Fragmentation of deprotonated cyclic dipeptides by electrospray ionization mass spectrometry

The fragmentation pathways of deprotonated cyclic dipeptides have been studied by electrospray ionization multi‐stage mass spectrometry (ESI‐MSⁿ) in negative mode. The results showed that the fragmentation pathways of deprotonated cyclic dipeptides depended significantly on the different substituents, the side chains of amino acid residues at the diketopiperazine ring. In the spectra of deprotonated cyclic dipeptides, the ion [M? H? substituent radical]^? was firstly observed in the ESI mode. The characteristic fragment ions [M? H? substituent radical]^? and [M? H? (substituent? H)]^? could be used as the symbols of particular cyclic dipeptides. The hydrogen/deuterium (H/D) exchange experiment, the high‐resolution mass spectrometry (Q‐TOF) and theoretical calculations were used to rationalize the proposed fragmentation pathways and to verify the differences between the fragmentation pathways. The relative Gibbs free energies (ΔG) of the product ions and possible fragmentation pathways were estimated using the B3LYP/6–31++G(d, p) model. The results have some potential applications in the structural elucidation and interpretation of the mass spectra of homologous compounds and will enrich the gas‐phase ESI‐MS ion chemistry of cyclic dipeptides. Copyright © 2009 John Wiley & Sons, Ltd.     

Studies on cyclic dipeptides, II. Methylated modifications ofcyclo-[Phe-His]

Summary Synthesis of seven new cyclic dipeptides and their conformational analysis based on¹HNMR spectra is reported as well as their application as models to elucidate the mechanism of cyclic dipeptide catalysis in enantioselective mandelonitrile formation. Further evidence is presented to support the view that a highly ordered supramolecular complex of dipeptides acts as catalyst.

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Untersuchungen an cyclischen Dipeptiden, 2. Mitt.: Methylierte Derivate von cyclo-[Phe-His]

Zusammenfassung Es wird die Synthese sieben neuer cyclischer Dipeptide, ihre Konformationsanalyse (basierend auf¹H-NMR-Daten) und ihre Anwendung als Modelle zur Aufklärung des Mechanismus der dipeptidkatalysierten enantioselektiven Mandelsäurenitrilsynthese beschrieben. Weitere Hinweise zur Stützung der Annahme, daß ein hoch geordneter supramolekularer Komplex aus Dipeptiden für die Katalyse ausschlaggebend ist, werden vorgelegt.

     

Synthesis,Conformation, and Interactions with Small Molecules of Bis (Cyclic Dipeptides)

Bis (cyclic dipeptides), cyclo and S, S ′-bis(cyclo(hemiCys-Pro)), were synthesized. These bis (cyclic dipeptides) very efficiently formed complexes with Ba²⁺ and Na⁺ owing to intramolecular cooperation of two cyclicdipeptide moieties, the bis-effect. Cyclo stacked sodium 8-anilino-1-naphthalensulfonate in aqueous solution. These properties of complexation were controlled by the nature of the bridge connecting two cyclic dipeptide moieties. The geometry of the complex between S, S′-bis (cyclo (hemiCys-Pro)) and metal ion was investigated with the help of circular dichroism, nuclear magnetic resonance, and Raman spectroscopy.     

Antibacterial activity of cyclo(L-Pro-L-Tyr) and cyclo(D-Pro-L-Tyr) from Streptomyces sp. strain 22-4 against phytopathogenic bacteria

Two bioactive cyclic dipeptides, cyclo(L-Pro-L-Tyr) and cyclo(D-Pro-L-Tyr), were isolated from the culture broth of Streptomyces sp. strain 22-4 and tested against three economically important plant pathogens, Xanthomonas axonopodis pv. citri, Ralstonia solanacearum and Clavibacter michiganensis. Both cyclic dipeptides were active against X. axonopodis pv. citri and R. Solanacearum with MIC of 31.25 μg/mL. No activity could be observed against C. michiganensis.     

α-酮酯和α-酮酰胺的Henry反应

用三乙胺催化环状α-酮酯和α-酮酰胺同硝基甲烷的Henry反应, 首次合成了12个多官能团的β-硝基醇, 它们的结构用元素分析、红外光谱和核磁共振进行了表征. 这一反应速度较快, 室温下进行, 条件温和, 产率较好, 是合成多官能团硝基醇的有效方法.     

Synthesis,stereochemistry and conformational properties of diastereomeric cyclic dipeptides containing tetrahydro-1,4-thiazine-3,5-dicarboxylic acid

The synthesis of linear dipeptides containing N-protected L-phenylalanine and (3R-cis)-tetrahydro-1,4-thiazine-3,5-dicarboxylic acid dialkyl diester residues is described. N-Deprotection of these dipeptides by hydrogenolysis on palladium afforded directly a mixture of cis and trans dioxopiperazines. The stereochemistry and the solution conformational properties of the cyclic dipeptides are determined.     

Prepatellamide A, a new cyclic peptide from the ascidian Lissoclinum patella

A new cyclic peptide, prepatellamide A (1), along with three known cyclic peptides (2)— (4), was isolated from the ascidianLissoclinum patella. The structure of prepatellamide A was determined from one- and two-dimensional¹H and¹³C NMR spectra. The known cyclic peptides were identified as patellamides A (2), B (3) and C (4).     

Investigation of Reaction Mechanism of Amino Acids and Phosphorus Trichloride by 31P NMR and ESI‐MS/MS

The reaction of amino acids and phosphorus trichloride in THF was studied by ³¹P NMR tracing and ESI‐MS/MS. A series of hydridophoranes and cyclic dipeptides were obtained. The reaction presented interesting diversity and the reaction mechanism was proposed. The mechanism suggests that phosphorus plays an important role in the synthesis of amino acid hydridophorane and cyclic dipeptides. The results also show that ³¹P NMR and ESI‐MS/MS are useful tools for the investigation of reaction mechanism.     

Thermodynamic properties of peptide solutions. Part 15. Partial molar isentropic compressibilities of some glycyl dipeptides in aqueous solution at 15 and 35°C

The partial molar isentropic compressibilities at infinite dilution,K _s,2 ^o , have been obtained for eight glycyl dipeptides of sequence gly-X (X is an amino acid) in aqueous solution at the temperatures 15 and 35°C. The results have been combined with those obtained at 25°C, that were reported earlier, to evaluate the temperature dependences ofK _s,2 ^o for the dipeptides in the temperature range 15 to 35°C. TheK _s,2 ^o values for all the dipeptides are negative and increase (become more positive) with an increase in temperature. The slopes of the temperature dependences ofK _s,2 ^o for the dipeptides with typically hydrophobic side-chains are significantly larger than those for dipeptides with hydrophilic side-chains.     

Interfacial supramolecular biomimetic epoxidation catalysed by cyclic dipeptides

We synthesised a library of cis- and trans-cyclic dipeptides and evaluated their efficacy as catalysts in the asymmetric Weitz-Scheffer epoxidation of trans-chalcone. A thorough investigation relying on structure-activity studies and computational studies provided insights into the mechanism of the process. Our results revealed some structural features required for efficient conversion and for introduction of chirality into the product. The cyclic dipeptide acts as a catalyst by templating a supramolecular arrangement at the aqueous-organic interface required for efficient transformations to occur. Among all cyclic dipeptides investigated, cyclo(Leu-Leu) was the most efficient supramolecular catalyst.     

Fabrication of a novel Li<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>MoO<Subscript><Emphasis Type="Italic">y</Emphasis></Subscript> film modified electrode and its application as an electrochemical sensor of iodate

A novel organic gel film modified electrode was simply and conveniently fabricated by casting Li_xMoO_y and polypropylene carbonate (PPC) onto the surface of a gold electrode. The cyclic voltammetry and amperometry studies demonstrated that the Li_xMoO_y film modified electrode has a high stability and a good electrocatalytic activity for the reduction of iodate. In amperometry, a good linear relationship between the steady current and the concentration of iodate was obtained in the range from 3×10^–7 to 1×10^–4 mol L^–1 with a correlation coefficient of 0.9997 and a detection limit of 1×10^–7 mol L^–1.     

Thermodynamic properties of peptide solutions: 7. Partial molar isentropic pressure coefficients of some dipeptides in aqueous solution

The partial molar isentropic pressure coefficients at infinite dilution, K _S,2 ^o , have been determined for a number of dipeptides in aqueous solution at 25°C. For a series of dipeptides of sequence gly-X, where X is an amino acid with a neutral side chain, the K _S,2 ^o values are all more negative than that for diglycine. The results are discussed in terms of the hydration of the side chains. There are significant differences in the K _S,2 ^o values for sequence isomeric dipeptides. These differences can be rationalized in terms of the mutual interactions between the side chain and the ionic end groups in the dipeptides. Possible relationships between K _S,2 ^o and V ₂ ^o , the partial molar volume at infinite dilution, were investigated. For the dipeptides of sequence gly-X there is an interesting linear relationship between K _S,2 ^o /V ₂ ^o and V ₂ ^o .     

Conformational investigations on cyclic dipeptides containing a proline residue by means of 13C n.m.r. spectroscopy

The amounts of boat (A) and planar (B) forms for the equilibrium state in D₂O and CD₃OD/d₆-DMSO (1:1) were calculated for seven proline-containing cyclic dipeptides from their ¹³C n.m.r. spectra. For c-Pro-Val the thermodynamic functions for the conversion between the boat and planar forms have been obtained from measurements of equilibrium constants at different temperatures.     

Quantum chemical study of cyclic dipeptides

The preferred conformations of cyclic dipeptides were first studied systemically using the density functional theory (DFT) B3LYP method at the 6‐31G(d) level. The structural characteristics of cyclic dipeptides were revealed, most of which have not been confirmed until now. Our studies showed that the six‐member main circles of cyclic dipeptides composed of natural L ‐amino acid residues appeared as boat conformations. The important factors that influence conformations of cyclic dipeptides, such as molecular total energy, nuclear repulsion energy, molecular orbit, spatial effects, and reactive mechanism, are discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Kinetic and equilibrium study of the deprotonation of 4-nitrophenyl[bis(ethylsulphonyl)]methane by organic bases in acetonitrile in the presence of common cation BH<Superscript>+</Superscript> and tetrabutylammonium perchlorate

The results of kinetic and equilibrium experiments with the set of reaction of proton abstraction from 4-nitrophenyl[bis(ethylsulphonyl)]methane in acetonitrile are reported. Two strong organic bases are used: 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) and 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD). The rates of proton transfer reaction have been measured by T-jump method in the presence of perchlorate of the appropriate base as a common cation BH⁺ and supporting electrolyte-tetrabutylammonium perchlorate (TBAP) in the temperature range between 20–40°C are: k _H =1.32×10⁷−2.00×10⁷ and 2.82×10⁷−4.84×10⁷ dm ³mol⁻¹s⁻¹ for MTBD and TBD respectively. The enthalpies of activation ΔH _MTBD ^≠ =13.5 and ΔH _TBD ^≠ =18.1 kJmol⁻¹. The entropies of activation are negative: ΔS _MTBD ^≠ =−62.3 and ΔS _TBD ^≠ =−40.3 Jmol⁻¹K⁻¹. The change of the absorbance of the anion of 4-nitrophenyl[bis9ethylsulphonyl)]methane at the temperature 25°C in the presence of common cation BH⁺ gives the equilibrium constants K=705 and 906 M⁻¹ for MTBD and TBD respectively. Kinetic and equilibrium results are discussed. The possible mechanism of proton transfer reaction between 4-nitrophenyl[bis(ethylsulphonyl)]methane and cyclic organic bases: MTBD and TBD in acetonitrile is proposed.     

Topological investigations of the molecular species and molecular interactions that characterize pyrrolidin-2-one + lower alkanol mixtures

Molar excess volumes, V^E, molar excess enthalpies, H^E, and speeds of sound data, u, of pyrrolidin-2-one (i) + ethanol or propan-1-ol or propan-2-ol or butan-1-ol (j) binary mixtures have been determined over entire composition range at 308.15 K. The observed speeds of sound data have been utilized to predict excess isentropic compressibilities, of the investigated binary mixtures. The observed excess thermodynamic properties V^E, H^E and have been analyzed in terms of Graph theory. The analysis of V^E data by the Graph theory suggests that pyrrolidin-2-one exists mainly as a mixture of cyclic and open dimer; ethanol as a mixture of dimer and trimer; butan-1-ol and propan-2-ol as mixture of monomer and dimer and propan-1-ol as a dimer in the pure state, and their mixtures contain 1:1 molecular complex. The IR studies lend additional credence to the nature and extent of interactions for the proposed molecular entities in the mixtures. Also, it has been observed that V^E, H^E and values predicted by the Graph theory compare well to with their corresponding experimental values.     

Electrochemical studies of cytochrome c on gold electrodes with promotor of humic acid and 4-aminothiophenol

p-Aminothiophenol (PATP) and humic acids (HA or HAs) were applied jointly as the electron transfer accelerants of redox reactions of cytochrome c (Cyt c) on gold electrodes. The electrochemical properties of the modified electrodes were studied by field emission scanning electron microscope, ultraviolet-visible spectroscopy, electrochemical impedance spectroscopy, Raman spectroscopy and cyclic voltammetry. The immobilized Cyt c displayed a couple of stable and well-defined redox peaks with a formal potential of −0.101 V (vs. SCE) in pH 7.0 phosphate buffer solution. Cyt c adsorption is in the form of a monolayer with average surface coverage of 5.28 pmol cm⁻². The electron transfer rate constant was calculated to be 2.14 s⁻¹. It indicate that the HA film acted as a good adsorption matrix for Cyt c and an excellent accelerant for the redox of Cyt c. The Cyt c-HA modified gold electrode showed a new couple of well-marked redox peaks when 2,4-dichlorophenol was added to the test solution.     

An Isotope (<Superscript>18</Superscript>O, <Superscript>15</Superscript>N,and <Superscript>2</Superscript>H) Technique to Investigate the Metal Ion Interactions Between the Phosphoryl Group and Amino Acid Side Chains by Electrospray Ionization Mass Spectrometry

Cationic metal ion-coordinated N-diisopropyloxyphosphoryl dipeptides (DIPP-dipeptides) were analyzed by electrospray ionization multistage tandem mass spectrometry (ESI-MS ⁿ ). Two novel rearrangement reactions with hydroxyl oxygen or carbonyl oxygen migrations were observed in ESI-MS/MS of the metallic adducts of DIPP-dipeptides, but not for the corresponding protonated DIPP-dipeptides. The possible oxygen migration mechanisms were elucidated through a combination of MS/MS experiments, isotope (¹⁸O, ¹⁵N, and ²H) labeling, accurate mass measurements, and density functional theory (DFT) calculations at the B3LYP/6-31 G(d) level. It was found that lithium and sodium cations catalyze the carbonyl oxygen migration more efficiently than does potassium and participation through a cyclic phosphoryl intermediate. In addition, dipeptides having a C-terminal hydroxyl or aromatic amino acid residue show a more favorable rearrangement through carbonyl oxygen migration, which may be due to metal cation stabilization by the donation of lone pair of the hydroxyl oxygen or aromatic π-electrons of the C-terminal amino acid residue, respectively. It was further shown that the metal ions, namely lithium, sodium, and potassium cations, could play a novel directing role for the migration of hydroxyl or carbonyl oxygen in the gas phase. This discovery suggests that interactions between phosphorylated biomolecules and proteins might involve the assistance of metal ions to coordinate the phosphoryl oxygen and protein side chains to achieve molecular recognition.     

The opposite effect of K+ and Na+ on the hydrolysis of linear and cyclic dipeptides

Potassium and sodium are generally considered inert ‘spectator’ ions for organic reactions. Here, we report rate constants for the acid-promoted hydrolysis of the seven dipeptides of glycine (G) and alanine (A) and an unexpected pattern in how these rates differ in the presence of K⁺ and Na⁺. The linear dipeptides hydrolyze 12–18% percent slower in the presence of KCl versus an equal concentration of NaCl, while the cyclic dipeptides hydrolyze 5–13% faster in the presence of KCl (all P-values?<?0.025). We believe this is the first report of a general organic reaction—here, amide hydrolysis—for which some substrates react faster in the presence of K⁺ and others in Na⁺. The results offer a potential reason for life’s mysterious universal selection of intracellular potassium over sodium.