The Influence of the Rigidity of a Carbon Nanotube on the Structure and Dynamics of Confined Methanol Vitaly V. CHABAN, Oleg N. KALUGIN  , Bradley F. HABENICHT 1 , and Oleg V. PREZHDO 1y Department of Inorganic Chemistry, V. N. Karazin, Kharkiv National University, Kharkiv, Ukraine 1 Department of Chemistry, University of Washington, Seattle, WA 98195, U.S.A. (Received February 7, 2010; accepted April 13, 2010; published June 10, 2010) In this paper, we compare the behavior of liquid methanol confined by an open-ended single-walled nanotube (SWCNT) under four different simulation conditions by using the molecular dynamics (MD) simulations technique. The first model is a rigid and fixed SWCNT with all its carbon atoms fixed at their initial positions; the second is a flexible and fixed SWCNT with its centre-of-mass fixed at the center of the MD box and with the carbon–carbon bond potential applied; the third is a rigid and floating SWCNT, and the fourth is the most realistic flexible and floating SWCNT model — without fixed atoms and with bond potential. The microscopic structure and transport properties of bulk methanol confined by the four different SWCNTs were analyzed. No changes in the radial distribution functions of the hydrogen bond between MeOH molecules are found, and the self-diffusion constant and microscopic dipole relaxation time are essentially unaffected by the confinements. In spite of the flexible/rigid or fixed/floating ð15; 15Þ SWCNT model used, the structure and transport properties of confined MeOH are found to be very close in all the simulated cases. We conclude that using the approximation of rigid or/and fixed SWCNT does not lead to any systematic errors in properties of the confined liquid. The results show that simulations using rigid carbon nanotubes provide a reliable description of molecular diffusion and other solvent properties in a variety of applications, such electro-chemical devices, membranes and sensors that rely on these properties. KEYWORDS: confined fluid, carbon nanotube, molecular dynamics simulation, methanol, intramolecular poten- tials, diffusion coefficient, hydrogen bond DOI: 10.1143/JPSJ.79.064608 1. Introduction Confined liquids are now of exceptional interest because of their unusual properties 1–5) and high importance for industrial applications. 6–11) Molecular dynamics simulations of confined liquids have already become a common practice, 1,3,12–14) as their experimental investigation is a difficult problem. Open-ended single-walled carbon nano- tubes (SWCNT) with an ideal geometry (zigzag or armchair) provide an excellent model to study the properties of the confined liquids at the microscopic level. Our present study was inspired by a number of questions arising from earlier reported molecular dynamics (MD) simulations of confined non-aqueous liquids. 15–17) These investigations involved SWCNTs with fixed atomic coor- dinates and caused concern about how rigidity and fixation of the carbon nanotube can influence the properties of the molecules inside the confinements. The above mentioned problem, namely the effect of rigidity/flexibility was considered in a few recent pa- pers 12,18–20) devoted to the MD simulations of gases and water confined by SWCNTs. However, different results were obtained for confined gases and liquids. Chen et al. 18) investigated the influence of nanotube flexibility on the transport diffusion of methane (CH 4 ) in ð15; 0Þ and ð20; 0Þ tubes. According to their simulations, the diffusion of CH 4 is hugely reduced by SWCNT flexibility at pressure values close to zero but at pressures around 1 bar the corresponding values for rigid and flexible SWCNTs differ on average by less than a factor of two. Jakobtorweihen, et al. 12) confirmed the above results also for CH 4 at low loadings and showed how the influence of flexible walls can be taken into account by means of a Lowe–Andersen thermostat. 13,14) Other authors dealing with transport diffusion of argon 19) and with water structure 20) found almost no noticeable influence both on molecular structure and transport. Again, neglect of the velocities of the SWCNT sites during MD simulation can be a substantial approximation, possibly distorting dynamical constants of the molecules absorbed inside the SWCNT. We analyze this effect as well. Hence, in the present paper, we make a comparison among four differing models of the ð15; 15Þ SWCNT, representing the most common simplifications applied in practical simulations: rigidity instead of flexibility and centre-of-mass fixation instead of free nanotube motion across the MD cell. Liquid methanol (MeOH) at 298 K was chosen as a test media because of its specific structure in the bulk phase and the novel interest to ‘‘SWCNT–MeOH’’ systems in connection with green chemistry direct methanol fuel cells. 21) Below, we compare the structure and transport properties of MeOH confined inside the SWCNT: rigid fixed [the center of ð15; 15Þ SWCNT coincides with a center of the box], fixed flexible, rigid floating (initially placed at the center of the box and then allowed to float as an ordinary particle) and, eventually, flexible floating (the most realis- tic), denoted as systems I, II, III, and IV, respectively. 2. MD Simulations Details The four ‘‘SWCNT–MeOH’’ systems (Table I) consisted of the non-capped ð15; 15Þ armchair SWCNT with diameter,  E-mail: Oleg.N.Kalugin@univer.kharkov.ua y E-mail: prezhdo@u.washington.edu Journal of the Physical Society of Japan Vol. 79, No. 6, June, 2010, 064608 #2010 The Physical Society of Japan 064608-1