Intramolecular Hydrogen-atom Migration Research Articles

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.

Photoinduced reversible isomerization of 9H-fluorene into 1H-fluorene by means of hydrogen-atom migration and the lowest electronically excited triplet state studied by matrix-isolation FTIR spectroscopy

Photoinduced reversible intramolecular hydrogen-atom migration between 9H-fluorene and 1H-fluorene isolated in an Ar matrix is found by FTIR spectroscopy with an aid of DFT calculation. The forward isomerization from 9H-fluorene to 1H-fluorene occurs upon UV irradiation (λ ≥ 295 nm), while the backward isomerization occurs upon λ ≥ 320 nm light irradiation. The less stable isomer, 1H-fluorene, is identified by comparison of the measured IR spectrum with the corresponding simulated spectral pattern obtained at the B3LYP/6-31++G(d,p) level. In addition, an IR spectrum of 9H-fluorene in the T1 state is measured during UV irradiation (λ ≥ 275 nm).

Red-light induced photoreaction of ozone-dimethylamine complex; matrix-isolation infrared spectra of dimethylamine-N-oxide and N,N-dimethylhydroxylamine

Photoreaction of molecular complex composed of ozone and dimethylamine is investigated by matrix-isolation IR and UV–visible spectroscopies. The UV–visible spectrum of the molecular complex isolated in an Ar matrix shows two broad bands in the region between 400 and 700 nm. Upon red-light irradiation (λ ≥ 680 nm), dimethylamine-N-oxide is produced by intermolecular oxygen-atom transfer from O3 to the lone pair on the nitrogen atom of dimethylamine. Dimethylamine-N-oxide isomerizes to N,N-dimethylhydroxylamine by intramolecular hydrogen-atom migration upon the second light irradiation (λ ≥ 385 nm). The both photoproducts are identified by the DFT calculation at the B3LYP/6-31++G(d,p) level.

H-atom loss and migration in hydrogen-rich peptide cation radicals: The role of chemical environment

Hydrogen-atom loss and intramolecular hydrogen-atom migration in peptide radical and cation radical were investigated by quantum chemical calculations for models that include zero to three hydrogen bonds with the ammonium groups. Five different DFT functionals have been checked to study the geometry relaxation and fragmentation processes after electron attachment to peptide cations. The structural changes associated with the geometry relaxation are shown to be dependent on the level of calculation. Furthermore, comparison with CCSD(T) calculations indicates that an adequate description of the electronic state of the reduced protonated peptide is not a sufficient prerequisite to provide accurate energy barrier. Calculating fragmentation reactions of hydrogen-rich peptide cation radicals is pointed out to be a challenging task as none of the DFT functionals are fully effective to describe the whole process. M06-2X is an adequate choice if it provides the correct ground state, otherwise LC-BLYP should be chosen.The electron attachment site and the electron affinity value are highly sensitive to the number of hydrogen bonds with the ammonium group. An ammonium cation with zero, one, and, to a smaller extent, two hydrogen bonds easily captures an incoming electron and subsequently undergoes an H-atom loss process rather than a proton coupled electron transfer. This suggests an explanation for the low amount of c and z fragments observed upon ECD for small protonated peptides, where the ammonium groups cannot be highly intramolecularly “solvated”.

Cleavage of phosphorus-carbon (P-C) bonds of α-amino phosphonates with intramolecular hydrogen migration in the gas phase using electrospray ionization tandem mass spectrometry.

α-Amino phosphonates with intrinsic biological activities have been used in a wide variety of applications. Because of the widespread existence of natural organophosphorus compounds containing P-C bonds such as the α-amino phosphonates, it is important to investigate the gas-phase chemistry of P-C bonds in order to determine their basic properties, which might provide some insights into their biosynthesis and catalytic cleavage. Twenty α-amino phosphonates were successfully synthesized and their fragmentation behavior was systematically investigated using in-solution deuterium labeling in combination with high-resolution Fourier transform ion cyclotron resonance (FTICR) electrospray ionization tandem mass spectrometry. The fragmentation pathways of twenty α-amino phosphonates with different chemical structures were systematically studied. In general, P-C bonds could be easily cleaved via a novel intramolecular hydrogen atom migration from the amino group to the phosphoryl group through a five-membered-ring intermediate in the gas phase. A possible mechanism of the rearrangement of α-amino phosphonates is proposed. An interesting intramolecular hydrogen atom migration between the amino and phosphoryl groups was observed with cleavage of the P-C bond in the molecule through a five-membered-ring intermediate. This characteristic fragmentation pathway not only provides some insights into the basic chemistry of compounds with P-C bonds, but could also have some applications in the structural determination of the α-amino phosphonate analogues.

Intramolecular hydrogen atom migration along the backbone of cationic and neutral radical tripeptides and subsequent radical-induced dissociations

Dissociation of peptide radical ions involves competition between charge-induced and radical-induced reactions that can be preceded by isomerization. The isomeric radical cations of the peptide methyl ester [G˙GR-OMe](+) and [GG˙R-OMe](+) provide very similar collision-induced dissociation (CID) spectra, suggesting that isomerization occurs prior to fragmentation. They undergo characteristic radical-induced bond cleavage of the peptide N-terminal amide bond resulting in the y2(+) ion, and of the arginine side-chain's Cα-Cβ bond giving protonated allylguanidine {[CH2[double bond, length as m-dash]CHCH2NHC(NH2)2](+), m/z 100}. The absence of a y2(+) fragment ion in the CID of the radical cationic tripeptide [ACH3G˙R](+) and of an m/z 100 ion in the spectrum of [G˙ACH3R](+) (where ACH3 is an α-aminoisobutyric acid residue, which cannot form an α-carbon-centered radical through hydrogen atom transfer) establishes the importance of hydrogen atom migration along the peptide backbone prior to specific radical-induced fragmentations. Herein we use density functional theory (DFT) at the B3LYP/6-31++G(d,p) level to evaluate the barriers for interconversion between the α-carbon-centered radicals and for dissociation. The radical cations [G˙GR](+) and [GG˙R](+) have their radicals located on the α-carbon atoms of the peptide backbone and their charge densities largely sequestered on the guanidine groups of the side-chain of arginine residues. This is in contrast to the isomeric radical cations of [GGG]˙(+), in which the charge resides necessarily on the peptide backbone. The lower charge densities on the backbones of [G˙GR](+) and [GG˙R](+) result in greater structural flexibility, decreasing the barrier for interconversion between these α-carbon-centered radicals to 36.2 kcal mol(-1) (cf. 44.7 kcal mol(-1) for [GGG]˙(+)). The total absence of charge, assessed by examining intramolecular hydrogen atom transfers among the three α-carbon centers of the isomeric neutral α-carbon-centered triglycine radicals [GGG-H]˙, leads to an additional but slight reduction in enthalpy, to approximately 34 kcal mol(-1).

Ab Initio Study of Chemical Activation and Hydrogenation of White Phosphorus in Reaction with Rhodium Trihydride Complex

The four-stage mechanism of reaction of the rhodium trihydride complex [(triphos)RhH3] (triphos=1,1,1-tris(diphenylphosphanylmethyl)ethane) with the white phosphorus molecule resulting in the phosphane and the cyclo-P3 complex [(triphos)M(η3-P3] is analyzed on the basis of ab initio calculations of reactants, products, and intermediate complexes of reaction. It is shown that generation of the transient complex [(triphos)RhH(η1:η1-P4)] followed by intramolecular hydrogen atom migration from the metal to one of the phosphorus atoms is the energetically favourable process. Calculations also show that P4 molecule is activated by coordination to the above complex: the metal-bonded P-P edge is broken, and the tetrahedron P4 is opened to form the butterfly geometry. This activation is realized mainly due to the one-orbital back donation of 4d-electron density from the atom of Rh to the unoccupied antibonding triple degenerate t1*-MO of P4.

UV-induced intramolecular hydrogen-atom migration of 4-chlororesorcinol and 4,6-dichlororesorcinol in low-temperature argon matrices

UV-induced photoreactions of 4-chlororesorcinol (4-chloro-1,3-benzenediol; denoted as Cl-RN) and 4,6-dichlororesorcinol (4,6-dichloro-1,3-benzenediol; denoted as Cl-RN-Cl) in low-temperature argon matrices have been investigated by infrared (IR) spectroscopy and density-functional-theory (DFT) calculation. In the photolysis of Cl-RN, elimination of HCl occurred to produce a ketocarbene, which immediately changed to a five-membered ring ketene (3-hydroxy-2,4-cyclopentadiene-1-ylidenemethanone; denoted as HO-CPYM) by Wolff rearrangement. In addition, dissociation of CO from the CCO part of HO-CPYM occurred to produce 2,4-cyclopentadienone (CPDN) by intramolecular hydrogen-atom migration from the OH group to the carbene atom. Similarly, in the photolysis of Cl-RN-Cl, HO-CPYM-Cl was produced by elimination of HCl and Wolff rearrangement, which changed to Cl-CPDN by intramolecular hydrogen-atom migration. The conformations around the CO bonds of the reactants, Cl-RN and Cl-RN-Cl, and the intermediates, HO-CPYM and HO-CPYM-Cl, are determined by comparison of the observed IR spectra with the corresponding calculated spectral patterns obtained by the DFT method.

UV-induced single and double hydrogen-atom migrations in 3,6-diimino-1,4-cyclohexadiene-1,4-diamine in a low-temperature argon matrix

Isomerization induced by ultraviolet radiation due to intramolecular hydrogen-atom migration in 3,6-diimino-1,4-cyclohexadiene-1,4-diamine (DCD) was studied by matrix-isolation Fourier transform infrared (IR) spectroscopy and density functional theory (DFT) calculation. Two isomers produced by single and double inversion of the hydrogen atom(s) around the C N bond(s) were identified using the wavelength dependence of the IR band-intensity changes. In addition, the IR bands of an intermediate produced by single hydrogen-atom transfer from the amino to the imino group ( C – NH 2 ⋯ NH C ) in the hydrogen bond were measured and identified by a comparison with the calculated spectral patterns. These observations confirm stepwise photoisomerization of DCD.

EPR studies of amine radical cations, part 1: thermal and photoinduced rearrangements of n-alkylamine radical cations to their distonic forms in low-temperature freon matrices.

The thermal and photochemical transformations of primary amine radical cations (n-propyl 1.+, n-butyl 5.+) generated radiolytically in freon matrices have been investigated by using low-temperature EPR spectroscopy. Assignment of the spectra was facilitated by parallel studies on the corresponding N,N-dideuterioamines. The identifications were supported by quantum chemical calculations on the geometry, electronic structure, hyperfine splitting constants and energy levels of the observed transient radical species. The rapid generation of the primary species by a short exposure (1-2 min) to electron-beam irradiation at 77 K allowed the thermal rearrangement of 1.+ to be monitored kinetically as a first-order reaction at 125-140 K by the growth in the well-resolved EPR signal of the distonic radical cation .C(2CH2CH2NH3+. By comparison, the formation of the corresponding .CH2CH2CH2CH2NH3+ species from 5.+ is considerably more facile and already occurs within the short irradiation time. These results directly verify the intramolecular hydrogen-atom migration from carbon to nitrogen in these ionised amines, a reaction previously proposed to account for the fragmentation patterns observed in the mass spectrometry of these amines. The greater ease of the thermal rearrangement of 5.+ is in accordance with calculations on the barrier heights for these intramolecular 1,5- and 1,4-hydrogen shifts, the lower barrier for the former being associated with minimisation of the ring strain in a six-membered transition state. For 1.+, the 1,4-hydrogen shift is also brought about directly at 77 K by exposure to approximately 350 nm light, although there is also evidence for the 1,3-hydrogen shift requiring a higher energy. A more surprising result is the photochemical formation of the H2C=N. radical as a minor product under hard-matrix conditions in which diffusion is minimal. It is suggested that this occurs as a consequence of the beta-fragmentation of 1.+ to the ethyl radical and the CH2=NH2+ ion, followed by consecutive cage reactions of deprotonation and hydrogen transfer from the iminonium group. Additionally, secondary ion-molecule reactions were studied in CFCl2CF2Cl under matrix conditions that allow diffusion. The propane-1-iminyl radical CH3CH2CH=N. was detected at high concentrations of the n-propylamine substrate. Its formation is attributed to a modified reaction sequence in which 1.+ first undergoes a proton transfer within a cluster of amine molecules to yield the aminyl radical CH3CH2CH2N.H. A subsequent disproportionation of these radicals can then yield the propane-1-imine precursor CH3CH2CH=NH, which is known to easily undergo hydrogen abstraction from the nitrogen atom. The corresponding butane-1-iminyl radical was also observed.

Hydrogen-atom migration and Wolff rearrangement in photolysis of chlorohydroquinone to produce p-benzoquinone and 3-hydroxy-2,4-cyclopentadiene-1-ylidenemethanone

Photolysis of chlorohydroquinone in a low-temperature argon matrix was investigated by Fourier transform infrared spectroscopy with an aid of hybrid density-functional-theory (DFT) calculation. The new photoreaction pathways via a ketocarbene intermediate produced by dissociation of hydrogen chloride upon UV irradiation were found, where a five-membered ring ketene and p-benzoquinone were produced from the ketocarbene by Wolff rearrangement and intramolecular hydrogen-atom migration, respectively. The large H/D isotope effect in the branching ratio for the final products, ketene and p-benzoquinone, was found in the analysis of the growth behavior of the infrared bands, implying that the hydrogen-atom migration occurs by tunneling effect.

Mechanism and energetics of intramolecular hydrogen transfer in amide and peptide radicals and cation-radicals.

Intramolecular hydrogen transfer in five model amide and peptide radicals and cation-radicals was investigated by combined B3LYP-MP2 calculations. Hypervalent ammonium radicals produced by electron capture in protonated peptides undergo competitive elimination of ammonia, H-atom loss, and H-atom migration to neighboring amide carbonyls. The calculated transition state energies for H-atom migration are slightly but uniformly lower than those for H-atom loss. Transition state theory calculations with inclusion of quantum tunneling effects predict k(H migration)/k(H loss) branching ratios that increase with the ring size of the cyclic transition state for the migration. Intramolecular hydrogen-atom migration in amide and peptide radicals can be described by the proton-coupled electron transfer mechanism. The migrating hydrogen atom shows a negligible spin density and substantial positive charge that are typical of a proton migration. Electron transfer occurs through a pi-orbital system and proceeds in the same (clockwise) or opposite (counterclockwise) direction as the proton motion, depending on the electronic properties of the chain connecting the ammonium group and the amide bond.

Photoinduced dehydrogenation reaction of CH 3NH 2 by NO 2 in a cryogenic Ar matrix. Identification of the CH 2 = NH · H 2O complex

The visible light-induced reaction of NO 2 with methylamine (CH 3NH 2) in a cryogenic argon matrix has been investigated using an FTIR spectrometer. The photochemical products were identified as methyleneimine (CH 2 = NH), water and nitric oxide. This photoinduced dehydrogenation reaction, CH 3NH 2 + NO 2 + hν → CH 2 = NH + H 2O + NO, is interpreted by the following reaction sequence: (1) photoexcitation of NO 2, (2) oxygen atom transfer from excited NO 2 to methylamine and (3) isomerization from the methylamine N-oxide to methylhydroxylamine (intramolecular hydrogen atom migration), followed by (4) dissociation into methyleneimine and water. it was confirmed by the infrared spectrum that two of the dissociation products interact with each other in the matrix cage (CH 2 = NH · H 2O). This reaction mechanism is also supported by the formation of CD 2 = NH · HDO in the CD 3NH 2/NO 2 system.

Fragmentation of collisionally activated hydroxyphenoxide anions in the gas phase

AbstractLow‐energy collisionally activated dissociation of O‐deprotonated dihydroxybenzenes (catechol, resorcinol, hydroquinone) in the gas phase causes both fragmentation to form [C6H4O2]– ions by loss of the remaining oxygen‐bound hydrogen atom and intramolecular hydrogen atom migration from O to C. The rearranged anions then undergo ring‐cleavage reactions which are different in each case. Both catechol and hydroquinone produce fragments which are the result of the loss of two carbon atoms and both oxygen atoms but the proposed mechanisms are different. Resorcinol also produces a fragment which derives from the loss of carbon dioxide. For this process a mechanism is proposed which involves a 6‐methylpyranone anion intermediate.

Photosensibilisation (253,7 nm) et photolyse directe (184,9 nm) du cis-pentène-2 gazeux

The major primary process in the interaction of Hg(6 3P 1) with cis-pentene-2 is energy transfer to yield vibrationally excited pentene-2 molecules in the first triplet state (φ ⩾ 0.98). The quantum yield for paraffinic-type quenching is less than or equal to 0.02. At low pressures fragmentation of the vibrationally excited molecules yields many products, including the isoemrs 3-methylbutene-1 and pentene-1. At pressures greater than 40 Torr, the quantum yield for cis → trans isomerization is 0.50 ± 0.02. An isomer (probably ethylcyclopropane) as well as some of the pentene-1 are formed by intramolecular hydrogen-atom migration, followed by collissional stabilization. The steady-state ratio [ trans-pentene-2]/[ cis-pentene-2] is 1.04 ± 0.04. The direct photolysis of cis-pentene-2 at 184.9 nm yields an excited molecule which decomposes at low pressures to give methyl and α-methallyl radicals (φ ≈ 0.9). The effect of adding DI, D 2S or O 2 as a radical trap has been studied. The excited pentene-2 molecules (or excited isomers formed by intramolecular hydrogen atom migration) can be deactivated collisionally: addition of propane (at 2 atm or higher) leads to φ( cis-pentene-2 → isomers) = 0.44 ± 0.05. Since φ(trans → cis) = 0.38 ± 0.03 under these conditions, the total quantum yield for deactivation is φ(C 5H 10) = 0.82 ± 0.09.

Behavior of the13C lines in the ESR spectra of 3,6-di-tert-butyl-2-oxyphenoxyl with intramolecular hydrogen atom migration

1. Study has been made of the effect of unpaired electron hyperfine interaction with the13C nucleus on the ESR spectrum of 3,6-di-tert-butyl-2-oxyphenoxyl. 2. The spin density distribution has been calculated for the radical under both rapid and slow exchange, and13C hfi constants obtained for various positions.