Alkali Metal Complexes of the Dipeptides PheAla and AlaPhe: IRMPD Spectroscopy

The structure of the sodiated peptide GGGGGGGG-Na ϩ or G 8 -Na ϩ was investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD was carried out in both the fingerprint and N-H/O-H stretching regions. Modeling used the polarizable force field AMOEBA in conjunction with the replica-exchange molecular dynamics (REMD) method, allowing an efficient exploration of the potential energy surface. Geometries and energetics were further refined at B3LYP-D and MP2 quantum chemical levels. The IRMPD spectra indicate that there is no free C-terminus OH and that several N-Hs are free of hydrogen bonding, while several others are bound, however not very strongly. The structure must then be either of the charge solvation (CS) type with a hydrogen-bound acidic OH, or a salt bridge (SB). Extensive REMD searches generated several low-energy structures of both types. The most stable structures of each type are computed to be very close in energy. The computed energy barrier separating these structures is small enough that G 8 -Na ϩ is likely fluxional with easy proton transfer between the two peptide termini. There is, however, good agreement between experiment and computations in the entire spectral range for the CS isomer only, which thus appears to be the most likely structure of G 8 -Na ϩ at room temperature. (J Am Soc Mass Spectrom 2010, 21, 728 -738) © 2010 American Society for Mass Spectrometry T he biological importance of sodium in performing or facilitating essential biological processes, such as neurotransmission, osmotic balance, and cellular metabolism is well documented [1][2][3]. Mass spectrometric methods have been used extensively to provide insight into peptide sequences [4,5] starting from sodium-cationized species, however with considerable debate as to the structure of the parent species and the fragmentation mechanisms [6 -8]. In this context, sodiated oligoglycines have been used in the last decade as a valuable testing ground for new experimental developments designed to obtain refined energetic and/or structural data. These include ion mobility measurements for global shape information [9,10], H/D exchange extent and kinetics for isomeric/ conformational content [11], the kinetic [12, 13] and the threshold collision induced decomposition [14] methods for thermochemical measurements, as well as infrared multiple photon dissociation (IRMPD) spectroscopy [15] for identification of functional groups and their interactions. All these studies have been complemented by extensive molecular modeling as required for translating experimental data into properties of specific molecular structures.Oligoglycines owe their value as model peptides to their relative simplicity. While the number of residues is an obvious source of conformational complexity, the absence of side chains limits the number of factors shaping their structures and energies. On the one hand, the main components of sodium-molecule interactions are electrostatic and polarization, favoring m...

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Elimination Of Structural Families On the Basis Of Their Commentioning

confidence: 91%

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Structure of sodiated octa-glycine: IRMPD spectroscopy and molecular modeling

Semrouni

Balaj

Calvo

et al. 2010

“…Vibrational frequency calculations were performed on the structures optimized at the B3LYP/6-311++G(d,p) level of theory and used to determine whether optimized structures were true minima (no imaginary frequencies) or transition states (one imaginary frequency), to determine zero-point energy corrections to electronic energies (used unscaled), and to predict infrared spectra for comparison to experimental IRMPD spectra. For comparison of DFT spectra to IRMPD spectra, the computed frequencies were scaled by a factor of 0.98, which is known to be adequate at the current level of theory [53,54]. Theoretical IR spectra from the Gaussian output were convoluted with a 20 cm -1 FWHM Lorentzian line shape.…”

Section: Density Functional Theory Calculationsmentioning

confidence: 99%

Structure and Reactivity of theN-Acetyl-Cysteine Radical Cation and Anion: Does Radical Migration Occur?

Osburn

Berden

O’Hair

et al. 2011

Self Cite

The structure and reactivity of the N-acetyl-cysteine radical cation and anion were studied using ion-molecule reactions, infrared multi-photon dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations. The radical cation was generated by first nitrosylating the thiol of N-acetyl-cysteine followed by the homolytic cleavage of the S-NO bond in the gas phase. IRMPD spectroscopy coupled with DFT calculations revealed that for the radical cation the radical migrates from its initial position on the sulfur atom to the α-carbon position, which is 2.5 kJ mol -1 lower in energy. The radical migration was confirmed by time-resolved ion-molecule reactions. These results are in contrast with our previous study on cysteine methyl ester radical cation (Osburn et al., Chem. Eur. J. 2011, 17, 873-879) and the study by Sinha et al. for cysteine radical cation (Phys. Chem. Chem. Phys. 2010, 12, 9794-9800) where the radical was found to stay on the sulfur atom as formed. A similar approach allowed us to form a hydrogen-deficient radical anion of N-acetyl-cysteine, (M -2H)•-. IRMPD studies and ion-molecule reactions performed on the radical anion showed that the radical remains on the sulfur, which is the initial and more stable (by 63.6 kJ mol -1 ) position, and does not rearrange.

“…This spectrum is displayed in Figure 9, along with spectra of potassiated complexes of simpler peptides (monopeptide and dipeptide) to show the prominent features of the C-terminal group dominating the monopeptide case, the development of amide features in the dipeptide, and the complete take-over of the spectrum by the backbone amide groups in the protein [85].…”

Section: B Infrared Spectroscopy Of Ionsmentioning

confidence: 99%

Ion spectroscopy: Where did it come from; where is it now; and where is it going?

Baer¹,

Dunbar

2010

Self Cite

a large group of mass spectrometrists working in the area of ion spectroscopy. In this introduction to the field, we provide a brief history, its current state, and where it is going. Ion spectroscopy of intermediate size molecules began with photoelectron spectroscopy in the 1960s, while electronic spectroscopy of ions using the photodissociation "action spectroscopic" mode became active in the next decade. These approaches remained for many years the main source of information about ionization energies, electronic states, and electronic transitions of ions. In recent years, highresolution laser techniques coupled with pulsed field ionization and sample cooling in molecular beams have provided high precision ionization energies and vibrational frequencies of small to intermediate sized molecules, including a number of radicals. More recently, optical parametric oscillator (OPO) IR lasers and free electron lasers have been developed and employed to record the IR spectra of molecular ions in either molecular beams or ion traps. These results, in combination with theoretical ab initio molecular orbital (MO) methods, are providing unprecedented structural and energetic information about gas-phase ions. (J Am Soc Mass Spectrom 2010, 21, 681-693) © 2010 Published by Elsevier Inc. on behalf of American Society for Mass Spectrometry T here are at least three perspectives guiding research in molecular spectroscopy of ions, which have given rise to rather distinct research communities. First is the goal of finding the quantum energy levels (electronic, vibrational, rotational) with high accuracy and energy resolution. Benefiting from experimental convenience, a vast body of results of this sort has been accumulated from photoionization and photoelectron spectroscopy experiments where the initial sample is the neutral molecule corresponding to an ion of interest.Second is the question of "what color" the ion is, that is to say, taking the ion itself as the sample, observing the wavelengths and transition intensities of the optical absorptions or emissions of the ion. These experiments are difficult, but have great interest for the study of ions found in nature, as for instance among the community of astronomers trying to sort out the telescope spectra corresponding to molecular species existing in extraterrestrial environments.Third is the use of spectra as a window to the identification and structural characterization of ionic molecules formed from interesting precursors by any of a variety of ionization, ion-molecule reaction, or ionextraction techniques. Combined with mass spectrometry, this branch of ion spectroscopy has developed into a new structural approach comparable to MS/MS, thanks to its ability to distinguish small conformational or structural differences among iso-mass ions. These studies have been dominated by the use of "action spectroscopy" (multi-photon and ion tagging dissociation techniques) to provide convenient, although indirect, access to the spectra of interesting ions.The three major parts of thi...