Molecular level investigations of (organo)clays
Title: Molecular level investigations of (organo)clays
SNIC Project: SNIC 2021/5-56
Project Type: SNIC Medium Compute
Principal Investigator: Michael Holmboe <>
Affiliation: Umeå universitet
Duration: 2021-03-01 – 2022-03-01
Classification: 10506 10404 10406


This medium allocation proposal aims to continue my groups on-going computational research efforts enabled by previous allocations SNIC 2019/3-487, 2018/3-454, 2017/1-369, 2016/1-375, investigating the molecular organization and mobility of small inorganic solutes and organics in zeolites and sheet silicate interlayers (i.e. in lamellar pores between 1nm thick clay layers), using mainly MD simulations with Gromacs. Zeolite and smectite silicate clays have nanoporous structures and an extremely high surface area, enabling intercalation of large quantities of molecular substances leading to nanomaterials with novel and/or improved properties, that is hard to study experimentally (which we also do). For the first project, we will use a significant amount of core-hours for the continued use and development of a combined MATLAB+Gromacs protocol (the former acting as a wrapper for the latter) to optimize forcefield parameters of inorganic periodic and discrete molecules. This routine will eventually be part of my published atom MATLAB library (atom: A MATLAB PACKAGE FOR MANIPULATION OF MOLECULAR SYSTEMS, Clays and Clay Minerals, 2019, 67(5), 419–426). This forcefield optimization routine is instrumental for our on-going project on a new forcefield for clay minerals, and for collaborative projects on polyoxometalate chemistry with experimental collaborators, as stated in the activity report for our previous allocation SNIC 2019/3-487. In a second project, using primarily molecular dynamics simulations with Gromacs, we will study adsorption and interaction behavior of these nanoporous minerals with a range of inorganic and organic molecules, using methods developed during our previous (and ongoing) work of similarly hydrated systems, such as calculation of theoretical XRD diffractograms, vibrational power spectra as well as free energy perturbation and umbrella sampling methods. In a third project, we will be using MD to study interactions of different aminoacids with zeolites, in the context of organic-N-fertilizers, in a new collaboration with the SLU start-up Arevo ( and Prof. Torgny Näsholm. In a fourth project, we also collaborate with US researchers on uranyl complex diffusion through compacted Bentonite clay, as highlighted in the national press: and