QUANTUM AND QUANTUM-CLASSICAL CALCULATIONS OF CORE-IONIZED MOLECULES IN VARIED ENVIRONMENTS TUOMAS LÖYTYNOJA Nano and Molecular Systems Research Unit University of Oulu Finland Theoretical Chemistry and Biology School of Engineering Sciences in Chemistry, Biotechnology and Health Royal Institute of Technology Stockholm, Sweden Academic Dissertation to be presented with the assent of the Doctoral Train- ing Committee of Technology and Natural Sciences, University of Oulu, for public discussion in the Auditorium IT116, on June 1st, 2018, at 12 o’clock noon. REPORT SERIES IN PHYSICAL SCIENCES Report No. 119 OULU 2018 • UNIVERSITY OF OULU Opponent Prof. Jukka Tulkki, Aalto University, Finland Reviewers Prof. Andreas Larsson, Luleå University of Technology, Sweden Prof. Kari Laasonen, Aalto University, Finland Custos Prof. Marko Huttula, University of Oulu, Finland ISBN 978-952-62-1882-3 (print) ISBN 978-952-62-1883-0 (electronic) ISSN 1239-4327 TRITA-CBH-FOU-2018:20 JUVENES PRINT/US-AB Oulu 2018/Stockholm 2018 i Löytynoja, Tuomas Juhani: Quantum and quantum-classical cal- culations of core-ionized molecules in varied environments Nano and Molecular Systems Research Unit Faculty of Science P.O. Box 3000 FIN-90014 University of Oulu Finland Theoretical Chemistry and Biology School of Engineering Sciences in Chemistry, Biotechnology and Health SE-106 91 Royal Institute of Technology Stockholm, Sweden Abstract Computational quantum chemistry methods have been applied in two par- ticular cases: to provide insight to photoionization induced fragmentation of HgBr2 and HgCl2 molecules, and to study core-electron binding energies and chemical shifts of molecules in liquid, surface adsorbed and polymeric environments in the framework of quantum mechanics/molecular mechanics (QM/MM). In the photodissociation studies the computational work is based on the relativistic Dirac equation as the systems present strong spin-orbit interaction affecting the fragmentation processes. In the QM/MM studies of ethanol-water mixtures and molecules physisorbed on silver surfaces the structures are provided by classical molecular dynamics simulations to an- alyze the distribution of the binding energies of core-orbitals and effects of their surroundings. In the case of polymethyl methacrylate polymer the im- pact of a QM-MM boundary and a polymeric environment are studied. The theoretical backgrounds of the computational methods applied and the ob- tained results are discussed. Key words: Electron spectroscopy, UPS, XPS, photodissociation, binding en- ergy, ionization potential, computational, electronic structure, self-consistent field, DFT, QM/MM, gas phase, liquid, solution, physisorption, metallic sur- face, polymer, charge transfer ii Acknowledgments This work was carried out at the Nano and Molecular Systems Research Unit, formerly known as the Electron Spectroscopy Group, in the University of Oulu and at the Department of Theoretical Chemistry and Biology in the KTH Royal Institute of Technology, Stockholm, Sweden. I would like to thank the Heads of the former Department of Physics in University of Oulu and the Department of Theoretical Chemistry and Biology in the Royal Institute of Technology for placing the facilities at my disposal. The work was financially supported by The National Doctoral Programme in Materials Physics, Vilho, Yrjö and Kalle Väisälä Foundation and Univer- sity of Oulu Graduate School. CSC – IT Center for Science administrated by the Ministry of Education and Culture of Finland and the Swedish National Infrastructure for Computing (SNIC) are thanked for providing most of the computational resources consumed in this thesis. I am grateful for my first supervisor in Oulu, Dr. Sami Heinäsmäki for teaching me to aim to be at control of my life goals and also sometimes take it easy. I thank my current supervisor, Dr. Kari Jänkälä for his incredible patience and ability to find answers to all the questions I could imagine and his help during all stages of my studies. My supervisor in Stockholm, Prof. Hans Ågren I thank for sharing his vast view over the field of quantum chem- istry and pushing me forward so I could finish this thesis. I would also like to thank Prof. Marko Huttula for taking care of a lot of the background matters thus ensuring that I could keep doing my work. My assistant supervisor in Stockholm, Assoc. Prof. Zilvinas Rinkevicius is thanked for his help and is acknowledged for having a (special) sense of humor. I thank Dr. Johannes Niskanen for his introduction to the world of MD and QM/MM calculations, Dr. Esko Kokkonen for being a kind and hard- working collaborator, Dr. Alexander Karpenko for showing me how to run the relativistic QM calculations, Dr. Xin Li for his help in the surface MD calculations and Dr. Ignat Harczuk for the great collaboration during the PMMA study. I am also grateful to Dr. Lauri Hautala, Dr. Antti Kettunen and Prof. Olav Vahtras for the cooperation during the studies. Dr. Bogdan Frecus, Dr. Arul Murugan, Prof. Yaoquan Tu, Dr. Perttu Lantto and Dr. Wei Cao are thanked for their help and insightful discussions during this work. I would also like to present my gratitude for the other research group iii iv members in Oulu and Stockholm for creating a pleasant working environ- ments and enlightening the everyday life during my studies. I thank my fellow students, friends and relatives for all their support during my university career. I am especially grateful for my roommate Mr. Heikki Huhtamäki for enduring me all these years and ensuring that I don’t completely shut myself between four walls. Lastly, I thank my parents, Tarja and Vesa and my sisters Riikka and Sara for letting me make my own choices in life and for all their support and care over the years. Oulu, May 2018 Tuomas Löytynoja v LIST OF ORIGINAL PAPERS The following articles are included in this thesis and are referred by their Roman numerals. I. E. Kokkonen, T. Löytynoja, K. Jänkälä, J. A. Kettunen, S. Heinäsmäki, A. Karpenko, M. Huttula: Spin-orbit interaction mediated molecular dissociation, J. Chem. Phys. 140, 184304 (2014). II. E. Kokkonen, T. Löytynoja, L. Hautala, K. Jänkälä, M. Huttula: Frag- mentation of mercury compounds under ultraviolet light irradiation, J. Chem. Phys. 143, 074307 (2015). III. T. Löytynoja, J. Niskanen, K. Jänkälä, O. Vahtras, Z. Rinkevicius, H. Ågren: Quantum Mechanics/Molecular Mechanics Modeling of Pho- toelectron Spectra: The Carbon 1s Core-Electron Binding Energies of Ethanol-Water Solutions, J. Phys. Chem. B 118, 13217 (2014). IV. T. Löytynoja, X. Li, K. Jänkälä, Z. Rinkevicius and H. Ågren: Quan- tum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface, J. Chem. Phys. 145, 024703 (2016). V. T. Löytynoja, I. Harczuk, K. Jänkälä, O. Vahtras, and H. Ågren: Quantum-classical calculations of X-ray photoelectron spectra of polymers– Polymethyl methacrylate revisited, J. Chem. Phys. 146, 124902 (2017). Comment on author’s contributions All the articles included in this thesis are results of teamwork. The author of this thesis is responsible for all the calculations and data analysis of the computational results provided in the papers, exceptions in some cases being the first steps of molecular dynamics simulations in papers III and IV and optimization of the molecular mechanics force-fields in paper V. To papers I and II the author wrote the section describing the computations and helped in interpretation of the results. He was the main author in papers III–V being responsible for most of the text. In addition, the author has participated in writing of the following paper that is not included in this thesis. A. L. Hautala, K. Jänkälä, T. Löytynoja, M.-H. Mikkelä, N. Prisle, M. Tchaplyguine, and M. Huttula: Experimental observation of structural phase transition in CsBr clusters, Phys. Rev. B 95, 045402 (2017). vi Abbreviations and notation Abbreviations ADC algebraic diagrammatic construction BE binding energy CI configuration interaction CIY coincident ion yield DFT density functional theory DHF Dirac-Hartree-Fock HF Hartree-Fock MD molecular dynamics ML monolayer MM molecular mechanics MO molecular orbital PEPICO photoelectron-photoion coincidence PES photoelectron spectrum PMMA polymethyl methacrylate QM quantum mechanics QM/MM quantum mechanics/molecular mechanics QM/CMM quantum mechanics/capacitance molecular mechanics RELADC relativistic algebraic diagrammatic construction SCF self-consistent field SM single molecule UPS ultraviolet photoelectron spectroscopy VUV vacuum ultraviolet XPS X-ray photoelectron spectroscopy Physical constants e elementary charge h Planck’s constant ~ reduced Planck’s constant ke Coulomb’s constant me mass of electron c speed of light kB Boltzmann constant Contents Abstract i Acknowledgments ii List of original papers v Abbreviations and notation vi Contents vii 1 Introduction 1 2 Computational methods 5 2.1 Molecular quantum mechanics . .5 2.1.1 Schrödinger equation . .5 2.1.2 Born-Oppenheimer approximation . .6 2.1.3 Hartree-Fock method . .7 2.1.4 Electron correlation . 10 2.1.5 Density functional theory . 13 2.1.6 Relativistic quantum theory . 15 2.1.7 ∆-SCF method . 17 2.1.8 Basis sets . 19 2.2 Molecular dynamics simulations . 21 2.2.1 Initial conditions and settings . 21 2.2.2 Interactions . 22 2.2.3 Force-fields . 23 2.2.4 Ensemble control . 25 2.2.5 Integrators . 28 2.2.6 Simulations in practice . 28 2.2.7 Analysis of the simulation results . 29 2.3 Hybrid methods . 32 2.3.1 Quantum mechanics/molecular mechanics method . 32 2.3.2 Polarizable continuum model . 36 2.3.3 Error analysis . 37 vii viii CONTENTS 3 Phenomena in electron spectroscopy 39 3.1 Electronic structure of atoms and molecules . 39 3.1.1 Intra and intermolecular bonds . 39 3.1.2 Quantum numbers . 40 3.1.3 Configurations and term symbols . 44 3.2 Electronic transitions . 47 3.3 Photodissociation . 49 4 Experiments 51 4.1 Samples . 51 4.2 Synchrotron radiation . 52 4.3 Hemispherical electron energy analyzer .