An Investigation of Protonation Sites and Conformations of Protonated Amino Acids by IRMPD Spectroscopy

The protonation sites and structures of a series of protonated amino acids (Gly, Ala, Pro, Phe, Lys and Ser) are investigated by means of infrared multiple‐photon dissociation (IRMPD) spectroscopy and electronic‐structure calculations. The IRMPD spectra of the protonated species are recorded using the combination of a free‐electron laser (FEL) and an electrospray‐ion‐trap mass spectrometer. The structures of different possible isomers of these protonated species are optimized at the B3LYP/6‐311+G(d, p) level of theory and the IR spectra calculated using the same computational method. For every amino acid studied herein, the current results indicate that a proton is bound to the α‐amino nitrogen, except for lysine, in which the protonation site is the amino nitrogen in the side chain. According to the calculated and experimental IRMPD results, the structures of the protonated amino acids may be assigned unambiguously. For Gly, Ala, and Pro, in each of the most stable isomers the protonated amino group forms an intramolecular hydrogen bond with the adjacent carbonyl oxygen. In the case of Gly, the isomer containing a proton bound to the carbonyl oxygen is theoretically possible. However, it does not exist under the experimental conditions because it has a significantly higher energy (i.e. 26.6 kcal mol^?1) relative to the most stable isomer. For Ser and Phe, the protonated amino group forms two intramolecular hydrogen bonds with both the adjacent carbonyl oxygen and the side‐chain group in each of the most stable isomers. In protonated lysine, the protonated amino group in the side chain forms two hydrogen bonds with the α‐amino nitrogen and the carbonyl oxygen, which is a cyclic structure. Interestingly, for protonated lysine the zwitterionic structure is a local minimum energy isomer, but the experimental spectrum indicates that it does not exist under the experimental conditions. This is consistent with the fact that the zwitterionic isomer is 9.2 kcal mol^?1 higher in free energy at 298 K than the most stable isomer. The carbonyl stretching vibration in the range of 1760–1800 cm^?1 is especially sensitive to the structural change. In addition, IRMPD mechanisms for the protonated amino acids are also investigated.     

2,4-Dihydroxy and O2 Protonated Tautomers of dThd and Thd Coexist in the Gas Phase: Methylation Alters Protonation Preferences versus dUrd and Urd

The gas-phase structures of protonated thymidine, [dThd + H]⁺, and its modified form, protonated 5-methyluridine, [Thd + H]⁺, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy combined with electronic structure calculations. IRMPD action spectra are measured over the ranges extending from ~600 to 1900 cm^–1 and ~2800 to 3800 cm^–1 using the FELIX free electron laser and an optical parametric oscillator/amplifier (OPO/OPA) laser system, respectively. Comparisons between the B3LYP/6-311+G(d,p) linear IR spectra calculated for the stable low-energy conformers and the measured IRMPD spectra are used to determine the most favorable tautomeric conformations of [dThd + H]⁺ and [Thd + H]⁺ and to identify those populated in the experiments. Both B3LYP and MP2 levels of theory predict a minor 2,4-dihydroxy tautomer as the ground-state conformer of [dThd + H]⁺ and [Thd + H]⁺ indicating that the 2'-hydroxyl substituent of Thd does not exert a significant impact on the structural features. [dThd + H]⁺ and [Thd + H]⁺ share parallel IRMPD spectral profiles and yields in both the FELIX and OPO regions. Comparisons between the measured IRMPD and calculated IR spectra suggest that minor 2,4-dihydroxy tautomers and O2 protonated conformers of [dThd + H]⁺ and [Thd + H]⁺ are populated in the experiments. Comparison of this work to our previous IRMPD spectroscopy study of protonated 2'-deoxyuridine and uridine suggests that the 5-methyl substituent alters the preferences of O2 versus O4 protonation.

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Infrared spectra of protonated uracil, thymine and cytosine.

The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm(-1) in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.     

Infrared spectra of the protonated neurotransmitter histamine: competition between imidazolium and ammonium isomers in the gas phase

The infrared (IR) spectrum of protonated histamine (histamineH(+)) was recorded in the 575-1900 cm(-1) fingerprint range by means of IR multiple photon dissociation (IRMPD) spectroscopy. The IRMPD spectrum of mass-selected histamineH(+) ions was obtained in a Fourier transform ion cyclotron resonance mass spectrometer coupled to an electrospray ionization source and an IR free electron laser. A variety of isomers were identified and characterized by quantum chemical calculations at the B3LYP and MP2 levels of theory using the cc-pVDZ basis set. The low-energy isomers are derived from various favourable protonation sites--all of which are N atoms--and different orientations of the ethylamine side chain with respect to the heterocyclic imidazole ring. The measured IRMPD spectrum was monitored in the NH(3) loss channel and exhibits 14 bands in the investigated spectral range, which were assigned to vibrational transitions of the most stable isomer, denoted A. This imidazolium-type isomer A with protonation at the imidazole ring and gauche conformation of the ethylamine side chain is significantly stabilized by an intramolecular ionic Nπ-H(+)···Nα hydrogen bond to the ethylamino group. The slightly less stable ammonium-type isomer B with protonation at the ethylamino group is only a few kJ mol(-1) higher in energy and may also provide a minor contribution to the observed IRMPD spectrum. Isomer B is derived from A by simple proton transfer from imidazole to the ethylamino group along the intramolecular Nπ-H(+)···Nα hydrogen bond via a low barrier, which is calculated to be of the order of 5-15 kJ mol(-1). Significantly, the most stable structure of isolated histamineH(+) differs from that in the condensed phase by both the protonation site and the conformation of the side chain, emphasizing the important effects of solvation on the structure and function of this neurotransmitter. The effects of protonation on the geometric and electronic structure of histamine are evaluated by comparing the calculated properties of isomer A with those of the most stable structure of neutral histamine A(n).     

Determination of picomolar levels of flavins in natural waters by solid-phase ion-pair extraction and liquid chromatography

A method is described for the rapid determination of flavins in sea water, based on solid-phase extraction followed by ion-pair high-performance liquid chromatography (HPLC) with fluorescence detection. Riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) and their photochemical breakdown products, lumiflavin, formylmethylflavin, and lumichrome can be determined with subpicomolar detection limits. The method was used at sea in the analysis of coastal and open ocean waters. In both environments, riboflavin, lumiflavin and lumichrome were routinely observed at concentrations in the picomolar range; lumiflavin and lumichrome were generally confined to the photic zone while riboflavin was present throughout the water column. Formylmethylflavin, FMN, and FAD were only occasionally observed; when present, these flavins were observed at consistently higher concentrations than riboflavin, lumiflavin and lumichrome.     

The reaction of triplet flavin with indole. A study of the cascade of reactive intermediates using density functional theory and time resolved infrared spectroscopy

As a model for riboflavin, lumiflavin was investigated using density functional theory methods (B3LYP/6-31G* and B3LYP/6-31+G**) with regard to the proposed cascade of intermediates formed after excitation to the triplet state, followed by electron-transfer, proton-transfer, and radical[bond]radical coupling reactions. The excited triplet state of the flavin is predicted to be 42 kcal/mol higher in energy than the singlet ground state, and the pi radical anion lies 45.1 kcal/mol lower in energy than the ground-state flavin and a free electron in the gas phase. The former value compares to a solution-phase triplet energy of 49.8 kcal/mol of riboflavin. For the radical anion, the thermodynamically favored position to accept a proton on the flavin ring system is at N(5). A natural population analysis also provided spin density information for the radicals and insight into the origin of the relative stabilities of the six different calculated hydroflavin radicals. The resulting 5H-LF* radical can then undergo radical[bond]radical coupling reactions, with the most thermodynamically stable adduct being formed at C(4'). Vibrational spectra were also calculated for the transient species. Experimental time-resolved infrared spectroscopic data obtained using riboflavin tetraacetate are in excellent agreement with the calculated spectra for the triplet flavin, the radical anion, and the most stable hydroflavin radical.     

EXCITED-STATE REACTIONS OF OXIDIZED FLAVIN DERIVATIVES

Abstract— The reactivity of flavin mononucleotide and of lumiflavin triplets was studied by flash and laser photolysis. The rate constants of the triplets with oxygen, with flavin ground-state molecules, and with Br^- ions were determined. Although in solution at room temperature, the protonated flavin triplet, ³F1H⁺, is not formed directly from its very short lived singlet state, a transient, which we think is this triplet, results from protonation of the neutral triplet. This conclusion is based on a comparison between the neutral and the protonated triplet spectra in a low-temperature glass. It is proposed that the protonated triplet can also be formed by sensitization via the phenanthrene triplet.     

Infrared spectra of protonated neurotransmitters: serotonin

The gas-phase IR spectrum of the protonated neurotransmitter serotonin (5-hydroxytryptamine) was measured in the fingerprint range by means of IR multiple photon dissociation (IRMPD) spectroscopy. The IRMPD spectrum was recorded in a Fourier transform ion cyclotron resonance mass spectrometer coupled to an electrospray ionization source and an IR free electron laser. Quantum chemical calculations at the B3LYP and MP2 levels of theory using the cc-pVDZ basis set yield six low-energy isomers in the energy range up to 40 kJ/mol, all of which are protonated at the amino group. Protonation at the indole N atom or the hydroxyl group is substantially less favorable. The IRMPD spectrum is rich in structure and exhibits 22 distinguishable features in the spectral range investigated (530-1885 cm(-1)). The best agreement between the measured IRMPD spectrum and the calculated linear IR absorption spectra is observed for the conformer lowest in energy at both levels of theory, denoted g-1. In this structure, one of the three protons of the ammonium group points toward the indole subunit, thereby maximizing the intramolecular NH(+)-π interaction between the positive charge of the ammonium ion and the aromatic indole ring. This mainly electrostatic cation-π interaction is further stabilized by significant dispersion forces, as suggested by the substantial differences between the DFT and MP2 energies. The IRMPD bands are assigned to individual normal modes of the g-1 conformer, with frequency deviations of less than 29 cm(-1) (average <13 cm(-1)). The effects of protonation on the geometric and electronic structure are revealed by comparison with the corresponding structural, energetic, electronic, and spectroscopic properties of neutral serotonin.     

Infrared Multiple Photon Dissociation Action Spectroscopy and Theoretical Studies of Triethyl Phosphate Complexes: Effects of Protonation and Sodium Cationization on Structure

The gas-phase structures of protonated and sodium cationized complexes of triethyl phosphate, [TEP + H]⁺ and [TEP + Na]⁺, are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy using tunable IR radiation generated by a free electron laser, a Fourier transform ion cyclotron resonance mass spectrometer with an electrospray ionization source, and theoretical electronic structure calculations. Measured IRMPD action spectra are compared to linear IR spectra calculated at the B3LYP/6-31 G(d,p) level of theory to identify the structures accessed in the experimental studies. For comparison, theoretical studies of neutral TEP are also performed. Sodium cationization and protonation produce changes in the central phosphate geometry, including an increase in the alkoxy ∠OPO bond angle and shortening of the alkoxy P–O bond. Changes associated with protonation are more pronounced than those produced by sodium cationization.     

The photoinduced triplet of flavins and its protonation states

The photogenerated triplet states of riboflavin and flavin mononucleotide (FMN) have been examined by time-resolved electron paramagnetic resonance (EPR) spectroscopy at low temperature (T = 80 K). Because of the high time resolution of the utilized EPR instrumentation, the triplets are for the first time observed in the nonequilibrated electron-spin polarized state and not in their equilibrated forms with the population of the triplet sublevels governed by Boltzmann distribution. The electron-spin polarization pattern directly reflects the anisotropy of the intersystem crossing from the excited singlet-state precursor. Spectral analysis of the resulting enhanced absorptive and emissive EPR signals yields the zero-field splitting parameters, |D| and |E|, and the zero-field populations of the triplet at high accuracy. These parameters are sensitive probes for the protonation state of the flavin's isoalloxazine ring, as becomes evident by a comparison of the spectra recorded at different pH values of the solvent. The three protonation states of the flavins can furthermore be distinguished by the kinetics of the transient EPR signals, which are dominated by spin-lattice relaxation. The fastest decays are observed for the protonated FMN and riboflavin triplets, followed by the deprotonated flavin triplets. Slow decays are measured for the triplet states of neutral FMN and riboflavin. Because proton transfer is found to be slow on the time scale of spin-polarized triplet detection by transient EPR, the pH-dependent spin-relaxation and zero-field splitting parameters offer a novel approach to probe the protonation state of flavins in their singlet ground state through the characterization of their triplet-state properties.     

Infrared spectroscopy of ionized corannulene in the gas phase

The gas-phase infrared spectra of radical cationic and protonated corannulene were recorded by infrared multiple-photon dissociation (IRMPD) spectroscopy using the IR free electron laser for infrared experiments. Electrospray ionization was used to generate protonated corannulene and an IRMPD spectrum was recorded in a Fourier-transform ion cyclotron resonance mass spectrometer monitoring H-loss as a function of IR frequency. The radical cation was produced by 193-nm UV photoionization of the vapor of corannulene in a 3D quadrupole trap and IR irradiation produces H, H(2), and C(2)H(x) losses. Summing the spectral response of the three fragmentation channels yields the IRMPD spectrum of the radical cation. The spectra were analyzed with the aid of quantum-chemical calculations carried out at various levels of theory. The good agreement of theoretical and experimental spectra for protonated corannulene indicates that protonation occurs on one of the peripheral C-atoms, forming an sp(3) hybridized carbon. The spectrum of the radical cation was examined taking into account distortions of the C(5v) geometry induced by the Jahn-Teller effect as a consequence of the degenerate (2)E(1) ground electronic state. As indicated by the calculations, the five equivalent C(s) minima are separated by marginal barriers, giving rise to a dynamically distorted system. Although in general the character of the various computed vibrational bands appears to be in order, only a qualitative match to the experimental spectrum is found. Along with a general redshift of the calculated frequencies, the IR intensities of modes in the 1000-1250 cm(-1) region show the largest discrepancy with the harmonic predictions. In addition to CH "in-plane" bending vibrations, these modes also exhibit substantial deformation of the pentagonal inner ring, which may relate directly to the vibronic interaction in the radical cation.     

ELECTROSTATIC EFFECTS IN THE PHOTOREDUCTION OF FLAVINS BY EDTA

The anaerobic photoreduction of riboflavin, flavin mononucleotide, N(3)-carboxymethylriboflavin, N(3)-methyl-lumiflavin, and lumiflavin by EDTA was studied in aqueous solution over the pH range 2.5–10. The electrostatic effects of the electron donor-acceptor pair produce a secondary effect on the reactivity, and this effect can be predicted from the product of the charges (Z_D x Z_A). The trianonic and tetraanonic species of EDTA have nitrogens which are free from intramolecular hydrogen bonding, and these species are potentially the most reactive. However, in some pH regions the electrostatic effect can become the dominant factor when both the electron donor and acceptor become negatively charged. The excited states of flavins are susceptible to charge effects whether the charge is localized on the side chain or involves the isoalloxazine ring system.     

Infrared spectra of protonated neurotransmitters: dopamine

The infrared (IR) spectrum of the isolated protonated neurotransmitter dopamine was recorded in the fingerprint range (570-1880 cm(-1)) by means of IR multiple photon dissociation (IRMPD) spectroscopy. The spectrum was obtained in a Fourier transform ion cyclotron resonance mass spectrometer equipped with an electrospray ionization source, which was coupled to a free electron laser (FEL). The spectroscopic studies are complemented by quantum chemical calculations at the B3LYP and MP2 levels of theory using the cc-pVDZ basis set. Several low-energy isomers with protonation occurring at the amino group are predicted in the energy range 0-50 kJ mol(-1). Good agreement between the measured IRMPD spectrum and the calculated linear absorption spectra is observed for the two gauche conformers lowest in energy (ΔE) and free energy (ΔG) at both levels of theory, denoted g-1 and g+1. Minor contributions of higher lying gauche isomers cannot be ruled out spectroscopically but their calculated energies suggest only minor population in the sampled ion cloud. In all these gauche structures, one of the three protons of the ammonium group is pointing toward the catechol subunit, thereby maximizing the intramolecular NH-π interaction of the positive charge with the aromatic ring. In total, 16 distinct vibrational bands are observed in the IRMPD spectrum and assigned to individual normal modes of the energetically most stable g-1 conformer, with deviations of less than 24 cm(-1) (average 11 cm(-1)) between measured and calculated frequencies. Comparison with neutral dopamine reveals the effects of protonation on the geometric and electronic structure.     

Modified Quadrupole Ion Trap Mass Spectrometer for Infrared Ion Spectroscopy: Application to Protonated Thiated Uridines

Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s²Urd+H]⁺, and 4-thiouridine, [s⁴Urd+H]⁺. The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2′-endo and C3′-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine.

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Femtosecond pump-probe experiments on trapped flavin: optical control of dissociation

Femtosecond pump-probe experiments are performed on flavin biomolecules isolated in an ion trap. Mass spectra of the photoinduced fragments show that the fragmentation pathways can be modified using two-color two-photon excitation. In particular, when an infrared probe pulse (810 nm) is added subsequent to the first excitation step (excitation of the S(1) state of flavin mononucleotide at 405 nm), branching ratios between lumichrome and lumiflavin production are inverted relative to the single excitation case.     

Determination of the site of protonation of substituted benzenes in water chemical ionization mass spectrometry

The site of protonation of a substituted benzene may be determined using chemical onization mass spectrometry with D₂O as a reagent gas. The observation of extensive exchange of the ring hydrogens for deuteriums is linked to protonation on the benzene ring. The lack of this exchange coupled with the formation of cluster ions (the association of the protonated species with one or more D₂O molecules) is evidence of protonation on the substituent rather than the ring. Aniline, benzaldehyde and nitrobenzene are observed to protonate at the substituent while toluene, bromobenzene, biphenyl and iodobenzene protonate on the ring. The dimethylbenzenes protonate on the ring while the diaminobenzenes protonate at one of the substituents. The dihydroxybenzenes, as well as a number of other compounds in which an oxygen is attached directly to the ring, protonate predominantly at the substituent although a small amount of exchange of one ring hydrogen is observed.     

Protonation sites of isolated fluorobenzene revealed by IR spectroscopy in the fingerprint range

Protonated fluorobenzene ions (C6H6F+) are produced by chemical ionization of C6H5F in the cell of a FT-ICR mass spectrometer using either CH5+ or C2H5+. The resulting protonation sites are probed by IR multiphoton dissociation (IRMPD) spectroscopy in the 600-1700 cm-1 fingerprint range employing the free electron laser at CLIO (Centre Laser Infrarouge Orsay). Comparison with quantum chemical calculations reveals that the IRMPD spectra are consistent with protonation in para and/or ortho position, which are the thermodynamically favored protonation sites. The lack of observation of protonation at the F substituent, when CH5+ is used as protonating agent, is attributed to the low-pressure conditions in the ICR cell where the ions are produced. Comparison of the C6H6F+ spectrum with IR spectra of C6H5F and C6H7+ reveals the effects of both protonation and H F substitution on the structural properties of these fundamental aromatic molecules.     

Substituent effect and multisite protonation in the fragmentation of alkyl benzoates

The dissociation of protonated alkyl benzoates (para H, CN, OMe and NO(2)) into protonated benzoic acids and alkyl cations was studied in the gas phase. It was found that the product ratio depends on the substituent at the para position of the phenyl ring. The substituent effect is probably the result of the formation of an ion-neutral complex intermediate that decomposes to an ion and a neutral, according to the relative proton affinities of the two moieties. The experimental results and theoretical calculations indicate that the favored protonation site in these compounds is the ester's carbonyl and that proton transfer from the phenyl ring to the ester group is very likely to occur under chemical ionization conditions. It is most probable that the carbonyl protonated form is a common intermediate in the fragmentation process, regardless of the protonation site.     

Fingerprint vibrational spectra of protonated methyl esters of amino acids in the gas phase

Infrared spectra of the protonated monomers of glycine, alanine, valine, and leucine methyl esters are presented. These protonated species are generated in the gas phase via matrix assisted laser desorption ionization (MALDI) within the cell of a Fourier transform ion cyclotron resonance spectrometer (FTICR) where they are subsequently mass selected as the only species trapped in the FTICR cell. Alternatively, they have also been generated by electrospray ionization and transferred to a Paul ion-trap mass spectrometer where they are similarly isolated. In both cases IR spectra are then derived from the frequency dependence of the infrared multiple photon dissociation (IRMPD) in the mid-infrared region (1000-2200 cm(-1)), using the free electron laser facility Centre de Laser Infrarouge d'Orsay (CLIO). IR bands are assigned by comparison with the calculated vibrational spectra of the lowest energy isomers using density functional theory (DFT) calculations. There is in general good agreement between experimental IRMPD spectra and calculated IR absorption spectra for the lowest energy conformer which provides evidence for conformational preferences. The two different approaches to ion generation and trapping yield IRMPD spectra that are in excellent agreement.     

Electronic transition dipole moment directions of reduced anionic flavin in stretched poly(vinyl alcohol) films

The IR and UV/vis linear dichroic spectra of reduced anionic flavin mononucleotide (FMNH-) partially oriented in poly(vinyl alcohol) (PVA) films have been measured to determine the direction of the major electronic transition dipole moments. The IR linear dichroism (LD) was measured in the 1750-1350 cm(-1) region to provide the overall molecular orientation of the FMNH- in the stretched films. Time-dependent density functional theory using the B3LYP functional was used to calculate the normal modes and the transition dipole moments of reduced lumiflavin. The calculated normal modes assisted in IR band assignments and in the determination of the IR transition dipole moment directions which were required for the determination of the orientation parameters for FMNH- in PVA films. The UV/vis LD spectrum was measured over the 200-700 nm region and was resolved into contributions from three pi-->pi* transitions. The directions of the transitions are 90 degrees+/-4 degrees at 440 nm, 79 degrees+/-4 degrees at 350 nm, and 93 degrees+/-4 degrees at 290 nm with counterclockwise rotations with respect to the N5-N10 axis. Comparison of the calculated and experimentally determined transition dipole moments allowed for refined assignment of the transition dipole moment directions. To our knowledge, this is the first experimental evidence that the 350-450 nm absorption arises from two unique transitions. Remarkably, the two lowest energy transition dipole moments for FMNH- are nearly parallel to those obtained in prior studies for both oxidized and semiquinone flavin.