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Parameterization of the Am1* Semiempirical Molecular Orbital Method for the First-Row Transition Metals and Other Elements

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Parameterization of the Am1* Semiempirical Molecular Orbital Method for the First-Row Transition Metals and Other Elements PARAMETERIZATION OF THE AM1* SEMIEMPIRICAL MOLECULAR ORBITAL METHOD FOR THE FIRST-ROW TRANSITION METALS AND OTHER ELEMENTS Der Naturwissenschaftlichen Fakultät der Friedrich-Alexander-Universität Erlangen-Nürnberg zur Erlangung des Doktorgrades Dr. rer. nat. vorgelegt von Hakan Kayi aus Bursa, Türkei 2009 Als Dissertation genehmigt durch die Naturwissenschaftliche Fakultät der Friedrich-Alexander-Universität Erlangen-Nürnberg Tag der mündlichen Prüfung: 23.12.2009 Vorsitzender der Promotionskommission: Prof. Dr. Eberhard Bänsch Erstberichterstatter: Prof. Dr. Timothy Clark Zweitberichterstatter: Prof. Dr. Nicolai Burzlaff ACKNOWLEDGMENTS First of all I would like to express my deepest gratitude to my supervisor Prof. Dr. Timothy Clark for his endless support, patience, full confidence in me and for always encouraging me. Without his understanding and excellent guidance, I could never complete this project. I am also very thankful for his support on personal level, that has been very valuable during many difficult situations. I would like to thank Prof. Dr. Rudi van Eldik and Prof. Dr. Bernd Meyer for accepting to be examiners at my defense exam, and also Prof. Dr. Nicolai Burzlaff for his expertise. I am very thankful to Dr. Paul Winget and Anselm Horn for sharing their great experiences in programming and for their help in using of parameterization scripts, and Dr. Nico van Eikema Hommes for his support and advice for solving technical problems related to hardware, software and scripting. Additionally, my thanks go to my officemate Dr. Tatyana Shubina for her fruitful discussions. I am also very thankful for the help and very valuable discussions of Dr. Matthias Henneman. Many thanks go as well to my former and present colleagues for their friendliness and support in many different issues: Dr. Harald Lanig, Dr. Ralph Puchta, Dr. Gudrun Schürer, Dr. Kendall Byler, Dr. Florian Haberl, Dr. Olaf Othersen, Dr. Jr-Hung Lin, Dr. Frank Beierlein, Dr. Mateusz Wielopolski, Dr. Pawel Rodziewicz, Dr. Gül Özpinar, Dr. Adria Gil Mestres, Dr. Ute Seidel, Christian Kramer, Christof Jäger, Sebastian Schenker, Matthias “Döner” Wildauer, Angela Götz, Marcel Youmbi and Alexander Urban. I also would like to say thank you to my friends: Kurtulus Erdogan, Günay Kaptan and Can Metehan Turhan for all the unforgettable moments they shared with me in Erlangen, and those everywhere that stayed friends despite the separations of time and distance. For the financial support I thank Deutsche Forschungsgemeinschaft (GK312 “Homogeneous and Heterogeneous Electron Transfer” and SFB583 “Redox-Active Metal Complexes”). And finally, I would like to express my warmest and endless gratitude to my parents and my sister for their lifelong love, support and encouragement. i ii ZUSAMMENFASSUNG In dieser Doktorarbeit wird die Parametrisierung der semiempirischen AM1* Molekülorbitaltechnik für einige neue Elemente beschrieben. Dies beinhaltet Resultate und Parameter für Vanadium, Chrom, Mangan, Eisen, Kobalt, Nickel, Kupfer, Zink, Brom, Jod und Gold. Die AM1* Methode ist eine Erweiterung der ursprünglichen AM1 Molekülorbital Theorie. Sie benutzt d-Orbitale für Elemente ab der zweiten langen Reihe des Periodensystems und eine leichte Modifizierung von Voityuk und Rösch’s AM1(d) Parametern für Mo. Unsere ursprüngliche Motivation für die Parametrisierung von AM1* war, die Vorteile von AM1 (gute H-Brücken Energien, höhere Rotationsbarrieren für π-Systeme als MNDO oder PM3) für die Elemente H, C, N, O und F beizubehalten, während die Performanz für P-, S- und Cl- beinhaltende Substanzen verbessert werden sollte. Zusätzlich wollten wir endlich eine Parametrisierung für Übergangsmetalle auf Basis eine MNDO Methode publizieren. Im Laufe der Arbeit stellte sich heraus, dass es auch nötig ist, Brom und Jod zu parametrisieren, um die Bromide und Jodide der Übergangsmetalle in den Parametrisierungsdatensätzen adäquat zu nutzen. Während der Vorbereitung der Parametrisierungsdatensätze wurden experimentelle Daten aus mehreren Quellen gesammelt. Im Falle fehlender experimenteller Daten und um den Bereich des Parametrisierungsdatensatzes zu vergrößern wurden die Eigenschaften wichtiger prototypischer Strukturen auf hoher quantenmechanischer Niveau berechnet. Zusätzlich haben wir experimentelle Daten geringer Qualität mit den Ergebnissen von hochqualitativen quantenmechanischen Rechnungen verglichen und verbessert. In solchen Fällen wurde das B3LYP Hybrid-Funktional mit LANL2DZ Basis Satz und Polarisierungsfunktionen oder Coupled Cluster Rechnungen mit Einzel- und Doppelanregungen und Störungstheoriekorrekturen für Dreifachanregungen (CCSD(T)) mit dem 6-311+G(d) Basissatz benutzt. Nach der Zusammenstellung des Datensatzes wurde die Parametrisierung durchgeführt und die Performanz und typische Fehler von AM1* analysiert. Diese werden im Detail gezeigt und mit der Performanz von anderen Methoden, die die NDDO Nährung benutzen, verglichen. Zusammenfassend lässt sich sagen, dass der AM1* Hamiltonian für energetische, elektronische und strukturelle Eigenschaften den anderen verfügbaren Hamiltonians überlegen ist, insbesondere für die Beschreibung von Übergangsmetallen. iii iv ABSTRACT This thesis describes the parameterization of AM1* semiempirical molecular orbital technique for a series of new elements. Parameterization results for vanadium, chromium, manganese, iron, cobalt, nickel, copper, zinc, bromine, iodine and gold are reported. The AM1* methodology is an extension of the original AM1 molecular orbital theory uses d-orbitals for the elements starting from the second long row of the periodic table, and a slight modification of Voityuk and Rösch’s AM1(d) parameters for Mo. Our original motivation in parameterizing AM1* was to retain the advantages of AM1 (good energies for hydrogen bonds, higher rotation barriers for π-systems than MNDO or PM3) for the elements H, C, N, O and F and to improve performance over AM1 for P-, S- and Cl-containing compounds and eventually to produce a published parameterization for an MNDO-like method for the transition metals. Additionally, bromine and iodine have also been parameterized because parameters for these elements became necessary in order to be able to parameterize the transition metals adequately by including their bromides and iodides in the parameterization datasets. In the preparation of parameterization datasets, experimental target data were collected from several sources. In the case of lack of experimental data and also to extend the range of parameterization dataset, prototype compounds were used and their properties derived from high-level calculations. In addition to this, when we have determined that the available experimental data are of insufficient quality, we have also applied corrections to available values using results from high-level calculations. In such cases, the B3LYP hybrid functional with the LANL2DZ basis set including polarization functions or coupled cluster calculations with single and double excitations and a perturbational corrections for triples (CCSD(T)) with the 6-311+G(d) basis set were used and dataset became more reliable. Once the parameterization dataset has been assembled, the parameterization process is performed. After this parameterization process is successfully completed, the performance and the typical errors of AM1* are discussed and also compared with the other available neglect of diatomic differential overlap (NDDO) Hamiltonians. To summarize, the performance of the AM1* for energetic, electronic and structural properties is superior to other available Hamiltonians in many cases, especially for the transition metals. v vi CONTENTS 1 INTRODUCTION 1 1.1 Historical Development of Semiempirical Methods ....................................................... 1 1.1.1 Hückel (HMO), Pariser-Parr-Pople (PPP) and Extended Hückel Theory (EHT) ..... 1 1.1.2 CNDO, INDO ........................................................................................................... 1 1.1.3 NDDO ....................................................................................................................... 2 1.1.4 MINDO ..................................................................................................................... 3 1.1.5 MNDO ...................................................................................................................... 3 1.1.6 AM1 .......................................................................................................................... 4 1.1.7 PM3 ........................................................................................................................... 5 1.1.8 MNDO/d .................................................................................................................. 6 1.1.9 SAM1 ........................................................................................................................ 6 1.1.10 PM3(tm) .................................................................................................................. 7 1.1.11 AM1(d) ................................................................................................................... 7 1.1.12 PM5 ......................................................................................................................... 7 1.1.13 AM1* ...................................................................................................................... 8 1.1.14 RM1 .......................................................................................................................
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