Development and Application of Hybrid AIMD/cDFT Simulations for Atomic-to-Mesoscale Chemistry

Abstract

Many important geochemical and biogeochemical processes involve reactivity and dynamics in complex solutions. Gaining a fundamental understanding of these reaction mechanisms is a challenging goal that requires advanced computational and experimental approaches. However, important techniques such as molecular simulation have limitations in terms of scales of time, length and system complexity. Furthermore, among currently available solvation models, there are very few designed to describe the interaction between the molecular scale and mesoscale. To help address this challenge, here we establish a novel hybrid approach that couples first principle plane-wave density functional theory (DFT) with classical density functional theory (cDFT). In this approach, a region of interest described by ab initio molecular dynamics (AIMD) interacts with the surrounding medium described using cDFT to arrive at a self-consistent ground state. cDFT is a robust but efficient mesoscopic approach to accurate thermodynamics of bulk electrolyte solutions over a wide concentration range (up to 2 molar concentrations). Benchmarking against commonly used continuum models of solvation such as SMD, as well as experiment, demonstrates that our hybrid AIMD/cDFT method is able to produce reasonable solvation energies for a variety of molecules and ions. With this model, we also examined solvent effects on a prototype S$_N$2 reaction of the nucleophilic attack of a chloride ion on methyl chloride in solution. The resulting reaction pathway profile and the solution phase barrier agree well with the experiment, showing that our AIMD/cDFT hybrid approach can provide insight into the specific role of solvent on the reaction coordinate.

Geochemical factors associated with deposition of lower Aptian organic-rich sediments during OAE1a in the Basque-Cantabrian Basin, northern Spain

“…Iron (Fe) being the predominant siderophile and fourth most abundant element in the Earth's crust it is expected to be prevalent in primary rock-forming minerals. As a result, it is naturally widespread in secondary phases of weathering mafic minerals into iron oxides or clay minerals (Prietzel et al, 2007;Muñoz et al, 2013;Simonnin et al, 2017). It is needed because of its ability to transfer electrons (synthesis of chlorophyll for photosynthesis, bacterial metabolic enzymes, and others); therefore, it is non-conservative.…”

“…One could be ferric illite (Kossovskaya and Drits, 1970) being produced predominately in salt lakes or lagoons (Porrenga, 1968;Baker, 1997), although it is also believed to be formed in arid soils (Wilson, 1999;Meunier, 2005). The other possibility is from either smectite such as montmorillonite, or micas because they are the most iron bearing phyllosilicates from the terrigenous components (Simonnin et al, 2017). Non-etheless, because micas are missing in the studied Cuchía sediments, the excess Fe is most likely from ferric montmorillonite (Meunier, 2005).…”