The University of Southampton
University of Southampton Institutional Repository

New methods and applications of energy decomposition analysis based on large-scale first principles quantum mechanics

New methods and applications of energy decomposition analysis based on large-scale first principles quantum mechanics
New methods and applications of energy decomposition analysis based on large-scale first principles quantum mechanics
Molecular systems with functional domains serve as a practical motivation for understanding the factors that contribute to the interaction energy. The ability to decompose the interaction energy of a group of interacting subsystems is an important method in studying the chemical nature of the interactions. Energy decomposition analysis (EDA) is a family of schemes that allows such dissection of the interaction energy into chemically relevant components depending on the scheme used. Since different EDA schemes decompose the interaction energy differently, the interpretation of the resulting components differs among schemes. However, various EDA schemes provide complementary insights into the interactions between chemical entities. In this work, two EDA schemes are developed or extended: Hybrid Absolutely Localized Molecular Orbitals (HALMO) and Combined Localized Molecular Orbitals (CLMO). Both EDA schemes have been implemented as part of a linkable library alongside the computational chemistry package, ONETEP. Since ONETEP is a linear-scaling software package, an important application of such decomposition analysis is in the study of large, nontrivial molecular systems for more insightful understanding of chemical interactions, which in turn can lead to more accurate and focused design of chemical systems. Systems such as biomolecules usually contain several self-stabilizing domains that can fold independently and have important functions. Defining the fragments of a supermolecule is necessary in EDA, and if done appropriately given the context of a particular application, the fragmentation of a biomolecule can elucidate the intramolecular interactions that contribute to the functions of the system as a whole. Two major methods of self-consistent field for molecular interaction (SCF MI) are examined and made more mathematically transparent. SCF MI was originally designed to exclude basis set superposition error (BSSE) from molecular interactions. However, SCF MI is also used in separating charge transfer from polarization in HALMO EDA. Studying several SCF MI methods provides HALMO EDA alternatives for separating charge transfer as an EDA component. Due to ONETEP’s linear scaling, large biomolecules or large samples of biomolecules could be studied for their interactions or distributions of specific properties. The primary type of biomolecule studied in this work is double-stranded DNA (dsDNA) and how its stability relates to guanine-cytosine (GC) content, which is a measure of the amount of guanines or cytosines in nucleic acids. By examining the interaction energies in terms of EDA components, contributions to the variabilities within and across GC-content groups are examined and are correlated with differing stabilities despite having same GC content. Ensemble density-functional theory (EDFT) optimizes the molecular orbitals of a system at finite electronic temperatures and allows occupancies to be fractional when the band gap is sufficiently small. EDA methods are normally developed for the pure state and pose difficulties in decomposing the interaction energy of a conductor due to the fractional occupancies that are part of the optimization process in EDFT. As such, fractional occupancies have been incorporated in the EDA optimization process of the fragmented species, thereby allowing EDA to be applied to systems of relevance to catalysis and metallic systems. The adaptations of EDA and SCF MI to metallic systems are novel and were validated using samples from catalysis and batteries, and HALMO EDA has provided reasonable decompositions of interaction energies and revealed some trends from SCF MI that correlate with charge distributions and chemical intuition.
University of Southampton
Chen, Han
3f0c8bfb-38cc-41ad-aa92-6f77bfa0897b
Chen, Han
3f0c8bfb-38cc-41ad-aa92-6f77bfa0897b
Skylaris, Chris-Kriton
8f593d13-3ace-4558-ba08-04e48211af61

Chen, Han (2022) New methods and applications of energy decomposition analysis based on large-scale first principles quantum mechanics. University of Southampton, Doctoral Thesis, 174pp.

Record type: Thesis (Doctoral)

Abstract

Molecular systems with functional domains serve as a practical motivation for understanding the factors that contribute to the interaction energy. The ability to decompose the interaction energy of a group of interacting subsystems is an important method in studying the chemical nature of the interactions. Energy decomposition analysis (EDA) is a family of schemes that allows such dissection of the interaction energy into chemically relevant components depending on the scheme used. Since different EDA schemes decompose the interaction energy differently, the interpretation of the resulting components differs among schemes. However, various EDA schemes provide complementary insights into the interactions between chemical entities. In this work, two EDA schemes are developed or extended: Hybrid Absolutely Localized Molecular Orbitals (HALMO) and Combined Localized Molecular Orbitals (CLMO). Both EDA schemes have been implemented as part of a linkable library alongside the computational chemistry package, ONETEP. Since ONETEP is a linear-scaling software package, an important application of such decomposition analysis is in the study of large, nontrivial molecular systems for more insightful understanding of chemical interactions, which in turn can lead to more accurate and focused design of chemical systems. Systems such as biomolecules usually contain several self-stabilizing domains that can fold independently and have important functions. Defining the fragments of a supermolecule is necessary in EDA, and if done appropriately given the context of a particular application, the fragmentation of a biomolecule can elucidate the intramolecular interactions that contribute to the functions of the system as a whole. Two major methods of self-consistent field for molecular interaction (SCF MI) are examined and made more mathematically transparent. SCF MI was originally designed to exclude basis set superposition error (BSSE) from molecular interactions. However, SCF MI is also used in separating charge transfer from polarization in HALMO EDA. Studying several SCF MI methods provides HALMO EDA alternatives for separating charge transfer as an EDA component. Due to ONETEP’s linear scaling, large biomolecules or large samples of biomolecules could be studied for their interactions or distributions of specific properties. The primary type of biomolecule studied in this work is double-stranded DNA (dsDNA) and how its stability relates to guanine-cytosine (GC) content, which is a measure of the amount of guanines or cytosines in nucleic acids. By examining the interaction energies in terms of EDA components, contributions to the variabilities within and across GC-content groups are examined and are correlated with differing stabilities despite having same GC content. Ensemble density-functional theory (EDFT) optimizes the molecular orbitals of a system at finite electronic temperatures and allows occupancies to be fractional when the band gap is sufficiently small. EDA methods are normally developed for the pure state and pose difficulties in decomposing the interaction energy of a conductor due to the fractional occupancies that are part of the optimization process in EDFT. As such, fractional occupancies have been incorporated in the EDA optimization process of the fragmented species, thereby allowing EDA to be applied to systems of relevance to catalysis and metallic systems. The adaptations of EDA and SCF MI to metallic systems are novel and were validated using samples from catalysis and batteries, and HALMO EDA has provided reasonable decompositions of interaction energies and revealed some trends from SCF MI that correlate with charge distributions and chemical intuition.

Text
H Chen Phd Thesis - Version of Record
Available under License University of Southampton Thesis Licence.
Download (2MB)
Text
permission-to-deposit-thesis - Version of Record
Restricted to Repository staff only
Available under License University of Southampton Thesis Licence.

More information

Published date: June 2022

Identifiers

Local EPrints ID: 467576
URI: http://eprints.soton.ac.uk/id/eprint/467576
PURE UUID: 14c1c147-93ba-4036-b298-85d0f2659fde
ORCID for Han Chen: ORCID iD orcid.org/0000-0002-1152-7575
ORCID for Chris-Kriton Skylaris: ORCID iD orcid.org/0000-0003-0258-3433

Catalogue record

Date deposited: 14 Jul 2022 17:04
Last modified: 15 Jul 2022 01:55

Export record

Contributors

Author: Han Chen ORCID iD
Thesis advisor: Chris-Kriton Skylaris ORCID iD

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×