We report here infrared spectra of protonated and lithiated valine with varying degrees of hydration in the gas phase and interpret them with the help of DFT calculations at the B3LYP/6-31++G** level. In both the protonated and lithiated species our results clearly indicate that the solvation process is driven first by solvation of the charge site and subsequently by formation of a second solvation shell. The infrared spectra of Val x Li+ (H2O)4 and Val x H+ (H2O)4 are strikingly similar in the region of the spectrum corresponding to hydrogen-bonded stretches of donor water molecules, suggesting that in both cases similar extended water structures are formed once the charge site is solvated. In the case of the lithiated species, our spectra are consistent with a conformation change of the amino acid backbone from syn to anti accompanied by a change in the lithium binding from a NO coordination to OO coordination configuration upon addition of the third water molecule. This change in the mode of metal ion binding was also observed previously by Williams and Lemoff [J. Am. Soc. Mass Spectrom. 2004, 15, 1014-1024] using blackbody infrared radiative dissociation (BIRD). In contrast to the zwitterion formation inferred from results of the BIRD experiments upon addition of a third water molecule, our spectra, which are a more direct probe of structure, show no evidence for zwitterion formation with the addition of up to four water molecules.

We report here a new method to obtain electronic spectra of biomolecular ions that are produced in the gas phase by electrospray and cooled to approximately 10 K in a 22-pole ion trap, and we demonstrate this technique by applying it to protonated tryptophan and tyrosine. Cooling in the trap greatly simplifies the spectrum of protonated tyrosine, which exhibits a well-defined band origin and clearly resolved low frequency vibrational bands. In contrast, the spectrum of protonated tryptophan exhibits only broad features, even at low temperatures, suggesting that a fast nonradiative process broadens the individual vibronic features, even upon excitation at the electronic band origin. The method demonstrated here should be applicable to a wide variety of biological molecules.

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.

A combination of methods, including laser-induced fluorescence excitation, fluorescence-dip infrared ͑FDIR͒ spectroscopy, and UV-UV hole-burning spectroscopy, have been used to study the infrared and ultraviolet spectra of single conformations of two methyl-capped dipeptides: N-acetyl tryptophan amide ͑NATA͒ and N-acetyl tryptophan methyl amide ͑NATMA͒. Density functional theory calculations predict that all low-energy conformers of NATA and NATMA belong to one of two conformational families: C5, with its extended dipeptide backbone, or C7 eq , in which the dipeptide backbone forms a seven-membered ring joined by a H bond between the-amide NH and the-amide carbonyl groups. In NATA ͑NATMA͒, the LIF spectrum has contributions from two ͑three͒ conformers. FDIR spectroscopy has been used to record infrared spectra of the individual conformers over the 2800-3600 cm Ϫ1 region, free from interference from one another. The NH stretch region provides unequivocal evidence that one of the conformers of NATA is C5, while the other is C7 eq. Similarly, in NATMA, there are two C5 conformers, and one C7 eq structure. Several pieces of evidence are used to assign spectra to particular C5 and C7 eq conformers. NATA͑A͒ and NATMA͑B͒ are both assigned as C5͑AP͒ structures, NATA͑B͒ and NATMA͑C͒ are assigned as C7 eq ͑⌽P͒, and NATMA͑A͒ is assigned as C5͑A⌽͒. In both molecules, the C5 structures have sharp vibronic spectra, while the C7 eq conformers are characterized by a dense, highly congested spectrum involving long progressions that extend several hundred wave numbers to the red of the C5 S 1-S 0 origins. N-acetyl tryptophan ethyl ester ͑NATE͒, which can only form C5 conformers, shows only sharp transitions in its LIF spectrum due to four C5 conformers, with no evidence for the broad absorption due to C7 eq. This provides direct experimental evidence for the importance of the peptide backbone conformation in controlling the spectroscopic and photophysical properties of 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.