DPT tautomerization of the long Aa™A* Watson-Crick base pair formed by the amino and imino tautomers of adenine: combined QM and QTAIM investigation

被引:55
作者
Brovarets', Ol'ha O. [1 ,2 ,3 ]
Zhurakivsky, Roman O. [1 ,2 ]
Hovorun, Dmytro M. [1 ,2 ,3 ]
机构
[1] Natl Acad Sci Ukraine, Dept Mol & Quantum Biophys, Inst Mol Biol & Genet, UA-03680 Kiev, Ukraine
[2] Res & Educ Ctr, State Key Lab Mol & Cell Biol, UA-03680 Kiev, Ukraine
[3] Taras Shevchenko Natl Univ Kyiv, Dept Mol Biol Biotechnol & Biophys, Inst High Technol, UA-03127 Kiev, Ukraine
关键词
Amino and imino tautomers of adenine; Sweeps of the energetic; electron-topological; geometric and polar parameters along the IRC; The double proton transfer; Cooperativity of the H-bonds; CH center dot center dot center dot HC dihydrogen bond; B3LYP and MP2 levels of QM theory; QTAIM analysis; COMPREHENSIVE CONFORMATIONAL-ANALYSIS; MOLECULAR-ORBITAL METHODS; SET SUPERPOSITION ERROR; O HYDROGEN-BONDS; AB-INITIO; COMPLIANCE CONSTANTS; IONIZATION ENERGIES; MUTAGENIC TAUTOMERS; RIBOSOMAL-SUBUNITS; VIBRATIONAL-MODES;
D O I
10.1007/s00894-013-1880-2
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Combining quantum-mechanical (QM) calculations with quantum theory of atoms in molecules (QTAIM) and using the methodology of sweeps of the energetic, electron-topological, geometric and polar parameters, which describe the course of the tautomerization along the intrinsic reaction coordinate (IRC), we showed for the first time that the biologically important Aa (TM) A* base pair (C-s symmetry) formed by the amino and imino tautomers of adenine (A) tautomerizes via asynchronous concerted double proton transfer (DPT) through a transition state (TS), which is the A(+)a (TM) A(-) zwitterion with the separated charge, with C-s symmetry. The nine key points, which can be considered as electron-topological "fingerprints" of the asynchronous concerted Aa (TM) A*a dagger"A*a (TM) A tautomerization process via the DPT, were detected and completely investigated along the IRC of the Aa (TM) A*a dagger"A*a (TM) A tautomerization. Based on the sweeps of the H-bond energies, it was found that intermolecular antiparallel N6Dea <-N6 (7.01 kcal mol(-1)) and N1Ha <-N1 (6.88 kcal mol(-1)) H-bonds are significantly cooperative and mutually reinforce each other. It was shown for the first time that the Aa (TM) A*a dagger"A*a (TM) A tautomerization is assisted by the third C2Ha <-HC2 dihydrogen bond (DHB), which, in contrast to the two others N6Ha <-N6 and N1Ha <-N1 H-bonds, exists within the IRC range from -2.92 to 2.92 . The DHB cooperatively strengthens, reaching its maximum energy 0.42 kcal mol(-1) at IRC = -0.52 and minimum energy 0.25 kcal mol(-1) at IRC = -2.92 , and is accompanied by strengthening of the two other aforementioned classical H-bonds. We established that the C2Ha <-HC2 DHB completely satisfies the electron-topological criteria for H-bonding, in particular Bader's and all eight "two-molecule" Koch and Popelier's criteria. The positive value of the Grunenberg's compliance constant (5.203 /mdyn) at the TSAa (TM) A*a dagger"A*a (TM) A proves that the C2Ha <-HC2 DHB is a stabilizing interaction. NBO analysis predicts transfer of charge from sigma(C2-H) bonding orbital to sigma*(H-C2) anti-bonding orbital; at this point, the stabilization energy E-(2) is equal to 0.19 kcal mol(-1) at the TSAa (TM) A*a dagger"A*a (TM) A.
引用
收藏
页码:4223 / 4237
页数:15
相关论文
共 99 条
[61]   Properties of the C-H•••H dihydrogen bond:: An ab initio and topological analysis [J].
Lipkowski, P ;
Grabowski, SJ ;
Robinson, TL ;
Leszczynski, J .
JOURNAL OF PHYSICAL CHEMISTRY A, 2004, 108 (49) :10865-10872
[62]   Hydrogen bonding and density functional calculations: The B3LYP approach as the shortest way to MP2 results [J].
Lozynski, M ;
Rusinska-Roszak, D ;
Mack, HG .
JOURNAL OF PHYSICAL CHEMISTRY A, 1998, 102 (17) :2899-2903
[63]   Relationships between interaction energy, intermolecular distance and electron density properties in hydrogen bonded complexes under external electric fields [J].
Mata, I. ;
Alkorta, I. ;
Espinosa, E. ;
Molins, E. .
CHEMICAL PHYSICS LETTERS, 2011, 507 (1-3) :185-189
[64]   How Dependent are Molecular and Atomic Properties on the Electronic Structure Method? Comparison of Hartree-Fock, DFT, and MP2 on a Biologically Relevant Set of Molecules [J].
Matta, Cherif F. .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2010, 31 (06) :1297-1311
[65]   Structure and dynamics of 6-azacytidine by MNDO/H quantum-chemical method [J].
Mishchuk, YR ;
Potyagaylo, AL ;
Hovorun, DM .
JOURNAL OF MOLECULAR STRUCTURE, 2000, 552 :283-289
[66]   Identification of pseudodiatomic behavior in polyatomic bond dissociation: Reaction force analysis [J].
Murray, Jane S. ;
Toro-Labbe, Alejandro ;
Gutierrez-Oliva, Soledad ;
Politzer, Peter .
JOURNAL OF CHEMICAL PHYSICS, 2010, 132 (15)
[67]   Analysis of diatomic bond dissociation and formation in terms of the reaction force and the position-dependent reaction force constant [J].
Murray, Jane S. ;
Toro-Labbe, Alejandro ;
Clark, Tim ;
Politzer, Peter .
JOURNAL OF MOLECULAR MODELING, 2009, 15 (06) :701-706
[68]   How Flexible are DNA Constituents? The Quantum-Mechanical Study [J].
Nikolaienko, T. Yu. ;
Bulavin, L. A. ;
Hovorun, D. M. .
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2011, 29 (03) :563-575
[69]   The Escherichia coli 3-methyladenine DNA glycosylase AlkA has a remarkably versatile active site [J].
O'Brien, PJ ;
Ellenberger, T .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2004, 279 (26) :26876-26884
[70]  
Parr RG., 1989, DENSITY FUNCTIONAL T, DOI DOI 10.1007/978-94-009-9027-2_2