Protonated primary amines induced thymine quintets studied by electrospray ionization mass spectrometry and density functional theory calculations

Abstract

As the novel magic number clusters of nucleobases, the thymine quintets induced by ammonium ion (NH4(+)), 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 NH4(+) induced thymine quintet ([T5 + NH4](+)) reveals some new features including three additional hydrogen bonds between NH4(+) and its surrounding thymine molecules when compared with that of the alkali metal ions induced thymine quintets. In addition, the fourth hydrogen atom of NH4(+) 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 ([T5 + R - NH3](+)), 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.

Highly sensitive and specific detection of histamine via the formation of a self-assembled magic number cluster with thymine by mass spectrometry

“…S4 †), which is in accordance with the previously reported quintet cluster of thymine induced by the protonated amines. 26 But remarkably, no high-order magic number clusters of thymine (n $ 15) were observed. This is probably due to the fact that the high-order magic number clusters need more than one positively charged center to stabilize the structure, in accordance with our previous report that the doubly charged 15-mer ([T 15 + 2M] 2+ ) is stabilized by two metal ions.…”

“…In fact, many studies have been reported on the self-clustering of nucleobases. [18][19][20][21][22][23][24][25][26] In these previous reports, thymine can aggregate to form the magic number clusters in the presence of alkali metal ions or an ammonium cation through non-covalent interactions. [22][23][24] In other words, these magic number clusters enable the small target ions such as Na + , K + and NH 4 + to be detected by MS through a "mass-shi" to the higher mass range.…”

“…[22][23][24] In other words, these magic number clusters enable the small target ions such as Na + , K + and NH 4 + to be detected by MS through a "mass-shi" to the higher mass range. Moreover, the formation and stability of the magic number clusters of thymine are highly correlated to the size, proton affinity and other properties of the central cation, 21,24,26 which inspire us to utilize the magic number clusters to analyze the target ions with high specicity.…”

Isomer differentiation through supramolecular self-assembly in microdroplets of milliseconds life-time

“…Previous studies by our group, 11,12,19,20 have demonstrated that alkali metal ions or primary amine induced thymine (or analogs) were thermodynamically stable and can be detected by ESI-MS or DESI-MS. Tertiary amines were not able to induce such clusters, probably because the cavity in the thymine (or analogs) circle was too small to entrap the charged moiety in tertiary amines.…”

“…2c and d To explain the different behaviours in the cluster formation, theoretical calculations were made to study the relative stabilities of the clusters formed by thymine with 1,3-PDA and 1,2-PDA, respectively. The possible structures were proposed according to a previously established model, 11,12,19,20 in which 5 or 6 thymine molecules were arranged into circles via double complementary hydrogen bonds, and the circles entrapped the nitrogen charge centres. Schalley et al 21 have used molecular dynamics to calculate model structures of organometallic clusters formed in ESI-MS, and we applied similar theoretical methods in our study.…”