Atomistic mechanisms of the double proton transfer in the H-bonded nucleobase pairs: QM/QTAIM computational lessons

Abstract

In this Review, we have summarized and generalized the results of the investigation of the microstructural mechanisms of the tautomerization by the counter movement of the protons along the neighboring intermolecular H-bonds in 22 biologically important pairs of nucleotide bases in the framework of the original method, which allows to trace the evolution of the physicochemical parameters, that characterize these processes along the intrinsic reaction coordinate (IRC). It was demonstrated the performance of the introduction of the conception of the key points (KPs) (from nine to five, depending on the symmetry and nature of system), which exhaustively characterize the flow of the tautomerization processes. It was proved that for all tautomerizing base pairs the extrema of the first derivative of the electron energy of the complex by IRC coincide with the second and penultimate KPs, in which the Laplacian of the electron density equals zero at the corresponding (3,-1) bond critical points of the H-bonds. It was established the linear dependence of the width of the transition state zone of the DPT tautomerization on the degree of its asynchrony. Authors emphasize that the tautomerization reaction through the DPT of the H-bonded pairs of nucleotide bases can be considered successful in those and only in those case if the tautomerized complex is a dynamically stable system, during lifetime of which low-frequency intermolecular vibrations could develop. Perspectives of the application of the obtained approaches to the thorough study of the proton transfer processes in the biologically important objects have been briefly discussed.

Keywords:

• Double proton transfer
• mutagenic tautomerization
• intrinsic reaction coordinate
• sweep of the physicochemical parameters
• key point
• reaction regions
• transition state
• reagent
• product
• stepwise
• concerted
• synchronous
• asynchronous
• hydrogen bond
• nucleobase pair

Acknowledgments

The authors gratefully appreciate technical support and computational facilities of joint computer cluster of SSI “Institute for Single Crystals” of the National Academy of Sciences of Ukraine (NASU) and Institute for Scintillation Materials of the NASU incorporated into Ukrainian National Grid. This work was partially supported by the Grant of the NASU for young scientists, Grant of the President of Ukraine to support the research of young scientists [project number F70] from the State Fund for Fundamental Research of Ukraine of the Ministry of the Education and Science of Ukraine and by the Scholarship of Verkhovna Rada (Parliament) of Ukraine for the talented young scientists in 2017 year given to DrSci Ol’ha Brovarets’. O. O. B. expresses sincere gratitude to organizing committee for financial support of the participation in the “EMBO/FEBS Lecture Course Spetsai Summer School 2017 for Proteins and Organized Complexity” (September 24–October 1, 2017, Spetses, Greece), to Lawyers Association “AVER Lex” (Kyiv, Ukraine) for the sponsorship of the presenting the plenary lecture as invited speaker at the “EMN Meeting on Computation and Theory” (November 6–10, 2017, Dubai, United Arab Emirates) and to Max Plank Institute of Plant Physiology (hosted by Prof. Yariv Brotman) for the kind invitation and financial support of the invited lecture (November 29, 2017, Potsdam, Germany).