Microsolvation effects on the excited-state dynamics of protonated tryptophan

To better understand the complex photophysics of the amino acid tryptophan, which is widely used as a probe of protein structure and dynamics, we have measured electronic spectra of protonated, gas-phase tryptophan solvated with a controlled number of water molecules and cooled to approximately 10 K. We observe that, even at this temperature, the bare molecule exhibits a broad electronic spectrum, implying ultrafast, nonradiative decay of the excited state. Surprisingly, the addition of two water molecules sufficiently lengthens the excited-state lifetime that we obtain a fully vibrationally resolved electronic spectrum. Quantum chemical calculations at the RI-CC2/aug-cc-pVDZ level, together with TDDFT/pw based first-principles MD simulations of the excited-state dynamics, clearly demonstrate how interactions with water destabilize the photodissociative states and increase the excited-state lifetime.     

Photodissociation and spectroscopic study of cold protonated dipeptides

A photodissociation spectrometer, containing a spray ionization source and a temperature-variable multipole ion trap, has been constructed to examine the structure and reactivity of gas phase biological molecular ions at various temperatures. Ultraviolet (UV) and infrared (IR) photodissociation spectra of protonated alanyltryptophan (Ala-TrpH+) and tryptophanylglycine (Trp-GlyH+) have been measured. In UV spectra, the S1-S0 band origin of Ala-TrpH+ exhibits a significant red shift with respect to those of protonated tryptophan (TrpH+) and Trp-GlyH+. This red shift is ascribed to the stabilization of the excited state due to the strong interaction between the NH3+ group and indole ring. We also discuss the temperature effect on the structure and reactivity for these peptides. In addition to the UV photodissociation spectra of the dipeptides, IR spectra of the complex of Ala-TrpH+ with methanol are measured. IR photodissociation spectra of solvated ions show that Ala-TrpH+-methanol has the closed structure, which is consistent with the large spectral shift in UV spectrum of bare dipeptide.     

Conformation-specific infrared and ultraviolet spectroscopy of tyrosine-based protonated dipeptides

We present the spectroscopy and photofragmentation dynamics of two isomeric protonated dipeptides, H+AlaTyr and H+TyrAla, in a cold ion trap. By a combination of infrared-ultraviolet double resonance experiments and density functional theory calculations, we establish the conformations present at low temperature. Interaction of the charge at the N-terminus with the carbonyl group and the tyrosine pi-cloud seems to be critical in stabilizing the low-energy conformations. H+AlaTyr has the flexibility to allow a stronger interaction between the charge and the aromatic ring than in H+TyrAla, and this interaction may be responsible for many of the differences we observe in the former: a significant redshift in the ultraviolet spectrum, a much larger photofragmentation yield, fewer stable conformations, and the absence of fragmentation in excited electronic states.     

Conformation-specific spectroscopy and photodissociation of cold, protonated tyrosine and phenylalanine

We present here ultraviolet and infrared spectra of protonated aromatic amino acids in a cold, 22-pole ion trap. Ultraviolet photofragmentation spectra of protonated tyrosine and phenylalanine show vibronically resolved bands corresponding to different stable conformers: two for PheH+ and four in the case of TyrH+. We subsequently use the resolved UV spectra to perform conformer-specific infrared depletion spectroscopy. Comparison of the measured infrared spectra to density functional theory calculations helps assign the geometry of the various conformers, all of which exhibit NH...pi hydrogen bonds and NH...O=C interactions, with the COOH group oriented either anti or gauche to the aromatic ring. In both molecules the majority of the observed fragments result from dissociation on an excited electronic state. In TyrH+, different conformers excited with practically the same energy exhibit different fragmentation patterns, suggesting that the excited-state dynamics depend upon conformation.     

Photodissociation spectroscopy of trapped protonated tryptophan

We have coupled a quadrupole ion trap with a frequency doubled optical parametric oscillator laser. The photodissociation spectrum of the protonated tryptophan ion from 215 to 320 nm is reported. The yields of fragmentation on each mass channel as a function of the laser wavelength were obtained. We also report experiments involving multiple stages of laser induced dissociation and discuss possible structures for the fragmentation products.     

The use of van der waals molecules to identify spectroscopic origins

A technique for identifying the origin band of an electronic transition is described. The technique utilizes the increased linewidth of helium van der Waals complexes caused by vibrational predissociation when the molecular part of the complex is vibrationally excited. The method is applied to the visible spectrum of chromyl chloride, and we conclude that the d₅ band of chromyl chloride is not a second electronic origin.     

Ultrafast excited state dynamics in protonated GWG and GYG tripeptides

The excited state dynamics of two protonated tripeptides GWG and GYG has been investigated by pump/probe femtosecond measurements on photofragments, to explore the behavior of peptides where the terminal protonated amino group is not directly linked to the aromatic residue. The dynamics observed are short and surprisingly similar to the dynamics observed on the free protonated tryptophan and tyrosine aromatic amino acids. Specific photofragments observed for protonated GWG are related to the formation of a radical species WG degrees (+) after cleavage of the C(alpha)-N bond near the tryptophan residue.     

Gas-phase reactions of protonated tryptophan

The gas phase reactions of protonated tryptophan have been examined in a quadrupole ion trap using a combination of collision induced dissociation, hydrogen-deuterium exchange, regiospecific deuterium labeling and molecular orbital calculations (at the B3LYP/6-31G* level of theory). The loss of ammonia from protonated tryptophan is observed as the primary fragmentation pathway, with concomitant formation of a [M + H - NH(3)](+) ion by nucleophilic attack from the C3 position of the indole side chain. Hydrogen-deuterium exchange and regiospecific deuterium labeling reveals that scrambling of protons in the C2 and C4 positions of the indole ring, via intramolecular proton transfer from the thermodynamically preferred site of protonation at the amino nitrogen, precedes ammonia loss. Molecular orbital calculations have been employed to demonstrate that the activation barriers to intramolecular proton transfer are lower than that for NH(3) loss.     

THE PHOTOCHEMISTRY OF SPECIFIC TRYPTOPHAN RESIDUES IN PROTEINS AS ANALYZED BY THE FLUORESCENT SCANNING OF TRYPTIC PEPTIDE MAPS

Abstract— The fact that most proteins contain several tryptophans hinders the investigation of the photochemistry of a particular indole residue. A method is presented here that can be used to investigate the photochemistry of specific tryptophan residues in proteins. It consists simply of separating the peptides of a proteolytically digested protein by TLC and then scanning the peptides at the fluorescent maximum of tryptophan. The assignment of the resultant peaks to a particular peptide is based on the chromatographic comparison of the scans with peptide maps.
Using this method, the photochemistry of the tryptophan residues in alpha crystallin, a major protein of lenses, was investigated. Under photolytic conditions that mimic the transmission characteristics of the cornea (>293 nm), it was found that there is a differential photolysis of the tryptophan residues in the protein; with Trp-9 in the N-terminal peptide photolyzing at a considerably faster rate than Trp-60. In addition to tryptophan, photolytic losses of tyrosine were assessed by scanning the peptide maps at the tyrosine fluorescent maximum. Only one tyrosine residue photolyzes under these conditions. The differential photolysis of the tryptophan residues is explained in part by the presence of residues in the vicinity of the indole moieties.     

Electronic absorption spectra of the protonated polyacetylenes H2CnH+ (n = 4, 6, 8) in neon matrixes

Electronic absorption spectra of the protonated polyacetylenic chains H2CnH+ (n = 4, 6, 8) and the neutral H2C8H have been observed in 6 K neon matrixes after mass selection. The wavelength of the H2CnH+ electronic transitions depends quasi-linearly on n, typical of carbon chains. The origin band is at 286.0, 378.6, and 467.6 nm for n = 4, 6, and 8, respectively. Two ground-state vibrations of H2C4H+ in the IR absorption spectrum were also detected. On the basis of the spectroscopic trends and the assignment of the vibrational frequencies in the ground and excited electronic states, it is concluded that the H2CnH+ species are C(2v) linear carbon chains with one H atom on one end and two on the other.     

Detection of tyrosine phosphorylated peptides via skimmer collision-induced dissociation/ion trap mass spectrometry

Phosphorylation of proteins is an important post-translational protein modification in cellular response to environmental change and occurs in both prokaryotes and eukaryotes. Identification of the amino acid on individual proteins that become phosphorylated in response to extracellular stimulus is essential for understanding the mechanisms involved in the intracellular signals that these modifications facilitate. Most protein kinases catalyze the phosphorylation of proteins on serine, threonine or tyrosine. Although tyrosine phosphorylation is often the least abundant of the three major phosphorylation sites, it is important owing to its role in signal pathways. Currently available methods for the identification of phosphorylation sites can often miss low levels of tyrosine phosphorylations. This paper describes a method for the identification of phosphotyrosine-containing peptides using electrospray ionization on an ion trap mass spectrometer. Skimmer-activated collision-induced dissociation (CID) was used to generate the phosphotyrosine immonium ion at m/z 216. This method is gentle enough that the protonated molecule of the intact peptide is still observed. In-trap CID was employed for the verification of the phosphotyrosine immonium ion. Using this technique, low levels of phosphotyrosine-containing peptides can be identified from peptide mixtures separated by nanoflow micro liquid chromatography/mass spectrometry.     

Resonance theory for discrete models: methodology and isolated resonances

We here consider open quantum systems defined on discretized space, motivated by experimental and theoretical interest in the electronic conduction through nanoscale devices such as molecular junctions and quantum dots. We particularly focus on effects of resonances on the conductance through the systems. We develop a method of calculating the conductance with the use of Green's function expansion with respect to the eigenstates of the effective Hamiltonian for the open quantum systems. Unlike previous methodologies where one can treat only narrow resonances far from the band edges in a satisfactory manner with a Lorentzian profile, our method provides a novel resonance profile which can be used to describe any isolated resonance in the spectrum even close to the band edges.     

The role of tautomers in the UV absorption of urocanic acid

Tautomeric effects in the UV-absorption of trans-urocanic acid in the gas phase are investigated by means of quantum chemical calculations of sixteen tautomers at different levels, followed by absorption cross section simulations. It is shown that several trans tautomers give significant contributions to the total spectrum and that cis tautomers should not contribute to the spectrum at room temperature. The spectra of tautomers protonated at the N1 site of the imidazole ring are strongly red shifted in comparison to the spectra of tautomers protonated at the N3 site. As a consequence, excitation of the first absorption band at different wavelengths produces very different tautomeric populations. This effect helps to explain specific features observed in dispersion emission spectroscopy as well as the anomalous photophysics of urocanic acid.     

Laser spectroscopy of Si3C

The C 1B1<--X 1A1 band system of the potential interstellar species Si3C has been recorded in a silane/acetylene discharge by resonant two-color two-photon ionization spectroscopy. The origin band is located near 24,925 cm-1 (3.09 eV). Several other features in the spectrum are assigned to progressions in the Si-Si stretching modes as well as to sequence and hot band transitions. The assignment was facilitated by ab initio calculations, which also indicate that this is the strongest electronic transition of Si3C in the visible region of the spectrum. Features in the spectrum are broadened considerably (ca. 10 cm-1), and suggest an excited state lifetime of a few picoseconds. Possible reasons for the short-lived nature of the excited state are discussed.     

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 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.     

Contribution to the analysis of the predissociated rovibronic structure of the symmetric isotopomers 16O3 and 18O3 of ozone near 10,400 cm-1): [3A2(3(2)(0)) <-- X1A1(0(0)(0))] and 3B2 <-- X1A1

The absorption spectrum of ozone was recorded at low temperatures (down to -135 degrees C) by high resolution Fourier transform spectrometry and intra cavity laser absorption spectroscopy (ICLAS) near 10,400 cm-1. A preliminary analysis of the rotational structure of the absorption spectra of 16O3 and 18O3 shows that this spectral region corresponds to a superposition of two different electronic transitions, one with a very broad rotational structure, showing for the first time the asymmetric stretching frequency mode nu3 of the electronic state 3A2, the other formed by a completely diffuse band, probably the 2(1)(0) band of a new transition due to the triplet electronic state 3B2. Predissociation effects induce large broadening of the rotational lines for the transition centered at 10,473 cm-1 identified as the 3(2)(0) band of the 3A2 <-- X1A1 electronic transition. The rotational structure cannot be analyzed directly but instead the band contour method was used to confirm the symmetry of the transition and to estimate the spectroscopic constants for the 16O isotopomer. The origin of the band is at 10,473 +/- 3 cm-1 and the value of the 16O3(3A2) antisymmetric stretching frequency mode is equal to 460 +/- 2 cm-1. We believe that the diffuse band is due to the 3B2 state and is located at about 10,363 +/- 3 cm-1 for 16O3 and 10,354 +/- 3 cm-1 for 18O3. The isotopic rules confirm the different results obtained for 18O3 and 16O3.     

Control of bond-cleaving reactions of free protonated tryptophan ion by femtosecond laser pulses

The excited-state dynamics of protonated tryptophan ions is investigated by photoinduced fragmentation in the gas phase. In contrast to the neutral molecule that decays on the nanosecond time scale, the protonated species exhibits an ultrafast decay with two time constants of about 400 fs and 15 ps. In addition, after UV excitation by a pump photon at 266 nm, specific photofragments, and in particular the NH3-loss channel, can be enhanced by the absorption of a probe photon at 800 nm. The bond-cleaving reactions can thus be controlled by a variation of the pump/probe delay.     

Adaptation of a 3-D Quadrupole Ion Trap for Dipolar DC Collisional Activation

Means to allow for the application of a dipolar DC pulse to the end-cap electrodes of a three-dimensional (3-D) quadrupole ion trap for as short as a millisecond to as long as hundreds of milliseconds are described. The implementation of dipolar DC does not compromise the ability to apply AC waveforms to the end-cap electrodes at other times in the experiment. Dipolar DC provides a nonresonant means for ion acceleration by displacing ions from the center of the ion trap where they experience stronger rf electric fields, which increases the extent of micro-motion. The evolution of the product ion spectrum to higher generation products with time, as shown using protonated leucine enkephalin as a model protonated peptide, illustrates the broad-band nature of the activation. Dipolar DC activation is also shown to be effective as an ion heating approach in mimicking high amplitude short time excitation (HASTE)/pulsed Q dissociation (PQD) resonance excitation experiments that are intended to enhance the likelihood for observing low m/z products in ion trap tandem mass spectrometry.     

The use of paraquat as an NMR.- and charge-transfer-probe for solvent-exposed aromatic amino-acid side-chains

The purpose of this investigation was to find new and more potent charge-transfer probes for the study of certain aspects of polypeptide and protein conformation, especially of solvent-exposure of aromatic amino-acid side chains. N,N′-dimethyl-4,4′-dipyridylium ion (paraquat) was shown by NMR. to complex specifically with tryptophan, tyrosine, and phenylalanine. The long-wavelength absorption (electronic transitions) typical of charge-transfer complexes was detectable with tryptophan and tyrosine, not with phenylalanine. Paraquat forms slightly stronger complexes than N(1)-methyl-nicotinamidium ion, and appears to have different steric requirements. Im human calcitonin and human calcitonin-(11–32)-dokosipeptide all the aromatic amino-acid side-chains (Phe, Tyr) are accessible to paraquat in solution. This is true also for at least one of the two tyrosines and the tryptopha of ACTH-(1–24)-tetrakosipeptide, and for Trp (62) of chicken egg-white lysozyme. Paraquat is of special interest, because it generates a CT.-absorption band not only with tryptophan, but also with tyrosine, and because of its strong diamagnetic shielding effect.