Update 1 of: Electrophilicity Index

Electron-induced damage of DNA and its components: Experiments and theoretical models

6.1. Molecular Vibrations PR58 6.2. Molecular Internal Rotations PR58 6.3. Chemical Reactions PR58 7. Dynamical Variants PR62 7.1. Quantum Fluid Density Functional Theory PR62 7.2. Atom-Field Interactions PR62 7.3. Ion-Atom Collisions PR62 7.4. Chemical Kinetics PR62 8. Spin Dependent Generalizations PR63 8.1. {N, Ns, v(r b)} Representation PR63 8.2. {NR, N , v(r b)} Representation PR64 9. Conclusions PR65 10. Abbreviations and Symbols of Some Important Subjects/Quantities PR

Update 2 of: Electrophilicity Index

http://www-heparin.rpi.edu/main/files/papers/400.pdf

Electron detachment dissociation of glycosaminoglycan tetrasaccharides

The accumulation of proline (Pro) and overproduction of reactive oxygen species (ROS) by plants exposed to stress is well-documented. In vitro assays show that enzyme inactivation by hydroxyl radicals ((•)OH) can be avoided in the presence of Pro, suggesting this amino acid might act as a (•)OH scavenger. Although production of hydroxyproline (Hyp) has been hypothesized in connection with such antioxidant activity, no evidence on the detailed mechanism of scavenging has been reported. To elucidate whether and how Hyp might be produced, we used density functional theory calculations coupled to a polarizable continuum model to explore 27 reaction channels including H-abstraction by (•)OH and (•)OH/H2O addition. The structure and energetics of stable species and transition states for each reaction channel were characterized at the PCM-(U)M06/6-31G(d,p) level in aqueous solution. Evidence is found for a main pathway in which Pro scavenges (•)OH by successive H-abstractions (ΔG(‡,298) = 4.1 and 7.5 kcal mol(-1)) to yield 3,4-Δ-Pro. A companion pathway with low barriers yielding Δ(1)-pyrroline-5-carboxylate (P5C) is also supported, linking with 5-Hyp through hydration. However, this connection remains unlikely in stressed plants because P5C would be efficiently recycled to Pro (contributing to its accumulation) by P5C reductase, hypothesis coined here as the "Pro-Pro cycle".

Molecular mechanisms for the reaction between (˙)OH radicals and proline: insights on the role as reactive oxygen species scavenger in plant stress.

Laser-induced acoustic desorption/chemical ionization in Fourier-transform ion cyclotron resonance mass spectrometry

The gas-phase structures of five five-carbon monosaccharides (d-ribose, d-lyxose, 2-deoxy-d-ribose, d-xylose, and d-arabinose) were studied via ion−molecule reactions with dimethoxyphosphenium ion and 1,3-dioxolane-2-phosphenium ion in a Fourier transform ion cyclotron resonance mass spectrometer. These reagent ions have been earlier demonstrated to be sensitive to the three-dimensional structures of diastereomeric vicinal diols. They were found to display unique reactivity toward each monosaccharide. The results indicate that the gaseous monosaccharides are cyclic molecules. On the basis of a comparison of the reactions of monosaccharides introduced into the gas phase via two different methods, laser-induced acoustic desorption (LIAD) and thermal desorption, the monosaccharides are concluded to maintain their crystalline structure, a pyranose form, throughout the evaporation procedure. For all the monosaccharides in this study except for d-lyxose, the lowest-energy structure found computationally using d...

An Experimental and Computational Study of the Gas-Phase Structures of Five-Carbon Monosaccharides

Reactions of differently substituted phenyl radicals with components of nucleic acids have been investigated in the gas phase. A positively charged group located meta with respect to the radical si...

Reactivity of substituted charged phenyl radicals toward components of nucleic acids.

The reactivity of 10 charged phenyl radicals toward several amino acids was examined in the gas phase in a dual-cell Fourier transform ion cyclotron resonance mass spectrometer. All radicals abstract a hydrogen atom from the amino acids, as expected. The most electrophilic radicals (with the greatest calculated vertical electron affinities (EA) at the radical site) also react with these amino acids via NH2 abstraction (a nonradical nucleophilic addition–elimination reaction). Both the radical (hydrogen atom abstraction) and nonradical (NH2 abstraction) reaction efficiencies were found to increase with the electrophilicity (EA) of the radical. However, NH2 abstraction is more strongly influenced by EA. In contrast to an earlier report, the ionization energies of the amino acids do not appear to play a general reactivity-controlling role. Studies using several partially deuterium-labeled amino acids revealed that abstraction of a hydrogen atom from the α-carbon is only preferred for glycine; for the other a...

/pdf/reactivity-and-selectivity-of-charged-phenyl-radicals-toward-1a50uxytbi.pdf

Reactivity and Selectivity of Charged Phenyl Radicals toward Amino Acids in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

The vertical electron affinity is demonstrated to be a key factor in controlling the selectivity of charged phenyl radicals in hydrogen atom abstraction from isopropanol in the gas phase. The measurement of the total reaction efficiencies (hydrogen and/or deuterium atom abstraction) for unlabeled and partially deuteriumlabeled isopropanol, and the branching ratios of hydrogen and deuterium atom abstraction, by using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer, allowed the determination of the selectivity for each site in the unlabeled isopropanol. Examination of hydrogen atom abstraction from isopropanol by eight structurally different radicals revealed that the preferred site is the CH group. The selectivity of the charged phenyl radicals correlates with the radical’s vertical electron affinity and the reaction efficiency. The smaller the vertical electron affinity of a radical, the lower its reactivity, and the greater the preference for the thermodynamically favored CH group over the CH3 group or the OH group. As the vertical electron affinity increases from 4.87 to 6.28 eV, the primary kinetic isotope effects decrease from 2.9 to 1.3 for the CD group, and the mixture of primary and R-secondary kinetic isotopes decreases from 6.0 to 2.4 for the CD3 group.

Leonard P. Guler

Papers

Laser-induced acoustic desorption/chemical ionization in Fourier-transform ion cyclotron resonance mass spectrometry

An Experimental and Computational Study of the Gas-Phase Structures of Five-Carbon Monosaccharides

Reactivity of substituted charged phenyl radicals toward components of nucleic acids.

Reactivity and Selectivity of Charged Phenyl Radicals toward Amino Acids in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

The selectivity of charged phenyl radicals in hydrogen atom abstraction reactions with isopropanol.