Doctoral defence in Chemistry - Barði Benediktsson

Streymi

Ph.D. student: Barði Benediktsson

Dissertation title: Electronic structure calculations of spin-coupled iron-sulfur clusters

Opponents: 
Dr. Adam Kubas - Associate professor at the Institute of Physical Chemistry, Polish Academy of Sciences, Poland
Dr. Dimitrios A. Pantazis - Research group leader at the Max-Planck-Institut für Kohlenforschung, Germany

Advisor: Dr. Ragnar Björnsson, Researcher at the Laboratoire Chimie et Biologie des Métaux, CEA Grenoble, France

Doctoral committee: 
Dr. Hannes Jónsson , Professor at the Faculty of Physical Sciences, University of Iceland (Supervisor)
Dr. Asmus Ougaard Dohn, Specialist at the Science Institute, University of Iceland
Dr. Tobias Krämer, Lecturer at Maynooth University, Ireland

Chair of Ceremony: Dr. Oddur Ingólfsson, Professor and the Vice Head of the Faculty of Physical Sciences, University of Iceland

Abstract:
Iron-sulfur clusters are integral to the biochemistry of living organisms and a lot of effort has been devoted to research their structure and function. However, describing these polynuclear iron-sulfur clusters with computational chemistry poses a challenge due to their complicated open-shell electronic structure and the fact they are embedded within a protein. Many electronic structure methods (e.g. DFT) struggle with describing correctly the phenomena encountered in these clusters, such as their spin coupling. The overarching goal is to model these systems (QM or QM/MM), in particular the cofactors of the nitrogenase enzymes, and understand their electronic structure within the language of DFT. Firstly, the resting state of the iron-vanadium cofactor as it appears in the 1.35 Å resolution X-ray structure is found to be best described  as [VFe7S8C(CO3)]2−. Secondly, a test set of 11 dimeric spin-coupled Fe or Mo clusters and a test set of 5 dimeric Fe closed shell clusters are introduced and are demonstrated to behave differently w.r.t. density functional choice. Thirdly, the calculated nuclear resonance vibrational spectra (NRVS) of iron-sulfur proteins modelled by QM/MM is shown to be sensitive to functional choice and model size. NRVS is additionally a promising method in the study of nitrogenase and calculations suggest that a combined experimental-computational approach could help characterize the isolable states in the catalytic cycle of nitrogenase.

About the doctoral candidate:

Barði finished undergraduate studies at the University of Iceland with a BSc. degree in biochemistry and molecular biology and graduate studies in 2018 with a MSc. degree in chemistry. Along with studying, Barði has taught courses in physical chemistry at the University of Iceland. When Barði is not busy at the office, he can be usually be found on some mountain peak or photographing everything in between heaven and earth. Barði is born and raised in Akureyri and is the oldest of three siblings.