Non-covalent interactions and their role in biological and catalytic chemistry

HKR;Co-salen;Non-covalent interactions;Hydrolytic kinetic resolution

Kennedy, Matthew R. ; Sherrill, Charles D. Chemistry and Biochemistry Bongiorno, Angelo Brown, Kenneth R. Ludovice, Peter J. Jones, Chris W. ; Sherrill, Charles D.

University:Georgia Institute of Technology

Department:Chemistry and Biochemistry

关键词: HKR;    Co-salen;    Non-covalent interactions;    Hydrolytic kinetic resolution;   

Others  :  https://smartech.gatech.edu/bitstream/1853/53044/1/KENNEDY-DISSERTATION-2014.pdf

美国|英语

来源: SMARTech Repository

【 摘 要 】

The focus of this thesis is the question of how non-covalentinteractions affect chemical systems' electronic and structural properties.Non-covalent interactions can exhibit a range of binding strengths,from strong electrostatically-bound salt bridges or multiple hydrogenbonds to weak dispersion-bound complexes such as rare gas dimersor the benzene dimer.To determine the interaction energies (IE)of non-covalent interactions one generally takes the supermolecularapproach as described by the equation \begin{equation} E_{IE} = E_{AB} - E_{A} - E_{B}, \end{equation} where subscripts A and B refer totwo monomers and AB indicates the dimer.This interaction energy isthe difference in energy between two monomers interacting at a singleconfiguration compared to the completely non-interacting monomers atinfinite separation. In this framework, positive interaction energies arerepulsive or unfavorable while negative interaction energies signifya favorable interaction. We use prototype systems to understand systemswith complex interactions such as π-π stacking in curved aromatic systems,three-body dispersion contributions to lattice energies and transition metal catalystsaffect on transition state barrier heights.The current "gold standard" of computational chemistry is coupled-cluster theory with iterative single and double excitation and perturbative tripleexcitations [CCSD(T)].\cite{Lee:1995:47}Using CCSD(T) with large basis sets usually yields results that are in good agreement with experimental data.\cite{Shibasaki:2006:4397}CCSD(T) beingvery computational expensive forces us to use methods of a lower overallquality, but also much more tractable for some interesting problems.We must use the available CCSD(T) or experimental data availableto benchmark lower quality methods in order to ensure that the lowquality methods are providing and accurate description of the problemof interest. To investigate the effect of curvature on the nature of π-π interactions, we studied concave-convex dimers of corannulene and coronene in nested configurations. By imposing artificialcurvature/planarity we were able to learn about the fundamentalphysics of π-π stacking in curved systems.To investigate these effects, it was necessary to benchmark low level methodsfor the interaction of large aromatic hydrocarbons. With the coronene and corannulene dimers being 60 and 72 atoms, respectively, they are outside the limits of tractability for a large number ofcomputations at the level of CCSD(T).Therefore we must determine the most efficient and accurate method of describing the physics of these systems with a few benchmark computations.Using a few benchmark computations published by Janowski et al. (Ref. \cite{Janowski:2011:155})we were able to benchmark four functionals (B3LYP, B97, M05-2X and M06-2X) as well as four dispersion corrections (-D2, -D3, -D3(BJ), and -XDM) and wefound that B3LYP-D3(BJ) performed best. Using B3LYP-D3(BJ) we found that both corannulene and coronene exhibit stronger interaction energies as more curvature isintroduced, except at unnaturally close intermolecular distances or high degreesof curvature. Using symmetry adapted perturbation theory (SAPT)\cite{Jeziorski:1994:1887, Szalewicz:2012:254}, we were able to determine that this stronger interaction comes from stabilizing dispersion, induction and charge penetration interactions with smaller destabilizing interactions from exchange interactions. For accurate computations on lattice energies one needs to go beyond two-body effects to three-body effects if the cluster expansion is being used. Three-body dispersion is normally a smaller fraction of the latticeenergy of a crystal when compared to three-body induction. We investigatedthe three-body contribution using the counterpoise correctedformula of Hankins \textit{et al.}.\cite{Hankins:1970:4544}\begin{equation}\Delta ^{3} E^{ABC}_{ABC} = E^{ABC}_{ABC} - \sum_{i} E^{ABC}_{i} -\sum_{ij} \Delta ^{2} E^{ABC}_{ij},\end{equation}where the superscript ABC represents the trimer basis and the E(subscript i) denotes the energy of each monomer, where {\em i} countsover the individual molecule of the trimer.The last term is defined as \begin{equation}\Delta ^{2} E^{ABC}_{ij} = E^{ABC}_{ij} - E^{ABC}_{i} - E^{ABC}_{j},\end{equation}where the energies of all dimers and monomers are determined in thetrimer basis. Using these formulae we investigated the three-bodycontribution to the lattice energy ofcrystalline benzene with CCSD(T). By using CCSD(T) computations we resolved a debate in the literature about themagnitude of the non-additive three-body dispersion contribution to the lattice energy of the benzene crystal.Based on CCSD(T)computations, we report a three-body dispersion contribution of 0.89 kcal mol⁻¹, or 7.2\% of the total lattice energy. This estimate is smaller than many previous computational estimates\cite{Tkatchenko:2012:236402,Grimme:2010:154104,Wen:2011:3733,vonlilienfeld:2010:234109} of the three-body dispersion contribution, which fell between 0.92 and 1.67 kcal mol⁻¹.The benchmark data we provide confirm that three-body dispersion effects cannot beneglected in accurate computations of the lattice energy of benzene.Although this study focused on benzene, three-body dispersion effectsmay also contribute substantially to the lattice energy of otheraromatic hydrocarbon materials. Finally, density functional theory (DFT) was applied to the rate-limiting step of the hydrolytic kinetic resolution (HKR) of terminalepoxides to resolve questions surrounding the mechanism. We find that the catalytic mechanism is cooperative becausethe barrier height reduction for the bimetallic reaction is greater than the sum of the barrier height reductions forthe two monometallic reactions.We were also able to compute barrier heights for multiple counter-ions which react at different rates. Based onexperimental reaction profiles, we saw a good correlation between our barrier heights for chloride, acetate, and tosylate withthe peak reaction rates reported. We also saw that hydroxide, which is inactive experimentally is inactve because when hydroxide is the only counter-ionpresent in the system it has a barrier height that is 11-14 kJ mol⁻¹ higher than the other three counter-ions which are extremelyactive.