Public defence in Engineering Physics, M.Sc. Shukning Choi

Title of the thesis: Real-space observation of non-covalent interactions in planar and non-planar molecules using scanning probe microscopy

Doctoral student: Shukning Choi
Opponent: Professor Angelika Kühnle, Bielefeld University, Germany
Custos: Professor Peter Liljeroth, Aalto University School of Science, Department of Applied Physics

With the rapid advancement of supramolecular materials, the study of non-covalent interactions (NCIs) has become increasingly critical. These interactions are fundamental to biological and synthetic materials' formation, stability, and functionality. Scanning probe microscopy (SPM) offers an unparalleled platform for investigating NCIs within low-dimensional supramolecular self-assemblies on surfaces. It allows direct visualization and overcomes ensemble-averaging errors.

The emergence of electrospray deposition (ESD) in SPM has significantly broadened its applicability to non-volatile, fragile biomolecules. However, accurately imaging and confirming the precise 3D structures of such molecules remains a considerable challenge. Addressing this difficulty requires the development of efficient structure search and reconstruction methods, which are still relatively underexplored.

This thesis investigates the structural and functional implications of NCIs in low-dimensional supramolecular nanostructures on surfaces, progressing from planar molecules to non-planar small molecules and flexible biomolecules. This systematic approach demonstrates how to overcome the increasing complexity of the systems studied. The discussion begins with planar self-assemblies of DNA base molecules, which create dynamic confined environments that stabilize water dimers, revealing their influence in causing mismatched hydrogen bonding. It then advances to integrating machine learning (ML) to predict the structures of disordered water nanoclusters on metal surfaces, enabling the determination of complex hydrogen-bond patterns. Finally, the investigation focuses on glycosidic bond stereochemistry in carbohydrate self-assemblies, highlighting its critical role in regulating the charge distribution of groups attached to the non-anomeric carbon and governing chirality transfer in self-assemblies, using data-efficient, multi-fidelity structure search methods integrated with ML.

Through these studies, this thesis provides insights into addressing the challenges posed by increasingly complex systems. It also paves the way for more efficient methods to study NCIs and their impact on supramolecular materials at atomic resolution.

Keywords: scanning probe microscopy, electrospray deposition, non-covalent interactions

Thesis available for public display 10 days prior to the defence at: https://aaltodoc.aalto.fi/doc_public/eonly/riiputus/

Doctoral theses at the School of Science: https://aaltodoc.aalto.fi/handle/123456789/52