Infrared spectroscopy of hydrated amino acids in the gas phase: protonated and lithiated valine

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.     

Infrared spectra of amino acids and peptides

Summary The ionization constants of glycine, glycylglycine, DL--alanine, and -alanine have been determined from their IR spectra.Khimiya Priodnykh Soedinenii, Vol. 3, No. 2, pp. 197–201, 1967     

Hydrogen-deuterium exchange and selective labeling of deprotonated amino acids and peptides in the gas phase

Hydrogen-deuterium exchange reactions of deprotonated amino acids and small peptides were studied. Selective labeling can be carried out at the alpha-amino group of lysine (2 of 4 labile hydrogens undergo exchange with CF3CH2OD) and the guanidine side chain of arginine (3 of 6 labile hydrogens undergo exchange with CH3CH2OD and C6H5CH2OD). Differential labeling of peptides also was accomplished, and the extent of H/D exchange is dependent on the amino acids which are present as well as their order in the chain.     

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.     

Experimental and theoretical studies of potassium cation interactions with the acidic amino acids and their amide derivatives

The binding of K(+) to aspartic acid (Asp), glutamic acid (Glu), asparagine (Asn), and glutamine (Gln) is examined in detail by studying the collision-induced dissociation (CID) of the four potassium cation-bound amino acid complexes with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Formed by electrospray ionization, these complexes have energy-dependent CID cross sections that are analyzed to provide 0 K bond energies after accounting for unimolecular decay rates, internal energy of reactant ions, and multiple ion-molecule collisions. Quantum chemical calculations for a number of geometric conformations of each K(+)(L) complex are determined at the B3LYP/6-311+G(d,p) level with single-point energies calculated at B3LYP, B3P86, and MP2(full) levels using a 6-311+G(2d,2p) basis set. Theoretical bond dissociation energies are in good agreement with the experimental values. This coordinated examination of both experimental work and quantum chemical calculations allows for a comprehensive understanding of the molecular interactions of K(+) with the Asx and Glx amino acids. K(+) binding affinities for the amide complexes are systematically stronger than those for the acid complexes by 9+/-1 kJ/mol, which is attributed to an inductive effect of the OH group in the carboxylic acid side chain. Additionally, the K(+) binding affinity for the longer-chain amino acids (Glx) is enhanced by 5+/-1 kJ/mol compared to the shorter-chain Asx because steric effects are reduced. Further, a detailed comparison between experimental and theoretical results reveals interesting differences in the binding of K(+) and Na(+) to these amino acids.     

Hydration of potassiated amino acids in the gas phase

The thermochemistry of stepwise hydration of several potassiated amino acids was studied by measuring the gas-phase equilibria, AAK(+)(H(2)O)(n-1) + H(2)O = AAK(+)(H(2)O)(n) (AA = Gly, AL, Val, Met, Pro, and Phe), using a high-pressure mass spectrometer. The AAK(+) ions were obtained by electrospray and the equilibrium constants K(n-1,n) were measured in a pulsed reaction chamber at 10 mbar bath gas, N(2), containing a known partial pressure of water vapor. Determination of the equilibrium constants at different temperatures was used to obtain the DeltaH(n)(o), DeltaS(n)(o), and DeltaG(n)(o) values. The results indicate that the water binding energy in AAK(+)(H(2)O) decreases as the K(+) affinity to AA increases. This trend in binding energies is explained in terms of changes in the side-chain substituent, which delocalize the positive charge from K(+) to AA in AAK(+) complexes, varying the AAK(+)-H(2)O electrostatic interaction.     

Infrared matrix and microwave spectroscopy of the gas phase vinylchloride-ozone reaction

The gas phase ozonolysis of vinylchloride has been investigated by linear reaction-infrared matrix and -microwave spectroscopy. The reaction is shown to produce formaldehyde and chloroethylene oxide, besides already known products. Implications for the reaction mechanism will be discussed.     

Para-hydrogen induced polarization of amino acids, peptides and deuterium-hydrogen gas

Signal Amplification by Reversible-Exchange (SABRE) is a method of hyperpolarizing substrates by polarization transfer from para-hydrogen without hydrogenation. Here, we demonstrate that this method can be applied to hyperpolarize small amounts of all proteinogenic amino acids and some chosen peptides down to the nanomole regime and can be detected in a single scan in low-magnetic fields down to 0.25 mT (10 kHz proton frequency). An outstanding feature is that depending on the chemical state of the used catalyst and the investigated amino acid or peptide, hyperpolarized hydrogen-deuterium gas is formed, which was detected with (1)H and (2)H NMR spectroscopy at low magnetic fields of B(0) = 3.9 mT (166 kHz proton frequency) and 3.2 mT (20 kHz deuterium frequency).     

Aromatic amino acids providing characteristic motifs in the Raman and SERS spectroscopy of peptides

Raman and surface-enhanced Raman spectroscopies (SERS) are potentially important tools in the characterization of biomolecules such as proteins and DNA. In this work, SERS spectra of three cysteine-containing aromatic peptides: tryptophan-cysteine, tyrosine-cysteine, and phenylalanine-cysteine, bound to Au nanoshell substrates, were obtained, and compared to their respective normal Raman spectra. While the linewidths of the SERS peaks are significantly broadened (up to 70%), no significant spectral shifts (<6 cm (-1)) of the major Stokes modes were observed between the two modalities. We show that the Raman and SERS spectra of penetratin, a cell-penetrating peptide oligomer, can be comprised quite reliably from the spectra of its constituent aromatic amino acids except in the backbone regions where the spectral intensities are critically dependent on the length and conformations of the probed molecules. From this study we conclude that, together with protein backbone groups, aromatic amino acid residues provide the overwhelmingly dominant features in the Raman and SERS spectra of peptides and proteins when present. It follows that the Raman modes of these three small constructed peptides may likely apply to the assignment of Raman and SERS features in the spectra of other peptides and proteins.     

Coded amino acids in gas phase: the shape of isoleucine

The solid alpha-amino acid isoleucine has been vaporized by laser ablation and expanded in a supersonic jet, where the molecular conformations of the isolated molecule were probed using Fourier transform microwave spectroscopy. Two conformers of neutral isoleucine have been detected in gas phase, the most stable being stabilized by an intramolecular hydrogen bond N-H...O=C and a cis-COOH arrangement. The higher energy form is stabilized by an intramolecular hydrogen bond N...H-O. The sec-butyl side chain of the amino acid adopts the same configuration in the two observed conformers, with a staggered configuration at Cbeta similar to that observed in valine and a trans arrangement of Calpha and Cdelta. Ab initio calculations at MP2/6-311++G(d,p) level reproduce satisfactorily the experimental results.     

Infrared spectroscopy of hydrogen-bonded CHCl3-SO2 in the gas phase

A molecular association between chloroform and sulfur dioxide in the gas phase at room temperature was studied by Fourier transform infrared spectroscopy. Since the intensity of the CH-stretching fundamental vibration of monomer chloroform is very weak but much stronger upon complexation, a simple subtraction procedure isolated the CH-stretching vibration spectrum of the complex. The presence of a 1:1 complex was confirmed by two dilution series, where the monomer concentrations were varied. The molecular association manifested itself as a shift of the peak absorbance of the CH-stretching vibration of CHCl3-SO2 by +7 cm(-1) and of the CD-stretching vibration of CDCl3-SO2 by +5 cm(-1) to higher wave numbers compared to monomer chloroform, accompanied by a considerable broadening of the band contour. In agreement with previous ab initio calculations, this indicates a "blueshifting" or more appropriately, a "C-H contracting" hydrogen bond between chloroform and sulfur dioxide. An estimate of the complex concentration was made based on ab initio calculations for the integrated band strength and the measured spectrum. With this estimate, the equilibrium constant Kp (295 K)=0.014 (po=10(5) Pa) for the dimerization was calculated, providing one of the very few cases where the formation of a hydrogen-bonded gas phase complex at room temperature could be quantitatively studied by infrared spectroscopy.     

Fourier transform infrared spectroscopy and theoretical study of dimethylamine dimer in the gas phase

Dimethylamine (DMA) has been studied by gas-phase Fourier transform infrared (FTIR) spectroscopy. We have identified a spectral transition that is assigned to the DMA dimer. The IR spectra of the dimer in the gas phase are obtained by spectral subtraction of spectra recorded at different pressures. The enthalpy of hydrogen bond formation was obtained for the DMA dimer by temperature-dependence measurements. We complement the experimental results with ab initio and anharmonic local mode model calculations of monomer and dimer. Compared to the monomer, our calculations show that in the dimer the N-H bond is elongated, and the NH-stretching fundamental shifts to a lower wavenumber. More importantly, the weak NH-stretching fundamental transition has a pronounced intensity increase upon complexation. However, the first NH-stretching overtone transition is not favored by the same intensity enhancement, and we do not observe the first NH-stretching overtone of the dimer. On the basis of the measured and calculated intensity of the NH-stretching transition of the dimer, the equilibrium constant for dimerization at room temperature was determined.     

High resolution photofragment spectroscopy of the gas phase methyl iodide ion

Photodissociation spectra of the molecular ion CH₃I⁺ were obtained with a three stage quadrupole mass spectrometer. Starting from the \(\tilde X^2 E_{3/2} \) ground state, theà ² E _1/2 state was excited with a stilbene 3 cw dye laser. This state predissociates to CH ₊ ³ +I. Measuring the intensity of the CH ₊ ³ fragment ions as a function of the wavelength of the exciting laser, a spectrum showing vibrational and rotational structure was obtained. The vibrational structure was assigned to three progressions ofv ₃ and new vibrational frequencies were determined. From a computer simulation of the (0, 1, 10) band rotational constants were derived. In particular, their dependence on the vibrationv ₃ was studied.     

Vibrational signatures of protonated, phosphorylated amino acids in the gas phase

Structural characterization of protonated phosphorylated serine, threonine, and tyrosine was performed using mid-infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations. The ions were generated and analyzed by an external electrospray source coupled to a Paul ion-trap type mass spectrometer. Their fragmentation was induced by the resonant absorption of multiple photons from a tunable free electron laser (FEL) beam. IRMPD spectra were recorded in the 900-1850 cm(-1) energy range and compared to the corresponding computed IR spectra. On the basis of the frequency and intensity of two independent bands in the 900-1400 cm(-1) energy range, it is possible to identify the phosphorylated residue. IRMPD spectra for a 12-residue fragment of stathmin in its phosphorylated and nonphosphorylated forms were also recorded in the 800-1400 cm(-1) energy range. The lack of spectral congestion in the 900-1300 cm(-1) region makes their distinction facile. Our results show that IRMPD spectroscopy may became a valuable tool for structural characterization of small phosphorylated peptides.     

Nucleophilicities of amino acids and peptides

The kinetics of the reactions of amino acids with stabilized diarylcarbenium ions (Ar(2)CH(+)) have been studied photometrically in aqueous solution at variable pH. In the range of 10.5 < pH < 12, the amino acids react much faster than the competing nucleophiles hydroxide and water. Though the pK(aH) values of the amino acids vary by almost four units, the nucleophilic reactivities of all primary amino groups differ by less than a factor of 4. The secondary amino group of proline is 10(2) times more reactive, and the thiolate site in cysteine exceeds the reactivities of the primary amino groups by a factor of 10(4). Nucleophilicity parameters N as defined by the correlation log k(20 degrees C) = s(N + E) have been determined in order to include amino acids into the most comprehensive nucleophilicity scales presently available, which provide a direct comparison of n-, pi-, and sigma-nucleophiles.