Force field models in halogen bonding
Date
2019
Authors
Billman, Mardi Marie, author
Rappé, Anthony, advisor
Prieto, Amy, committee member
Strauss, Stephen, committee member
Ho, Pui Shing, committee member
Journal Title
Journal ISSN
Volume Title
Abstract
Halogen bonding schemes have been proposed to replace those of hydrogen bonding in biomolecules, such as proteins and DNA, because halogens can counter-intuitively attract a Lewis base. Unlike hydrogen bonding, halogen bonding strength is dependent on a number of factors, such as electrostatics, exchange repulsion, dispersion, and charge transfer. Understanding the underlying energetic components of halogen bonding at a fundamental level, defined herein to mean the subatomic level, is necessary to utilize halogen bonding in a biomolecular context. Our aspiration throughout this research has not been to quantify the strength of the underlying interactions. Instead, it has been to identify and explain the interactions as dependent on the uneven distribution of valence electrons inherent to the halogens, and apply our findings to developing force field models. Chapter 2: The Cambridge Structural Database was used to show that crystals of halogen bonding structures exhibit a distance-angle correlation. The correlation is similar to that present in crystals of hydrogen bonding structures, though with a diminished angular dependence beyond the sum of the van der Waals radii. Halogen bonding strength, approximated by bonding frequency, was found to be inversely proportional to non-bonding distance. The shape of the distance-angle correlation would continue to be studied in Chapters 3–4. Chapter 3: An angular dependence was illustrated in Chapter 2 at short non-bonding distances; the interaction energy must have been dependent on anisotropic, short-range components such as electrostatics and exchange repulsion. The electronic structure of halogen-containing compounds was studied independently as a function of distance and then as a function of angle. Electron-withdrawing and -donating moieties were used to observe the dependence of electrostatics, exchange repulsion, and dispersion on the polarizability of the halogen. Both substituent and periodic trends were observed, where halogen bonding strength increased with -hole and aspherical shape of the halogen atom. Chapter 4: Atomic halogens were used to study the anisotropic electrostatic potential and exchange repulsion directly, without influence of the substituent groups present in Chapter 3. Our hypothesis was that theoretical models of the electrostatic potential and exchange repulsion would display an angular dependence because of the inherent s2px2py2pz1 valence electron configuration. The halogen atoms were defined as a linear combination of core and valence s and p wavefunctions, fitted simultaneously to Hartree-Fock calculations of the orbital shapes, electrostatic potential, and exchange repulsion. The shape of the exchange repulsion model as a function of distance and angle, in conjunction with dispersion, could explain the distance-angle correlation of experimental and theoretical halogen bonding. The electrostatic potential, associated with the -hole model of halogen bonding, did not vanish at long distance. Instead, it was found that the presence of a dipole-dipole interaction was necessary to recreate experimental results. Chapter 5: The purpose of this study was to begin development on a multimolecular system to model solvent interactions with halogen bonding structures. We found that halogen bonding trimer systems have a cooperative non-bonding energy due to the electrostatics, dispersion, and partial charge transfer from Lewis base to halogen. The polarization of the model hydrogen-bond enhanced halogen bonds increased the electrostatic attraction within the trimer systems. The charge transfer stabilized the structure and lead to decrease in bond distances relative to the corresponding dimers. Because attractive dispersion interactions are inversely dependent on interaction distance, the overall dispersive attraction increased in the trimer system as well. Chapter 6: A novel model was created to examine the process of charge transfer as a function of distance in halogen bonding dimers. Two molecular models of borane with ammonia and diatomic bromine with ammonia were developed and fitted to computational calculations. The results of the models showed that the cross-term of the charge transfer interaction between reactant and product components contributes to the attraction between Lewis acids and bases.
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Subject
force field
inorganic
computational
theoretical
halogen bonding