Paper Citing NAMD - Abstract
Zobnina, V. G.; Chagovets, V. V.; Boryak, O. A.; Kosevich, M. V.
A mass spectrometric study and computer modeling of noncovalent interactions of cytosine with polyethylene glycol oligomers
JOURNAL OF ANALYTICAL CHEMISTRY, 70:1533-1541, DEC 2015
Data on intermolecular noncovalent interactions of nitrogen base components of nucleic acid with organic polyethers are of interest both for fundamental molecular biophysics and for applications in the production of pharmaceutical organic nanoparticles. In the present work, systems composed of pyrimidine nitrogen base cytosine (Cyt) or its methyl derivatives and polyethylene glycol PEG-400 oligomers M (n) have been examined by electrospray ionization (ESI) and fast atom bombardment mass spectrometry. Detection of a set of associates of the M (n) center dot Cyt center dot H+ type (n = 3-17) in ESI mass spectra evidences the formation of protonated complexes of the base with oligomers of different chain lengths in all of the studied systems. Computer modeling by molecular dynamics gave answers to the questions concerning the stability and structure of these complexes under different conditions. It has been shown that M (n) center dot Cyt center dot H+ clusters in the gas phase (vacuum) adopt a compact structure with a quasi-cyclic or quasi-helical self-organization of the polymer chain around the protonated base. It has been found that the compact structure of the M-8 center dot Cyt center dot H+ complex characteristic for its state in the gas phase is preserved in a liquid medium of methanol (used as a solvent in ESI). The results of simulation of the evolution of a methanol droplet in vacuum, which mimics the droplet disintegration under ESI conditions, have shown that the M-8 center dot Cyt center dot H+ complex initially present in the droplet does not disintegrate in the course of droplet evaporation. After the completion of desolvation, the complex returns to the conformation characteristic for the gas phase. Thus, the evidence has been found confirming that the M-8 center dot Cyt center dot H+ clusters recorded in ESI mass spectra adequately reflect the presence of corresponding noncovalent complexes in the analyzed liquid solution.
