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Modeling the Heat of Formation of Organic Compounds Using SPARC Modeling the Heat of Formation of Organic Compounds Using SPARC by Tad S. Whiteside (Under the direction of Lionel Carreira) Abstract Typically, the interaction of chemicals with the environment is governed through physic- ochemical properties. The Environmental Protection Agency has developed several models to predict the fate of chemicals in the environment. SPARC (SPARC Performs Automated Reasoning in Chemistry) has been developed as a method to predict the properties of envi- ronmentally sensitive compounds. SPARC uses computational algorithms based on chemical structure theory to calculate chemical properties, including the heat of formation. Molecular structures are broken into simple functional units (reactophores) with intrinsic properties. Each reactophore is analyzed and the effects of appended molecular structures are quantified through perturbation theory. Standard enthalpies of formation (∆Hf ) were calculated with models developed using the computer program SPARC. The ∆Hf models have been completely developed using all known data for saturated and unsaturated hydrocarbons and halogenated hydrocarbons. Basic models have also been developed for alcohols, aldehydes, and ketones. The structures of these compounds vary from chains and conjugated rings to poly-benzoic aromatic hydro- carbons. The 587 hydrocarbons have a SPARC calculated RMS of 4.50 kJ mol-1. Halogenated hydrocarbons have a calculated RMS deviation of 5.18 kJ mol-1 for 202 compounds. The effect of stereochemistry on the standard enthalpy of formation was also modeled. Chiral centers are found in a variety of molecules and help define the overall structure of a compound. The local atomic environment determines the strain energy in each chiral center. There are four local environments in which chiral centers are found: Linear, Single, Bridge, and SideShare. These are modeled independently and the total contribution of stere- ochemistry to the heat of formation is determined by summing the energy found in these environments. The 169 experimentally determined compounds with chiral centers were used to develop this model. To provide a benchmark of SPARC’s capabilities, the heat of formation of the compounds used to develop the models was also calculated using the semi-empirical PM3 method and the group additivity method developed by Benson, as implemented by NIST in their chemical webbook. SPARC outperforms both of these methods in terms of speed and accuracy. Index words: enthalpy of formation, heat of formation, hydrocarbons, halohydrocarbons, SPARC, stereochemistry Modeling the Heat of Formation of Organic Compounds Using SPARC by Tad S. Whiteside B.S., Erskine College, 2000 B.A., Erskine College, 2000 A Dissertation Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Athens, Georgia 2004 c 2004 Tad S. Whiteside All Rights Reserved Modeling the Heat of Formation of Organic Compounds Using SPARC by Tad S. Whiteside Approved: Major Professor: Lionel Carreira Committee: Michael Duncan Jonathan Amster Electronic Version Approved: Maureen Grasso Dean of the Graduate School The University of Georgia December 2004 Dedication To my family iv Acknowledgments I would like to thank Dr. L. Carreira for his support and encouragement over the past four years. I appreciate the time and effort he has expended on my behalf. I would also like to thank the members of my committee, Dr. J. Amster and Dr. M. Duncan, for providing sound advice. I appreciate Dr. S. Hilal’s insight into the heat of formation models and SPARC in general. I also give special thanks to Raj Ayyampalayam for allowing me to be impatient and short-tempered. This research was sponsored in part by the U.S. Environmental Protection Agency under the cooperative agreement No. CR83138401 with the University of Georgia. v Table of Contents Page Acknowledgments ................................. v ListofFigures ................................... ix ListofTables ................................... xi Chapter 1 Introduction ................................ 1 1.1 Introduction ............................ 1 1.2 SPARC................................ 2 1.3 TheHeatofFormation . 3 1.4 Calculating the Heat of Formation . 3 1.5 Structure of Dissertation . 6 1.6 Data ................................. 7 2 Prediction of the Enthalpy of Formation of Hydrocarbons UsingSPARC ................................ 8 2.1 Introduction ............................ 9 2.2 TheoreticalMethodology . 10 2.3 ∆Hf AdjustmentModels . 19 2.4 ResultsandDiscussion . 28 2.5 Conclusion ............................. 31 2.6 References ............................. 32 3 Prediction of the Enthalpy of Formation of Halogenated HydrocarbonsUsingSPARC. 35 vi vii 3.1 Introduction ............................ 36 3.2 TheoreticalMethodology . 37 3.3 ResultsandDiscussion . 49 3.4 Conclusion ............................. 50 3.5 References ............................. 52 4 Stereochemistry and the Enthalpy of Formation . 54 4.1 Introduction ............................ 55 4.2 TheoreticalMethodology . 56 4.3 Data ................................. 65 4.4 ResultsandDiscussion . 65 4.5 Conclusion ............................. 69 4.6 References ............................. 70 5 OtherModeling .............................. 72 5.1 Introduction ............................ 72 5.2 Alcohols .............................. 72 5.3 Aldehydes.............................. 73 5.4 Ketones ............................... 73 5.5 Assortedprojects. 74 6 Tools..................................... 75 6.1 Introduction ............................ 75 6.2 TheSPARCDatabase . 75 6.3 TrainingFileTools. 77 6.4 SPARC Data Viewer / Comparer . 78 6.5 QualityControlofSPARC. 78 6.6 CommonUserArea ........................ 79 6.7 Summary............................... 80 viii 7 Conclusions................................. 81 7.1 ReviewofFindings ........................ 81 7.2 FutureStudies........................... 83 Bibliography .................................... 85 Appendix A SPARCTools................................ 88 A.1 Databasemanagementtools. 88 A.2 QualityControlPrograms . 122 A.3 CommonAreaScript ....................... 125 B CompoundsUsedtoDeveloptheModel . 129 B.1 Hydrocarbons ........................... 129 B.2 HalogenatedHydrocarbons. 154 C The heat of formation PROLOG code . 163 C.1 HF.pro................................ 163 C.2 HF ring2.pro ............................ 232 C.3 other arom.pro .......................... 263 C.4 HF chiral.pro ........................... 268 C.5 HF data.pro............................. 302 List of Figures 2.1 The ethylenic reaction center can experience interactions at four locations . 13 2.2 trans-andcis-cyclooctene . 14 2.3 Interactions in 1,2-dimethyl cyclohexane . ......... 14 2.4 Possible interactions between substituents and an n-membered ring in an exo- ethylenicreactioncenter.. 14 2.5 Interaction between two n-membered rings joined by an exodoublebond. 15 2.6 Pyrene, which has examples of bridge and buried atoms. ........ 16 2.7 The steric interaction sites on an aromatic reaction center. .......... 19 2.8 The five possible connectivity locations in an aromatic reaction center. 23 2.9 Ring strain versus ring size for cyclo-X-anes . ..... 24 2.10 The various ring structures SPARC identifies . ....... 26 2.11 The difference in the confirmations of cis- and trans- dimethylcyclohexane. 27 2.12 SPARC versus Observed for 587 heats of formation . ..... 31 3.1 The five unique substituent locations in an aromatic reaction center. 40 3.2 Halogenated methyl, showing the Br-F, Cl-F, and Br-Cl Halo interactions. 42 3.3 The Xi interaction of halogens on the bonds of neighboring atoms. 44 3.4 A perfluorinated alkane showing the Per parameter(s) used for interactions betweenreactioncenters.. 45 3.5 The interactions affecting one atom in an ethylenic reaction center. 46 3.6 Outer and Inner substituents in an aromatic reaction center ......... 48 3.7 SPARV vs Observed for 202 heats of formation of halohydrocarbons ..... 51 4.1 The three ring environments with stereochemistry . ........ 57 4.2 Oxolane-3,4-dioldinitrate . ..... 59 ix x 4.3 Two bridge sections showing the three local environments of OtherCAs. Also shown is a ChiralBridgeAtom (CBA) and a ChiralSideShareAtom (CSA). 61 4.4 The various interactions which occur between the three unique bridge envi- ronments (x,x,x; y,x,y; x,x,y). 62 4.5 No stereochemistry specified in either a. Tetrahydroanthracene or b. Tri- cyclo[4.2.0.02,5]octane ([3]-ladderane) . ......... 64 4.6 Linear Chiral Centers calculated versus observed values for 11 stereoisomers. 67 4.7 Calculated versus observed for 37 stereoisomers of chiral centers in single rings. 67 4.8 Bridge Rings Calculated versus observed for seven stereoisomers containing a bridge........................................ 68 4.9 Calculated versus observed for the seventeen sideshare stereoisomers. 69 List of Tables 2.1 Calculating the heat of formation of pyrene using the SPARC parameters. 17 -1 2.2 Comparison of experimental and calculated values of ∆Hf (kJ mol ) for PBAHsusingSPARC,PM3,andGroupAdditivity. 18 2.3 Individual components of the SPARC calculated series methane, ethane, propane, 2-methyl propane, and neopentane. ..... 30 2.4 Comparison of the error in observed values with the SPARC, PM3, and Group Additivity calculated RMS values. Also included is the R2 value. ....... 32 3.1 The parameters, interactions, and energies associated with the Halo interac- tion, grouped
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