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A Computational Study of Small Gold Clusters with H2S, Thiols, H2O, and Alcohols Silvija C

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A Computational Study of Small Gold Clusters with H2S, Thiols, H2O, and Alcohols Silvija C Wilfrid Laurier University Scholars Commons @ Laurier Theses and Dissertations (Comprehensive) 2014 A Computational Study of Small Gold Clusters with H2S, Thiols, H2O, and Alcohols Silvija C. Smith Wilfrid Laurier University, [email protected] Follow this and additional works at: http://scholars.wlu.ca/etd Part of the Physical Chemistry Commons Recommended Citation Smith, Silvija C., "A Computational Study of Small Gold Clusters with H2S, Thiols, H2O, and Alcohols" (2014). Theses and Dissertations (Comprehensive). 1640. http://scholars.wlu.ca/etd/1640 This Thesis is brought to you for free and open access by Scholars Commons @ Laurier. It has been accepted for inclusion in Theses and Dissertations (Comprehensive) by an authorized administrator of Scholars Commons @ Laurier. For more information, please contact [email protected]. A Computational Study of Small Gold Clusters with H2S, Thiols, H2O, and Alcohols Silvija C. Smith Bachelor of Science, Honours Chemistry, Wilfrid Laurier University, 2012 THESIS Submitted to the Department of Chemistry in partial fulfillments of the requirements for the degree of Master of Science Wilfrid Laurier University Waterloo, Ontario, Canada ©Silvija C. Smith 2014 Abstract Bulk gold is known to be one of the least reactive metals. In contrast, gold colloids and gold nanoclusters exhibit unique chemical and physical properties, due to their stability, uniformity, and size related characteristics. These interesting attributes cause gold nanoclusters to have promising applications in catalysis, biosensors, and optoelectronics. In particular, many of the applications for gold nanoclusters are in the fields of biomedicine and biotechnology. These potential applications require aggregation resistant, water-soluble nanoparticles capable of withstanding an environment within living organisms. Additionally, previous studies have shown that supported gold nanoclusters can be used as catalysts for many hydrogenation and oxidation reactions at low temperatures. These reactions include the oxidation of carbon monoxide (CO) and nitric oxide (NO), partial oxidation of propylene, and partial and complete hydrogenation of acetylene and ethylene, respectively. In this thesis, density functional theory (DFT) calculations are used to obtain energies of equilibrium structures from geometry optimizations and vibrational frequencies of small gold clusters, with one to four gold atoms bonded to a water molecule, small alcohols, or short-chain thiols, SHR, wth R=H, CH3, CH3CH2. Additionally, density functional theory, Møller-Plesset Perturbation theory, and coupled cluster theory calculations were used to obtain energies, optimal geometries, vibrational frequencies, activation energies, and the rate of reaction for the hydrogen atom transfer from sulphur to gold of the RSH-Aun and RSAunH complexes. These complexes consist of small gold clusters, with n=1-4 and short-chain thiols wth R=H, CH3, and CH3CH2. The Gibbs free energies were calculated to determine whether the hydrogen atom transfer occurs as a thermodynamically spontaneous reaction. Additionally, common trends of the cluster i complexes including bond lengths and characteristic gold-sulphur and gold-oxygen vibrational stretching were examined. Depending on the ligand attached to the gold cluster and the overall charge of the complex, bridge-bonding to different pairs of gold atoms in the cluster can occur with the hydrogen atom that has been transferred and the sulphur atom or oxygen atom. These theoretical studies are used to expand on the limited understanding of gold clusters and their interesting characteristics. Additionally, these studies determine the versatility of various basis functionals and basis sets when used on many electron atoms, such as gold. The results from this study are compared to similar studies involving gold clusters. ii Acknowledgments I would like to thank my supervisor Dr. Ian Hamilton for giving me the opportunity to complete my Master of Science degree as a member of his lab. The support and guidance which he provided was invaluable. I am extremely grateful for all that I have learned under his supervision, as it will be helpful in my future educational endeavours. I would also like to thank Dr. Hind Al-Abadleh and Dr. Vladimir Kitaev for graciously lending their time as committee members and providing valuable insight into similar fields of study. I would like to thank my family for their continued support with my educational career. A special thank you to my father, who encouraged me to pursue a career in science. Without his continuous guidance, this opportunity would not have been possible. Finally, I would like to thank the founding agencies who allowed this research to be possible: Wilfrid Laurier University, Compute Canada, Sharcnet, and NSERC (Natural Sciences and Engineering Research Council of Canada). iii Table of Contents Abstract ..........................................................................................................................................i Acknowledgements ………………………………………………………………………….......iii Table of Contents …………………………………………………………………………….......iv List of Abbreviations and Symbols……………………………………………………………..viii List of Tables……………………………………………………………………………………..ix List of Schemes…………………………………………………………………………………xiii Chapter 1 Introduction………………………………………………………………………….1 1.1 Gold clusters…………………………………………………………………………………..1 1.1.1 Gold nanoparticles………………………………………………………………….1 1.1.2 Small gold clusters………………………………………………………………….2 1.2 Thiols………………………………………………………………………………………….2 1.3 Chemical synthesis of thiolate-protected gold clusters…………………………………...….3 1.4 Complexes of small gold clusters with H2S and small thiols, HSCH3 and HSC2H5…………5 1.5 Complexes of small gold clusters with H2O and small alcohols, CH3OH and C2H5OH…….6 1.6 Computational Theories……………………………………………………………………...6 1.6.1 Density Functional Theory………………………………………………………...6 1.6.1.1 BP86……………………………………………………………………...8 1.6.1.2 M06-2X…………………………………………………………………..9 1.6.2 Perturbation Theory………………………………………………………………...9 1.6.2.1 Rayleigh-Schrödinger perturbation theory………………….……………9 1.6.2.2 Møller-Plesset Perturbation Theory……………………………………..11 1.6.3 Coupled Cluster Calculations……………………………………………………...14 1.7 Transition State Theory………………………………………………………………………15 1.8 Research Goals and Objectives……………………………………………………………...17 1.9 References…………………………………………………………………………………....19 Chapter 2 Hydrogen atom transfer in alkane thiol-gold cluster complexes: A density functional theory study…………………………………………………………………………31 2.0 Abstract………………………………………………………………………………………31 iv 2.1 Introduction………………………………………………………………………...………..31 2.2 Computational Method………………………………………………………………………33 2.3 Results and Discussion………………………………………………………………………34 2.3.1 Geometries of the complexes……………………………………………...………35 + - 2.3.1.1 Geometries of the AunSHR, AunSHR , and AunSHR complexes………36 + - 2.3.1.2 Geometries of HAunSR, HAunSR and HAunSR complexes…………..36 + - 2.3.2 Vibrations of HAunSR, HAunSR and HAunSR complexes………………………37 2.3.3 Energetics of hydrogen atom transfer……………………………………………...37 2.3.4 Activation energies of hydrogen atom transfer…………………………………....38 2.4 Conclusions…………………………………………………………………………………..38 2.5 Acknowledgments……………………………………………………………………………39 2.6 References……………………………………………………………………………………40 Chapter 3 Hydrogen atom transfer in gold-oxygen cluster complexes: A density functional theory study……………………………………………………………………………………..48 3.0 Abstract………………………………………………………………………………………48 3.1 Introduction………………………………………………………………………………….48 3.2 Computational Method………………………………………………………………………50 3.3 Results and Discussion………………………………………………………………………51 3.3.1 Geometries of the complexes……………………………………………………..52 + - 3.3.1.1 Geometries of AunOH2 , AunOH2, and AunOH2 complexes …..………52 + - 3.3.1.2 Geometries of HAunOH , HAunOH, and HAunOH complexes ….…….53 + - 3.3.2 Vibrations of HAunOH , HAunOH, and HAunOH complexes ….………………..53 3.3.3 Energetics of hydrogen atom transfer……………………………………………..54 3.3.4 Activation energies of hydrogen atom transfer……………………………………55 3.4 Conclusions…………………………………………………………………………………..56 3.5 Acknowledgements…………………………………………………………………………..56 3.6 References……………………………………………………………………………………57 v Chapter 4 Transition state theory of hydrogen atom transfer in alkane thiol-gold cluster complexes………………………………………………………………………………………..66 4.0 Abstract………………………………………………………………………………………66 4.1 Introduction………………………………………………………………………………….66 4.2 Computational Method………………………………………………………………………68 4.3 Results and Discussion………………………………………………………………………69 4.3.1 BP86 results………………………………………………………………………..69 4.3.1.1 Geometries of the complexes……………………………………………69 4.3.1.1.1 Geometries of the AunSHR complexes……………………….70 4.3.1.2 Vibrations of the AunSHR complexes…………………………………..71 4.3.1.3 Energetics of hydrogen atom transfer…………………………………...71 4.3.1.4 Activation energies of hydrogen atom transfer………………………….72 4.3.1.5 Reaction rate constants of hydrogen atom transfer……………………..72 4.3.2 M06-2X results…………………………………………………………………….72 4.3.2.1 Geometries of the complexes……………………………………………72 4.3.2.1.1 Geometries of the AunSHR complexes……………………….73 4.3.2.2 Vibrations of the AunSHR complexes…………………………………..74 4.3.2.3 Energetics of hydrogen atom transfer…………………………………...74 4.3.2.4 Activation energies of hydrogen atom transfer………………………….75 4.3.2.5 Reaction rate constants of hydrogen atom transfer………………………75 4.3.3 MP2 results.………………………………………………………………………..75 4.3.3.1 Geometries of the complexes…………………………………………….75 4.3.3.1.1
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