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On the Nature of Weak Intermolecular Forces: a First Principles Approach to Hydrogen Bonding and Pi-Type Interactions

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On the Nature of Weak Intermolecular Forces: a First Principles Approach to Hydrogen Bonding and Pi-Type Interactions University of Mississippi eGrove Electronic Theses and Dissertations Graduate School 2012 On the Nature of Weak Intermolecular Forces: a First Principles Approach to Hydrogen Bonding and Pi-Type Interactions Kari Lorene Copeland Follow this and additional works at: https://egrove.olemiss.edu/etd Part of the Physical Chemistry Commons Recommended Citation Copeland, Kari Lorene, "On the Nature of Weak Intermolecular Forces: a First Principles Approach to Hydrogen Bonding and Pi-Type Interactions" (2012). Electronic Theses and Dissertations. 83. https://egrove.olemiss.edu/etd/83 This Dissertation is brought to you for free and open access by the Graduate School at eGrove. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of eGrove. For more information, please contact [email protected]. On the Nature of Weak Intermolecular Forces: A First Principles Approach to Hydrogen Bonding and π-Type Interactions A Dissertation presented in partial fulfillment of requirements for the degree of Doctor of Philosophy in the Department of Chemistry and Biochemistry The University of Mississippi by Kari L. Copeland April 2012 c 2012 Kari L. Copeland ALL RIGHTS RESERVED ABSTRACT Computational quantum chemistry is a branch of chemistry that is based on quantum mechanics. In this field, chemical phenomena is represented in mathematical form and com- puters are used to provide numerical solutions to rigorous mathematical equations. Through this medium, the properties of atoms and molecules are calculated with high accuracy. Chapter 1 opens with a general discussion of science, the development of atomic the- ory and computational chemistry. Electronic structure theory is more extensively reviewed in Chapter 2. Hydrogen bonding and dispersion forces are defined in Chapter 3, and the procedures used to computationally study these type interactions are considered. Chapter 4 discusses the effects of π-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures. The 26 toluene/(N9-methyl-) adenine model configurations constructed from protein/ligand crystal structures are inves- tigated with explicitly correlated methods. In Chapter 5, electronic structure computations are used to systematically examine nine small hydrocarbon molecules interacting with wa- ter. The structures, energetics and nature of hydrocarbon/water interactions in 30 hydro- carbon/water dimer configurations are examined. ii DEDICATION To my family; my parents: Ruth Copeland and Esker Copeland my siblings: Catina, Trena, Mark, Trey and Shaun and my grandparents: Edna (Ayunda) and Woodrow (Willie Boy) Richardson iii ACKNOWLEDGMENTS I would like to thank God, the supreme being and creator of the universe: I could not have accomplished any of this without your help, strength and guidance. I would also like to thank the following human beings: Dr. Gregory S. Tschumper: for being my Ph.D. advisor. Dr. Maurice Eftink and Dr. Donald Cole: for your immeasurable comfort and support. Harriet Hearn and Margo Montgomery: for being my homegirls and keeping it real. Jeffrey Veals: for being my closest companion and confidant. Dr. Murrell Godfrey: for being a mentor and a friend. Ginger Tarpley and Bei Cao: for your support and empathy when no one else could understand. Dr. Desiree Bates: for your help and advice. There are so many other individuals who listened when I whined, comforted me when I cried or simply smiled at me on the street, who, knowingly or not, brightened some of my dark days. To you all: thank you for helping me to complete this degree. Lastly, I would like to thank my dog, Milo: your astounding excitement to see me (when no one else seemed to have that same enthusiasm) after a long day was priceless. I would also like to sincerely thank my dissertation committee (Drs. Gregory S. Tschumper, Steven R. Davis, Murrell Godfrey, Nathan I. Hammer and Donald R. Cole), the past and present members of the Tschumper research group and my research collaborators at Murray State University. The research in this dissertation was financially supported by the National Science iv Foundation (EPS–0132618, CHE–0517067, EPS–0556308, EPS–0903787, CHE–0957317 and EPS–100698). In addition, I have been supported by the Southern Regional Education Board (SREB), the National Organization for the Professional Advancement of Black Chemists and Chemical Engineers (NOBCChE), the Alliance for Graduate Education in Mississippi (AGEM), the Mississippi Center for Supercomputing Research (MCSR), the Center for En- abling New Technologies Through Catalysis (CENTC), the Mississippi Experimental Pro- gram to Stimulate Competitive Research (ESPCoR), the University of Mississippi Depart- ment of Chemistry and Biochemistry and the University of Mississippi Graduate School. v “Imagine that you are explaining your ideas to your former smart, but ignorant, self, at the beginning of your studies!” Richard Feynman − vi Contents Chapter 1 Introduction 1 1.1 TheScienceofChemistry . .. .. 1 2 Electronic Structure Theory 6 2.1 Introduction.................................... 6 2.2 Wave functions: Molecular Orbital Approximation . .......... 9 2.3 Molecular Orbitals: Linear Combination of Atomic Orbitals ......... 11 2.4 ModelChemistries ................................ 12 2.5 QuantumChemistryBasisSets . .. 13 2.6 QuantumChemistryMethods . 14 2.6.1 HartreeFockTheory ........................... 14 2.6.2 ConfigurationInteractionTheory . ... 16 2.6.3 CoupledClusterTheory . .. .. .. 17 2.6.4 Møller-Plesset Perturbation Theory . ..... 18 2.6.5 Explicitly Correlated Methods . ... 18 2.6.6 DensityFunctionalTheory. 19 vii 3 Non-covalent Interactions 21 3.1 WeakIntermolecularForces . ... 21 3.2 Prototypes of Non-Covalent Interactions . ........ 23 3.2.1 HydrogenBonding: WaterDimer . 24 3.2.2 π-Type Interactions: Benzene Dimer . 24 3.3 QuantumChemistryComputations . ... 24 3.3.1 ComputationalCostsandScaling . .. 24 3.3.2 BasisSetSuperpositionError . .. 26 4 Probing Phenylalanine/Adenine π-Stacking Interactions in Protein Com- plexes with Explicitly Correlated and CCSD(T) Computations∗ 28 4.1 Abstract...................................... 28 4.2 Introduction.................................... 29 4.3 TheoreticalMethods .............................. 32 4.4 ResultsandDiscussion . .. .. .. 36 4.5 Conclusions .................................... 41 4.6 Acknowledgments................................. 42 4.7 SupportingInformationAvailable . ...... 42 5 Hydrocarbon/Water Interactions: Encouraging Energetics and Structures from DFT but Disconcerting Discrepancies for Hessian Indices† 43 5.1 Abstract...................................... 43 5.2 Introduction.................................... 44 5.3 ComputationalMethods . 47 viii 5.4 ResultsandDiscussion . .. .. .. 50 5.4.1 Structures................................. 50 5.4.2 CBS Limit Interaction Energies . .. 51 5.4.3 Comparison of Optimized Structures . ... 53 5.4.4 Comparison of Interaction Energies . .... 55 5.4.5 Comparison of Hessian Indices . .. 56 5.5 Conclusion..................................... 57 5.6 SupportingInformationAvailable . ...... 59 5.7 Acknowledgments................................. 60 6 Concluding Remarks 70 Bibliography 74 Appendix 94 Vita 133 ix List of Figures 3.1 Water dimer configuration for modeling hydrogen bonding interactions. 24 3.2 Typical configurations of the benzene dimer for modeling π-type interactions. 25 4.1 Overlay of the 26 crystal structures for the toluene/9MeA(adenine) model complexes. The β-carbon of Phe is orange and H atoms are not shown. 33 4.2 Overlay of the six unique MP2/DZP++ optimized toluene/9MeA(adenine) structures. The β-carbon of Phe is orange and H atoms are not shown. 34 4.3 Overlay of the most and least stable crystal structures: 1C0A most stable at MP2 CBS limit, 1E22 most stable at CCSD(T) CBS limit, 1FW6 least stable at MP2 and CCSD(T) CBS limits. The β-carbon of Phe is orange and H atomsarenotshown................................ 40 5.1 Configurations of water interacting with 2 simple alkanes (methane and ethane) 66 5.2 Configurations of water interacting with 2 linear alkynes (acetylene and di- acetylene) ..................................... 67 5.3 Configurations of water interacting with 2 acyclic alkynes (ethene and 1,3- butadiene)..................................... 68 5.4 Configurations of water interacting with 3 unsaturated cyclic hydrocarbons (1,3-cyclobutadiene, 1,3-cyclopentadiene and benzene) . ............ 69 6.1 Alternative configurations of water interacting with benzene ......... 101 x List of Tables 4.1 Intermolecular distances (in A),˚ angles (in degrees) and CBS limit interaction 1 energies (in kcal mol− ) of the 26 crystal toluene/9MeA(adenine) structures . 38 4.2 Intermolecular distances (in A),˚ angles (in degrees) and CBS limit interaction 1 energies (in kcal mol− ) of the 6 optimized toluene/9MeA(adenine) structures 39 1 5.1 CBS limit interaction energies (Eint in kcal mol− ) and higher-order correla- CCSD(T) 1 tion effects (δMP2 in kcal mol− ) for MP2 optimized stationary points of hydrocarbon/waterdimers. 61 5.2 Deviations of MP2/haTZ and DFT/haTZ interaction energies (∆Eint in kcal 1 avg mol− ) from the average of the CCSD(T)/CBS interaction energies (Eint in 1 kcal mol− )..................................... 62 5.3 The intermolecular distance (R in A)˚ for the MP2 optimized structures, and the deviations (∆R and RMSD in A)˚ of the DFT optimized structures from theMP2referencegeometries. 63 a 1
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