Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization.
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2013-11-04
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Abstract
Here we apply the harmonic Fourier beads HFB path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical QM and hybrid QM molecular mechanical QM MM potential energy surfaces To improve efficiency of the path optimization on such computationally demanding potentials we combined HFB with conjugate gradient CG optimization The combined CG HFB method was used to study two biologically relevant reactions namely L to D alanine amino acid inversion and alcohol acylation by amides The optimized paths revealed several unexpected reaction steps in the gas phase For example on the B3LYP 6 31G d p potential we found that alanine inversion proceeded via previously unknown intermediates 2 iminopropane 1 1 diol and 3 amino 3 methyloxiran 2 ol The CG HFB method accurately located transition states aiding in the interpretation of complex reaction mechanisms Thus on the B3LYP 6 31G d p potential the gas phase activation barriers for the inversion and acylation reactions were 50 5 and 39 9 kcal mol respectively These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins We conclude that the combined CG HFB method further advances QM and QM MM studies of reaction mechanisms