Characterization of Protonated Formamide-Containing Clusters by Infrared Spectroscopy and Ab Initio Calculations:  I. O-Protonation

Abstract

Characterization of protonated formamide clusters by vibrational predissociation spectroscopy confirms theoretical predictions that O-protonation occurs in preference to N-protonation in formamide. The confirmation is made from a close comparison of the infrared spectra of H + [HC(O)NH 2 ] 3 and NH 4 + [HC(O)NH 2 ] 3 produced by a supersonic expansion with the spectra produced by ab initio calculations. For NH 4 + [HC(O)NH 2 ] 3 , prominent and well-resolved vibrational features are observed at 3436 and 3554 cm -1 . They derive, respectively, from the symmetric and asymmetric NH 2 stretching motions of the three formamide molecules linked separately to the NH 4 + ion core via three N-H + ‚‚‚O hydrogen bonds. Similarly distinct absorption features are also found for H + [HC(O)NH 2 ] 3 ; moreover, they differ in frequency from the corresponding vibrational modes of NH 4 + [HC(O)NH 2 ] 3 by less than 10 cm -1 . The result is consistent with a picture of proton attachment to the oxygen atom, rather than the nitrogen atom in H + [HC(O)NH 2 ] 3 . We provide in this work both spectroscopic and computational evidence for the O-protonation of formamide and its clusters in the gas phase.

Secondary and tertiary structures of gaseous protein ions characterized by electron capture dissociation mass spectrometry and photofragment spectroscopy

“…These are greatly increased in their (Ac-Lys-OMe) 2 (Ac-Asp-OH)H ϩ trimer in which salt bridge stabilization is possible. Hydrogen-bonded stretching frequencies are usually several hundred wavenumbers less than the corresponding free stretching frequencies (40,41), consistent with hydrogen bonding as a major factor in the tertiary structure of the 6ϩ to 9ϩ ions. This photodissociation, apparently a multiphoton process, requires further study.…”

Progressive Stabilization of Zwitterionic Structures in [H(Ser)2–8]+ Studied by Infrared Photodissociation Spectroscopy

“…Because of the complexity of the system, even for monomeric serine itself, [24,25] a complete search for all possible potential minima was impractical. Nonetheless, a wide range of hydrogen-bonding network structures, including those of neutral and zwitterionic forms, were designed based on our previous studies of protonated ammonia, [19] methanol, [18] and formamide [26] clusters and optimized with the semiempirical method, AM1. Ten salt-bridge conformations and 100 ionmolecule conformations were then selected and optimized by the DFT calculation at the B3LYP/6-31 + G* level.…”

Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase

“…Several ways of overcoming the number density restriction have now been developed, each based upon the coupling of ionisation techniques such as electro-spray (ESI), or matrix assisted laser desorption (MALDI), [17][18][19][20][21][22][23][24][25], or electron impact, [26][27][28][29][30][31][32][33] or electrical discharge [34][35][36][37][38] with mass filtering, and cumulative storage in ion traps to enhance their number densities. Their molecular structures have been probed through resonant single, or multiphoton infrared photodissociation spectroscopy.…”

“…Their molecular structures have been probed through resonant single, or multiphoton infrared photodissociation spectroscopy. In general, single photon absorption is sufficient for dissociation of weakly bound complexes (typically, with 'reporter' partners such as Ar, N 2 or H 2 O) [26][27][28][29][30][31][32][33][34][35][36][37][38] but resonantly enhanced multi-photon absorption is required to fragment the bare, uncomplexed ions or proton bound complexes [17,21,22]. Comparisons with high-level quantum chemical calculations facilitate spectral assignments to specific structures and the sensitivity of their near infrared bands, in particular those associated with OH and NH stretching modes, to local hydrogen bonded environments, identifies specific inter-and intramolecular interactions.…”

“…On the negative side (but see below) the resolution is currently inferior to that provided by infrared ion-dip spectroscopy of jet-cooled neutral molecules [1][2][3][4][5][6][7]14] and protonated molecular complexes [26][27][28][29][30][31][32][33][34][35][36][37][38] and the width of the spectral bands limits the ability to distinguish between species with similar vibrational spectra. The NH stretch region of APE where a partially resolved shoulder on the principal band (3360 cm -1 ) was tentatively assigned to an alternative complex, see Figure 4, provides a good example.…”