Authors: Ziling Luo
Source: eScholarship@McGill (McGill) (article, 2021-01-01)
Field: Materials Science — Surfaces, Coatings and Films

Exploring and exploiting locality in computer modeling of electrons and atomic nuclei With rapid advances in computer hardware and algorithms, computational chemistry plays an increasingly important role in interpreting ambiguous experimental data, analyzing complex relations between observables and predicting new chemical phenomena.To further expand the applicability of computational chemistry, new simulation methodologies must be constantly proposed, tested and improved.Since the strength of all relevant interactions decreases with distance, most chemical phenomena are local.Methodological developments presented in this thesis are united by their reliance on the locality principle in computer modeling of electrons and atomic nuclei.Spatially localized molecular orbitals are of tremendous importance in electronic structure theory as they are widely used to describe chemical bonding and speed up calculations.This work introduces a new approach to orbital localization called variable-metric localization.In this approach, the constraints, which are normally imposed when localizing orbitals, are replaced with a single restriction.This simple restriction specifies the maximum allowed deviation from the orthogonality for a set of localized orbitals.This reformulation, which can be viewed as a generalization of existing localization methods, allows to sacrifice orthogonality of the orbitals in order to achieve better locality.The variable-metric approach also allows to perform orbital localization using a straightforward unconstrained minimization procedure.Numerous iterative variable-metric localization algorithms were designed and implemented in CP2K -a massivelyparallel freely-distributed software package for modeling of materials and molecules.The best algorithms were found to be efficient and robust, enabling localization of not only occupied but substantially more challenging virtual orbitals.Variable-metric localization was demonstrated to produce well-localized orthogonal and nonorthogonal, occupied and virtual orbitals for a variety of molecules and periodic materials including large systems with non-trivial bonding.With regard to the utility of the locality principle for modeling atomic nuclei, local adjustments to atomic positions were used to explain why progesterone (PRO) molecules form cocrystals with a wide variety of aromatic systems whereas pregnenolone (PRE), a steroid with a very similar structure, cocrystallizes only with few.In order to generate experimentally inaccessible meta-stable cocrystals of PRE that closely resemble those obtained for PRO without relying on prohibitively expensive crystal structure prediction methods, a simple and inexpensive computational procedure was designed based only on local insertions and deletions of atoms.This procedure enabled a direct comparison of the strength of typical interactions that control the binding in both cocrystals and allowed us to attribute the difference in the observed behavior of PRO and PRE to the different stability of the cocrystals relative to their pure components: organic and steroid crystals.It was found that, for a wide range of aromatic molecules, the cocrystallization process tends to be thermodynamically favorable in the case of PRO and unfavorable in the case of PRE.This difference in relative stability is mostly because of strong hydrogen bonds in the pure PRE crystal.The fundamental analysis of this work has important practical implications for designing new steroids-containing crystals, selective biomolecular steroid receptors and steroid-specific drugs.Unlike previous works, it suggests that a strategy for designing selective binding of steroids should focus primarily on tuning the strength of hydrogen bonding. Locality ; Physics ; Electron ; Computer science ; Quantum mechanics Electron and X-Ray Spectroscopy Techniques