IRMPD Spectroscopy of a Protonated,Phosphorylated Dipeptide

The protonated, phosphorylated dipeptide [GpY+H]⁺ is characterized by mid‐infrared multiple‐photon dissociation (IRMPD) spectroscopy and quantum‐chemical calculations. The ions are generated in an external electrospray source and analyzed in a Fourier transform ion cyclotron resonance mass spectrometer, and their fragmentation is induced by resonant absorption of multiple photons emitted by a tunable free‐electron laser. The IRMPD spectra are recorded in the 900–1730 cm^?1 range and compared to the absorption spectra computed for the lowest energy structures. A detailed calibration of computational levels, including B3LYP‐D and coupled cluster, is carried out to obtain reliable relative energies of the low‐energy conformers. It turns out that a single structure can be invoked to assign the IRMPD spectrum. Protonation at the N terminus leads to the formation of a strong ionic hydrogen bond with the phosphate P?O group in all low‐energy structures. This leads to a P?O stretching frequency for [GpY+H]⁺ that is closer to that of [pS+H]⁺ than to that of [pY+H]⁺ and thus demonstrates the sensitivity of this mode to the phosphate environment. The COP phosphate ester stretching mode is confirmed to be an intrinsic diagnostic for identification of which type of amino acid is phosphorylated.     

Infrared Multiple Photon Dissociation Spectroscopy of Hydrated Cobalt Anions Doped with Carbon Dioxide CoCO2(H2O)n−, n=1–10, in the C−O Stretch Region

We investigate anionic [Co,CO₂,nH₂O]⁻ clusters as model systems for the electrochemical activation of CO₂ by infrared multiple photon dissociation (IRMPD) spectroscopy in the range of 1250–2234 cm⁻¹ using an FT-ICR mass spectrometer. We show that both CO₂ and H₂O are activated in a significant fraction of the [Co,CO₂,H₂O]⁻ clusters since it dissociates by CO loss, and the IR spectrum exhibits the characteristic C−O stretching frequency. About 25 % of the ion population can be dissociated by pumping the C−O stretching mode. With the help of quantum chemical calculations, we assign the structure of this ion as Co(CO)(OH)₂⁻. However, calculations find Co(HCOO)(OH)⁻ as the global minimum, which is stable against IRMPD under the conditions of our experiment. Weak features around 1590–1730 cm⁻¹ are most likely due to higher lying isomers of the composition Co(HOCO)(OH)⁻. Upon additional hydration, all species [Co,CO₂,nH₂O]⁻, n≥2, undergo IRMPD through loss of H₂O molecules as a relatively weakly bound messenger. The main spectral features are the C−O stretching mode of the CO ligand around 1900 cm⁻¹, the water bending mode mixed with the antisymmetric C−O stretching mode of the HCOO⁻ ligand around 1580–1730 cm⁻¹, and the symmetric C−O stretching mode of the HCOO⁻ ligand around 1300 cm⁻¹. A weak feature above 2000 cm⁻¹ is assigned to water combination bands. The spectral assignment clearly indicates the presence of at least two distinct isomers for n ≥2.     

2,4-Dihydroxy and O2 Protonated Tautomers of dThd and Thd Coexist in the Gas Phase: Methylation Alters Protonation Preferences versus dUrd and Urd

The gas-phase structures of protonated thymidine, [dThd + H]⁺, and its modified form, protonated 5-methyluridine, [Thd + H]⁺, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy combined with electronic structure calculations. IRMPD action spectra are measured over the ranges extending from ~600 to 1900 cm^–1 and ~2800 to 3800 cm^–1 using the FELIX free electron laser and an optical parametric oscillator/amplifier (OPO/OPA) laser system, respectively. Comparisons between the B3LYP/6-311+G(d,p) linear IR spectra calculated for the stable low-energy conformers and the measured IRMPD spectra are used to determine the most favorable tautomeric conformations of [dThd + H]⁺ and [Thd + H]⁺ and to identify those populated in the experiments. Both B3LYP and MP2 levels of theory predict a minor 2,4-dihydroxy tautomer as the ground-state conformer of [dThd + H]⁺ and [Thd + H]⁺ indicating that the 2'-hydroxyl substituent of Thd does not exert a significant impact on the structural features. [dThd + H]⁺ and [Thd + H]⁺ share parallel IRMPD spectral profiles and yields in both the FELIX and OPO regions. Comparisons between the measured IRMPD and calculated IR spectra suggest that minor 2,4-dihydroxy tautomers and O2 protonated conformers of [dThd + H]⁺ and [Thd + H]⁺ are populated in the experiments. Comparison of this work to our previous IRMPD spectroscopy study of protonated 2'-deoxyuridine and uridine suggests that the 5-methyl substituent alters the preferences of O2 versus O4 protonation.

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Effects of Aromatic Fluorine Substitution on Protonated Neurotransmitters: The Case of 2‐Phenylethylamine

Fluorination of pharmaceutical compounds is a common tool to modulate their physiochemical properties. We determine the effects of site‐specific aromatic fluorine substitution on the geometric, energetic, vibrational, and electronic properties of the protonated neurotransmitter 2‐phenylethylamine (xF‐H⁺PEA, x=ortho, meta, para) by infrared multiphoton photodissociation (IRMPD) in the fingerprint range (600–1750 cm^?1) and quantum chemical calculations at the B3LYP‐D3/aug‐cc‐pVTZ level. The IRMPD spectra of all ions are assigned to their folded gauche conformers stabilized by intramolecular NH⁺???π hydrogen bonds (H‐bonds) between the protonated amino group and the aromatic ring. H→F substitution reduces the symmetry and allows for additional NH⁺???F interactions in oF‐H⁺PEA, leading to three distinct gauche conformers. In comparison to oF‐H⁺PEA, the fluorination effects on the energy landscape (energy ordering and isomerization barriers) in pF‐H⁺PEA and mF‐H⁺PEA with one and two gauche conformers are less pronounced. The strengths of the intramolecular NH⁺???F and NH⁺???π bonds are analyzed by the noncovalent interaction (NCI) method.     

Spectroscopic evidence for an oxazolone structure of the b2 fragment ion from protonated tri-alanine

Infrared multiple photon dissociation (IRMPD) spectroscopy is used to identify the structure of the b ₂⁺ ion generated from protonated tri-alanine by collision induced dissociation (CID). The IRMPD spectrum of b ₂⁺ differs markedly from that of protonated cyclo-alanine-alanine, demonstrating that the product is not a diketopiperazine. Instead, comparison of the IRMPD spectrum of b ₂⁺ to spectra predicted by density functional theory provides compelling evidence for an oxazolone structure protonated at the oxazolone N-atom.     

The Shape of the Simplest Non-proteinogenic Amino Acid α-Aminoisobutyric Acid (Aib)

The simplest non-proteinogenic amino acid α-aminoisobutyric acid (Aib), an analogue of glycine and alanine, has been vaporized by laser ablation and probed by high-resolution Fourier transform microwave spectroscopic techniques. Comparison of the experimental rotational and ¹⁴N nuclear quadrupole constants with that predicted ab initio has allowed the identification of three conformers of Aib exhibiting three types of hydrogen-bond interactions I (NH⋅⋅⋅O=C, cis-COOH), II (OH⋅⋅⋅N, trans-COOH), and III (N−H⋅⋅⋅O−H, cis-COOH) within the amino acid backbone. The observation of conformer III, not detected previously for related proteinogenic amino acids with a nonpolar side chain in a supersonic expansion, indicates that the presence of the methyl groups should restrict the conformational relaxation from conformer Aib-III to Aib-I. For conformer Aib-II, the rotational spectra of the ¹³C isotopomers reveal a tunneling motion arising from the two equivalent methyl groups in the molecule. The observation of a single spectrum at the midpoint between those predicted for the two ¹³C of the methyl groups has been explained by considering a double-minimum potential function with a low-energy interconversion barrier for a large amplitude internal motion. This singular fact has been corroborated by the anomalous centrifugal distortion effects determined in conformer Aib-II.     

Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid

Two conformers of protonated pyruvate, CH₃C⁺(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the C? C? C plane have been studied using the ab initio SCF/3-21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the C? COO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH₃COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a C? COO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6-311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone-type isomer of protonated pyruvate, which contains a C? C? O ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3-21G basis set. The most stable complex is predicted to occur between trans-methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ? OC hydrogen bond. © 1993 John Wiley & Sons, Inc.     

Quantum chemical topology: The electronic structure of the alkaline nitrites MONO (M = Li,Na, K) studied by means of topological analysis of the electron localization function

In the search of the protocovalent bonding, previously recognized in the nitrous acid (HONO), a nature of the chemical bonds in the alkaline nitrites MONO (M = Li, Na, K) has been studied by means of the topological analysis of the Electron Localization Function (ELF) and Electron Localizability Indicator (ELI‐D). Calculations carried out with the B3LYP and MP2(full) methods, in conjunction with the aug‐cc‐pVTZ and 6‐311++G(3df,3pd) basis sets, revealed the cis (C_2v, more stable) and trans (C_s) isomers as minima on PES. Alkaline nitrites consist of the alkali metal cation M^δ+ interacting, mainly via electrostatic forces, with the nitrite anion [ONO]^δ− (δ ≈ 1e). The covalent N O bonds are characterized by disynaptic basins V(N,O) with the basin populations: 1.58÷1.62e for cis‐M^δ+[ONO]^δ− but 1.39÷1.49e for single N O bond and 1.81÷1.87e for formally double NO bond in trans M^δ+[O NO]^δ−. The protocovalent nitrogen–oxygen bond has not been observed. The N O bonds are slightly polarized towards the nitrogen atom with the polarity index p_NO ≤ 0.12. Two different sets of the hybrid (Lewis) structures are compared leading to different pictures of the bonding. According to NBO data there is a delocalization between the single N O and double NO type bonds, meanwhile results of the ELF analysis emphasize an electron delocalization between the single N O and ionic O⁻N⁺ hybrids. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Stereochemical effects in the chemical ionization mass spectra of cyclic diols

The chemical ionization mass spectra of configurational isomers of many cyclic diols give substantial differences which are characteristic of their stereochemistry. For the cis-isomer of 1,3- and 1,4-cyclohexanediols, formation of a stable intramolecular proton bridge involving the OH groups gives rise to dominant MH⁺ peaks, suppressing the (M-H)⁺ peaks found in the spectra of the trans-isomers and monoalcohols. The stability of the proton bridge in cis-1,3-cyclohexanediol structures is decreased by a sterically interfering cis-5-methyl substituent, but increased by a cis-5-OH group due to additional proton solvation. cis-Stereochemistry also gives increased formation of the dimeric M₂H⁺ ions, but decreased formation of trimers, at higher diol concentrations, for the 1,3- and 1,4-diols. The similarity of the CI spectra of cis- and trans-1,2-cyclohexanediol are explicable in terms of the similarities of the most stable proton-bridged conformers; the reduced ring flexibility in cis- and trans-1,2-cyclopentanediols makes such similar structures unfavorable, as shown by the substantial differences between their CI spectra. The substantial, but expected, variations in behavior with temperature and reagent gas are useful for maximizing stereochemical effects on CI spectra; conditions of lowest energy are usually, but not always, the most useful.     

Cover Feature: OH Radical-Induced Oxidation in Nucleosides and Nucleotides Unraveled by Tandem Mass Spectrometry and Infrared Multiple Photon Dissociation Spectroscopy (ChemPhysChem 23/2023)

OH⋅-induced oxidation products of DNA nucleosides and nucleotides have been structurally characterized by collision-induced dissociation tandem mass spectrometry (CID-MS²) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. CID-MS² results have shown that the addition of one oxygen atom occurs on the nucleobase moiety. The gas-phase geometries of +16 mass increment products of 2’-deoxyadenosine (dA(O)H⁺), 2’-deoxyadenosine 5’-monophosphate (dAMP(O)H⁺), 2’-deoxycytidine (dC(O)H⁺), and 2’-deoxycytidine 5’-monophosphate (dCMP(O)H⁺) are extensively investigated by IRMPD spectroscopy and quantum-chemical calculations. We show that a carbonyl group is formed at the C8 position after oxidation of 2’-deoxyadenosine and its monophosphate derivative. For 2’-deoxycytidine and its monophosphate derivative, the oxygen atom is added to the C5 position to form a C−OH group. IRMPD spectroscopy has been employed for the first time to provide direct structural information on oxidative lesions in DNA model systems.     

NMR-Spectroscopic, computational and mass-spectrometric investigations on the cis/trans analogues of 2,3,4-trihydronaphthalene-1-one

NMR-Spectroscopic, computational and mass-spectrometric studies of the cis/trans isomers of N-[8-(acetylamino)-4-(2,2-dimethyl-1,1-diphenyl-silapropoxy)-6-fluoro-5-methyl-1-one-2,3,4-trihydronaphthyl]acetamide (1a and 1b), obtained as intermediates in the synthesis of an important class of alkaloid molecules, are reported. ¹H and ¹³C NMR analyses show an unusual axial preference of the TBDPSi- (tert-butyldiphenylsilyl) group in position 4 in both the isomers. Mass spectrometric evidence demonstrates that trans isomer has a higher affinity for ammonium ions than the cis isomer and that only the ammonium adduct [1b+NH₄]⁺ and the protonated molecule [1b+H]⁺ show the fragmentation in which loss of benzene is observed. Moreover, molecular mechanics and semi-empirical calculations indicate that a group of trans conformers tend to place one of the phenyl rings of the TBDPSiO- group in a offset π-stacked geometry with the compound's aromatic ring. The combination and the detailed analyses of these experimental and theoretical results could support the π-π interaction obtained as a conformational preference in the trans isomer.     

Stereochemical applications of mass spectrometry. II—Chemical ionization mass spectra of isomeric dicarboxylic acids and derivatives

The H₂ and CH₄, chemical ionization mass spectra of the cis dicarboxylic acids, maleic and citraconic acid, show much more extensive loss of H₂O from [MH]⁺ than the trans isomers, fumaric acid and mesaconic acid. Similarly, esters of maleic acid show a much more facile loss of ROH (R=alkyl or phenyl) from [MH]⁺ than do esters of fumaric acid. Similar differences are observed in the chemical ionization mass spectra of the isomeric phthalic and isophthalic acids and derivatives, where the ortho isomers show more extensive fragmentation of [MH]⁺ than the meta isomers. The facile fragmentation of [MH]⁺ for the cis and ortho isomers is attributed to ROH elimination involving interaction between the two carboxylate functions and forming the stable cyclic anhydride structure for the fragment ion. By contrast ROH elimination from [MH]⁺ for the trans and metu isomers requires a symmetry-forbidden [1,3]-H migration in the carboxyl protonated species and cannot lead to the cyclic anhydride structure. The chemical ionization mass spectra of cis and trans cyclohexane-1,2-dicarboxylic acids are essentially identical and show extensive fragmentation of the [IMH]⁺ ion. Experiments using deuterium labelling show extensive carboxyl group interactions for both isomers. The chemical ionization mass spectra of maleanilic and phthalanilic acids and of the related anhydrides and imides also are reported, as are the electron impact mass spectra of diphenyl maleate, diphenyl fumarate, diphenyl phthalate, maleanilic acid and phthalanilic acid.     

An experimental and ab inttio molecular orbital study of benzaldehyde and isomeric phthalaldehydes

Analysis of the dipole moments of phthalaldehyde, isophthalaldehyde and terephthalaldehyde in benzene at 13.7 and 54.3°C indicates that the first two molecules exist mainly in a cis-trans conformation, and that the third is present as a nearly equimolecular mixture of cis and trans conformera. For isophthalaldehyde and terephthalaldehyde, these results are supported by the total molecular energies of the conformers obtained using STO-3G ab initio molecular orbital calculations. The π-electron distribution in benzaldehyde and all planar conformers of the three isomeric phthalaldehydes, the dipole moments and ^πc-co Mulliken overlap populations have also been calculated and are briefly discussed.     

Stereochemical applications of mass spectrometry. 3—Energy dependence of the fragmentation of stereoisomeric methylcyclohexanols

Breakdown graphs have been constructed from charge exchange data for the epimeric 2-methyl-, 3-methyl- and 4-methyl-cyclohexanols. Although the breakdown graphs for epimeric pairs are essentially identical above ～12 eV recombination energy, significant differences are observed for the epimeric 2-methyl- and 4-methyl-cyclohexanols at low internal energies. For the 2-methylcyclohexanols the ratio ([M? H₂O]^+·/[M]^+·)_cis/([M? H₂O]^+·/[M]^+·)_trans is 3.2 in the [C₆F₆]^+· charge exchange mass spectra. This is attributed to both energetic and conformational effects which favour the stereospecific cis-1,4-H₂O elimination for the cis epimer. The breakdown graph for trans-4-methylcyclohexanol shows a sharp peak in the abundance of the [M? H₂O]^+· ion at ～10 eV recombination energy which is absent from the breakdown graph for the cis epimer. This peak is attributed to the stereospecific cis-1,4-elimination of water from the molecular ion of the trans isomer; the reaction appears to have a low critical energy but a very unfavourable frequency factor, and alternative modes of water loss common to both epimers are observed at higher energies. As a result, in the [C₆F₆]^+· charge exchange mass spectra the ([M? H₂O]^+·/[M]^+·)_trans/([M? H₂O]^+·/[M]^+·)_cis ratio is ～24, compared to the value of 13 observed in the 70 eV EI mass spectra. No differences are observed in either the metastable ion abundances or the associated kinetic energy releases for epimeric molecules.     

Nachweis einer ‘Wagner-Meerwein’- Ringkontraktion bei der Protoneninduzierten H2O-Eliminierung aus Cyclohexan-1.2-diol

From collisional activation data it is concluded that the non-decomposing [MH? H₂O]⁺ ions from both cis-and trans-1,2-cyclohexanediol possess the structure of protonated cyclopentanecarboxaldehyde. The mechanism of this process as well as alternatives are discussed.     

Synthesis and physico-chemical characterization of coordination compounds of 3d metals with bis(hydroxylammonium)bicyclo[2.2.1]-hept-5-en-endo-2,3-cis-dicarboxylate

Summary The reaction of aqueous solutions of 3d metal salts with bis(hydroxylammonium) bicyclo[2.2.1]-hept-5-en-endo-2,3-cis-dicarboxylate in a 12 mole ratio yielded complexes of the general formula [MⁿL₂(NH₃OH)₂]·nH₂O and [Fe^IIIL₂(NH₃OH)H₂O]·H₂O, where M^II=Mn, Fe, Co, Ni, Cu and Zn, and L=bicyclo[2.2.1]-hept-5-en-endo-2,3-cis-dicarboxylate dianion.The compounds were characterized by i.r. spectra and thermal analysis. For all complexes, an octahedral structure is proposed which is formed bytrans coordination of two bidentate (OO) ligands (L) and two NH₃OH⁺ cations attrans positions, coordinated also through oxygen atoms; and similarlytrans positions for NH₃OH⁺ and H₂O in the case of the Fe^III complex.     

Substitution reactions under NH3 chemical ionization conditions in cis-/trans-1,2-dihydroxybenzosuberans

The nucleophilic substitution reaction under NH₃ chemical ionization (CI) conditions in cis- and trans-1,2-dihydroxybenzosuberans (1–4) has been studied with the help of ND₃ CI and metastable data. The results indicate that in the parent diols 1 (cis) and 2 (trans), the substitution ion [M_sH]⁺, is produced mainly by the loss of H₂O from the [MNH₄]⁺ ion (S_Ni reaction) while in their 7-methoxy derivatives 3 and 4, the ion-molecule reaction between [M? OH]⁺ and NH₃ seems to be the major pathway for the formation of [M_sH]⁺. The substitution ion from 1 and 2 and the [MH]⁺ ion from trans-1-amino-2-hydroxybenzosuberan give similar collision-induced dissociation mass-analysed ion kinetic energy spectra. Interestingly, their diacetates do not undergo the substitution reaction.     

Diagnostic NH and OH Vibrations for Oxazolone and Diketopiperazine Structures: b<Subscript>2</Subscript> from Protonated Triglycine

We present infrared multiple photon dissociation (IRMPD) spectra in the hydrogen stretching region of the simplest b fragment, b₂ from protonated triglycine, contrasted to that of protonated cyclo(Gly-Gly). Both spectra confirm the presence of intense, diagnostic vibrations linked to the site of proton attachment. Protonated cyclo(Gly-Gly) serves as a reference spectrum for the diketopiperazine structure, showing a diagnostic O-H⁺ stretch of the protonated carbonyl group at 3585 cm^–1. Conversely, b₂ from protonated triglycine exhibits a strong band at 3345 cm^–1, associated with the N-H stretching mode of the protonated oxazolone ring structure. Other weaker N-H stretches can also be discerned, such as the amino NH₂ and amide NH bands. These results demonstrate the usefulness of the hydrogen stretching region, and hence benchtop optical parametric oscillator/amplifier (OPO/A) set-ups, in making structural assignments of product ions in collision-induced dissociation (CID) of peptides.     

Interpretation of vibrational and NMR spectra of allyl acrylate: An evidence for several conformers

The mid-IR, far-IR, and Raman spectra of allyl acrylate were measured and interpreted with support of the B3LYP/aug-cc-pVDZ calculated anharmonic vibrational spectra followed by the potential energy distribution analysis. The experimental ¹H and ¹³C NMR spectra of allyl acrylate dissolved in CDCl₃ or C₆D₆ were interpreted by means of the B3LYP/aug-cc-pVDZ-su2 calculated NMR chemical shifts and J(¹H,¹H) and J(¹H,¹³C) coupling constants. Exactly ten stable allyl acrylate conformers (five s-cis and five s-trans) were found after careful B3LYP/aug-cc-pVDZ and MP2/aug-cc-pVDZ scan of the conformational space. The experimental IR and Raman spectra are in good agreement with the theoretical spectra of the most stable conformers 1 with a presence of the second stable conformer 2, both exhibiting cis arrangement of the acrylic moiety. There are however two bands in the IR spectra, at ca. 1270 and 1260 cm⁻¹, that definitely indicate the conformers with trans arrangement of the acrylic moiety to be present in liquid allyl acrylate. The bands at ca. 2990 and 1650 cm⁻¹ are suggested to be due to Fermi resonances engaging CH and CC stretching vibrations, respectively. The careful inspection of the room temperature ¹H and ¹³C NMR spectra of allyl acrylate suggest that a dominating form of the allyl acrylate molecule in an inert solvent exhibits the cis conformation of the acrylic moiety and an extended allyl group.     

Synthesis of macrocyclic tris-cis-tris-trans- dodeca[(phenyl)(hydroxy)]cyclododecasiloxane in carbonic acid solution

The possibility to synthesize stereoregular tris-cis-tris-trans- dodeca[(phenyl)(hydroxy)]cyclododecasiloxane (tris-cis-tris-trans-[PhSi(O)OH]12) in an inorganic liquid medium – aqueous carbonic acid solution – was shown. The interaction of polyhedral phenylcoppersodiumsiloxane, {[(C₆H₅Si(O)O^?]₁₂(Cu₂⁺)₄(Na⁺)₄}*(L)_m (L?=?Buⁿ OH, H₂O), with carbonic acid can be considered as a new ‘green’ method to obtain functional organosiloxane macrocycles. In contrast to the known methods, no organic solvents were used during the reaction. The identification of the structure of the end compound was performed by means of NMR and Infrared spectroscopy as well as X-ray crystallography.