POSITRON Vol. 13, No. 1 (2023), Hal. 14 - 20 This work is licensed under a Creative Commons Attribution 4.0 International License. 14 DOI: 10.26418/positron.v13i1.63670 Protonation Process of Porous Silica Cluster Surface using Molecular Dynamics Method Raihan Alfaridzi a , Bintoro S. Nugroho b , Yudi Rosandi c* a Department of Chemistry, Universitas Padjadjaran, Sumedang 45363, Indonesia b Program Studi Fisika FMIPA Universitas Tanjungpura, Jl. Prof. Dr. H. Hadari Nawawi, Pontianak c Department of Geophysics, Universitas Padjadjaran, Sumedang 45363, Indonesia *Email : rosandi@geophys.unpad.ac.id (Received 10 March 2023; Revised 15 May 2023; Accepted 27 May 2023; Published 31 May 2023) Abstract Using molecular dynamic simulation, we developed an algorithm to protonate the surface of an amorphous porous silica grain particle model and study its effect. In this work, the silica grain model can be used to study cosmic dust coagulation. The surface of the silica cluster was protonated by placing H atoms on oxygen atoms having only a single bond, namely, the non-bridging oxygens. The H atoms are placed opposite the Si –O bond with a distance of around 1 Å to form silanol (Si –O–H) group termination on the silica surface. The angular conformation of the silanol was optimized by relaxing the surface at low temperature. We evaluated the number of silanol groups, the angular distribution of the Si-O-H bond, and the average distance between Si-O particles using the radial distribution function (RDF). The result of the study shows that minimizing the energy of the silica surface changes the angular distribution of the silanol from 180° to about 110° and between 140°- 160°. However, the average distance between Si-O particles remains at 1 Å, which demonstrates the correctness of the atomic interaction model. The addition of protons on the silica surface is an essential factor in the simulation of cosmic dust collision since the modification of the surface chemistry may alter the contact surface energy, thus changing the probability of particle coagulation. Keywords: cosmic dust, molecular dynamics, protonation, silica nanoparticle 1. Background Cosmic dust, also known as interstellar dust, is a collection of particle materials that exist throughout the galaxy. This particle ranges from a few molecules to 100 micrometers, with a complex structure formed by small grain aggregates and varying compositions. Regarding the formation of rocky planets, a class of silica and ice grain are the most interesting ones. Remnants of these dust particles can be found in the solar system, including in planetary rings, comet tails, and interplanetary space [1,2]. Cosmic dust has a significant role in the astrophysics of planet formation processes, especially in the formation and evolution of rocky planets in the protoplanetary disk, which consists of collision events that lead to the aggregation of dust particles in space. This initial process makes the formation of larger and more complex structures possible. The content of dust in the protoplanetary disk, which is the birthplace of planets, is very likely a mixture of silicates and carbons, with a size distribution from ~100 Å to maximum radii of ~0.2–0.3 µm, based on the observation with a variety of techniques and over a large range of wavelengths [3,4]. In situ data from spacecraft in the Saturnian system also indicate the presence of major rock-forming elements (magnesium, silicon, iron and calcium) in cosmic abundances [5]. In order to accurately model the dust collision phenomenon in outer space, the silica model has to be compatible with existing theories. In this study, we developed an algorithm to protonate the surface of silica grain particle models and evaluate its effect on particle bonding. The produced silica grain models can be used for further cosmic dust coagulation studies. Research on the collision process of silica nanoparticles has been actively done previously. The research was conducted, one of which was to prove the theories regarding the collision of silica nanoparticles, such as the Johnson-Kendall- Roberts (JKR) collision theory on a porous silica cluster on an atomic scale. This theory explains the collision between two particles macroscopically