Scope of Computational Organometallic Chemistry Structure, Reactivity and Properties Manuel Ángel Ortuño Maqueda PhD Thesis Theoretical and Computational Chemistry Supervisors: Gregori Ujaque Pérez Agustí Lledós Falcó Departament de Química Facultat de Ciències 2014 Universitat Autònoma de Barcelona Departament de Química Unitat de Química Física Memoria presentada para aspirar al Grado de Doctor por Manuel Ángel Ortuño Maqueda Manuel Ángel Ortuño Maqueda Visto bueno Gregori Ujaque Pérez Agustí Lledós Falcó Bellaterra, 9 de Septiembre de 2014 Acknowledgments I am delighted to dedicate this section to all people who have been involved, either actively or passively, in the dissertation. Unofficial Acknowledgments is mostly written in Spanish, my native language, whilst Official Acknowledgments is composed in English. Unofficial Acknowledgments “Al César lo que es del César”. Todo este trabajo ha sido posible gracias a mis directores de tesis, Gregori Ujaque y Agustí Lledós. Les estoy enormemente agradecido por la ciencia y los valores que me han enseñado, así como por la confianza que han depositado en mí todos estos años. I would also like to express my gratitude to Prof. Michael Bühl (University of St. Andrews) for his pleasant treatment and great support. Pero no habría sido capaz de llegar hasta aquí sin la excelente disciplina que aprendí de mis profesores en la Universidad de Almería, Ignacio Fernández de las Nieves y Fernando López Ortiz. Me acogieron en su laboratorio cuando aún estaba en la carrera y me transmitieron su gran motivación por la investigación. A toda la unidad de química física de la UAB por su cálida acogida. Mención especial para Carles Acosta, el sysadmin que más me ha aguantado, Xavi Solans, con quien he compartido —y sufrido— horas y horas de docencia biotecnóloga, ¡y la máquina Nespresso! To my colleagues abroad, particularly to Ludovic, Ava, Neetika and Lazaros, who made easier my stay in Scotland. I enjoyed the way we changed British tea time into Magic time. Al grupo transmet y a toda la gente que ha pasado por él: Aleix, Gabor y Óscar, entre otros muchos. A Salva por guiar mis primeros pasos sobre terreno computacional. A Pietro que, por lo mucho que me ha enseñado, podría haber sido mi tercer director de tesis. A Max, quien ha sido mi ejemplo a seguir durante todos estos años. A Laia Sparrow y Almudena por su agradable compañía. A Luca por sacarme siempre una carcajada con sus extrañas anéctodas. Y finalmente a Sergi, que pese a sus bacallades, ha sido un compañero genial y un amigo excepcional. A la célula biomet, con Jean-Didier a la cabeza. A Lur por sus deliciosos brownies y a Jaime por el humor absurdo con el que tanto nos reímos. A Bea por su eterna y contagiosa risa. A Victor por todas las pissarres y situaciones divertidas que sólo él es capaz de crear. A Elisabeth por la complicidad que nos caracteriza y los incontables Dunkins, cafés y frikadas varias que hemos disfrutado juntos. Last but not least, a Rosa por su gran ayuda y sinceridad; su amistad es una de las mejoras cosas que me llevo de esta etapa de mi vida. Volviendo al sur, a todos mis amigos de Almería, en particular a Alba, Alberto, Cristóbal, Jesús, Miguel, Nacho y Samanta. A pesar de todas las técnicas computacionales que he aprendido durante el doctorado, su apoyo moral sigue siendo incalculable. Por último, a mi padre Manuel, a mi madre Llani y a mi hermana Marta. Sé que la familia no se elige, pero si existiera tal posibilidad, no habría mejor elección que vosotros. Tenéis mi eterno agradecimiento por estar ahí siempre. Official Acknowledgments I would like to thank the Ministerio de Educación, Cultura y Deporte (Government of Spain) for (i) the predoctoral FPU fellowship that made possible the present PhD thesis and (ii) the travel scholarship that allowed me to stay for three months in the research group of Prof. Michael Bühl (University of St. Andrews). CESCA and BSC are also acknowledged for providing computational resources. Prof. Salvador Conejero (CSIC–Universidad de Sevilla, Instituto de Investigaciones Científicas) and Prof. Ernesto de Jesús (Universidad de Alcalá) are acknowledged for their collaboration in some of the studies presented herein. Make it simple, but significant. Don Draper in Mad Men List of Abbreviations The most common abbreviations used along the dissertation are collected as follows. Abbreviation Meaning AIMD Ab initio molecular dynamics B3LYP Becke’s three parameters, Lee–Yang–Parr density functional BZ Benzene CN Coordination number COD 1,5-Cyclooctadiene D3 Grimme’s dispersion function DCM Dichloromethane DFT Density functional theory Dipp 2,6-Diisopropylphenyl DMF Dimethylformamide DZ Double-ζ (zeta) en Ethylenediamine GIAO Gauge-including atomic orbitals HE Heck mechanism HI Hiyama mechanism HR Heck-reinsertion mechanism HT Heck-transmetalation mechanism IMe 1,3-Dimethylimidazol-2-ylidene IMes 1,3-Bis(2,4,6-trimethylphenyl)imidazol-2-ylidene IMes* 1,3-Bis(2,4,6-trimethylphenyl)-4,5-dimethylimidazol-2-ylidene IPr 1,3-Bis(2,6-diisopropylphenyl)imidazol-2-ylidene ItBu 1,3-Di-tert-butylimidazol-2-ylidene JTE Jahn–Teller effect M06 Zhao and Truhlar’s Minnesota 06 density functional MAD Mean absolute deviation MD Molecular dynamics MM Molecular mechanics NHC N-Heterocyclic carbene NHC' Cyclometalated N-heterocyclic carbene NMR Nuclear magnetic resonance OA Oxidative addition P–P Bis(phosphine) PBE0 Perdew–Burke–Ernzerhof hybrid density functional QM Quantum mechanics RDF Radial distribution function RE Reductive elimination σ-CAM σ-Complex assisted metathesis SMD Solvent model density SOMO Single occupied molecular orbital THF Tetrahydrofuran TOL Toluene TS Transition state TZ Triple-ζ (zeta) XC Exchange–correlation Atom Caption H Br C N I O F Rh Si Pd P Cl Pt Preface Long time ago, a younger version of myself decided to join the computational chemistry community in blind way. No regrets nowadays, it was totally worthy. Nobody could expect the outstanding and extensive knowledge I have received during these years of research training. I have learnt the potential of computation in resolving chemical problems as well as in understanding the essential engine of phenomena. After all, the final outcome has been captured in the text you already have in your hands. The dissertation I proudly present here pursues to reflect both the competence and the impact of computational chemistry in the organometallic chemistry scene. Forthcoming chapters are lightly overviewed as follows. Introduction gathers the general concepts of the topics under further discussion and provides a simplistic sketch of the theoretical methodology employed. Objectives points towards the general targets this work pretends to achieve. The body of the results is divided into three different parts. Structure analyses the geometry of paramagnetic Pt(III) complexes and evaluate the presence of agostic interactions in low-coordinate Pt(II) species. Reactivity unravels the reaction mechanisms of selected transition metal-mediated processes, i.e., C–H bond activation and cross-coupling reactions. Properties applies several computational methods to reproduce and predict some properties of transition metal compounds, in particular, NMR chemical shifts and acid dissociation constants. Conclusions collects the most important remarks obtained along the study. Ultimately, in Annex A and Annex B one can find the first page of the published material I am co-author of. I hope you enjoy the dissertation as much as I did. Thanks for reading and have fun! Manu Contents CHAPTER I: INTRODUCTION ............................................................................. 1 1. Organometallic Chemistry .................................................................................... 3 1.1. Structure of Transition Metal Complexes ................................................................. 6 1.1.1. Four-coordinate Pt(III) species .......................................................................................... 7 1.1.2. Three-coordinate Pt(II) species ......................................................................................... 9 1.2. Reaction Mechanisms .............................................................................................. 11 1.2.1. Pt(II) C–H bond activation .............................................................................................. 13 1.2.2. Cross-coupling reactions .................................................................................................. 14 1.2.3. Heck reaction ................................................................................................................... 16 1.3. Acidity of Dihydrogen Complexes .......................................................................... 17 1.4. Nuclear Magnetic Resonance of Transition Metals ................................................ 18 2. Computational Methods ...................................................................................... 21 2.1. Density Functional Theory ...................................................................................... 22 2.1.1. Classification of density functionals ................................................................................ 24 2.1.2. Which functional should one choose? ............................................................................ 27 2.2. Molecular Mechanics ............................................................................................... 29 2.3. Molecular Dynamics ...............................................................................................