Premium
Protonated primary amines induced thymine quintets studied by electrospray ionization mass spectrometry and density functional theory calculations
Author(s) -
Qin Zhen,
Qiu Bo,
Sun Jiamu,
Zhao Wenbo,
Luo Hai
Publication year - 2014
Publication title -
journal of mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.475
H-Index - 121
eISSN - 1096-9888
pISSN - 1076-5174
DOI - 10.1002/jms.3334
Subject(s) - chemistry , thymine , protonation , aryl , alkyl , nucleobase , electrospray ionization , molecule , hydrogen bond , density functional theory , computational chemistry , photochemistry , crystallography , medicinal chemistry , ion , organic chemistry , dna , biochemistry
As the novel magic number clusters of nucleobases, the thymine quintets induced by ammonium ion (NH 4 + ), and particularly by its derivatives such as protonated alkyl amines and protonated aryl amines, have been studied by electrospray ionization mass spectrometry (ESI‐MS) and density functional theory (DFT) calculations. The DFT‐optimized geometry of NH 4 + induced thymine quintet ([T 5 + NH 4 ] + ) reveals some new features including three additional hydrogen bonds between NH 4 + and its surrounding thymine molecules when compared with that of the alkali metal ions induced thymine quintets. In addition, the fourth hydrogen atom of NH 4 + is sticking out the assembly, and, thus, it might be replaced by an organic group R to form the protonated primary amine induced thymine quintet ([T 5 + R − NH 3 ] + ), a hypothesis that has been confirmed by both DFT calculations and ESI‐MS experiments. Furthermore, the relative abilities of the different protonated primary amines for inducing the thymine quintets are investigated by ESI‐MS competition experiments, and the results have shown a clear trend of stronger ability as the alkyl chain gets longer or as the aryl ring gets larger for the alkyl amines or the aryl amines. Two basic influence factors are consequently identified: one is the ability of the alkyl amine to accept proton, another is the π–π stacking interaction between the aryl ring and the π ‐surface of the thymine molecule(s), whose explanations are strongly supported by multiple types of thermochemical data, various control experiments and DFT calculations. Copyright © 2014 John Wiley & Sons, Ltd.