Proton Migration in a Chain of Tyrosine Residues

Proton migration in a tyrosine residue chain which is a model for a proton channel in a series ofproteins, including tubulin, has been studied. Magnesium(2+) complex within the guanosinetri phosphatemoiety favors dissociation one of the coordinated water molecules. The dissociation initiates proton shiftsalong the tyrosine chain composed of spatially separated tyrosine residues. The shifts are thermodynamicallyallowed (G298 < 0). The barrier to the proton shift does not exceed 3.15 kJ/mol. When applied, externalelectric field of low intensity, which mimicks the electret properties of some proteins, favors proton migrationby large distances.     

Configurational and conformational preferences in stereoselective acylations of <Emphasis Type="Italic">N</Emphasis>-methyl-1,3-diaminopropane with acyl chlorides

Evidence for a stereoinduction profile of the reaction of N-methyl-1,3-diaminopropane with acyl chlorides has been provided. A possibility to engage in intramolecular CH₂⋯HN and Cl⋯H-N interactions and the proton migration process to the methylamino group leads to the E secondary amides carrying the N⋯H⁺⋯N or N-H⋯N bridges, that show unusual spectroscopic images. Empirical relations between the Δδ _C chemical shift differences, the polarizability of the CO(S) groups and hydrogen bonding strength have been found. Both ¹H-¹⁵N-GHSQC and GHMBC experiments provide insight into the nature of hydrogen bonding and confirm the cyclic array of atoms.     

A Non‐damaging Method to Analyze the Configuration and Dynamics of Nitrotyrosines in Proteins

Often, deregulation of protein activity and turnover by tyrosine nitration drives cells toward pathogenesis. Hence, understanding how the nitration of a protein affects both its function and stability is of outstanding interest. Nowadays, most of the in vitro analyses of nitrated proteins rely on chemical treatment of native proteins with an excess of a chemical reagent. One such reagent, peroxynitrite, stands out for its biological relevance. However, given the excess of the nitrating reagent, the resulting in vitro modification could differ from the physiological nitration. Here, we determine unequivocally the configuration of distinct nitrated‐tyrosine rings in single‐tyrosine mutants of cytochrome c. We aimed to confirm the nitration position by a non‐destructive method. Thus, we have resorted to ¹H‐¹⁵N heteronuclear single quantum coherence(HSQC) spectra to identify the ³J(N? H) correlation between a ¹⁵N‐tagged nitro group and the adjacent aromatic proton. Once the chemical shift of this proton was determined, we compared the ¹H‐¹³C HSQC spectra of untreated and nitrated samples. All tyrosines were nitrated at ε positions, in agreement to previous analysis by indirect techniques. Notably, the various nitrotyrosine residues show a different dynamic behaviour that is consistent with molecular dynamics computations.     

Ring opening reaction of protonated polyfluorinated benzenes in the gas phase. A theoretical MNDO study

The MNDO calculations of protonated polyfluorobenzenes [Ph-F_n]H⁺ indicate the possibility of a relatively free migration of the hydrogen proton with energy barriers of 125–145 kJ mol^?1. At a higher degree of substitution (n) the protonation of the ipso carbon atom occupied by fluorine becomes energetically feasible, along with analogous migrations of fluorine, which, however, are energetically the most advantageous (ΔE_a ～ 230 kJ mol^?1). In addition to bridged fluoronium ions, relatively stable cyclic intermediates were also found, which make possible a rearrangement to the difluoromethylenecyclopentadienyl cation and thus the elimination of CF₂ observed in collision-induced dissociation mass spectra.     

Evidence for the Prerequisite Formation of Phenoxyl Radicals in Radical-Mediated Peptide Tyrosine Nitration In Vacuo

The elementary mechanism of radical-mediated peptide tyrosine nitration, which is a hallmark of post-translational modification of proteins under nitrative stress in vivo, has been elucidated in detail by using an integrated approach that combines the gas-phase synthesis of prototypical molecular tyrosine-containing peptide radical cations, ion–molecule reactions, and isotopic labeling experiments with DFT calculations. This reaction first involves the radical recombination of ^.NO₂ towards the prerequisite phenoxyl radical tautomer of a tyrosine residue, followed by proton rearrangements, finally yielding the stable and regioselective 3-nitrotyrosyl residue product. In contrast, nitration with the π-phenolic radical cation tautomer is inefficient. This first direct experimental evidence for the elementary steps of the radical-mediated tyrosine nitration mechanism in the gas phase provides a fundamental insight into the regioselectivity of biological tyrosine ortho-nitration.     

Multiple bond migration with participation of a protophilic agent

The pathways of migration of the multiple bond in propene and propyne molecules involving the hydroxide ion were investigated by theab initio (RHF/6-31+G^* and MP2/6-31+G^*) methods. Stationary points corresponding to stable complexes between the molecules under study and the hydroxide ion and between corresponding carbanions and water molecule were found on the potential energy surfaces of the proton transfer reactions. In the presence of hydroxide ion, migration of the multiple bond can occur by an “intramolecular” mechanism of the proton transfer involving the proton of hydroxide ion bound in the complex with propene or propyne molecule. For the propene system, such a mechanism seems to be quite realistic and more preferable energetically than a traditional two-stage mechanism with a passage of the proton into the medium. For the system with the triple bond, an equal expenditure of energy is required to follow any mechanism (without taking into account the effects of solvation and the interaction with a cation), whereas the formation of the stable [H₂C=C=CH·H₂O]⁻ complex can prevent further transformations. For Part 1, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 35–41, January, 1999.     

A Cucurbit[8]uril 2:2 Complex with a Negative pKa Shift

A viologen derivative carrying a benzimidazole group ( V-P-I ²⁺; viologen–phenylene–imidazole V-P-I ) can be dimerized in water using cucurbit[8]uril (CB[8]) in the form of a 2:2 complex resulting in a negative shift of the guest pK_a, by more than 1 pH unit, contrasting with the positive pK_a shift usually observed for CB-based complexes. Whereas 2:2 complex protonation is unclear by NMR, silver cations have been used for probing the accessibility of the imidazole groups of the 2:2 complexes. The protonation capacity of the buried imidazole groups is reduced, suggesting that CB[8] could trigger proton release upon 2:2 complex formation. The addition of CB[8] to a solution containing V-P- I ³⁺ indeed released protons as monitored by pH-metry and visualized by a coloured indicator. This property was used to induce a host/guest swapping, accompanied by a proton transfer, between V-P-I ³⁺ ⋅ CB[7] and a CB[8] complex of 1-methyl-4-(4-pyridyl)pyridinium. The origin of this negative pK_a shift is proposed to stand in an ideal charge state, and in the position of the two pH-responsive fragments inside the two CB[8] which, alike residues engulfed in proteins, favour the deprotonated form of the guest molecules. Such proton release triggered by a recognition event is reminiscent of several biological processes and may open new avenues toward bioinspired enzyme mimics catalyzing proton transfer or chemical reactions.     

Quantum-chemical calculation of a spillover model on a graphite support

The simplest quantum-chemical models of hydrogen spillover over a graphite-like surface as a proton or radical have been considered. The condensed planar C₂₄H₁₂ molecule was used as a model surface. Theab initio calculations of the interaction of hydrogen with the model surface were carried out by the restricted Hartree-Fock (HF) method in the STO-3G and 6-31 G^* basis sets. The radical hydrogen can not bind to such a surface, whereas the proton binds to it with an energy release of 186 kcal mol⁻¹. The activation energy of the transfer of the proton between two neighboring carbon atoms (10 kcal mol⁻¹) has been determined. The simplest model of the hydrogen migration as a proton over the model surface can be used for describing the spillover of hydrogen over the graphite surface. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 428–430, March, 1997.     

Kinetics for tautomerizations and dissociations of triglycine radical cations

Fragmentations of tautomers of the α-centered radical triglycine radical cation, [GGG^•]⁺, [GG^•G]⁺, and [G^•GG]⁺, are charge-driven, giving b-type ions; these are processes that are facilitated by a mobile proton, as in the fragmentation of protonated triglycine (Rodriquez, C. F. et al. J. Am. Chem. Soc. 2001, 123, 3006–3012). By contrast, radical centers are less mobile. Two mechanisms have been examined theoretically utilizing density functional theory and Rice-Ramsperger-Kassel-Marcus modeling: (1) a direct hydrogen-atom migration between two α-carbons, and (2) a two-step proton migration involving canonical [GGG]^•+ as an intermediate. Predictions employing the latter mechanism are in good agreement with results of recent CID experiments (Chu, I. K. et al. J. Am. Chem. Soc. 2008, 130, 7862–7872).     

Kinetics of mixed-controlled oxygen reduction at nafion-impregnated Pt-alloy-dispersed carbon electrode by analysis of cathodic current transients

The effects of Co alloying to Pt catalyst and Nafion pretreatment by NaClO₄ solution on the rate-determining step (RDS) of oxygen reduction at Nafion-impregnated Pt-dispersed carbon (Pt/C) electrode were investigated as a function of the potential step ΔE employing potentiostatic current transient (PCT) technique. For this purpose, the cathodic PCTs were measured on the pure Nafion-impregnated and partially Na⁺-doped Nafion-impregnated Pt/C and PtCo/C electrodes in an oxygen-saturated 1 M H₂SO₄ solution and analyzed. From the shape of the cathodic PCTs and the dependence of the instantaneous current on the value of ΔE, it was confirmed that oxygen reduction at the pure Nafion-impregnated electrodes is controlled by charge transfer at the electrode surface mixed with oxygen diffusion in the solution below the transition potential step |ΔE _tr| in absolute value, whereas oxygen reduction is purely governed by oxygen diffusion above |ΔE _tr|. On the other hand, the RDS of oxygen reduction at the partially Na⁺-doped Nafion-impregnated electrodes below |ΔE _tr| is charge transfer coupled with proton migration, whereas above |ΔE _tr|, it becomes proton migration in the Nafion electrolyte instead of oxygen diffusion. Consequently, it is expected in real fuel cell system that the cell performance is improved by Co alloying since the electrode reaches the maximum diffusion (migration) current even at small value of |ΔE|, whereas the cell performance is aggravated by Nafion pretreatment due to the decrease in the maximum diffusion (migration) current.     

Dissociation of the N-C(alpha) bond and competitive formation of the [z(n) - H](+) and [c(n) + 2H](+) product ions in radical peptide ions containing tyrosine and tryptophan: the influence of proton affinities on product formation

Dissociations at the N-C_α bond of tryptophan and tyrosine residues are the prevalent pathways in the fragmentations of radical cations of tripeptides that contain such as residues. This process involves a proton transfer from the β-carbon of the tryptophan or tyrosine residue to the carbonyl oxygen of the amide group, followed by cleavage of the N-C_α bond, generating low-lying proton-bound dimers that dissociate to give each an ionic and a neutral product. Formation of the [z _n −H]^∢+ or [c _n +2H]⁺ ion is a competition between the two incipient fragments for the proton in a dissociating proton-bound dimer.     

Double proton shifts in associates of formic acid with hydrides of third period elements

The mechanisms of double proton shift in associates HC(O)OH ... X of formic acid with hydrides (X = SiH₄, PH₃, PH₅, H₂S, SH₄, CIH, and CIH₃) were studied by theab initio method (SCF/3G*). The activation barriers to this reaction in associates with PH₃, H₂S, SH₄, CIH, and CIH₃ are equal to 68.3, 10.0, 26.0, 1.0, and 0.4 kcal mol^–1, respectively. For X = SiH₄ and PHS₅ transition states for the double proton shift were not determined, and in all of the other cases studied they are synchronous (concerted or one-step).Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 817–822, April, 1996.     

Asymmetric Donor–π‐Acceptor‐Type Benzo‐Fused Aza‐BODIPYs: Facile Synthesis and Colorimetric Properties

Novel aza‐diisoindolylmethene and their BF₂‐chelating complexes (benzo‐fused aza‐BODIPYs) were synthesized on a large scale and in a facile manner from phthalonitrile in tBuOK‐DMF solution. The unique asymmetric donor–π‐acceptor structure facilitates B? N bond detachment in the presence of trifluoroacetic acid (TFA) in dichloromethane, resulting in sharp color change from red to colorless, with over 250 nm hypsochromic shift in the absorption maximum. This colorimetric process can be reversed by adding a very small amount of proton‐accepting solvents or compounds. A ¹H and ¹¹B NMR spectroscopy study and also density functional theory (DFT) calculations suggest that TFA‐induced B? N bond cleavage may disrupt the whole π‐conjugation of the BODIPY molecule, resulting in significant colorimetric behavior.     

Quantum chemical study of the nature of the interaction between the proton and phosphoryl compounds in the H+ ...OPX3 complex

Based on CNDO/2 (spd basis) quantum chemical calculations of the proton affinity, we propose a model describing the nature of the interaction between the proton and the molecule of phosphoryl compounds in the monocation X₃POH⁺. We have established that in the series of phosphoryl compounds, the change in the proton affinity is subject to two effects: the shift in electron density from the base to the proton, and the ionic interaction between the proton complexing agent and the phosphorus atom and substituents; and in the latter case we observe electrostatic repulsion for the substituents R, OR, NR₂ and attraction for F.A. N. Nesmeyanov Institute of Heteroorganic Compounds, Russian Academy of Sciences, 117813 Moscow. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 11, pp. 2579–2583, November, 1992.     

Characterization of di- and trimethoxybenzaldehydes by analysis of deshielding gradients obtained with Eu(fod)3 shift reagent

Eu(fod)₃ shift reagent was used to simplify PMR spectra from isomeric mono-, di and trimethoxybenzaldehydes. Deshielding gradients, obtained by plotting induced shift vs. molar ratio of [Eu(fod)₃]/[substrate] made it possible to assign methoxyl proton signals to the correct positional substituent in polymethoxylated benzaldehydes. Anomalous upfield shifts for the aldehydic protons of 2,6-dimethoxy- and 2,4,6-trimethoxybenzaldehyde were observed with Eu(fod)₃ Various instances of long-range (⁵J) proton coupling between the aldehydic proton and a meta-proton provide insight to the geometry of the substrate in the complexed state with Eu(fod)₃. Di- and trimethoxybenzaldehydes are important precursors for the synthesis of the correspondingly methoxylated amphetamines which are of pharmacological and forensic interest because of abuse and illicit manufacture.     

Multiple bond migration with participation of a protophilic agent

The pathways of migration of the double bond in the 1-methoxy-2-propene molecule with participation of a hydroxide ion were investigated by theab initio RHF/6-31+G^* and MP2/6-31+G^* methods. Stationary points corresponding to complexes between the molecule under study and the hydroxide ion and between the corresponding carbanion and a water molecule were found on the potential energy surfaces of the proton transfer reactions. As in the propene molecule, migration of the double bond in the 1-methoxy-2-propene molecule can occur in the gas phase by the mechanism of intramolecular proton transfer involving the proton of the hydroxide ion. Conformational isomerism of the initial molecule and reaction products was considered. The proposed mechanism of 1,3-hydrogen shift involving the proton-containing base suggests the formation of bothE- andZ-products with predominance of the latter irrespective of the nature of the substituent. In this case the direction of multiple bond migration will be completely determined by the energy difference between the initial reagents and final products.     

Cationic grafting of olefins from PVC: The effect of reaction conditions

The cationic grafting of isobutylene, styrene, α-methylstyrene, and β-pinene from a poly(vinyl chloride) (PVC) backbone was investigated. Grafting-from was induced by Et₂AlCl in 1,2-dichloroethane and methylene dichloride solutions from 20 to −70 °C. The effects of temperature and proton trap [2,6-di-tert-butylpyridine (DtBP)] on grafting-from efficiency (G_eff), extent of grafting, branch length (molecular weight), and number of branches per PVC molecule were determined. Reducing the temperature invariably increased the G_eff and the molecular weight of polyisobutylene, polystyrene, poly(α-methylstyrene), and poly(β-pinene) branches attached to PVC. The magnitude of the effects was different with the various olefins and depended on the reaction conditions. The effect of DtBP was examined in the 5 × 10⁻⁴–4 × 10⁻³ mol/L range. By increasing the DtBP concentration the G_eff increased; however, the number-average molecular weight of the grafted branches decreased. The lengths of the grafted branches can be controlled, and G_eff's close to 100% were obtained. The fact that the proton trap reduced the molecular weights of grafted branches suggests that besides proton scavenging, DtBP may also abstract protons from the growing carbenium ion site. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 1675–1680, 2001     

A comparison of the fragmentation pathways of [Cu(II)(Ma)(Mb)]•2+ complexes where Ma and Mb are peptides containing either a tryptophan or a tyrosine residue

[Cu^II(M_a)(M_b)]^?2+ complexes, where M_a and M_b are dipeptides or tripeptides each containing either a tryptophan (W) or tyrosine (Y) residue, have been examined by means of electrospray tandem mass spectrometry. Collision‐induced dissociations (CIDs) of complexes containing identical peptides having a tryptophan residue generated abundant radical cations of the peptides; by contrast, for complexes containing peptides having a tyrosine residue, the main fragmentation channel is dissociative proton transfer to give [M_a + H]⁺ and [Cu^II(M_b – H)]^?+. When there are two different peptides in the complex, each containing a tryptophan residue, radical cations are again the major products, with their relative abundances depending on the locations of the tryptophan residue in the peptides. In the CIDs of mixed complexes, where one peptide contains a tryptophan residue and the other a tyrosine residue, the main fragmentation channel is formation of the radical cation of the tryptophan‐containing peptide and not proton transfer from the tyrosine‐containing peptide to give a protonated peptide. Copyright © 2010 John Wiley & Sons, Ltd.     

An experimental and computational investigation on the fragmentation behavior of enaminones in electrospray ionization mass spectrometry

The dissociation pathways of protonated enaminones with different substituents were investigated by electrospray ionization tandem mass spectrometry (ESI‐MS/MS) in positive ion mode. In mass spectrometry of the enaminones, Ar? CO? CH?CH? N(CH₃)₂, the proton transfers from the thermodynamically favored site at the carbonyl oxygen to the dissociative protonation site at ipso‐position of the phenyl ring or the double bond carbon atom adjacent to the carbonyl leading to the loss of a benzene or elimination of C₄H₉N, respectively. And the hydrogen? deuterium (H/D) exchange between the added proton and the proton of the phenyl ring via a 1,4‐H shift followed by hydrogen ring‐walk was witnessed by the D‐labeling experiments. The elemental compositions of all the ions were confirmed by ultrahigh resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FTICR‐MS/MS). The enaminones studied here were para‐monosubstituted on the phenyl ring and the electron‐donating groups were in favor of losing the benzene, whereas the electron‐attracting groups strongly favored the competing proton transfer reaction leading to the loss of C₄H₉N to form a benzoyl cation, Ar‐CO⁺. The abundance ratios of the two competitive product ions were relatively well‐correlated with the σ_p⁺ substituent constants. The mechanisms of these reactions were further investigated by density functional theory (DFT) calculations. Copyright © 2010 John Wiley & Sons, Ltd.     

Multinuclear two-dimensional NMR: Assignments of natural abundance polypeptide 13C, 1H and 15N chemical shifts and demonstration of isomer interconversion

The polypeptide carbobenzoxy-glycyl-L -prolyl-L -leucyl-L -alanyl-L -proline (0.2 M in DMSO-d₆) was investigated using ¹³C, ¹H and ¹⁵N NMR in natural abundance at 4.7 tesla. The existence of cis–trans-Gly-Pro and -Ala-Pro bonds permits up to four isomers, and all four were observed (in a 60:30:7:3 ratio). ¹³C shifts of the proline β-CH₂ resonances are consistent only with the 60% form being trans–trans. The 30% form is either trans–cis or cis–trans (order as above) and was tentatively assigned as cis-trans on the basis of relaxation behavior. Refocused INEPT studies aided the ¹³C assignments. The ¹⁵N data were obtained using both NOE and INEPT excitation, with signals evident for the three major isomers. The spectra were analysed by starting from the ¹³C data, which were assigned based on known regularities in peptide spectra. A ¹³C? ¹H heteronuclear two-dimensional chemical shift correlation experiment allowed direct assignment of proton shifts for major and minor isomers. The NH proton shifts were assigned by running a homonuclear two-dimensional chemical shift correlation experiment and noting the correlation with the previously assigned α-CH protons. The ¹⁵N resonances were then assigned from a ¹⁵N? ¹H heteronuclear two-dimensional chemical shift correlation experiment, relating the ¹⁵N signals directly to the NH proton resonances. Isomer interconversion between the two major isomers was demonstrated by performing a magnetization transfer homonuclear 2D experiment. Off-diagonal intensity was noted relating the major and minor isomer alanine NH proton, as well as for the major and minor isomer leucine NH protons.