Cation-pi Interactions and oxidative effects on Cu+ and Cu2+ binding to Phe, Tyr, Trp, and His amino acids in the gas phase. Insights from first-principles calculations

The coordination properties of the four natural aromatic amino acids (AA(arom) = Phe, Tyr, Trp, and His) to Cu+ and Cu2+ have been exhaustively studied by means of ab initio calculations. For Cu+-Phe, Cu+-Tyr and Cu+-Trp, the two charge solvated tridentate N/O/ring and bidentate N/ring structures, with the metal cation interacting with the pi system of the ring, were found to be the lowest ones, relative DeltaG(298K) energies being less than 0.5 kcal/mol. The Cu+-His ground-state structure has the metal cation interacting with the NH2 group and the imidazole N. For these low-lying structures vibrational features are also discussed. Unlike Cu+ complexes, the ground-state structure of Cu2+-Phe, Cu2+-Tyr, and Cu2+-Trp does not present cation-pi interactions due to the oxidation of the aromatic ring induced by the metal cation. The ground-state structure of Cu2+-His does not present oxidation of the amino acid, the coordination to Cu2+ being tridentate with the oxygen of the carbonyl group, the nitrogen of the amine, and the N of the imidazole. Other less stable isomers, however, show oxidation of His, particularly of the imidazole ring, which can induce spontaneous proton-transfer reactions from the NH of the imidazole to the NH2 of the backbone. Finally, the computed binding energies for Cu+-AA(arom) and Cu2+-AA(arom) systems have been computed, the order found for the single charged systems being Cu+-His > Cu+-Trp > Cu+-Tyr > Cu+-Phe, in very good agreement with the experimental data.     

Sites of reaction of pilocarpine

Analysis of the sites of reaction of a biologically important compound, pilocarpine, a molecule with imidazole and butyrolactone rings connected by a methylene bridge, has been accomplished in a quadrupole ion trap with the aim of characterizing its structure/reactivity relationships. Ion-molecule reactions of pilocarpine with chemical ionizing agents, dimethyl ether (DME), 2-methoxyethanol, and trimethyl borate (TMB), along with collision-activated dissociation elucidated the reaction sites of pilocarpine and made possible the comparison of structural features that affect sites of reaction. Based on MS/MS experiments, methylation occurs on the imidazole ring upon reactions with CH3OCH2+ or (CH3OCH2CH2OH)H+ ions but methylation occurs on the lactone ring for reactions with (CH3O)2B+ ions. Bracketing experiments with two model compounds, alpha-methyl-gamma-butyrolactone and N-methyl imidazole, show the imidazole ring to have a greater gas-phase basicity and methyl cation affinity than the lactone ring. The contrast of methylation by TMB ions on the lactone ring is explained by initial addition of the dimethoxyborinium ion, (CH3O)2B+, on the imidazole ring with subsequent collisional activation promoting an intramolecular transfer of a methyl group to the lactone ring with concurrent loss of CH3OBO. Semiempirical molecular orbital calculations are undertaken to further address the favored reaction sites.     

Infrared spectra and the structure of salts of imidazoles

The IR spectra of nitro- and polynitroimidazoles, and their salts are investigated. Salt formation with nitroimidazoles is shown to involve one nitro group, with conversion of the imidazole ring to an isoimidazole one. Assignment of frequencies to valence vibrations of NO in charged and uncharged NO₂ groups, and to skeleton vibrations of the ring, is made for nitroimidazoles, so that these data can be used to identify newly synthesized compounds.     

Structural analysis of phosphatidylcholines by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The utility of post-source decay (PSD) matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was investigated for the structural analysis of phosphatidylcholine (PC). PC did not produce detectable negative molecular ion from MALDI, but positive ions were observed as both [PC+H](+) and [PC+Na](+). The PSD spectra of the protonated PC species contained only one fragment corresponding to the head group (m/z 184), while the sodiated precursors produced many fragment ions, including those derived from the loss of fatty acids. The loss of fatty acid from the C-1 position (sn-1) of the glycerol backbone was favored over the loss of fatty acid from the C-2 position (sn-2). Ions emanating from the fragmentation of the head group (phosphocholine) included [PC+Na-59](+), [PC+Na-183](+) and [PC+Na-205](+), which corresponded to the loss of trimethylamine (TMA), non-sodiated choline phosphate and sodiated choline phosphate, respectively. Other fragments reflecting the structure of the head group were observed at m/z 183, 146 and 86. The difference in the fragmentation patterns for the PSD of [PC+Na](+) compared to [PC+H](+) is attributed to difference in the binding of Na(+) and H(+). While the proton binds to a negatively charged oxygen of the phosphate group, the sodium ion can be associated with several regions of the PC molecule. Hence, in the sodiated PC, intermolecular interaction of the negatively charged oxygen of the phosphate group, along with sodium association at multiple sites, can lead to a complex and characteristic ion fragmentation pattern. The preferential loss of sn-1 fatty acid group could be explained by the formation of an energetically favorable six-member ring intermediate, as apposed to the five-member ring intermediate formed prior to the loss of sn-2 fatty acid group.     

X-ray structure of a novel histidine-copper(II) complex

A new crystal structure of the dichloro(L-histidine)copper(II) half-hydrate is reported. In this complex, histidine acts as a bidentate ligand to the copper(II) cation. The coordination sphere of the copper cation is created by the carboxyl oxygen and the amine nitrogen from main chain group of histidine. Two additional chloride anions complete the square coordination of the central Cu⁺² cation. In the crystal, the copper cations are additionally surrounded by two chloride anions from neighboring complex molecules, which are located in the distant axial position and fill up the stretched octahedral coordination sphere Cu⁺². In the presented complex, the histidine molecule exists as a zwitter ion with an unprotonated negatively charged carboxyl group and with double protonated positively charged imidazole ring. Crystallographic study was supported by IR measurements confirming the presence of water in the crystal structure.     

Cu(II)-氨基酸-核苷酸三元配合物的合成和表征

合成和表征Na~2[Cu(L-Ala)~2(5'-GMP)].2H~2O、Na~2[Cu(L-Ala)~2(5'-IMP)].6H~2O、Na~2[Cu(L-His)(5'-GMP)Cl~2^2.2H~2O和Na~2[Cu(L-His)(5'-IMP)Cl~2].H~2O四个新的三元配合物, 其中两个L-Ala分子通过羧基O和α-氨基N与Cu(II)成反式配位, 一个L-His分子通过羧基O和咪唑环上的N与Cu(II)配位; 一个5'-GMP或5'-IMP分子嘌呤环上的N(7)与Cu(II)配位; 5'-GMP的磷酸根上可能存在强氢键, 而5'-IMP的磷酸根上不存在强氢键; 在含L-Ala三元配合物中, 5'-GMP的C(6)=0可能参与配位或形成强氢键, 而5'-IMP的C(6)=0不参与配位或形成配位或形成强氢键; 在含L-His三元配合物中, 5'-IMP的C(6)=0的表现则相反。     

Synthesis and PMR spectra of 7-hydroxyalkylguanosinium acetates

Guanosine and 9-methylguanine treated with epoxides in glacial acetic acid are hydroxyalkylated stereoselectively at the N₇ position of the guanine moiety. Previously unreported 7-(hydroxyalkyl)guanosinium acetates from the reactions of six epoxides with guanosine and 7-(hydroxyalkyl)-9-methylguaninium acetates from the reactions of two epoxides with 9-methyl guanine in glacial acetic acid have been prepared and characterized by their pmr spectra. By using an excess of epoxide, quantitative conversion of guanosine or 9-methylguanine to the corresponding 7-hydroxyalkylguanosinium or 7-hydroxyalkyl-9-methylguaninium acetate was achieved. Comparisons of the pmr spectra of the 7-(hydroxyalkyl)guanosinium acetates in DMSO-d₆ to the spectrum of guanosine reveal that the H₈ and amino group proton absorptions common to guanosine are shifted to a lower field, the absorptions of the H₁ proton is absent, and the coupling constant of the H′₁-H′₂ protons of the ribosyl group is decreased from about 5.7 ± 0.1 Hz in guanosine to about 3.5 ± 0.1 Hz in the products. The use of the pmr spectral features of 7-(hydroxyalkyl)-9-methylguaninium compounds in characterizing 7-hydroxyalkylguanosinium compounds is discussed. Evidence is presented which suggests that extensive delocalization of positive charge exists in both the pyrimidine and imidazole rings of N₇-hydroxyalkylated guanosine and N₇-hydroxyalkylated-9-methylguanine. The possible effects of charge delocalization upon the hydrogen bonding potential of 7-hydroxyalkylated guanine moieties in DNA is discussed.     

Formation of O6,7-dimethylguanine residues in calf thymus deoxyribonucleic acid treated with carcinogenic N-methyl-N-nitrosourea in vitro

Treatment of calf thymus deoxyribonucleic acid (DNA) in vitro with a methylating carcinogen, N-methyl-N-nitrosourea (MNU), in phosphate buffer (pH 7.2) resulted in formation of O6,7-dimethylguanine residues in DNA besides the well-known methylated DNA adducts, 7-methylguanine, O6-methylguanine and 3-methyladenine. The product ratio (%) of O6,7-dimethylguanine versus 7-methylguanine was 0.32 after one MNU treatment. The significance of formation of O6,7-dimethylguanine residues in DNA is discussed briefly in relation to the carcinogenicity of MNU.     

Computational calculations of pKa values of imidazole in Cu(II) complexes of biological relevance

The imidazole ring is part of the lateral chain of histidine. One of the main features of this amino acid is the ability to coordinate copper, especially Cu(2+), because of the intermediate base nature of its imidazole ring, which has a great biological relevance. Proteins such as cytochrome c oxidase, a crucial enzyme in the respiratory chain, and β-amyloid peptide, implicated in the pathology of Alzheimer's disease, are examples of proteins containing histidines in their coordination sphere. Several studies indicate that the presence of this metal ion produces a decrease in the pK(a) of the imidazole ring of histidine. However, there are no reports of systematic studies of pK(a) variation in these types of metal cation complexes. In this work we use density functional theory to study the dependence of imidazole pK(a) with the number of imidazole rings in Cu(2+) coordination environments. The pK(a) of isolated imidazole (ImH), and the pK(a) of imidazole in Cu(2+)(ImH)(m)(H(2)O)(4-m) (m=1-3) complexes have been studied using two different functionals, B3LYP and MPWB1K, which have different percentage of exact exchange, and the highly-correlated CCSD(T) method. Results show that imidazole pK(a) decreases between 2 and 7 units depending on the method employed and the number of imidazole rings coordinating the metal cation. Taking into account that the pK(a) of imidazole is 14, this decrease could be relevant in biological processes.     

Synthesis of imidazole and imidazolium porphyrins

A new porphyrin compound, where an imidazole group was attached through the 1‐position nitrogen to a phenyl ring located on the porphyrin periphery has been synthesized and characterized. The second nitrogen on the imidazole is available for further chemistry as demonstrated by the attachment of bromopentane forming the imidazolium porphyrin complex. This is the first example of an imidazolium group covalently attached to the porphyrin periphery in which the porphyrin is attached through the nitrogen on the imidazole ring rather than a carbon atom.     

Elucidation of the fragmentation pathways of different phosphatidylinositol phosphate species (PIPx) using IRMPD implemented on a FT-ICR MS

This work reports on the fragmentation of phosphoinositides by tandem mass spectrometry (MS/MS) and MS3 experiments on a hybrid apex-Qe Fourier transform-ion cyclotron resonance mass spectrometer (FT-ICR MS) using internal infrared multiphoton dissociation (IRMPD). The fragmentation behavior of diacylphophatidylinositol triphosphate was intensively studied since an abundant loss of inositol biphosphate was observed. This loss was suggested to occur via phosphate migration along the inositol head group. Substantiation by MS3 experiments showed that this neutral loss is formed after the loss of water from the precursor ion, indicating phosphate migration along the inositol ring to the glycerol backbone. Further fragmentation of the ion formed by the loss of inositol biphosphate from diacylphophatidylinositol triphosphate resulted in the formation of a product ion with a molecular formula of C(3)H(5)O(7)P(2), corresponding to a glycerol backbone linked to two phosphate groups. We suggested different structures for this ion and compared their stability using modeling experiments.     

Tryptic hydrolysis of inorcanic pyrophosphate modified by phosphate and O-phosphoethanolamine

By the peptide map method, a phosphorylated peptide has been isolated from a tryptic hydrolysate of phosphorylated yeast inorganic pyrophosphatase (I), and this is a direct proof of the formation of a covalent bond between (I) and phosphate in the course of this reaction. The isolation and analysis of the peptide from the tryptic hydrolysate shows that the phosphate acceptor is probably the aspartic acid residue 240 or 248. Analysis of a tryptic hydrolysate of (I) modified with O-phosphoethanolamine has shown that O-phosphoethanolamine forms an amide bond with the carboxy group of the same aspartic acid residue. In an alkaline medium, the phosphate residue migrates to the imidazole ring of a histidine residue, apparently that present in position 222.     

Ion trap collisional activation of the deprotonated deoxymononucleoside and deoxydinucleoside monophosphates

Deoxymononucleoside and deoxydinucleoside monophosphate anions formed by electrospray have been subjected to ion trap collisional activation. The threshold for decomposition via loss of base is significantly lower for the deoxymononucleoside 3′-monophosphates than for the corresponding 5′-monophosphates, which indicates that the presence of a charged 3′ phosphate group facilitates base loss. The behavior of the bases among each class of isomers shows slight variation in threshold and tandem mass spectrometry efficiency with tile notable exception of 2′-deoxyguanosine 5′-monophosphate. This ion is exceptionally stable toward decomposition via base loss, which reflects a strong hydrogen bonding interaction between the base and the phosphate group. All dinucleotides fragment via similar mechanisms, but the propensity for neutral base loss relative to loss of a charged base is highly dependent on the identities of both the 5′ and 3′ bases. The behavior of the dinucleotides under collisional activation conditions supports the proposal that base loss proceeds via a proton-bound dimer intermediate in which loss of the charged base directly competes with loss of the neutral base. Application of the kinetic method allows for quantitative predictions of the differences of the gas-phase acidities of the dimer components.     

Adsorption of l-histidine on copper surface as evidenced by surface-enhanced Raman scattering spectroscopy

The adsorption of l-histidine on a copper electrode from H₂O- and D₂O-based solutions is studied by means of surface-enhanced Raman scattering (SERS) spectroscopy. Different adsorption states of histidine are observed depending upon pH, potential, and the presence of the SO²⁻₄ and Cl⁻ ions. In acidic solutions of pH 1.2 the imidazole ring of the adsorbed histidine remains protonated and is not involved in the chemical coordination with the surface. The SO²⁻₄ and Cl⁻ ions compete with histidine for the adsorption sites. In solutions of pH 3.1 three different adsorption states of histidine are observed depending on the potential. Histidine adsorbs with the protonated imidazole ring oriented mainly perpendicularly to the surface at potentials more positive than −0.2 V. Transformation of that adsorption state occurs at more negative potentials. As this takes place, histidine adsorbs through the α-NH₂ group and the neutral imidazole ring. The Cl⁻ ions cause the protonation and detachment of the α-NH₂ group from the surface and the formation of the ion pair NH⁺₃ … Cl⁻ can be observed. In the neutral solution of pH 7.0 histidine adsorbs through the deprotonated nitrogen atom of the imidazole ring and the α-COO⁻ group at E ≥ −0.2 V. However, this adsorption state is transformed into the adsorption state in which the α-NH₂ group and/or neutral imidazole ring participate in the anchoring of histidine to the surface, once the potential becomes more negative. In alkaline solutions of pH 11.9 histidine is adsorbed on the copper surface through the neutral imidazole ring.     

UV photodissociation of phospho-seryl-containing peptides: laser stabilization of the phospho-seryl bond with multistage mass spectrometry

Protonated precursor ions of phosphorylated peptides containing a tyrosyl residue have been subjected to UV laser-induced dissociation (LID) at a wavelength of 220 nm and to collision-induced dissociation (CID) in an ion trap. As expected, neutral loss of the phosphate group is one of the predominant fragmentation channels during CID together with H2O elimination. In contrast, LID leads mainly to the homolytic cleavage of the tyrosyl side chain and a restrained loss of the phosphate group. Interestingly, the intensity of the dephosphorylated fragment ion is greatly minimized when CID is carried out next on the radical precursor ion of the singly and doubly charged species.     

A new and selective capillary column coated with cationic diazacrown ether for separation of organic and inorganic anions by capillary electrophoresis

A new coated capillary has been introduced for capillary electrophoretic separation of anions by using a positively charged diazacrown ether with a 12-membered ring. A positive charge spread over the inner capillary surface led to a substantial anodic electroosmotic flow (EOF) over the range of migrating buffer of pH 2-11. Under the optimum conditions of 25 mM phosphate buffer at pH 7, the diazacrown-coated capillary showed a successful simultaneous separation of 7 inorganic anions and 13 aromatic anions (including positional isomers) in less than 15 min. The migration times of the sample anions and EOF marker for consecutive runs on a single column were highly reproducible, giving a relative standard deviation of 1%. Theoretical treatment of the migration behavior clearly demonstrated that ion association between the diazacrown and analyte anions is strongly dependent on the nature of the functional groups of anions (e.g., sulfonate groups > carboxyl groups) and the number of negative charges (e.g., trivalent anions > divalent anions > monovalent anions) on the analyte.     

Neutral loss of water from the b ions with histidine at the C-terminus and formation of the c ions involving lysine side chains

Neutral loss of water from the amide bond induced by the His side chain has been reported. The proposed fragmentation pathway is a retro-Ritter reaction catalyzed by the imidazole nitrogen. In our MS/MS study of the neuropeptide GAHKNYLRFamide, we observed that the neutral loss of water from the b(3) ion is abundant. The b(3) ion has a His residue at the C-terminus. As reported previously, in the b ions with His at the C-terminus, the imidazole residue is connected to the carbonyl carbon to form a five-membered ring. Therefore, it is unlikely that the neutral loss of water from the b(3) ion is catalyzed by the imidazole nitrogen. Through MS2 and MS3 studies of a synthetic peptide standard AGHKLL and its chemically labeled and isotope-encoded forms, we discovered that the water loss from the b(3) ion involves the carbonyl group of His, the hydrogen connected to the alpha-carbon of Gly, and the amide hydrogen of His. We also discovered the formation of an unusual c(x) ion in peptides with a Lys or Arg residue at the (x + 1) position of the peptide.     

Influence of pH on the micelle-to-vesicle transition in aqueous mixtures of sodium dodecyl benzenesulfonate with histidine

Small unilamellar vesicles (approximately 100 nm in diameter) form spontaneously in aqueous mixtures of histidine and sodium dodecyl benzenesulfonate. By manipulating pH, a gradual transition from micelles to vesicles to bilayers to precipitate is observed. The self-assembly of vesicles occurs over a wide range of compositions when the solution pH is lower than 6.0, the pKa of the imidazole moiety on the histidine molecule. This phenomenon is likely the result of attractive interactions between the negatively charged benzenesulfonate headgroups and the positively charged imidazole group in the amino acid. Similar results are obtained when imidazole salt itself is used.     

Mass spectra and structure of halo-substituted 2- and 4-aminopyrimidines

The mass spectra of methyl- and halo-substituted 2- and 4-aminopyrimidines at an ionizing electron energy of 70 eV were studied. It is shown that the molecular ion of the investigated compounds corresponds primarily to the imine form. This structure determines the principal direction of disintegration, which proceeds through the formation of pseudomolecular ions with an imidazole or pyrazole structure, depending on the position of the amino group in the pyrimidine ring.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1689–1693, December, 1973.     

On isomers and tautomers of Nitro-1-deazapurine: A DFT study

The 1-deazapurine molecules substituted by the NO₂ group at three different positions of the six-membered ring were subject of computational study performed at the B3LYP/cc-pVTZ level. For each substitution three tautomers were considered. The N3H tautomers are relatively instable in the gas and water phases which is due to significant decrease in aromaticity of the N3H forms. In the gas phase, the equilibria between the N7H and N9H tautomers are determined by a competition of the repulsive and attractive intermolecular interaction of different moieties of Nitro-1-deazapurine. The close neighborhood of the two tertiary N atoms and attractive close neighborhood of the tertiary N atom and the NH group result in preference of the N9H tautomer over the N7H one by ca. 3.5 kcal/mol. By comparing energy of different forms and proposed isodesmic reaction we showed that the Gibbs free energy of the attractive interaction between the NO₂ and HN groups is equal to ca. 1.0 kcal/mol, whereas the repulsive interaction between the NO₂ group and the tertiary N atom of the imidazole is equal to ca. 6.4 kcal/mol. It was shown also that the increase in dipole moment in the water media is the crucial effect influencing the N7H/N9H tautomeric equilibria of Nitro-1-deazapurines. For the three isomers dissolved in water, the two tautomers, N7H and N9H, are predicted to be observed and the former should dominate slightly for the 2-Nitro isomer whereas the latter for the 6-Nitro and 1-Nitro isomers. The NBO analysis showed that the NO₂ group withdraws 0.3 e of the σ-electrons from the pyridine ring of 1-deazapurine and has no influence on the σ-electrons of the imidazole ring. The NBO analysis shows also that the ratio between number of π-electrons which are withdrawed from imidazole vs. pyridine ring is characteristic for position of the substitution. The isodesmic reaction used revealed also that the NO₂ group destabilizes the N3H-1-deazapurine system, whereas it stabilizes the N7H- and N9H-1-deazapurine systems.