A molecular mechanics implementation of the cyclic cluster model
Author:
Samaniego-Rojas Juan Diego1, Gaumard Robin2, Alejandre José3, Mineva Tzonka2, Geudtner Gerald1, Köster Andreas M.1
Affiliation:
1. Departamento de Química , CINVESTAV , Av. Instituto Politécnico Nacional 2508, A.P. 14-740 , Ciudad de México , C.P. 07360 , Mexico 2. ICGM, Université Montpellier, CNRS, ENSCM , Montpellier , France 3. Departamento de Química , UAM-Iztapalapa , San Rafael Atlixco 186, A.P. 55-534 , Ciudad de México , C.P. 09340 , Mexico
Abstract
Abstract
The implementation of the cyclic cluster model (CCM) for molecular mechanics is presented in the framework of the computational chemistry program deMon2k. Because the CCM is particularly well-suited for the description of periodic systems with defects, it can be used for periodic QM/MM approaches where the non-periodic QM part is treated as a defect in a periodic MM surrounding. To this end, we present here the explicit formulae for the evaluation of the Ewald sum and its first- and second-order derivatives as implemented in deMon2k. The outlined implementation was tested in molecular dynamics (MD) simulations and periodic structure optimization calculations. MD simulations of an argon system were carried out using the Nosé-Hoover chain (NHC) thermostat and the Martyna-Tobias-Klein (MTK) barostat to control the temperature and pressure of the system, respectively. For the validation of CCM structure optimization a set of molecular crystals were optimized using the Ewald method for the evaluation of the electrostatic interactions. Two optimization procedures for the determination of the atomic positions and CCM cell parameters were tested. Our results show that the simultaneous optimization of the atomic positions and cell parameters is most efficient.
Publisher
Walter de Gruyter GmbH
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