Inverse Sandwich Cyclopentadienyl Complexes of Sodium in the Gas Phase.

Infrared multiple photon dissociation (IRMPD) experiments and electronic structure computations have been used to explore the structures and energetics of binding in gas phase sodium cyclopentadienyl complexes of the general form Na nCp n-1+. Computational work for the analogous anionic Na nCp n+1- complexes reveals nearly identical energetics for the loss of neutral NaCp units from both cationic and anionic species leading to the conclusion that the binding in the gas phase species is largely electrostatic, arising primarily from ion-ion and ion-dipole interactions. This is supported by an examination of the molecular orbitals of these species, which show no orbital overlap between the Na and Cp moieties. Observation of peaks in the IRMPD spectra, which do not correspond to any of the computed linear absorption frequencies, strongly suggest the contribution of overtone and combination bands.

Deamidation reactions of protonated asparagine and glutamine investigated by ion spectroscopy.

RATIONALE: Deamidation of Asn and Gln residues is a primary route for spontaneous post-translational protein modification. Several structures have been proposed for the deamidation products of the protonated amino acids. Here we verify these structures by ion spectroscopy, as well as the structures of parallel and sequential fragmentation products. METHODS: Infrared ion spectroscopy using the free electron laser FELIX has been applied to the reaction products from deamidation of protonated glutamine and asparagine in a tandem mass spectrometer. IR spectra were recorded over the 800-1900 cm(-1) spectral range by infrared multiple-photon dissociation (IRMPD) spectroscopy. Molecular structures of the fragment ions are derived from comparison of the experimental spectra with spectra predicted for different candidate structures by density functional theory (DFT) calculations. RESULTS: [AsnH(+) -NH3](+) is found to possess a 3-aminosuccinic anhydride structure protonated on the amino group. The dissociation reaction involving loss of H2O and CO forms a linear immonium ion. For [GlnH(+)-NH3](+), the N-terminal nitrogen acts as the nucleophile leading to an oxo-proline product ion structure. For [GlnH(+)-NH3](+), a sequential loss of [CO + H2O] is found, leading to a pyrolidone-like structure. We also confirm by IR spectroscopy that dehydration of protonated aspartic acid (AspH(+)) and glutamic acid (GluH(+)) leads to identical structures as to those found for the loss of NH3 from AsnH(+) and GlnH(+). CONCLUSIONS: The structure determined for AsnH(+) is in agreement with the suggested structure derived from measured and computed activation energies. IR ion spectra for the NH3 -loss product from GlnH(+) establish that a different reaction mechanism occurs for this species as compared to AsnH(+). For both amino acids, loss of NH3 occurs from the side chain.

Divalent Metal-Ion Complexes with Dipeptide Ligands Having Phe and His Side-Chain Anchors: Effects of Sequence, Metal Ion, and Anchor.

Conformational preferences have been surveyed for divalent metal cation complexes with the dipeptide ligands AlaPhe, PheAla, GlyHis, and HisGly. Density functional theory results for a full set of complexes are presented, and previous experimental infrared spectra, supplemented by a number of newly recorded spectra obtained with infrared multiple photon dissociation spectroscopy, provide experimental verification of the preferred conformations in most cases. The overall structural features of these complexes are shown, and attention is given to comparisons involving peptide sequence, nature of the metal ion, and nature of the side-chain anchor. A regular progression is observed as a function of binding strength, whereby the weakly binding metal ions (Ba(2+) to Ca(2+)) transition from carboxylate zwitterion (ZW) binding to charge-solvated (CS) binding, while the stronger binding metal ions (Ca(2+) to Mg(2+) to Ni(2+)) transition from CS binding to metal-ion-backbone binding (Iminol) by direct metal-nitrogen bonds to the deprotonated amide nitrogens. Two new sequence-dependent reversals are found between ZW and CS binding modes, such that Ba(2+) and Ca(2+) prefer ZW binding in the GlyHis case but prefer CS binding in the HisGly case. The overall binding strength for a given metal ion is not strongly dependent on the sequence, but the histidine peptides are significantly more strongly bound (by 50-100 kJ mol(-1)) than the phenylalanine peptides.

Gas-phase solvation of protonated amino acids by methanol.

The enthalpy and entropy changes for the formation of the 1:1 complexes of methanol with various gaseous protonated amino acids have been measured using pulsed-ionization high-pressure mass spectrometry. The enthalpy changes for formation of the clusters Gly(MeOH)H(+), Ala(MeOH)H(+), Val(MeOH)H(+), Leu(MeOH)H(+), Ile(MeOH)H(+), and Pro(MeOH)H(+) have been determined to be -92.0, -83.3, -82.4, -79.5, -78.7, and -73.6 kJ mol(-1), respectively. These values agree very well with the energetic values computed at the MP2(full)/6-311++G(2d,2p)//B3LYP/6-311+G(d,p) level of theory for the lowest energy adducts in each system. Both experimental observations and computational determinations of the potential energy surface for the glycine system suggest that a mixture of low-lying isomers may be present for each of the cluster systems examined. The primary structural motif for these clusters is the coordination of the methanol molecule to the ammonium group of the protonated amino acid via a strong ionic hydrogen bond. For the amino acids studied here, computational results reveal that one methanol molecule does not sufficiently stabilize any zwitterionic structure such that no appreciable extent of proton transfer from the amino acid to methanol was observed.

Structural investigation of protonated azidothymidine and protonated dimer.

Infrared multiple photon dissociation (IRMPD) spectroscopy experiments and quantum chemical calculations have been used to explore the possible structures of protonated azidothymidine and the corresponding protonated dimer. Many interesting differences between the protonated and neutral forms of azidothymidine were found, particularly associated with keto-enol tautomerization. Comparison of computational vibrational and the experimental IMRPD spectra show good agreement and give confidence that the dominant protonated species has been identified. The protonated dimer of azidothymidine exhibits three intramolecular hydrogen bonds. The IRMPD spectrum of the protonated dimer is consistent with the spectrum of the most stable computational structure. This work brings to light interesting keto-enol tautomerization and exocyclic hydrogen bonding involving azidothymidine and its protonated dimer. The fact that one dominant protonated species is observed in the gas phase, despite both the keto and enol structures being similar in energy, is proposed to be the direct result of the electrospray ionization process in which the dominant protonated dimer structure dissociates in the most energetically favorable way.

Consecutive fragmentation mechanisms of protonated ferulic acid probed by infrared multiple photon dissociation spectroscopy and electronic structure calculations.

Protonated ferulic acid and its principle fragment ion have been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311 + G(d,p) level of theory. Due to its extensively conjugated structure, protonated ferulic acid is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. The first pathway involves proton transfer, resulting in the loss of water and subsequently carbon monoxide, producing fragment ions m/z 177 and 149, respectively. Optimization of m/z 177 yields a species containing an acylium group, which is supported by a diagnostic peak in the IRMPD spectrum at 2168 cm(-1). The second pathway involves an alternate proton transfer leading to loss of methanol and rearrangement to a five-membered ring.

Experimental and theoretical investigation of the proton-bound dimer of lysine.

The structure of the proton-bound lysine dimer has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations. The structures of different possible isomers of the proton-bound lysine dimer have been optimized at the B3LYP/6-31 + G(d) level of theory and IR spectra calculated using the same computational method. Based on relative Gibbs free energies (298 K) calculated at the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d) level of theory, LL-CS01, and followed closely (1.1 kJ mol(-1)) by LL-CS02 are the most stable non-zwitterionic isomers. At the MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + (d,p) levels of theory, isomer LL-CS02 is favored by 3.0 and 2.3 kJ mol(-1), respectively. The relative Gibbs free energies calculated by the aforementioned levels of theory for LL-CS01 and LL-CS02 are very close and strongly suggest that diagnostic vibrational signatures found in the IRMPD spectrum of the proton-bound dimer of lysine can be attributed to the existence of both isomers. LL-ZW01 is the most stable zwitterionic isomer, in which the zwitterionic structure of the neutral lysine is well stabilized by the protonated lysine moiety via a very strong intermolecular hydrogen bond. At the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d), MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + G(d,p) levels of theory, the most stable zwitterionic isomer (LL-ZW01) is less favored than LL-CS01 by 7.3, 4.1 and 2.3 kJ mol(-1), respectively. The experimental IRMPD spectrum also confirms that the proton-bound dimer of lysine largely exists as charge-solvated isomers. Investigation of zwitterionic and charge-solvated species of amino acids in the gas phase will aid in a further understanding of structure, property, and function of biological molecules.

Tridentate ionic hydrogen-bonding interactions of the 5-fluorocytosine cationic dimer and other 5-fluorocytosine analogues characterized by IRMPD spectroscopy and electronic structure calculations.

Ionic hydrogen-bonding interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, along with the cationic (proton-bound) dimer have been characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD action spectra, in combination with calculated spectra and relative energetics, indicate that it is most probable that predominantly a single isomer exists in each experiment. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest-energy isomer convincingly matches the experimental spectrum. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) involving a tridentate ionic hydrogen-bonding interaction. The three sites of intermolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significant calculated binding energy of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, suggests that a tridentate-proton-bound dimer was observed predominantly in the experiments. Comparison of the calculated relative Gibbs free energies (298 K) for this species and several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV.

Infrared vibrational spectra as a structural probe of gaseous ions formed by caffeine and theophylline.

Ionic hydrogen bond (IHB) interactions, resulting from the association of ammonia and the two protonated methylxanthine derivatives, caffeine and theophylline, have been characterized using infrared multiphoton dissociation (IRMPD) spectroscopy and electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. The proton-bound dimer (PBD) of caffeine and ammonia exhibits a low binding energy and was found to be elusive under the experimental conditions due, most probably, to collision-induced dissociation of the complex with helium buffer gas before IRMPD irradiation. The IRMPD spectrum of a PBD of theophylline and ammonia was obtained and revealed bidentate IHB formation within the complex, which greatly increased the binding energy relative to the most stable isomer of the PBD of caffeine and ammonia. The IRMPD spectra of the protonated forms of caffeine and theophylline have also been obtained. The spectrum of protonated caffeine showed dominant protonation at the N(9) site, whereas the spectrum of protonated theophylline showed a mixture of two isomers. The first protonated isomer of theophylline exhibits protonation at the N(9) site and the second isomer demonstrated protonation at the C(6) carbonyl oxygen. The protonated carbonyl isomer of theophylline cannot be produced as a result of direct protonation and is thus suggested to be a consequence of proton-transport catalysis (PTC) initiated by the electrostatic interaction between water and N(9) protonated theophylline. Calculated anharmonic spectra have been simulated at the B3LYP/6-311+G(d,p) level of theory. It is shown that calculated anharmonic frequencies significantly outperform calculated harmonic frequencies in providing simulated IRMPD spectra in all cases.