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
[51]   Reaction force constant and projected force constants of vibrational modes along the path of an intramolecular proton transfer reaction [J].
Jaque, Pablo ;
Toro-Labbe, Alejandro ;
Politzer, Peter ;
Geerlings, Paul .
CHEMICAL PHYSICS LETTERS, 2008, 456 (4-6) :135-140
[52]   ELECTRON-AFFINITIES OF THE 1ST-ROW ATOMS REVISITED - SYSTEMATIC BASIS-SETS AND WAVE-FUNCTIONS [J].
KENDALL, RA ;
DUNNING, TH ;
HARRISON, RJ .
JOURNAL OF CHEMICAL PHYSICS, 1992, 96 (09) :6796-6806
[53]   CHARACTERIZATION OF C-H-O HYDROGEN-BONDS ON THE BASIS OF THE CHARGE-DENSITY [J].
KOCH, U ;
POPELIER, PLA .
JOURNAL OF PHYSICAL CHEMISTRY, 1995, 99 (24) :9747-9754
[54]   Prototropic molecular-zwitterionic tautomerism of xanthine and hypoxanthine [J].
Kondratyuk, IV ;
Samijlenko, SP ;
Kolomiets, IM ;
Hovorun, DM .
JOURNAL OF MOLECULAR STRUCTURE, 2000, 523 :109-118
[55]   SELF-CONSISTENT MOLECULAR-ORBITAL METHODS .20. BASIS SET FOR CORRELATED WAVE-FUNCTIONS [J].
KRISHNAN, R ;
BINKLEY, JS ;
SEEGER, R ;
POPLE, JA .
JOURNAL OF CHEMICAL PHYSICS, 1980, 72 (01) :650-654
[56]  
Kwiatkowski J.S., 1990, J. Mol. Struct, V208, P35
[57]   Is there a hydrogen bond radius? Evidence from microwave spectroscopy, neutron scattering and X-ray diffraction results [J].
Lakshmi, B ;
Samuelson, AG ;
Jose, KVJ ;
Gadre, SR ;
Arunan, E .
NEW JOURNAL OF CHEMISTRY, 2005, 29 (02) :371-377
[58]   DEVELOPMENT OF THE COLLE-SALVETTI CORRELATION-ENERGY FORMULA INTO A FUNCTIONAL OF THE ELECTRON-DENSITY [J].
LEE, CT ;
YANG, WT ;
PARR, RG .
PHYSICAL REVIEW B, 1988, 37 (02) :785-789
[59]   Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs [J].
Lee, JC ;
Gutell, RR .
JOURNAL OF MOLECULAR BIOLOGY, 2004, 344 (05) :1225-1249
[60]  
Lehninger AL., 1970, Biochemistry: The molecular basis of cell structure and function