Program

P.3 -- Poster, IWTCP-3

Date: Wednesday, 29 July 2015

Time: 08h30 - 10h00

Estimation of partial atomic charges of calcite (CaCO3) by Electrostatic Potential Fitting method

Phan Van Cuong

Department of Physics, Nha Trang University 02 Nguyen Dinh Chieu Street. Nha Trang, Vietnam. Email: cuongpv@ntu.edu.vn

Atomic charge cannot be observed experimentally because they do not correspond to any unique physical property [1]. Molecules are traditionally considered as “composed” of atoms, in a more general sense, as a collection of charged particles, positive nuclei and negative electrons [2]. Researchers have so far developed several approaches and techniques for estimating the partial atomic charges of the molecule. In this paper, we will discuss two different relevant methods widely used to estimate the partial charges: Quantum chemistry and Empirical fitting method. Quantum chemistry method based on the Electrostatic Potential Fitting technique has many advantages, in this technique all ion charges of the molecule are varied in calculation processes but constraining their sum to zero. The method has been implemented in the Maestro/Jaguar quantum chemistry package [3, 4]. Here, we utilize this package to estimate the partial atomic charges of calcite (CaCO3). Calcite crystals and calcite slabs were built using CrystalMaker software, version 2.1.4 for Windows [5]. In this work, calcite structural parameters from American Mineralogist Crystal Structure Database (AMCSD) [6, 7] were used. Calcite slabs differing in shape and size were cleaved along the (1-0-1 overbar-4) surface of the calcite crystal. After cleaving, all the broken bonds of carbon, oxygen, and calcium were deleted. The resulting calcite slabs were exported directly from CrystalMaker to Protein Data Bank (PDB) format [8]. The PDB files were then imported into Maestro/Jaguar software package, version 7.6. The estimation of the atomic charge of different calcite slabs has been done for many times, and proven to be quite challenging. For the first try, calcite structure with 30 atoms in total was used in our first attempt, which was successful. Then the total number of atoms in the calcite slab was increased to 60, 80, 90, 100, and up to 210. The average values of partial calcite atomic charges are quite comparable to those found in Fisler et al. [9] used the Empirical fitting method, where the calcium ion charges were kept fixed at +2, and the focus was only on the carbonate group, allowing carbon, oxygen core, and oxygen shell charges to vary but constraining their sum to -2. References: [1] D. C. Young, Computational Chemistry. (John Wiley \& Sons INC., New York, 2001). [2] F. Jensen, Introduction to Computational Chemistry. (John Wiley \& Sons Ltd, 2007). [3] Maestro, Version 9.0 (Schrödinger, LLC, New York, 2009). [4] Jaguar, Version 7.6 (Schrödinger, LLC, New York, 2009). [5] CrystalMaker (CrystalMaker Software Limited, Oxford, England, 2008). [6] S. A. Markgraf and R. J. Reeder, "High-temperature structure refinements of calcite and magnesite," American Mineralogist 70 (5-6), 590-600 (1985). [7] R. T. Downs and M. H. Wallace, "American Mineralogist Crystal Structure Database," American Mineralogist 88 (1), 247-250 (2003). [8] F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, "PROTEIN DATA BANK - COMPUTER-BASED ARCHIVAL FILE FOR MACROMOLECULAR STRUCTURES," Journal of Molecular Biology 112 (3), 535-542 (1977). [9] D. K. Fisler, J. D. Gale, and R. T. Cygan, "A shell model for the simulation of rhombohedral carbonate minerals and their point defects," American Mineralogist 85, 217-224 (2000).

Presenter: Phan Van Cuong