecules with applications in biology and industry. Notably, their structural properties are scarcely understood. To assess structural and thermodynamic properties of dotriacontane (C32) molecules adsorbed on a SiO 2 surface, we conducted all-atom molecular dynamics (MD) simulations. By analyzing potentials of mean force, order parameters and self-diffusion, we com- pared the stability and preferential orientation between ordered and disordered systems. Our data con- firm the presence of one parallel layer of C32 followed by a mixture of disordered C32 segments exhibiting no thermodynamic preference. This semi-ordered structural model shed light to the interac- tions between C32 and a SiO 2 surface. Ó 2017 Elsevier B.V. All rights reserved. 1. Introduction Medium-chain alkanes are the main constituents of several molecules with biological and industrial relevance. They are important for biosensing and bio-remediation of fossil fuels [1], as microlubricants, anticorrosive agents, and surfactants [2]. Con- sequently, their structural and dynamical properties have been the focus of both experimental and theoretical studies [3–10]. Given their simplicity and due to their role as prototypes for more complex polymers including biologically relevant molecules such as membranes, alkanes have been used to study the behavior of nano-scale materials such as polymeric thin films [11,12]. Using a variety of tools including atomic force microscopy, X-ray diffrac- tion, high-resolution ellipsometry and more recently, molecular dynamics, it is currently accepted that the behavior of alkane thin films is mainly dominated by surface effects [5,10,13–16]. According to experimental evidence published by Volkmann et al. [17,18], the growth of dotriacontane (C 32 H 66 , C32) thin films, a linear medium-chain alkane, supported on amorphous silica sur- faces covered with their native oxide layer (SiO 2 ) begins with the formation of a bilayer of C32 molecules with their long axis orien- tated parallel to the surface. On top of this parallel bilayer, a per- pendicular layer is formed, i.e., a layer of C32 molecules with their long axis lays perpendicular to the surface. This layer will continue to grow adding as much perpendicular layers, one on top of each other, as more C32 molecules are added to the system, until the formation of mesoparticles is achieved. This mechanism is known as Stranski-Krastanov growth and is commonly accepted as the growth mechanism for medium-sized alkanes supported on inorganic surfaces such as SiO 2 [19–21]. Despite the advancements represented by these studies, fundamental questions remain to be answered regarding the nature of the physicochemical properties governing the interaction between inorganic surfaces and organic molecules. Moreover, shading lights on these questions is a key step to support the development of nanotechnological systems with application in biotechnology [9,12]. A relevant tool to gain insights with atomic resolution on the behavior of molecules is by using a whole spectrum of computer simulation techniques called Molecular Dynamics (MD). MD tech- niques offer a set of methods suitable to investigate complex inter- actions between molecules in heterogeneous systems. During the last years, it has emerged as a powerful tool to study diverse phe- nomena at the atomic scale, ranging from protein folding, structure-function relationships in proteins, to inorganic/biological interactions [9,12]. In particular, several molecular dynamics sim- ulations of alkanes have been previously reported [3,4,6,8,11,13– 16,22–26]. Most simulations performed to date have used united http://dx.doi.org/10.1016/j.cplett.2017.01.065 0009-2614/Ó 2017 Elsevier B.V. All rights reserved. ⇑ Corresponding author at: Computational Biology Lab (DLab), Fundacion Ciencia & Vida, Av. Zañartu 1482, Santiago, Region Metropolitana, P.O. 7780272, Chile. E-mail addresses: sebastian@dlab.cl (S.E. Gutierrez-Maldonado), jgarate@dlab.cl (J.A. Garate), moretama@uc.cl (M.J. Retamal), mncister@uc.cl (M.A. Cisternas), volkmann@fis.puc.cl (U.G. Volkmann), tomas@dlab.cl (T. Perez-Acle). Chemical Physics Letters 674 (2017) 64–70 Contents lists available at ScienceDirect Chemical Physics Letters journal homepage: www.elsevier.com/locate/cplett