Photofragmentation in selected tautomers of protonated adenine

The photofragmentation by UV excitation of selectively prepared 1(+) and 3(+) tautomers of protonated adenine is studied after excitation at a 266 and 263 nm wavelengths with two different experimental set-ups located in Seoul and Orsay. While the production of 1(+) tautomers with an electrospray ion source is now well accepted, calculations were used to ascribe the preparation of 3(+) tautomers from cold adenine dimers. The fragmentation patterns are rather similar for both tautomers, suggesting similar mechanisms as a statistical fragmentation in the ground electronic state after internal conversion.     

Gas-phase tautomers of protonated 1-methylcytosine. Preparation, energetics, and dissociation mechanisms

Tautomers of 1-methylcytosine that are protonated at N-3 (1+) and C-5 (2+) have been specifically synthesized in the gas phase and characterized by tandem mass spectrometry and quantum chemical calculations. Ion 1+ is the most stable tautomer in aqueous and methanol solution and is likely to be formed by electrospray ionization of 1-methylcytosine and transferred in the gas phase. Gas-phase protonation of 1-methylcytosine produces a mixture of 1+ and the O-2-protonated tautomer (3+), which are nearly isoenergetic. Dissociative ionization of 6-ethyl-5,6-dihydro-1-methylcytosine selectively forms isomer 2+. Upon collisional activation, ions 1+ and 3+ dissociate by loss of ammonia and [C,H,N,O], whose mechanisms have been established by deuterium labeling and ab initio calculations. The main dissociations of 2+ following collisional activation are losses of CH2=C=NH and HN=C=O. The mechanisms of these dissociations have been elucidated by deuterium labeling and theoretical calculations.     

Gaseous arginine conformers and their unique intramolecular interactions

Extensive ab initio calculations were employed to characterize stable conformers of gaseous arginine, both the canonical and zwitterionic tautomers. Step-by-step geometry optimizations of possible single-bond rotamers at the B3LYP/6-31G(d), B3LYP/6-31++G(d,p), and MP2/6-31++G(d,p) levels yield numerous structures that are more stable than any known ones. The final electronic energies of the conformers were determined at the CCSD/6-31++G(d,p) level. The lowest energies of the canonical and zwitterionic structures are lower than the existing values by 2.0 and 2.3 kcal/mol, respectively. The relative energies, rotational constants, dipole moments, and harmonic frequencies of the stable conformers remain for future experimental verification. The conformational distributions at various temperatures, estimated according to thermodynamic principles, consist almost exclusively of the newly found structures. One striking feature is the occurrence of blue-shifting hydrogen bonds in all six of the most stable conformers. A unique feature of important conformations is the coexistence of dihydrogen and blue- and red-shifting hydrogen bonds. In addition to the hydrogen bonds, the stereoelectronic effects were also found to be important stabilization factors. The calculated and measured proton affinities agree within the theoretical and experimental uncertainties, affirming the high quality of our conformational search. The theoretical gas-phase basicity of 245.9 kcal/mol is also in good agreement with the experimental value of 240.6 kcal/mol. The extensive searches establish firmly that gaseous arginine exists primarily in the canonical and not the zwitterionic form.     

Fragmentation of protonated dipeptides containing arginine. Effect of activation method

The fragmentation reactions of the protonated dipeptides Gly-Arg and Arg-Gly have been studied using collision-induced dissociation (CID) in a quadrupole ion trap, by in-source CID in a single-quadrupole mass spectrometer and by CID in the quadrupole cell of a QqTOF mass spectrometer. In agreement with earlier quadrupole ion trap studies (Farrugia, J. M.; O'Hair, R. A. J., Int. J. Mass Spectrom., 2003, 222, 229), the CID mass spectra obtained with the ion trap for the MH(+) ions and major fragment ions are very similar for the two isomers indicating rearrangement to a common structure before fragmentation. In contrast, in-source CID of the MH(+) ions and QqTOF CID of the MH(+), [MH - NH(3)](+) and [MH <23 HN = C(NH(2))(2)](+) ions provide distinctly different spectra for the isomeric dipeptides, indicating that rearrangement to a common structure has not occurred to a significant extent under these conditions even near the threshold for fragmentation in the QqTOF instrument. Clearly, under normal operating conditions significantly different fragmentation behavior is observed in the ion trap and beam-type experiments. This different behavior probably can be attributed to the shorter observation times and concomitant higher excitation energies in the in-source and QqTOF experiments compared to the long observation times and lower excitation energies relevant to the ion trap experiments. Based largely on elemental compositions derived from accurate mass measurements in QqTOF studies fragmentation schemes are proposed for the MH(+), [MH - NH(3)](+), and [MH - (HN = C(NH(2))(2))](+) ions.     

Photoisomerization of naphthylquinolylethylenes in neutral and protonated forms

The quantum yield of the trans-cis photoisomerization of 1-(1-naphthyl)-2-(2-quinolyl)ethylene and 1-(2-naphthyl)-2-(2-quinolyl)ethylene is close to the theoretical limit (0.5) for diabatic photoisomerization and does not change on passing from the neutral to the protonated form. The data obtained indicate the absence of the α-effect for the test compounds, which consists in an increase in the trans-cis photoisomerization quantum yield to values of >0.5 upon protonation of some azadiarylethylenes with the nitrogen atom in the α-position to the ethylene group.     

A computational study of azaphospholes: anions and neutral tautomers

One hundred and eleven azaphospholes (31 anions and 80 neutral compounds) have been studied theoretically at the B3LYP/6-311++G(d,p) level. Among the analyzed properties, there are the geometries, mainly the non-planarity of the PH tautomers, the isomerism of the anions, the NH/PH tautomerism of neutral compounds, the chemical shifts and spin–spin coupling constants. The aromaticity has been assessed through Schleyer’s NICS values, preferably NICS(1). Finally, we have compared our calculations with previous ones as well as with the available experimental data for the calculated compounds and for related ones.     

The exceptional hydrogen-bond properties of neutral and protonated lobeline

The X-ray diffraction structure of (-)-lobeline, a high affinity nicotinic ligand, has been determined. A comparison with its hydrobromide and hydrochloride salts shows the great flexibility of the two lateral chains of the N-methylpiperidine ring. Infrared studies carried out on the same species, in the solid state and in solution, reveal the propensity of this molecular framework to accommodate very specific hydrogen bonds (HBs) depending on the state-neutral or protonated-of the molecule. In solution, a strong internal HB between the hydroxyl group and the piperidine nitrogen gives an exceptionally high HB affinity to the hydroxyl oxygen of the lobeline base. In the ionic form, both NH+ and OH groups of the molecule cooperate as HB donors to chelate the counterion. These interactions provide very stable structures and indicate that protonated lobeline can also act as a strong HB donor.     

Photoisomerization of 2-styrylquinoline in neutral and protonated forms

The quantum yields of the trans-cis and cis-trans photoisomerization of 2-styrylquinoline (2SQ) and its several derivatives were measured in neutral, protonated, and quaternized forms. It was shown that electron-donor substituents in the styryl moiety increase the quantum yield of trans-cis photoisometization ?_tc in the neutral form as a result of stabilization of the intermediate zwitterionic perpendicular conformer. On passing from the neutral to the positively charged forms (protonated or quaternized), an increase in the quantum yields to ?_tc > 0.5 was observed, thus suggesting in terms of the classical diabatic mechanism of photoisomerization via the perpendicular conformer the shift of the minimum on the potential energy surface (PES) of the S ₁ state relative to the maximum of the S ₀ state PES to the cis-isomer or a possible contribution of the adiabatic route to the photoisomerization of the 2SQ cations.     

Modeling of the gas-phase ion chemistry of protonated arginine

Arginine is often involved at the C-terminus of peptides obtained from tryptic digests of proteins. The very basic guanidine group of the side-chain of arginine has a large effect on the backbone fragmentation of protonated peptides. Furthermore, arginine exhibits specific fragmentation reactions involving its side-chain. Various tautomerization states, conformers and side-chain dissociation channels of protonated arginine were studied using theoretical methods. The guanidine loss of protonated arginine is proved to be an S(N)2 substitution on the delta-carbon of the side-chain, starting from species containing the N(epsilon)H-C(+)(N(eta)H(2))(N(eta')H(2)) or -N(epsilon) (+)H(2)-C(N(eta)H)(N(eta')H(2)) moieties and leads to formation to either protonated guanidine or protonated proline. In the corresponding transition structures the proline moiety is protonated. Under low-energy collision conditions the extra proton transfers to the guanidine moiety, leading to the formation of C(+)(NH(2))(3). On the other hand, the lifetime of the fragmenting species under high-energy collision conditions is shorter, resulting in enhanced formation of protonated proline and its dissociation products. The first step of ammonia loss is the leaving of a preformed NH(3) from tautomers containing the -N(epsilon)H-C(N(eta)H(3) (+))(N(eta')H) or -N(epsilon)-C(N(eta)H(3) (+))(N(eta')H(2)) moieties. The resulting protonated carbodiimide group can be stabilized by intramolecular nucleophilic attack, leading to ring formation. Overall, reactions involved in the ammonia loss from protonated arginine can be considered as an S(N)1 substitution on the central zeta-carbon of the guanidine group.     

Protonation of 1,4,5-tri- and 1,4,5,8-tetrahydroxyanthraquinones in sulfuric acid: Multistep reaction involving tautomers and conformers

The fine structure of the ??_l,??*-absorption of hydroxyanthraquinones solutions in sulfuric acid arises due to the existence of the protonated forms as equilibrium mixtures of tautomers and conformers distinguished by the positions of the ??-bonds, charges, and the number of intramolecular hydrogen bonds. Using quantum-chemical calculations and correlation analysis of the absorption spectra tautomers were identified of mono- and dications of 1,4,5-trihydroxyanthraquinone of 9,10-, 1,4-, and 1,10-isomeric structure. For 1,4,5,8-tetrahydroxyanthraquinone 9,10-, 1,4-, 1,10-, and 1,5-isomeric mono- and dications and their conformers were found.     

Photochemical properties of 9-azidoacridine in neutral and protonated forms

It was found that the quantum yield of 9-azidoacridine photodissociation was equal to 0.95 (in acetonitrile) and remained unchanged upon protonation. Quantum-chemical calculations on the structures of the azide and its cation in the ground (S ₀) and the lower single excited (S ₁) state were performed using semiempirical (PM3) and ab initio (HF, B3LYP) methods. The σ _NN ^* antibonding orbital at the N-N₂ bond was occupied in both of the azides in the S ₁ state; this fact is consistent with the photochemical activity of these compounds. Because of the presence of absorption bands in the visible region of the spectrum, 9-azidoacridinium hydrochloride is sensitive to visible light, and, among all of the currently known arylazides, it is sensitive to light with the longest wavelength: the quantum yield of its photodissociation is 0.65 on irradiation with 470-nm light.     

Conformational study of protonated,neutral, and deprotonated formamide

Neutral, protonated, and deprotonated formamide isomers were studied at the 3-21G SCF level with complete geometry optimization. Ten stable structures, ten first-order saddle points, and three second-order saddle points (conformational maxima) are reported. [Total energies are reported in hartrees (1 hartree = 627.51 kcal/mol = 2625.5 kJ/mol) and energy differences are reported in kJ/mol (1 kJ/mol = 0.239 kcal/mol).] Rotational barriers and proton affinities are discussed and compared to isoelectronic amidine species.     

DFT studies on the favored and rare tautomers of neutral and redox cytosine

The complete tautomeric mixture consisting of nine prototropic tautomers has been studied in the gas phase at the DFT(B3LYP)/6-311+G(d,p) level for neutral, oxidized, and reduced cytosine. Rotational isomerism of the exo –OH group and geometrical isomerism of the exo =NH group have also been considered. Tautomeric conversions possible for cytosine have been compared with those for its structural models, 4-amino- and 2-hydroxypyrimidine. Effects of intramolecular interactions between neighboring groups for cytosine are analogous to those observed for model compounds. Although they are not very strong, they are sufficient to influence tautomeric equilibria and relative stabilities of individual tautomers. One-electron oxidation and one-electron reduction change tautomeric preferences. Tautomers that are rare forms for neutral cytosine become favored ones for oxidized and reduced cytosine. Aromaticity is not the main factor that dictates the tautomeric preferences. Stability of functional groups seems to be more important than full electron delocalization.     

Compression elastic modulus of neutral and protonated poly(N-vinylimidazole) hydrogels

The compression modulus of poly(N-vinylimidazole) (PVI) hydrogels synthesized by cross-linking polymerization in aqueous solution, was measured at room temperature in several related systems: i) just after polymerization, ii) swollen at equilibrium in deionized water, iii) swollen in HCl (aq) (pH=2.5), iv) swollen in HCl (pH=2.5) and 1 M NaCl (aq) solution and v) swollen in H₂SO₄ (pH=2.5) (aq) solution. Samples of the first and second groups are neutral whereas hydrogels of the other three groups are ionic because of protonation of basic imidazole groups. The experimental results were fitted with the Erman-Monnerie theory, applied to compression measurements for the first time, to determine the phantom modulus, [f_ph*], and the parameter κ_G which measures the constraining role of entanglements on the fluctuations of chains between knots.     

Cyclic tautomers of tryptamines and tryptophans. V. Formation and reactions of cyclic tautomers of cyclo-L-tryptophanyl-L-proline

Two stereoisomeric cyclic tautomers ($\text{5}$ and $\text{6}$ of cyclo-L-tryptophanyl-L-proline whose stereochemistry was established by x-ray analysis, gave 5- and 6-hydroxytryptophanyl derivatives ($\text{10}$), $\text{11}$, and $\text{19}$) on the hydroxylation with lead tetraacetate in trifluoroacetic acid.     

πl,π*-Absorption bands as a valuable source of information on the structure of tautomers and conformers

The presence of several π_l,π*-absorption bands in the electronic spectrum of hydroxyanthraquinones indicates the occurrence of tautomeric and conformational equilibria. The structure of tautomers and conformers can be determined from the correlation between λ_max and the sums of the constants σ^A of hydroxy and oxido groups, calculated for each isomer.     

Characterization of neutral fragments issued from the photodissociation of protonated tryptophane

New information on the photo-fragmentation of biomolecules is obtained from the detection of neutral and ionic fragments using a time and position resolved coincidence technique that reveals whether an ionic photofragment is associated with one or more neutral fragments. In the case of a sequential dissociation, both fragmentation channels are identified as well as their time ordering.     

Substitution effects on neutral and protonated pyridine derivatives along the periodic table

A theoretical study of the monosubstitution effects of all atoms of the second and third rows of the periodic table on the α, β and γ positions of neutral and protonated pyridine has been carried out by means of B3LYP/6-31 + G(d,p) DFT calculations. The geometric and electronic properties, calculated using the Atoms in Molecules methodology, and the electrostatic potential have been analysed. Concurrently, three separate aromaticity indexes (NICS(0), NICS(1) and HOMA) have been evaluated and compared to the above results. Furthermore, the effect of protonation on these parameters has been investigated. A comparison with analogous results for benzene derivatives has also been carried out.