Written by V Erastova for Phyllosophical News of the Clay Minerals Group, 2024, Issue 1.
Read the complete issue of the newsletter here.
The first theoretical calculations in chemistry go back nearly a hundred years (Heitler, W. et al., (1927) Z. Physik, 44, 455–472). However, it was not until the advent of computers a couple of decades later that the calculations of multi-atomic systems became feasible. Today, propelled by advancements in both hardware and algorithms, computational chemistry has blossomed, with many techniques developed, granting us unprecedented access to molecular scales with unparalleled accuracy and detail.
At the heart of this revolution is molecular modelling, a computational approach that seeks to elucidate the behaviour of systems with atomistic detail. While computational chemistry encompasses a wide array of techniques, from quantum mechanics to classical molecular dynamics simulations, in its basis, it relies on mathematical models and computational algorithms to solve the equations governing interactions and motions of atoms that comprise molecules and materials. Leveraging the power of supercomputers, we now can simulate complex molecular systems, from ultra-fast chemistry of excited states to large biomolecular assemblies and inorganic materials.
The utility of molecular modelling goes beyond its applications in chemistry and extends across disciplines. In the field of clay science, it has proven itself as a powerful tool for understanding the structure, dynamics, and reactivity of clay minerals at the molecular level. Here, the primary motivation for performing molecular simulations is their ability to elucidate the complex interplay between clay minerals and their surrounding environment, describe processes at the interface, and understand how the structure of clays defines their function. To this end, simulating interactions between clay minerals and water, ions, and organic molecules gives us insights into fundamental clay properties, such as ionic exchange or swelling, and allows us to predict the capacity of clays for various applications, from targeted pollution remediation to drug delivery (Cygan, R. T. et al., (2009) J. Mater. Chem., 19, 2470-2481).
While simulations only provide insights into processes at the atomistic scales and over nano/microsecond timescales, their ability to model many system perturbations allows us to leverage statistics and create a probabilistic representation of the macroscopic phenomenon. This gives modelling a predictive power and an ability to extrapolate the processes and system’s evolution over extended time and size scales.
As an example, in the quest for solutions to environmental challenges, molecular modelling supports efforts in nuclear pollution management. To this end, molecular simulations of clay mineral interactions with radionuclides under relevant environmental conditions offer a safe tool for predicting the nuclear contaminant spread, identifying routes to pollution remediation, and guiding the development of clay-based materials for long-term nuclear waste storage (Ma, Z. et al., (2018) Appl. Clay Sci., 168, 436-44; Liu, X. et al., (2022) Nature Rev. Earth & Env., 3.7, 461-476).
Furthermore, molecular models establish themselves as a powerful tool to study otherwise unattainable conditions of far-gone past or at locations in the distant universe. In such cases, even a laboratory experiment will still be a simulation. The subject of such a quest is unravelling the origin of life or searching for its extraterrestrial evidence in the form of biosignatures. Through sequences of molecular simulations, we can test our hypothesis and identify a set of attainable laboratory experiments for further validation. In the end, the timescales available for life-forming processes could have spanned beyond the duration of human life, let alone a graduate student degree (Erastova V., et al., (2017) Nat. Commun., 8, 2033).
At the same time, with the developments in space missions, the search for evidence of extraterrestrial past life is now becoming a reality. Martian Rovers are now examining clay-rich soils, as those provide the optimal environment for biosignature preservation. However, identifying organic materials must be scrutinised before any conclusions can be made about their potential as evidence of ancient life. Yet, unable to return the samples to Earth, simulations are well posed to offer guidance on the location-specific chemistry at the mineral interface, assisting in the search for biosignatures. (Pollak, H. et al., (2023) Goldschmidt 2023 Conference)
In the grand tapestry of science, molecular modelling not only illuminates microscopic phenomena but also informs our understanding of macroscopic processes, connecting time and space across our Universe.