Static and Dynamic Polarizabilities of Conjugated Molecules and Their Cations

The sodium cation affinities of six commonly used MALDI matrices are determined here using guided ion beam tandem mass spectrometry techniques. The collision-induced dissociation behavior of six sodium cationized MALDI matrices, Na + (MALDI), with Xe is studied as a function of kinetic energy. The MALDI matrices examined here include: nicotinic acid, quinoline, 3-aminoquinoline, 4-nitroaniline, picolinic acid, and 3-hydroxypicolinic acid. In all cases, the primary dissociation pathway corresponds to endothermic loss of the intact MALDI matrix. The cross section thresholds are interpreted to yield zero and 298 K Na + −MALDI bond dissociation energies (BDEs), or sodium cation affinities, after accounting for the effects of multiple ionneutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* and MP2(full)/6-311+G(2d,2p)//B3LYP/6-31G* levels of theory are used to characterized the structures and energetics for these systems. The calculated BDEs exhibit very good agreement with the measured values for most systems. The experimental and theoretical Na + −MALDI BDEs determined here are compared with those previously measured by cation transfer equilibrium methods.

Section: Theoretical Calculationsmentioning

confidence: 99%

Sodium Cation Affinities of Commonly Used MALDI Matrices Determined by Guided Ion Beam Tandem Mass Spectrometry

Chinthaka¹,

Rodgers²

2012

“…A theoretical calculation of the polarizability of TMP based on a dipole electric field was carried out at the PBE0/6-311ϩG(2d,2p) level of theory. This level of theory was chosen because it has been shown to provide polarizabilities that are in better agreement with experimentally determined polarizabilities than values computed using the B3LYP functional used here for the structures and energetics of these systems [48].…”

Section: Theoretical Calculationsmentioning

confidence: 99%

“…Good reproduction of the data is obtained over energy ranges exceeding 1.5 eV and cross section magnitudes of at least a factor of 100. Table 1 frequencies is the same [48] for all of the M ϩ (TMP) complexes. Because the density of states of the complex at threshold depends on the measured BDE, the kinetic shift is expected to directly correlate with BDE.…”

Section: Threshold Analysismentioning

confidence: 99%

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

Ruan

Huang

Rodgers

2008

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...

“…Thus, the isotropic molecular polarizabilities of the ground-state conformations of the neutral and protonated AcAAs and 18C6 are calculated using PBE0 hybrid functional and the 6-311+G(2d,2p) basis set using the B3LYP/6-31G* optimized geometries. This level of theory was chosen because polarizabilities determined using the PBE0 functional [43] exhibit much better agreement with experimentally determined polarizabilities than the B3LYP and M06 functionals employed for energetics here [44]. Figure S1 of the Supplemental Information.…”

Section: Theoretical Calculationsmentioning

confidence: 99%

Structural and Energetic Effects in the Molecular Recognition of Acetylated Amino Acids by 18-Crown-6

Chen

Rodgers

2012

Absolute 18-crown-6 (18C6) binding affinities of four protonated acetylated amino acids (AcAAs) are determined using guided ion beam tandem mass spectrometry techniques. The AcAAs examined in this work include: N-terminal acetylated lysine (N α -AcLys), histidine (N α -AcHis), and arginine (N α -AcArg) as well as side chain acetylated lysine (N ε -AcLys). The kinetic-energydependent cross sections for collision-induced dissociation (CID) of the (AcAA)H + (18C6) complexes are analyzed using an empirical threshold law to extract absolute 0 and 298 K (AcAA)H + −18C6 bond dissociation energies (BDEs) after accounting for the effects of multiple collisions, kinetic and internal energy distributions of the reactants, and unimolecular dissociation lifetimes. Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the AcAAs as well as the proton bound complexes of these species, (AcAA)H + (18C6), at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31 G* and M06/6-311+G(2d,2p)//B3LYP/6-31G* levels of theory. For all four (AcAA)H + (18C6) complexes, loss of neutral 18C6 corresponds to the most favorable dissociation pathway. At elevated energies, products arising from sequential dissociation of the primary CID product, H + (AcAA), are also observed. Protonated N α -AcLys exhibits a greater 18C6 binding affinity than other protonated N α -AcAAs, suggesting that the side chains of Lys residues are the preferred binding sites for 18C6 complexation to peptides and proteins. N α -AcLys exhibits a greater 18C6 binding affinity than N ε -AcLys, suggesting that binding of 18C6 to the side chain of Lys residues is more favorable than to the N-terminal amino group of Lys.