A computational study of intramolecular proton transfer in gaseous protonated glycine

The minimum energy paths for intramolecular proton transfer between the amino nitrogen and carbonyl oxygen atoms in gaseous protonated glycine were estimated at the Hartree-Fock (HF) and second-order M?ller-Plesset Perturbation (MP2) levels of theory. Potential energy profiles and their associated reactant, transition state, and product species calculated at the MP2/6-31G* level were shown to differ significantly from those obtained at the HF/6-31G* level. Effects of electron correlation and basis functions on the calculated geometries and energies of relevant species were examined at the HF, MP2, MP4, CCSD, and B3LYP levels using the 6-31G*, 6-31G**, 6-31+G**, 6-311+G**, 6-31+G(2d,2p), 6-311+G(3df,2p), cc-pVDZ, aug-cc-pVDZ, and cc-pVTZ basis sets. The HF and MP2 optimized levels with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** bases were used to calculate the thermodynamic and kinetic properties of the proton transfer reaction at 298.15 K and 1 atm, which include enthalpy, entropy, Gibbs free energy, equilibrium constant, potential energy barriers, tunneling transmission coefficients, and rate constants. Results indicate that the proton in a carbonyl O-protonated glycine undergoes a rapid migration to the amino nitrogen atom, while the reverse process is extremely unfavorable. The objective of this work is to develop practical theoretical procedures for studying proton transfer reactions in amino acids and peptides and to assemble physical data from these model calculations for future references.     

Cyclization and rearrangement reactions of a(n) fragment ions of protonated peptides

a(n) ions are frequently formed in collision-induced dissociation (CID) of protonated peptides in tandem mass spectrometry (MS/MS) based sequencing experiments. These ions have generally been assumed to exist as immonium derivatives (-HN(+)═CHR). Using a quadrupole ion trap mass spectrometer, MS/MS experiments have been performed and the structure of a(n) ions formed from oligoglycines was probed by infrared spectroscopy. The structure and isomerization reactions of the same ions were studied using density functional theory. Overall, theory and infrared spectroscopy provide compelling evidence that a(n) ions undergo cyclization and/or rearrangement reactions, and the resulting structure(s) observed under our experimental conditions depends on the size (n). The a(2) ion (GG sequence) undergoes cyclization to form a 5-membered ring isomer. The a(3) ion (GGG sequence) undergoes cyclization initiated by nucleophilic attack of the carbonyl oxygen of the N-terminal glycine residue on the carbon center of the C-terminal immonium group forming a 7-membered ring isomer. The barrier to this reaction is comparatively low at 10.5 kcal mol(-1), and the resulting cyclic isomer (-5.4 kcal mol(-1)) is more energetically favorable than the linear form. The a(4) ion with the GGGG sequence undergoes head-to-tail cyclization via nucleophilic attack of the N-terminal amino group on the carbon center of the C-terminal immonium ion, forming an 11-membered macroring which contains a secondary amine and three trans amide bonds. Then an intermolecular proton transfer isomerizes the initially formed secondary amine moiety (-CH(2)-NH(2)(+)-CH(2)-NH-CO-) to form a new -CH(2)-NH-CH(2)-NH(2)(+)-CO- form. This structure is readily cleaved at the -CH(2)-NH(2)(+)- bond, leading to opening of the macrocycle and formation of a rearranged linear isomer with the H(2)C═NH(+)-CH(2)- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. This rearranged linear structure is much more energetically favorable (-14.0 kcal mol(-1)) than the initially formed imine-protonated linear a(4) ion structure. Furthermore, the barriers to these cyclization and ring-opening reactions are low (8-11 kcal mol(-1)), allowing facile formation of the rearranged linear species in the mass spectrometer. This finding is not limited to 'simple' glycine-containing systems, as evidenced by the IRMPD spectrum of the a(4) ion generated from protonated AAAAA, which shows a stronger tendency toward formation of the energetically favorable (-12.3 kcal mol(-1)) rearranged linear structure with the MeHC═NH(+)-CHMe- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. Our results indicate that one needs to consider a complex variety of cyclization and rearrangement reactions in order to decipher the structure and fragmentation pathways of peptide a(n) ions. The implications this potentially has for peptide sequencing are also discussed.     

Fragmentation characteristics of b(n) (n=2-15) ions from protonated peptides

The fragmentation reactions of protonated oligoalanines (trialanine, tetraalanine and pentaalanine) and the fragments present in the electrospray ionization (ESI) mass spectrum of polyalanine have been studied by collisionally activated dissociation (CAD) mass spectrometry (MS(2) and MS(3) experiments). The MS(n) experiments provided strong evidence that the m/z 71n+1 ion series in the ESI mass spectrum of polyalanine is a b(n) series. These ions are formed via the b(n) -y(m) pathway of amide bond cleavage, which results in the formation of a proton-bound complex of an oxazolone and a peptide/amino acid. Also, the MS(2) spectra of the b(n) series from polyalanine revealed that the chain length of b(n) ions influences significantly the dissociations taking place. For example, b(n) ions start losing H(2)O at n ≥5 and the losses of CO and CO+NH(3) decrease in intensity from b(2) to b(15). The elimination of H(2)O+NH(3) and the elimination of 61 mass (HN=C=O+H(2)O) commence with b(6); their abundances initially increase up to ~ b(8)-b(9) and then gradually decrease until b(15) (largest fragment studied). The tandem mass spectrometry experiments help to elucidate the dissociation mechanisms of the observed structures of biopolymer fragments.     

脂肪胺分子离子及质子化脂肪胺分子的碎裂反应

应用碰撞诱导解离(CID)技术研究了电子轰击方法产生的脂肪胺分子离子和化学电离方法产生的质子化脂肪胺分子的碎裂反应。质子化脂肪胺碰撞活化后的主要碎裂通道包括丢失C~XH~2~X、C~XH~2~X~+~1、C~XH~2~X~+~2单元及NH~3和生成[C~yH~2~y~+~1]^+及CH~3CH=NH~2^+离子。脂肪胺分子离子碰撞活化后的主要碎裂通道是丢失C~XH~2~X、C~XH~2~X~+~1及NH~3和生成[C~mH~2~m~-~1]^+、CH~2NH~2^+及CH~3CHNH~2^+离子。随着碰撞能的增加，远电荷碎裂反应和电荷诱导碎裂反应之间竞争引起产物离子的分布发生变化，如[C~mH~2~m~-~1]^+和[C~yH~2~y~+~1]^+离子。自由基机理可以解释质子化脂肪胺分子的远电荷反应。分子内氢抽取可以解释脂肪胺分子离子的碎裂反应。     

A novel mechanism of proton transfer in protonated peptides

The study presents quantum-chemical calculations on proton transfer in protonated N-acetylglycyl-N1-methylglycinamide (AGA) as a short oligopeptide model. All calculations employ the B3LYP functional and the 6-31++G** basis set. Two different mechanisms of proton transfer are discussed. The rate-determining step of the first mechanism exhibits an energy barrier of about 17.7 kcal mol-1, and it is represented by an isomerization of the proton around the double bond of the carbonyl group. The second mechanism is based on the large conformational flexibility of AGA, where all carbonyl oxygens cooperate. The rate-determining step of this mechanism exhibits an energy barrier of only 8.3 kcal mol-1.     

“Slow exchange” of unpaired electron in diphenylmethane an ion-radical

Conclusions In diethyl ether, containing 10% hexametapol, in the EPR spectra of the anion-radicals obtained by the action of potassium on diphenylmethane, a transition from the spectra, corresponding to a dynamic delocalization of the unpaired electron throughout the entire diphenylmethane molecule, to spectra that testify to its localization in one phenyl ring, is realized when the temperature is lowered.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 10, pp. 2370–2371, October, 1973.     

Non‐covalent dimers of the lysine containing protonated peptide ions in gaseous state: electrospray ionization mass spectrometric study

Study of the non‐covalent molecular complexes in gas phase by electrospray ionization mass spectrometry (ESI‐MS) represents a promising strategy to probe the intrinsic nature of these complexes. ESI‐MS investigation of a series of synthetic octapeptides containing six alanine and two lysine residues differing only by their positions showed the formation of non‐covalent dimers, which were preserved in the gas phase. Unlike the monomers, the dimers were found to show only singly protonated state. The decrease in the solvent polarity from water to alcohol showed enhanced propensity of formation of the dimer indicating that the electrostatic interaction plays a crucial role to stabilize the dimer. Selective functionalization studies showed that ε‐NH₂ of lysine and C‐terminal amide (? CONH₂) facilitate the dimerization through intermolecular hydrogen bonding network. Copyright © 2010 John Wiley & Sons, Ltd.     

Octahedral-tetrahedral equilibrium and solvent exchange of cobalt(II) ions in primary alkylamines

The enthalpy differences (Delta H degrees ) of the equilibrium between the octahedral and tetrahedral solvated cobalt(II) complexes were obtained in some primary alkylamines such as propylamine (pa, 36.1 +/- 2.3 kJ mol(-1)), n-hexylamine (ha, 34.9 +/- 1.0 kJ mol(-1)), 2-methoxyethylamine (meea, 44.8 +/- 3.1 kJ mol(-1)), and benzylamine (ba, 50.1 +/- 3.6 kJ mol(-1)) by the spectrophotometric method. The differences in the energy levels between the two geometries of the cobalt(II) complexes in the spherically symmetric field (Delta E(spher)) were estimated from the values of Delta H degrees by offsetting the ligand field stabilization energies. It was indicated that the value of Delta E(spher) is the decisive factor in determining the value of Delta H degrees and is largely dependent on the electronic repulsion between the d-electrons and the donor atoms and the interelectronic repulsion in the d orbitals. The comparison between activation enthalpies (Delta H(++)) for the solvent exchange reactions of octahedral cobalt(II) ions in pa and meea revealed that the unexpectedly large rate constant and small Delta H(++) in pa are attributed to the strong electronic repulsion in the ground state and removal of the electronic repulsion in the dissociative transition state, which can give the small Delta E(spher) between the ground and transition states. Differences in the solvent exchange rates and the DeltaH(++) values of the octahedral metal(II) ions in some other solvents are discussed in connection with the electronic repulsive factors.     

Formation and stability of gaseous tolyl ions

Collisional activation mass spectra confirm that tolyl ions can be produced from a variety of CH₃C₆H₄Y compounds. High purity o-, m- and p-tolyl ions are prepared by chemical ionization of the corresponding fluorides (Y=F) as proposed by Harrison. In electron ionization of CH₃C₆H₄Y formation of the more stable tropylium and benzyl ionic isomers usually accompanies that of the o-, m- and p-tolyl ions. Isomerization of low energy [CH₃C₆H₄Y]⁺? to [Y–methylenecyclohexadiene]⁺? is proposed to account for most [benzyl]⁺ formation, while the tropylium ion appears to arise from the isomerization of tolyl ions formed with higher internal energies, [o-, m-, p-tolyl]⁺→ [benzyl]⁺→ [tropylium]⁺, consistent with Dewar's predictions from MINDO/3 calculations.     

Transacetalization with gaseous carboxonium and carbosulfonium ions

Primary carboxonium (H2C=O+-R) and carbosulfonium (H2C=S+-R) ions (R = CH3, C2H5, Ph) and the prototype five-membered cyclic carboxonium ion are found to react in the gas phase with cyclic acetals and ketals by transacetalization to form the respective O-alkyl-1,3-dioxolanium and S-alkyl-1,3-oxathiolanium ions. The reaction, which competes mainly with proton transfer and hydride abstraction, initiates by O-alkylation and proceeds by ring opening and recyclization via intramolecular displacement of the carbonyl compound previously protected in its ketal form. As indicated by product ion mass spectra, and confirmed by competitive reactions, carbosulfonium ions are, by transacetalization, much more reactive than carboxonium ions. For acyclic secondary and tertiary carboxonium ions bearing acidic alpha-hydrogens, little or no transacetalization occurs and proton transfer dominates. This structurally related reactivity distinguishes primary from both secondary and tertiary ions, as exemplified for the two structural isomers H2C=O+-C2H5 and CH3C(H)=O+-CH3. The prototype five- and six-membered cyclic carboxonium ions react mainly by proton transfer and adduct formation, but the five-membered ring ion also reacts by transacetalization to a medium extent. Upon CID, the transacetalization products of the primary ions often dissociate by loss of formaldehyde, and a +44 u neutral gain/-30 u neutral loss MS3 scan is shown to efficiently detect reactive carboxonium and carbosulfonium ions. Transacetalization with either carboxonium or carbosulfonium ions provides a route to 1,3-oxathiolanes and analogs alkylated selectively either at the sulfur or oxygen atom.     

A coarse-graining approach for the proton complex in protonated aluminosilicates

We have developed a computational framework for the adsorption of linear alkanes in protonated aluminosilicates. These zeolites contain trace amounts of water that form hydrated proton complexes. The presence of hydrated protons makes the simulations at the fully atomistic level difficult. Instead of constructing an elaborate and complex model, we show that an approach based on a coarse-graining of the proton-complex accurately describes the available experimental isotherms, Henry coefficients, heats of adsorption, and oxygen-proton distances. Our approach is supported by MP2 quantum mechanical simulations. The model gives remarkably good agreement with experimental data beyond the initial calibration set.     

Vibrations of a chelated proton in a protonated tertiary diamine

Vibrational spectra of the conjugate acid of Me(2)NCH(2)CH(2)CH(2)CH(2)NMe(2) (N,N,N',N'-tetramethylputrescine) have been examined in the gaseous and crystalline phases using Infrared Multiple Photon Dissociation (IRMPD) spectroscopy, Inelastic Neutron Scattering (INS), and high pressure Raman spectroscopy. A band observed near 530 cm(-1) is assigned to the asymmetric stretch of the bridging proton between the two nitrogens, based on deuterium substitution and pressure dependence. The NN distance measured by X-ray crystallography gives a good match to DFT calculations, and the experimental band position agrees with the value predicted from theory using a 2-dimensional potential energy surface. The reduced dimensionality potential energy surface, which treats the ion as though it possesses a linear NHN geometry, shows low barriers to proton transit from one nitrogen to the other, with zero point levels close to the barrier tops. In contrast, two other related systems containing strong hydrogen bonds do not exhibit the same spectroscopic signature of a low barrier hydrogen bond (LBHB). On the one hand, the IRMPD spectra of the conjugate acid ions of the amino acid N,N,N',N'-tetramethylornithine (in which the two nitrogens have different basicities) show fewer bands and no comparable isotopic shifts in the low frequency domain. On the other hand, the IRMPD spectrum of the shorter homologue Me(2)NCH(2)CH(2)CH(2)NMe(2) (N,N,N',N'-tetramethyl-1,3-propanediamine), for which the NHN bond angle deviates substantially from linearity, displays more than one band in the 1100-1400 cm(-1) domain, which vanish as a consequence of deuteration.     

Study on poly(imide-ethylene glycol) and graphene oxide-based hybrid proton exchange membrane

In this study, novel poly(imide-ethylene glycol) (PIEG) was prepared via polycondensation of ethylenediaminetetraacetic dianhydride, 4-aminophenyl sulfone, and poly(ethylene glycol) bis(amine). Later, thermally stable and mechanically robust undoped and acid-doped proton exchange membranes were prepared using the graphene oxide (GO) nanofiller. Field emission scanning electron microscope revealed a unique hexagonal imprinted morphology of the fractured surface. Increasing the GO content from 1 to 5 wt% increased tensile strength (59.7–65.9 MPa) and the modulus (20.3–23.9 GPa) of the undoped PIEG/GO series. Thermal properties of the undoped PIEG/GO 1–5 membranes were also higher, i.e., T₁₀ = 438–487°C. However, dop-PIEG/GO 1–5 membranes have a higher ion exchange capacity (IEC) of 2.4–2.9 mmol/g and proton conductivity 1.8–2.7 S cm^?1 (94% RH).     

Balance of xanthophylls molecular and protonated molecular ions in electrospray ionization

This paper reports the chemical evidence of the balance between radical molecular ions and protonatedmolecules of xanthophylls (an oxygen-containing carotenoid) with a conjugated pi-system (polyene) and oxygen as a heteroatom in ESI and HRESI mass spectrometry. The ionization energy of neutral xanthophylls was calculated by semi-empirical methods. The results were compared with those previously published for carotenoids and retinoids, which have also been shown in ESI-MS to form M(+*) and [M + H](+), respectively. This study demonstrates, for the first time, the correlation of an extended conjugation and the presence of oxygen in the formation and balance of M(+*) or [M + H](+) for the carotenoids, neoxanthin, lutein, violaxanthin and zeaxanthin.