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Automated Structure Generation for First-Principles Transition-Metal Automated structure generation for first-principles transition-metal catalysis by Efthymios Ioannis Ioannidis Diploma Chemical Engineering National Technical University of Athens (2013) M.S. Chemical Engineering Practice Massachusetts Institute of Technology (2014) Submitted to the Department of Chemical Engineering in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Engineering Practice at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY June 2018 ⃝c Massachusetts Institute of Technology 2018. All rights reserved. Author................................................................ Department of Chemical Engineering June 2018 Certified by. Heather J. Kulik Joseph R. Mares ’24 Career Development Professor in Chemical Engineering Thesis Supervisor Accepted by . Patrick S. Doyle Robert T. Haslam (1911) Professor of Chemical Engineering Chairman, Committee for Graduate Students 2 Automated structure generation for first-principles transition-metal catalysis by Efthymios Ioannis Ioannidis Submitted to the Department of Chemical Engineering in June 2018, in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Engineering Practice Abstract Efficient discovery of new catalytic materials necessitates the rapid but selective gen- eration of candidate structures from a very wide chemical space and the efficient estimation of their properties. We developed an efficient and reliable software utility for high-throughput screening of inorganic complexes that enables chemical discov- ery by automating molecular and intermolecular complex structure generation, job preparation as well as post-processing analysis to elucidate correlations of electronic or geometric descriptors with energetics. The developed software was then used to unveil different binding modes of small anions on organometallic complexes as well as functionalizations that allow for selective binding. We additionally employed our ma- terials design framework to study the binding of carbon monoxide on functionalized metalloporphyrins providing tuning strategies and uncertainty estimation. Compu- tational approaches such as density functional theory (DFT) that directly simulate the electronic properties have been increasingly used as tools for materials design mainly due to recent developments in computational speed and accuracy. DFT re- casts the many-body problem of interacting electrons into an equivalent problem of non-interacting electrons, greatly simplifying the solution procedure. This approach introduces certain approximations that are effectively modeled with an exchange and correlation functional that accounts for the many-body effects that are not included in the simplified problem. The functional choice is an important modeling decision and therefore computational predictions can be sensitive to user selection. This sensitivity is maximized for systems with highly localized electrons such as transition metals due to self-interaction error, where one electron interacts with its own mean field resulting in an unphysical delocalization of the electron density. We studied extensively how the incorporation of the widely employed Hartree-Fock and meta-GGA-type exchange functionals affects DFT predictions on transition metal complexes. Thesis Supervisor: Heather J. Kulik Title: Joseph R. Mares ’24 Career Development Professor in Chemical Engineering 3 4 Acknowledgments At the verge of completing my PhDCEP thesis I would like to express my gratitude to all the people that have helped me shape this amazing journey. First and foremost, I would like to thank my academic advisor, Prof. Heather Kulik who despite the short 3-year research period of the PhDCEP program provided me with all I needed to jump start the thesis and then let me construct my own path with proper and invaluable feedback and guidance. Being one of the first students in the Kulik lab and helping start up the group was a great experience and watching it gradually grow and take its own shape and character has been very fulfilling for me. I would like to additionally thank my thesis committee members Prof. Bill Green and Prof. Yuriy Roman for their continuous support in our thesis committee meetings and the advice they offered me during the term of this research project. I have been extremely fortunate to be part of a very special research group for the past 3 years. I would like to thank everybody who is or has been a member of the Kulik lab including Natasha, Lisi, Niladri, Qing, Helena, Yusu, Jeong Yun, JP and especially Terry for their valuable feedback and fruitful discussions on matters concerning various aspects of my thesis. I would also like to thank all my dear friends back home that have been supporting me these years I have been away. Despite the distance I am grateful that we are still close and I do consider you my life-long friends. Also, I am grateful for the new friends I made here in Boston, the Greek community and my friends from the chemical engineering department at MIT, all of them being special people that have helped me through the transition of living and studying in the US. I cherish every moment that I have spent with you and I am looking forward to even more exciting ones. I would not have been here if it weren’t for my parents, Liana and Ippokratis and my sisters Dioni and Eleonora. They have always been my driving force, my source of energy and motivation and have supported every decision that I have made in my life. This thesis is dedicated to you. 5 6 Contents 1 Introduction 19 1.1 Density functional theory (DFT) .................... 19 1.1.1 Introduction to density functional theory ............ 19 1.1.2 Spin density functional theory .................. 23 1.2 DFT for transition metal catalysis .................... 24 1.3 Ligand field theories ........................... 26 1.3.1 Crystal field theory ........................ 26 1.3.2 Ligand field theory ........................ 28 1.4 High-throughput screening ........................ 30 1.5 Thesis outline ............................... 33 2 Effect of Hartree-Fock exchange 35 2.1 Computational details .......................... 38 2.2 Dependence of spin-state ordering on functional choice ........ 40 2.3 Dependence of spin-state ordering on HF exchange .......... 43 2.3.1 Spin-state ordering dependence with Fe(III) complex test cases 44 2.3.2 Spin-state ordering: comparison with Fe(II) complexes .... 47 2.4 Trends in charge localization measures ................. 50 2.5 Corroborating geometric and energetic relationships .......... 56 2.6 Quantitative vs. qualitative spin-state ordering ............ 57 2.7 Conclusions ................................ 58 7 3 Effect of meta-GGA exchange 61 3.1 Theory ................................... 62 3.2 Computational details .......................... 65 3.3 Effect of meta-GGA exchange on single ions spin-state splittings ... 68 3.4 Dependence of spin-state ordering on meta-GGA exchange ...... 69 3.5 Trends in charge localization measures ................. 74 3.6 Combined effect of HF exchange and meta-GGA exchange ...... 79 3.7 Conclusions ................................ 83 4 Automatic structure generation 85 4.1 Code overview ............................... 86 4.2 Code architecture ............................. 87 4.3 Structure generation ........................... 89 4.3.1 General approach ......................... 89 4.3.2 Customized cores ......................... 95 4.3.3 Modify function .......................... 96 4.4 Additional features ............................ 97 4.4.1 Random generation ........................ 97 4.4.2 Database search .......................... 98 4.4.3 Supramolecular complex building ................ 99 4.4.4 Simulation automation ...................... 101 4.4.5 Structure-property correlation and analysis ........... 102 4.5 Benchmarking molSimplify ........................ 105 4.6 Conclusions ................................ 111 5 Selective anion binding by functionalized organometallics 113 5.1 Computational details .......................... 114 5.2 Binding modes .............................. 115 5.3 Selective binding ............................. 118 5.3.1 Hydrogen bonding ........................ 120 5.3.2 Additional correlations ...................... 123 8 5.4 Conclusions ................................ 126 6 CO binding on metalloporphyrins 129 6.1 Computational details .......................... 131 6.2 Structures ................................. 133 6.3 Binding energies .............................. 135 6.4 Charge measures ............................. 141 6.5 Sensitivity analysis ............................ 143 6.6 Conclusions ................................ 146 7 Concluding remarks 149 8 Market analysis of the Catalysis industry: Capstone paper 153 8.1 Introduction ................................ 153 8.2 Types of Catalysts ............................ 154 8.3 Catalyst market segments ........................ 156 8.4 Environmental catalysts ......................... 157 8.5 Refining catalysts ............................. 160 8.6 Polymer catalysts ............................. 161 8.7 Chemical catalysts ............................ 163 8.8 Global Catalysis Market Trends ..................... 163 8.8.1 Toward higher activity and selectivity of catalysts ....... 164 8.8.2 Changes in feedstock and more effective use of feedstock ... 165 8.8.3 Lower Operating Temperatures ................. 166 8.8.4 Energy efficiency ......................... 166 8.8.5 Creation of processes around catalyst
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