A simple model for metal cation-phosphate interactions in nucleic acids in the gas phase: Alkali metal cations and trimethyl phosphate

Abstract

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of complexes of alkali metal cations to trimethyl phosphate, TMP. Endothermic loss of the intact TMP ligand is the only dissociation pathway observed for all complexes. Theoretical calculations at the B3LYP/6-31G* level of theory are used to determine the structures, vibrational frequencies, and rotational constants of neutral TMP and the M ϩ (TMP) complexes. Theoretical BDEs are determined from single point energy calculations at the B3LYP/6-311ϩG(2d,2p) level using the B3LYP/6-31G* optimized geometries. The agreement between theory and experiment is reasonably good for all complexes except Li ϩ (TMP hosphate esters are integral parts of many biologically active molecules ranging from nucleic acids, lipids, and ATP to pesticides and nerve agents [1][2][3]. Serving as link components in nucleic acids, phosphate esters connect thousands of base pairs to form large molecules that contain the genetic information. These phosphate groups are deprotonated under physiological conditions. The resulting negative charges along the phosphate backbone are stabilized and neutralized by the binding of metal cations. Metal cations can and often do exert a significant influence on nucleic acid structure and genetic information transfer [4]. Metal cation binding reduces the repulsion between neighboring nucleotide units, and therefore influences the stabilization and structural dynamics of nucleic acids and lipids in membranes. For example, alkali and alkaline earth metal cations, including the most biologically important of these cations, Na ϩ and Mg 2ϩ , prefer to bind to a phosphate group rather than to the nucleobases or sugar moieties [5]. Mg 2ϩ is found to increase the melting temperature of DNA [6]. Metal cations may also be involved in the functioning of nucleic acids, e.g., metal cations are required for the proper functioning of all ribozymes [7]. Metal cation-nucleic acid interactions are currently of great interest because metal cations and metal cation-ligand complexes bind to DNA and regulate gene expression, act as drugs, or can be used as tools for molecular biology studies [8]. Hendry and Sargeson studied metal cation-promoted phosphate ester hydrolysis and found that the rate of hydrolysis is modulated by the size of the metal cation and the ease of formation of a four-membered chelate ring [9]. Dempcy and Bruice found a pentacoordinate intermediate for the catalysis of alkyl phosphate diesters [10]. Schneider and Kabelac et al. [11] studied the distribution of five metal cations (i.e., Na, and Zn 2ϩ ) and water around a negatively charged phosphate group from various crystal structures, and found that all of the cations prefer asymmetric monodentate coordination over bidentate coordination. Their ab initio calculations suggest that bidentate binding of these metal cations to an isolated phosphate group is preferred, but that the presence of even a single water molecule alters this preference. Ab...

Gas-Phase Lithium Cation Basicity: Revisiting the High Basicity Range by Experiment and Theory

“…The LiCA(TMP) value from TCID measurements at 0 K [81] is much larger than the calculated one: 280.8 versus 239.0 kJ mol −1 . The TCID evaluation of LiCB starts from dissociation energy at 0 K, which is obtained by fitting the experimental cross section for the dissociative collision between Xe and the Li + adduct, the bare Li + being the expected ion product.…”

“…The TCID evaluation of LiCB starts from dissociation energy at 0 K, which is obtained by fitting the experimental cross section for the dissociative collision between Xe and the Li + adduct, the bare Li + being the expected ion product. From the Supplementary Material of Reference [81], the data for the TMP adduct appears to be rather noisy compared with other alkali metal cations. In fact, Rodgers and Armentrout have admitted that the determination of the true thermodynamic threshold may be impaired by difficulties with collecting the light lithium ion [43].…”

Multistage mass spectrometry of phospholipids using collision-induced dissociation (CID) and metastable atom-activated dissociation (MAD)

“…The potassiated adduct clearly favors internal electron capture through reaction (1) despite the fact that it has the lowest electron affinity of the three cations. At present, we can only speculate that the binding energy of the cations is a dominant factor in these reactions [38] and that conformational differences are a possible secondary factor [39]. Potassium has the lowest binding affinity for POPC of the three cations and is therefore most readily lost [38].…”

Rapid quantification of highly polar trimethyl phosphate in wastewater via direct analysis in real-time mass spectrometry

“…TMP is believed persistence in nature [7]. The extensive use of TMP causes its release into the environment, and uptake by organisms.…”