Atom Adducts Research Articles

Investigation of strength and nature of the weak intermolecular bond in NH2 radical-noble gas atom adducts and evaluation of their basic spectroscopic features

The NH2-Ng intermolecular interactions are characterized exploiting a combined theoretical-phenomenological approach that suggests the use of effective interaction potential energy curves for the evaluation of fundamental spectroscopic properties of the formed weakly bound adducts. Lifetime studies reveal that, with the exception of NH2-He, all other compounds are considered stable in the 200–500 K temperature range. CCSD(T)/aug-cc-pVTZ calculations and NBO analysis suggest that induction-polarization interaction contribution plays a limited role and that charge transfer is small and appreciable only in complexes formed by the heavier Ng. SAPT0 and NCI analyses confirm that NH2-Ng systems are held together by van der Waals forces.

Charge‐Tagged DNA Radicals in the Gas Phase Characterized by UV/Vis Photodissociation Action Spectroscopy

AbstractAdenosine radicals tagged with a fixed‐charge group were generated in the gas phase and structurally characterized by tandem mass spectrometry, deuterium labeling, and UV/Vis action spectroscopy. Experimental results in combination with Born–Oppenheimer molecular dynamics, ab initio, and excited‐state calculations led to unambiguous assignment of adenosine radicals as N‐7 hydrogen atom adducts. The charge‐tagged radicals were found to be electronically equivalent to natural DNA nucleoside radicals.

Charge-Tagged DNA Radicals in the Gas Phase Characterized by UV/Vis Photodissociation Action Spectroscopy.

Adenosine radicals tagged with a fixed-charge group were generated in the gas phase and structurally characterized by tandem mass spectrometry, deuterium labeling, and UV/Vis action spectroscopy. Experimental results in combination with Born-Oppenheimer molecular dynamics, ab initio, and excited-state calculations led to unambiguous assignment of adenosine radicals as N-7 hydrogen atom adducts. The charge-tagged radicals were found to be electronically equivalent to natural DNA nucleoside radicals.

Guanine-adenine interactions in DNA tetranucleotide cation radicals revealed by UV/vis photodissociation action spectroscopy and theory.

Hydrogen-rich cation radicals (GATT + 2H)+˙ and (AGTT + 2H)+˙ represent oligonucleotide models of charged hydrogen atom adducts to DNA. These tetranucleotide cation radicals were generated in the gas phase by one-electron reduction of the respective (GATT + 2H)2+ and (AGTT + 2H)2+ dications in which the charging protons were placed on the guanine and adenine nucleobases. We used wavelength-dependent UV/Vis photodissociation in the valence-electron excitation region of 210-700 nm to produce action spectra of (GATT + 2H)+˙ and (AGTT + 2H)+˙ that showed radical-associated absorption bands in the near-UV (330 nm) and visible (400-440 nm) regions. Born-Oppenheimer molecular dynamics and density-functional theory calculations were used to obtain and rank by energy multiple (GATT + 2H) dication and cation-radical structures. Time-dependent density functional theory (TD-DFT) calculations of excited-state energies and electronic transitions in (GATT + 2H)+˙ were augmented by vibronic spectra calculations at 310 K for selected low-energy cation radicals to provide a match with the action spectrum. The stable product of one-electron reduction was identified as having a 7,8-dihydroguanine cation radical moiety, formed by intramolecular hydrogen atom migration from adenine N-1-H. The hydrogen migration was calculated to have a transition state with a low activation energy, Ea = 96.5 kJ mol-1, and positive activation entropy, ΔS‡ = 75 J mol-1 K-1. This allowed for a fast isomerization of the primary reduction products on the ion-trap time scale of 150 ms that was substantially accelerated by highly exothermic electron transfer.

The AHA Moment: Assessment of the Redox Stability of Ionic Liquids Based on Aromatic Heterocyclic Anions (AHAs) for Nuclear Separations and Electric Energy Storage.

Because of their extended conjugated bond network, aromatic compounds generally have higher redox stability than less saturated compounds. We conjectured that ionic liquids (ILs) consisting of aromatic heterocyclic anions (AHAs) may exhibit improved radiation and electrochemical stability. Such properties are important in applications of these ILs as diluents in radionuclide separations and electrolytes in the electric energy storage devices. In this study, we systematically examine the redox chemistry of the AHAs. Three classes of these anions have been studied: (i) simple 5-atom ring AHAs, such as the pyrazolide and triazolides, (ii) AHAs containing an adjacent benzene ring, and (iii) AHAs containing electron-withdrawing groups that were introduced to reduce their basicity and interaction with metal ions. It is shown that fragmentation in the reduced and oxidized states of these AHAs does not generally occur, and the two main products, respectively, are the H atom adduct and the imidyl radical. The latter species occurs either as an N σ-radical or as an N π-radical, depending on the length of the N-N bond, and the state that is stabilized in the solid matrix is frequently different from that having the lowest energy in the gas phase. In some instances, the formation of the sandwich π-stack dimer radical anions has been observed. For trifluoromethylated anions, H adduct formation did not occur; instead, there was facile loss of fluoride from their fluorinated groups. The latter can be problematic in nuclear separations, but beneficial in batteries. Overall, our study suggests that AHA-based ILs are viable candidates for use as radiation-exposed diluents and electrolytes.

The Fate of H Atom Adducts to 3′-Uridine Monophosphate

The stabilities of the adducts deriving from H free radical addition to the O2, O4, and C5 positions of 3'-uridine monophosphate (3'UMP) are studied by the hybrid density functional B3LYP approach. Upon H atom addition at the O2 position, a concerted low-barrier proton-transfer process will initially occur, followed by the potential ruptures of the N-glycosidic or beta-phosphate bonds. The rupture barriers are strongly influenced by the rotational configuration of the phosphate group at the 3' terminal, and are influenced by bulk solvation effects. The O4-H adduct has the highest thermal stability, as the localization of the unpaired electron does not enable cleavage of either the C1'-N1 or the C3'-O(P) bonds. For the most stable adduct, with H atom added to the C5 position, the rate-controlled step is the H2'a abstraction by the C6 radical site, after which the subsequent strand rupture reactions proceed with low barriers. The main unpaired electron densities are presented for the transient species. Combined with previous results, it is concluded that the H atom adducts are more facile to drive the strand scission rather than N-glycosidic bond ruptures within the nucleic acid bases.

Mass-spectrometric and computational study of tryptophan radicals (Trp + H)˙ produced by collisional electron transfer to protonated tryptophan in the gas phase

Hydrogen atom adducts to tryptophan were generated for the first time in the gas phase by collisional electron transfer to protonated tryptophan at 7170 eV kinetic energy. The radicals showed fast dissociations by C(α)-C(β) bond cleavage and cross-ring cleavages occurring on the 7.3 μs time scale. The mechanism of the C(α)-C(β) bond cleavage was explained by ab initio computational analysis of the radical potential energy surface. This showed spontaneous isomerization of the primary tryptophan radical by ammonium hydrogen atom migration to the carboxyl group. The stable intermediate formed by the isomerization can undergo radical-induced scission of the C(α)-C(β) bond in competition with H-atom migrations to the C-2 and C-4 positions of the indole ring. RRKM calculations of unimolecular rate constants on the B3-ROMP2/6-311++G(2d,p) potential energy surface indicated that the C(α)-C(β) bond cleavage was the fastest unimolecular reaction of the radical intermediates within the range of internal energies acquired upon electron transfer. We also report an updated G2(MP2) proton affinity of tryptophan (PA = 946 kJ mol(-1)) and hydrogen atom affinities of the tryptophan indole ring of relevance to electron-based peptide dissociations.

AN EFFICIENT CRITERION FOR THE FORMATION ENERGIES AND REACTIVITIES OF DEFECTS IN CNTs AND BNNTs

Directional curvature KD, was proposed as a simple and efficient criterion for the formation energies and reactivities of defects in carbon and boron nitride nanotubes. Using the periodic density functional theory, the formation energies of Stone–Wales (SW) and divacancy (DV) defects in their armchair (5,5) and zigzag (10,0) nanotubes, as well as the binding energies of the O atom adducts on these defect sites are calculated. These calculated results are found to fit well with the theoretical predictions by the directional curvature KD.

Modeling Deoxyribonucleic Acid and Ribonucleic Acid Damage in the Gas Phase

This short review outlines the tandem mass spectrometric methods for the generation and analysis of transient nucleobase radicals relevant to deoxyribonucleic acid and ribonucleic acid damage. Radical hydrogen atom adducts to uracil, adenine, cytosine and N-methylcytosine were generated by femtosecond electron transfer to the corresponding gas-phase cations in fast beams at 8 keV kinetic energy. Radical unimolecular dissociations were monitored by product analysis following collisional ionization to cations or anions using neutralization-reionization mass spectrometry. The radical energetics and dissociation kinetics were further analyzed by mapping the potential energy surfaces by high-level ab initio calculations in combination with Rice-Remsberger-Kassel-Marcus calculations of unimolecular rate constants. This first- principles-based approach allows one to model radical dissociations occurring from doublet ground electronic states of radical intermediates, assign reaction mechanisms and derive quantitative branching ratios for dissociation channels that are in agreement with experiments. Theoretical analysis also provides distinction between radical dissociations occurring on the ground and excited electronic state potential energy surfaces. Specific characterization of excited state dissociations of nucleobase and other polyatomic radicals remains a challenging topic for both experimentalists and computational chemists.

Proton and hydrogen atom adducts to cytosine. An experimental and computational study

Cytosine cations were generated by chemical ionization and fast-atom bombardment of cytosine, and their dissociations in the gas phase were studied by tandem mass spectrometry and quantum chemistry calculations at levels of theory up to CCSD(T)/aug-cc-pVTZ. Metastable cytosine cations undergo loss of NH 3, H 2O, and [CHNO] molecules as major dissociations. Mechanisms for these dissociations were established by a combination of MS 3, deuterium labeling, and calculations. Several tautomers of protonated cytosine were identified to exist as local energy minima. The tautomers are predicted to undergo facile prototropic isomerizations at internal energies below the lowest ion-dissociation thresholds. The lowest-energy elimination of ammonia proceeds from open-ring structures and is accompanied by exchange of the N-3 and N-7 positions in cytosine, so that either nitrogen atom can be lost in the ammonia molecule. Cytosine radicals corresponding to hydrogen atom adducts are stable when formed by femtosecond electron transfer to the cations. A fraction of the radicals dissociate by loss of hydrogen atom to form cytosine tautomers. Ring-cleavage dissociations leading to the loss of CO and HNCO are less abundant, and are predicted to proceed from excited electronic states accessed by vertical electron transfer.

Dissociation mechanisms of neutral methyl stearate and its hydrogen atom adduct formed from the respective positive ions by electron transfer

The mechanism of dissociation of neutral methyl stearate and its hydrogen atom adduct was investigated by charge inversion mass spectrometry using an alkali metal target. Migrations of functional groups in fatty acid ester ions are often observed during the dissociation of the cations in collisionally activated dissociation (CAD). In the charge inversion spectrum, the main dissociation channels of methyl stearate molecule are the loss of a CH3 radical or a H atom. To identify the source of the CH3 radical and the H atom, the charge inversion spectra of partially deuterated methyl stearate (C17H35COOCD3) were measured. The loss of CH3 occurred through elimination from the methoxy methyl group and that of H occurred through elimination from the hydrocarbon chain of the fatty acid group. In the protonated ester, a simultaneous loss of CH3 (from the methoxy methyl group) and a H atom or a H2 molecule was observed. The charge inversion process gave the dissociation fragments with almost no migration of atoms. Only a few peaks that were structure sensitive were observed in the higher mass region in the charge inversion spectra; these peaks were associated with dissociations of energy-selected neutral species, unlike the case of CAD spectra in which they result from dissociation of ions. Charge inversion mass spectrometry with alkali metal targets provided direct information on the dissociation mechanism of methyl stearate and its hydrogen atom adduct without any migration of functional groups.

Rate Constant and Activation Energy Measurement for the Reaction of Atomic Hydrogen with Thiocyanate and Azide in Aqueous Solution

Arrhenius parameters for the reaction of hydrogen atoms with azide and thiocyanate in aqueous solution have been determined using electron pulse radiolysis and electron paramagnetic resonance free induction decay attenuation measurements. Absolute values for SCN-, N3(-), and HN3 were well-described over the temperature range of 9-81 degrees C by the equations log k5 = (12.03 +/- 0.12) - [(21.05 +/- 0.66 kJ mol(-1))/2.303RT], log k10 = (12.75 +/- 0.21) - [(18.43 +/- 1.22 kJ mol(-1))/2.303RT], and log k15 = (11.59 +/- 0.12) - [(21.44 +/- 0.69 kJ mol(-1))/2.303RT], corresponding to room temperature (22 degrees C) rate constants of (2.07 +/- 0.03) x 10(8), (3.15 +/- 0.08) x 10(9), and (6.31 +/- 0.05) x 10(7) M(-1) s(-1) and activation energies for these chemicals of 21.05 +/- 0.66, 18.4 +/- 1.2, and 21.44 +/- 0.69 kJ mol(-1), respectively. The similarity of these three measured activation energies, taken together with the available information on reaction products, suggests a similar reaction mechanism, which is proposed to be an initial hydrogen atom adduct formation in these molecules, followed by single bond breakage.

Detection of Hydrogen Atom Adduct of Spin-Trap DEPMPO. The Relevance for Studies of Biological Systems

We proposed EPR spectroscopy using spin-trap DEPMPO as a novel method for the detection of a hydrogen atom (*H) produced by chemical and biological systems. In complex EPR spectra of DEPMPO adducts in biological systems, spectral lines of unknown origin have been observed. We have assumed (Bacić, G.; Mojović, M. Ann. N. Y. Acad. Sci. 2005, 1048, 230-243) that those lines represent the spectrum of a hydrogen atom (*H) adduct i.e., DEPMPO/H. An electrochemical system known to produce only *H radicals was used here in order to obtain a separate spectrum of the DEPMPO/H adduct. An acquired spectrum as well as a computer spectral simulation of the DEPMPO/H adduct showed considerable resemblance with additional lines in the EPR spectra of DEPMPO adducts in biological systems-plant plasma membranes and cell walls. This shows that such a radical is produced by plants as well as that DEPMPO is suitable for detection in both electrochemical and biological systems.

Adenine Radicals in the Gas Phase: An Experimental and Computational Study of Hydrogen Atom Adducts to Adenine

The elusive hydrogen atom adduct to the N-1 position in adenine, which is thought to be the initial intermediate of chemical damage, was specifically generated in the gas phase and characterized by neutralization-reionization mass spectrometry. The N-1 adduct, 1,2-dihydroaden-2-yl radical (1), was generated by femtosecond electron transfer to N-1-protonated adenine that was selectively produced by electrospray ionization of adenine in aqueous-methanol solution. Radical 1 is an intrinsically stable species in the gas phase that undergoes specific loss of the N-1-hydrogen atom to form adenine, but does not isomerize to the more stable C-2 adduct, 1,2-dihydroaden-1-yl radical (5). Radicals 1 that are formed in the fifth and higher electronically excited states of DeltaE > or = 2.5 eV can also undergo ring-cleavage dissociations resulting in expulsion of HCN. The relative stabilities, dissociation, and transition state energies for several hydrogen atom adducts to adenine have been established computationally at highly correlated levels of theory. Transition state theory calculations of 298 K rate constants in the gas phase, including quantum tunnel corrections, indicate the branching ratios for H-atom additions to C-8, C-2, N-3, N-1, and N-7 positions in adenine as 0.68, 0.20, 0.08, 0.03, and 0.01, respectively. The relative free energies of adenine radicals in aqueous solution point to the C-8 adduct as the most stable tautomer, which is predicted to be the predominating (>99.9%) product at thermal equilibrium in solution at 298 K.

Toward a general mechanism of electron capture dissociation

The effects of positive charge on the properties of ammonium and amide radicals were investigated by ab initio and density functional theory calculations with the goal of elucidating the energetics of electron capture dissociation (ECD) of multiply charged peptide ions. The electronic properties of the amide group in N-methylacetamide (NMA) are greatly affected by the presence of a remote charge in the form of a point charge, methylammonium, or guanidinium cations. The common effect of the remote charge is an increase of the electron affinity of the amide group, resulting in exothermic electron capture. The N-Calpha bond dissociation and transition state energies in charge-stabilized NMA anions are 20-50 kJ mol(-1) greater than in the hydrogen atom adduct. The zwitterions formed by electron capture have proton affinities that were calculated as 1030-1350 kJ mol(-1), and are sufficiently basic for the amide carbonyl to exothermically abstract a proton from the ammonium, guanidinium and imidazolium groups in protonated lysine, arginine, and histidine residues, respectively. A new mechanism is proposed for ECD of multiply charged peptide and protein cations in which the electron enters a charge-stabilized electronic state delocalized over the amide group, which is a superbase that abstracts a proton from a sterically proximate amino acid residue to form a labile aminoketyl radical that dissociates by N-Calpha bond cleavage. This mechanism explains the low selectivity of N-Calpha bond dissociations induced by electron capture, and is applicable to dissociations of peptide ions in which the charge carriers are metal ions or quaternary ammonium groups. The new amide superbase and the previously proposed mechanisms of ECD can be uniformly viewed as being triggered by intramolecular proton transfer in charge-reduced amide cation-radicals. In contrast, remote charge affects N-H bond dissociation in weakly bound ground electronic states of hypervalent ammonium radicals, as represented by methylammonium, CH3NH3*, but has a negligible effect on the N-H bond dissociation in the strongly bound excited electronic states. This refutes previous speculations that loss of "hot hydrogen" can occur from an excited state of an ammonium radical.

An Anionic Zerovalent Nickel Carbonyl Complex Supported by a Triphosphine Borate Ligand: An Ni−C⋮O−Li Isocarbonyl

An anionic zerovalent nickel carbonyl complex, [Ni(PhBP3)(CO)][Li(TMED)] (1), supported by a triphosphine borate ligand was prepared and structurally characterized. The solid state structure shows the coordination of Li+ to the O atom of the CO ligand. The isocarbonyl structure indicates strong electron donor ability of the [PhBP3] ligand and charge redistribution to the carbonyl oxygen. Results of a DFT calculation support this view. Complex 1 represents the first example of a Lewis acid O atom adduct of a Ni(0) carbonyl complex.

Electron-Rich Radicals by Neutralization—Reionization Mass Spectrometry. Generation, Dissociations and Energetics of the Hydrogen Atom Adduct to Acetamide

Protonated acetamide exists as two planar conformers, the more stable anti-form (anti-1(+)) and the syn-form (syn-1(+)), DeltaG(degree) (298) (anti-->syn) = 10.8 kJ mol(-1). Collisional neutralization of 1(+) produces 1-hydroxy-1-amino-1-ethyl radicals (anti-1 and syn-1) which in part survive for 3.7 micros. The major dissociation of 1 is loss of the hydroxyl hydrogen atom (approximately 95%) which is accompanied by loss of one of the methyl hydrogen atoms (approximately 3%) and loss of the methyl group (approximately 2%). The most favorable dissociation of the OH bond is calculated to be only 34 kJ mol(1) endothermic but requires 88 kJ mol(-1) in the transition state. Other dissociations of 1, e.g., loss of one of the amide hydrogens, methyl hydrogens, and loss of ammonia are calculated to proceed through higher- energy transition states and are not kinetically competitive if proceeding from the ground doublet electronic state of 1. The unimolecular dissociation of 1 following collisional electron transfer is promoted by large Franck-Condon effects that result in 8090 kJ mol(-1) vibrational excitation in the radicals. Radicals 1 are calculated to exoergically abstract hydrogen atoms from acetamide in water, but not in the gas phase. The different reactivity is due to solvent effects that favor the products, (.)CH(2)CONH(2) and CH(3)CH(OH)NH(2), over the reactants.

Avoided Level Crossing Muon Spectroscopy of Free Radicals Formed by Muonium Addition to the Constituents of DNA

Avoided level crossing muon spectra (ALC-μSR) of the free radicals formed by muonium addition to nucleic acid bases adenine, cytosine, guanine, thymine, and uracil are reported and assigned by using ab initio DFT calculations. The following radicals and their hyperfine constants, Aμ, were identified: adenine, C8 (the radical formed by adding Mu to the C8 carbon of adenine) = 424.1 MHz; cytosine, C5 = 406.1 MHz and C6 = 593.0 MHz; guanine, C5 = 657.1 MHz and C8 = 407.5 MHz; thymine, C5 = 494.3 MHz and O2 = 409.7 MHz; and uracil, C5 = 381.7 MHz, C6 = 553.6 MHz, O2 = 418.1 MHz, and O4 = 149.7 MHz. No ALC-μSR resonances were observed from polycrystalline samples of the sugar ribose or potassium phosphate at 300 K. Preliminary ALC-μSR spectra of a double stranded (ds) DNA sample are reported and found to show additional resonances to those of the nucleic acid bases, indicating the behavior of implanted muons in dsDNA to be more complex than a simple sum of the behaviors found with the bases. The reported data are also pertinent to H atom adducts of these materials, where the hyperfine parameters are scaled by the ratio of the gyromagentic ratio of the muon to that of the proton.

Triplet excited states and radical intermediates formed in electron pulse radiolysis of amino-substituted fluorenones

Electron pulse radiolysis of four differently substituted amino derivatives of fluorenone, namely, 1-amino-, 2-amino- 3-amino-, and 4-aminofluorenone, has been carried out to study the effect of structure on the spectroscopic and kinetic characteristics of the triplet excited states as well as the transient free radical intermediates formed under reducing and oxidizing conditions. The triplet states of these compounds have been generated in benzene by pulse radiolysis and in other solvents by flash photolysis technique and their spectral and kinetic properties have been investigated. Hydrated electron (e aq −) has been found to react with these fluorenone derivatives to form the anion radical species with a diffusion-controlled rate constant. The spectral and kinetic properties of the transient ketyl and anion radicals have been studied by generating them in aqueous solutions of suitable pH. The pK a values of ketyl⇌anion radical equilibria are in the range of 6.8–7.7 for these derivatives. The oxidized species have been generated by reaction with the azide radical. Hydrogen atom adducts as well as the cation radicals of these derivatives have also been generated by pulse radiolysis and characterized.

Reactions of Electrons on the Surface of γ-Al2O3. A Pulse Radiolytic Study with 0.4 MeV Electrons

Radiolysis of γ-alumina produces electrons, e-, and positive holes, h+. These species rapidly migrate to the surface to produce products of surface adsorbed compounds. The electrons are also trapped by surface OH groups giving rise to short-lived (<10 μs) trapped electrons, . Heating the γ-Al2O3 produces Lewis acid sites and decreases the OH content of the surface. Such material produces much lower yields of trapped electrons, as e- then reacts predominantly with the Lewis acid sites. Hydrogen gas is produced on radiolysis of γ-Al2O3 via H atom formation from e-. The H atoms may recombine, producing H2, or react with surface adsorbed materials (e.g., pyrene) to produce H atom adducts. The basic radiation chemistry is similar to that observed in zeolites (but not SiO2), where ionization predominates. These studies illustrate for the first time the production of electrons in a γ-Al2O3 surface and the consequent two-dimensional kinetics of these species on the surface.