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Application of X-Ray Diffraction Methods and Molecular Mechanics Simulations to Structure Determination and Cotton Fiber Analysis

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Application of X-Ray Diffraction Methods and Molecular Mechanics Simulations to Structure Determination and Cotton Fiber Analysis University of New Orleans ScholarWorks@UNO University of New Orleans Theses and Dissertations Dissertations and Theses 12-19-2008 Application of X-ray Diffraction Methods and Molecular Mechanics Simulations to Structure Determination and Cotton Fiber Analysis Zakhia Moore University of New Orleans Follow this and additional works at: https://scholarworks.uno.edu/td Recommended Citation Moore, Zakhia, "Application of X-ray Diffraction Methods and Molecular Mechanics Simulations to Structure Determination and Cotton Fiber Analysis" (2008). University of New Orleans Theses and Dissertations. 888. https://scholarworks.uno.edu/td/888 This Dissertation is protected by copyright and/or related rights. It has been brought to you by ScholarWorks@UNO with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This Dissertation has been accepted for inclusion in University of New Orleans Theses and Dissertations by an authorized administrator of ScholarWorks@UNO. For more information, please contact [email protected]. Application of X-ray Diffraction Methods and Molecular Mechanics Simulations to Structure Determination and Cotton Fiber Analysis A Dissertation Submitted to the Graduate Faculty of the University of New Orleans in partial fulfillment of the Requirements for the Degree of Doctor of Philosophy in the Department of Chemistry by Zakhia Moore B.S., Xavier University, 2000 M.S., University of New Orleans, 2005 December, 2008 ACKNOWLEDGEMENTS Giving all glory to God for His many blessings, whom without I could not have completed this long journey. The work took longer than what I expected, but I’m glad it’s finally behind me and now I can continue to another chapter in my life. This dissertation is dedicated to my beloved grandmothers, Dorothy Moore and Pernella Collins. Both of these beautiful women never stopped believing in me and always gave me words of encouragement. My parents, Vanest and Denise Moore have always been there for me every step of the way; I thank them for their constant unwavering love and support. To my best girls, Chanel Fortier, RaShante Gilford, Ebony Terrance, and Stephanie Anderson, there aren’t words I could say that would come close to how much your friendship and love has helped me overcome many obstacles and brought me to where I am today. Thanks for everything all of you have given to me. To my co- workers, the U.S. Customs and Border Patrol Agriculture Specialists and Officers, too many to name, thanks for your support. My co-worker and editor, Dr. Yi He, thanks for your patience and for reading all this stuff! To Devron Thibodeaux, for showing me his passion for his work and family, thanks for being a great colleague and friend. Finally Dr. Edwin D. Stevens, you have put up with me for eight years, my ups and downs, the constant changes in my life. I thank you the most for not only being a great professor, but also a great advisor and friend. ii TABLE OF CONTENTS List of Tables ........................................................................................................ v List of Figures ..................................................................................................... vii Abstract ............................................................................................................... ix Chapter I Introduction to X-ray Diffraction 1.1 The Significance of X-ray Technology .........................................................1 1.2 Properties and Production of X-rays ............................................................5 1.3 Geometry of X-ray Diffraction and Bragg’s Law ..........................................8 1.4 The X-Ray Diffractometer ..........................................................................11 1.5 Area Detectors ..........................................................................................12 Chapter II Identification and Structure Determination of Ethylene Glycol Bis(Tropane -3- Carboxylate) by Single-Crystal X-Ray Diffraction 2.1 The Use of Single Crystal X-ray Diffraction in Structure Determinations ... 19 2.2 Description of Unit Cell and Lattices ..........................................................22 2.3 Miller Indices .............................................................................................27 2.4 The Reciprocal Lattice and Ewald Sphere ................................................ 29 2.5 Crystal Selection .......................................................................................32 2.6 Diffraction of x-ray by Crystals ...................................................................34 2.7 The Crystallography Project ......................................................................40 a. Unit Cell Determination ........................................................................40 b. Data Collection .....................................................................................45 c. Integration of Intensity ..........................................................................47 d. Creation of a Trial Structure .................................................................53 f. Crystal Structure ....................................................................................57 Chapter III Correlations Between the Structural Properties and the Strength Properties of Cotton Fibers Grown In Various Countries 3.1 Introduction ...............................................................................................80 3.2 Cotton Fiber Structure ...............................................................................82 3.3 X-ray Analysis ...........................................................................................84 a. Apparatus ................................................................................................84 b. Sampling, Preparation, and Analysis .......................................................85 c. Calibration ...............................................................................................89 3.3 Results ......................................................................................................91 3.4 Discussion ...............................................................................................101 3.5 Data Treatment .......................................................................................104 3.6 Crystallinity Estimate ............................................................................... 107 3.7 Crystallite Size .........................................................................................110 3.8 Crystallite Orientation ..............................................................................111 3.9 Conclusion ..............................................................................................114 iii Chapter IV Determining the Crystal Structure of Cellulose Iii by Molecular Modeling 4. Introduction ............................................................................................... 116 4.2 Methods ..................................................................................................118 4.3 Results and Discussion ...........................................................................123 Bibliography ......................................................................................................140 Vita ....................................................................................................................146 iv LIST OF TABLES TABLE PAGE 2.1 Laue Lattices…………………………………………………………………. 24 2.2 Summary of Unit Cell Parameters and Reflections……………………... 43 2.3 Summary of Preliminary Crystallographic Data …………………………50 2.4 Crystal Structure Refinement Data ………………………………………… 59 2.5 Published Results of Ethylene Glycol BIS(tropane-3-carboxylate) ……. 75 2.6 Atomic Coordinates ………………………………………………………….. 76 2.7 Bond Lengths and Angles ……………………………..…………………… 77 2.8 Anisotropic displacement parameters …………………………………….. 78 2.9 Hydrogen Atom Coordinates ……………………………………………….. 78 3.1 Calibration Results ………………………………………………………...… 90 3.2 Diffraction Measurements - 002 Peak …………………………………….. 91 3.3 Diffraction Measurements - 002 Peak …………………………………….. 92 3.4 Crystallinity Results ……….…………………………………………………. 93 3.5 Crystallinity Results ………………………………………………………….. 94 3.6 Crystallite Size Estimates …………………………………………………… 95 3.7 Crystallite Size Estimates …………………………………………………… 96 3.8 Crystallite Orientation ……………………………………………………….. 97 3.9 Crystallite Orientation ……………………………………………………….. 98 3.10 Measured Strengths of Cotton Fibers ……………………………………...99 3.11 Measured Fiber Strengths ………………………………………………… 101 v 4.1 Energies (kcal) and hydroxyl torsion angles (º) for two central glucose residues from the best tetraose-based models …………………………..124 4.2 Calculated energies and unit cell dimensions of hexamer models …. 126 4.3 Intra - and Intermoleculara hydrogen bonds in best “up” model ……… 128 4.4 Atomic coordinates of modeled glucose monomer of up cellulose IIII ……………………………………………………………135 4.5 Atomic coordinates of modeled glucose monomer of down cellulose IIII ……………………………………………………...… 137 vi LIST OF FIGURES FIGURE PAGE 1.1 Bragg’s Law ……………………………………………………………………….. 11 1.2 HI-STAR Detector ………………………………………………………………….15
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