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64.See supplementary material http://dx.doi.org/10.1063/1.4826470 for the details of the combined CG-HFB method, its latest stand-alone implementation, and practical aspects of applying the method to study reaction mechanisms. The results of CG-HFB path optimizations for alanine inversion on the HF/6-31G(d,p) potential are provided. In addition, the energy profile for the full 360° rotation of the geminal diol –C(OH)2H group at the B3LYP/6-31G(d,p) potential is provided. HF/6-31G(d,p) energy profiles for methanol acylation in both large and small systems are also provided. [Supplementary Material]
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/content/aip/journal/jcp/139/16/10.1063/1.4826470
2013-10-25
2016-09-26

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, - to -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.

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