15N NMR spectroscopy. 30—structure/shift relationships of oligopeptides and copolypeptides,including gramicidin S

The ¹⁵N NMR spectra of various oligopeptide derivatives of the Z? X? Y? Y? OMe structure, where X and Y are variable amino acids and Z is the benzyloxycarbonyl group, were measured in several protic and aprotic solvents. The shift difference of the ¹⁵N of the Y? Y and X? Y bond (neighbouring residue effect) is discussed with respect to the nature of X and Y with respect to the solvent. Oligopeptides of the Z? X? Y? Y? OH and n?H₃? X? Y? Y? OMe structures were compared with the Z-pëptide esters to investigate the spectroscopic influence of the protecting groups. The methyl ester hydrochlorides of the 25 most common amino acids were measured in water and DMSO to elucidate the solvent dependence of the substituent effects. Moreover, the methyl ester hydrochlorides were compared with Z-amino acids and N-acetyl-amino acid methyl esters in DMSO to establish whether the substituent effects depend on the nature of the amino acid derivatives. In this connection the assignments of the serine, threonine and glycine signals are discussed with respect to silk proteins. Furthermore, the assignments of the signals of copolypeptides by comparison with oligo- and homo-polypeptides are discussed. Finally, it was demonstrated that intramolecular H bonds cause downfied shifts of 7–10 ppm of the acceptor amide groups.     

Correlations between conformational isomerism and chromatographic diastereoselectivity of bis amino amide s-triazine derivatives

NMR spectroscopy was used to probe the conformational behavior of diastereomeric s-triazine derivatives containing two chiral amino amide substituents, in order to shed light onto the mechanism of chromatographic diastereoselectivity. Utilizing the amino hydrogen signals in the proton NMR spectrum, the population of the conformations caused by rotation about the bond between the amino nitrogen and aromatic carbon atoms could be observed. The population distribution between the three possible conformations was similar but not identical between the two diastereomers, with similar trends being observed for both bis alanine amide and bis valine amide derivatives. Based on a simple model in which it is assumed that adsorption to the hydrophobic RP-LC stationary phase occurs only for the conformations having both amino amide R-groups on the same side of the triazine ring plane, the different conformation populations between the two diastereomers obtained by NMR was consistent with the observed RP-LC elution order (L-L diastereomer followed by L-D). The predicted diastereoselectivity values from NMR data were compared to RP-LC diastereoselectivity values obtained using both C18 and polymeric columns, with both acetonitrile/water and DMSO/water mobile phases. Values obtained with the polymeric column were in better agreement with calculated values than those obtained with the C18 column, suggesting that the simple adsorption model used to calculate the diastereoselectivity is more relevant towards a simple hydrophobic polymeric surface rather than a more complex C18 stationary phase. This study indicates that proton NMR is a useful tool for studying the diastereoselective mechanism of these derivatives, due to the relatively slow C-N bond rotation caused by the significant sp(2) character of the amino nitrogen atoms.     

Vibrational spectroscopic detection of H-bonded β- and γ-turns in cyclic peptides and glycopeptides

The conformation of N-glycoproteins and N-glycopeptides has been the subject of many spectroscopic studies over the past decades. However, except for some preliminary data, no detailed study on the vibrational spectroscopy of glycosylated peptides has been published until recently.

This paper reports FTIR spectroscopic properties in DMSO and TFE of the N-glycosylated cyclic peptides cyclo[Gly-Pro-Xxx(GlcNAc)-Gly-δ-Ava] 3a and 3b in comparison with data on the non-glycosylated parent peptides cyclo(Gly-Pro-Xxx-Gly-δ-Ava) 2a and 2b [a, Xxx = Asn; b, Xxx = Gln; δ-Ava = NH-(CH₂)₄-CO] and N-acetyl 2-acetamido-2-deoxy-β- -gluco pyranosylamine (GlcNAc-NHAc, 4). The assignment of amide I band frequencies to conformation is based on ROESY experiments and determination of the temperature coefficients in DMSO-d₆ solution. (For the synthesis and NMR characterization of 2a and 3a see Ref. [19].)

Cyclic peptides are expected to adopt folded (β- and/or γ-turn) conformations which may be fixed by intramolecular H-bonding(s). A comparison of the temperature coefficients of the NH protons and amide I band frequencies and intensities suggests that in DMSO there is no significant difference in the backbone conformation and H-bond system of the N-glycosylated models and their parent cyclic peptides. The common feature of the backbone conformation of models 2 and 3 is the predominance of a 1 ← 4 (C₁₀) H-bonded type II β-turn encompassing Pro-Xxx or Pro-Xxx(GlcNAc), respectively. The ROESY connectivities in the Asn(GlcNAc) model (3a) have not been found to reflect intramolecular H-bondings between the peptide and the sugar.

The unique feature of the FTIR spectra in DMSO of the cyclic models is the lack or weakness of low-frequency (< 1640 cm⁻¹) amide I component bands. In TFE the amide I region of the FTIR spectra shows an increased number of components below 1650 cm⁻¹ reflecting a mixture of open and H-bonded β- and γ-turn conformers.

Because of its destabilizing effect upon γ-turns and other weakly H-bonded structures, DMSO decreases the number of backbone conformers. DMSO also destroys side-chain-backbone H-bondings of type C₇, C₆ or C₈. Possible ‘glyco’ C₇ H-bondings in GlcNAc-NHAc (4) or in glycopeptides 3a and 3b cannot resist the effect of DMSO either.

The FTIR data in TFE of models 2–4 suggest that the acceptor amide group of strong C₇ H-bondings in peptides and glycopeptides absorbs at 1630 ± 5 cm⁻¹ and that of bifurcated H-bondings between 1600–1620 cm⁻¹.     

功能单体对分子烙印手性固定相手性拆分能力的影响

系统考察了功能单体对非共价分子烙印手性固定相手性分离能力的影响,发现在非共价分子烙印手性固定相的制备中,功能单体与烙印分子之间存在着匹配性。丙烯酰胺可以与氨基酸衍生物的酰胺基团形成较强的氢键作用,碱性功能单体2-乙烯基吡啶则与其羧基形成较离子作用,两者的协同作用使复合功能单体丙烯酰胺+2-乙烯基吡啶对于氨基酸衍生物具有良好的烙印效果。竞争溶剂乙酸对样品与分子固定相间的非共价作用力有较大的影响,增加流动相中的竞争溶剂乙酸的含量,将减弱分子手性固定相与样品的酰胺键和羧基的氢键及离子作用,导致对样品的容量因子、手性选择性α及分离度f/g的减小。     

Amino acids and peptides—IV: Novel peptide bond formation catalysed by metal ions—II Formation of optically active peptide esters

The novel peptide bond formation previously reported in the reaction of glycine ester with Cu(II) ion in an anhydrous solvent, was examined using several kinds of optically active amino acid esters. Various reaction conditions were studied in detail for Phe-OEt. From Phe-OEt, Ala-OMe, Leu-OMe, Trp-OMe, Ser-OMe, and Met-OMe, the expected dipeptide esters with the same amino acid components were obtained without racemization. Asp(OEt)-OEt, and Glu(OMe)-OMe gave only optically active α-dipeptide esters. No formation of dipeptide esters was observed with Ile-OMe, Cys-OMe, His-OMe, and Pro-OEt. However, Lys-OMe, and Orn-OMe afforded optically active lactam derivatives. Some explanations of these abnormal observations have been given.Attempts to prepare di- and tri-peptide esters carrying different kinds of amino acid units were also studied.     

Sensitized Photooxidation of Di- and Tripeptides of Tyrosine*

This paper studies the dye-sensitized photooxidation of tyrosine (tyr) and tyr di- and tripeptides (tyr-tyr and tyr-tyr-tyr) mediated by singlet molecular oxygen (O,[l]) in alkaline media. Photooxidation quantum efficiencies (φ_r) were obtained by determining the overall and reactive rate constants of interaction with the oxidative species, employing the time-resolved O,(l) phosphorescence detection method and static-photolysis actinometric method, respectively. The interaction of O,(l)-tyr derivatives occurs through an intermediate encounter complex with polar character. Ionization of the phenolic OH group of tyr derivatives and the polarity of the solvent favors the overall interaction. Nevertheless, & values decrease when changing from water to MeCN-water medium. This indicates that the reactive deactivation of the encounter complex, probably an entropy-controlled step, may be affected by solvent polarity in the same way as those processes in which charg- es are neutralized along the reaction pathway. Photooxidation quantum efficiencies indicate that the contribution to O,(′) physical quenching (a second alternative deactivation route for the encountered complex [O,(′)-tyr derivatives]) increases with the complexity of the peptide. As a result, the selfprotection of the peptidic entity against physical quenching also increases. The information obtained from the fractional consumption mol OJmol tyr derivative (in tyr, the di- and tripeptides and the respective methyl ester of tyr and the tripeptide), together with the evolution (either consumption and/or generation) of primary amino groups upon photosensitized irradiation of the same compounds clearly indicates that the photooxidation of di- and tri-tyr peptides proceeds with the breakage of peptidic bonds. As a consequence, in the final balance each tyr unity behaves as an independent photooxidizable target.     

Synthesis of α-fluoroalkyl substituted peptides via enzymatic fragment condensation

A peptide library consisting of di- and tripeptide esters and tripeptide amides, respectively, containing α-Tfm amino acids in different positions was synthesized and tested for enzymatic fragment condensations catalyzed by the proteases α-chymotrypsin, trypsin and clostripain.     

Effect of C-terminal modification on the self-assembly and hydrogelation of fluorinated Fmoc-Phe derivatives

The development of hydrogels resulting from the self-assembly of low molecular weight (LMW) hydrogelators is a rapidly expanding area of study. Fluorenylmethoxycarbonyl (Fmoc) protected aromatic amino acids derived from phenylalanine (Phe) have been shown to be highly effective LMW hydrogelators. It has been found that side chain functionalization of Fmoc-Phe exerts a significant effect on the self-assembly and hydrogelation behavior of these molecules; fluorinated derivatives, including pentafluorophenylalanine (F(5)-Phe) and 3-F-phenylalanine (3-F-Phe), spontaneously self-assemble into fibrils that form a hydrogel network upon dissolution into water. In this study, Fmoc-F(5)-Phe-OH and Fmoc-3-F-Phe-OH were used to characterize the role of the C-terminal carboxylic acid on the self-assembly and hydrogelation of these derivatives. The C-terminal carboxylic acid moieties of Fmoc-F(5)-Phe-OH and Fmoc-3-F-Phe-OH were converted to C-terminal amide and methyl ester groups in order to perturb the hydrophobicity and hydrogen bond capacity of the C-terminus. Self-assembly and hydrogelation of these derivatives was investigated in comparison to the parent carboxylic acid compounds at neutral and acidic pH. It was found that hydrogelation of the C-terminal acids was highly sensitive to solvent pH, which influences the charge state of the terminal group. Rigid hydrogels form at pH 3.5, but at pH 7 hydrogel rigidity is dramatically weakened. C-terminal esters self-assembled into fibrils only slowly and failed to form hydrogels due to the higher hydrophobicity of these derivatives. C-terminal amide derivatives assembled much more rapidly than the parent carboxylic acids at both acidic and neutral pH, but the resultant hydrogels were unstable to shear stress as a function of the lower water solubility of the amide functionality. Co-assembly of acid and amide functionalized monomers was also explored in order to characterize the properties of hybrid hydrogels; these gels were rigid in unbuffered water but significantly weaker in phosphate buffered saline. These results highlight the complex nature of monomer/solvent interactions and their ultimate influence on self-assembly and hydrogelation, and provide insight that will facilitate the development of optimal amino acid LMW hydrogelators for gelation of complex buffered media.     

The solute molecule—Rigid or partially flexible? calculation of benzodiazepineR F values as an example

Summary The liquid-chromatographic separation of the enantiomers of amino acid esters as benzophenone Schiff-base derivatives on polysaccharide-derived chiral stationary phases (CSPs) is described. The performance of Chiralcel OF was superior to that of the other CSPs for resolution of benzophenone imine derivatives of amino acid ethyl and methyl esters. The enantiomers of most of the amino acid esters examined as their benzophenone imine derivatives were resolved to baseline on Chiralcel OF. The L-(−) enantiomers of all the analytes were preferentially retained on Chiralcel OF. The resolution of several imine derivatives of amino acid esters was investigated, as was the effect of eluent composition on the resolution of amino acid ethyl esters as their benzophenone imine derivatives.     

Synthesis and spectroscopic investigations of iron(III) complexes with chlorides and dianionic,symmetrically halogen substituted phthalocyanines as ligands

The synthesis of iron(III) complexes of general formula FeCl(R-pc), where R-pc are dianionic, symmetrically halogen substituted phthalocyanines at the positions 2,9,16,23 or 1,8,15,22, from the corresponding amino substituted derivatives is described (R=Cl, Br, I). The complexes are characterized by UV-visible and infrared spectra, powder X-ray diffraction and magnetic susceptibility measurements. The effect of substituents at the periphery and the basicity of the solvents used on the electronic spectra are discussed. The Q band of the electronic spectra for symmetrically halogen substituted derivatives are redshifted and the substituents at 2,9,16,23- positions are more effective in redshifting the Q bands than those at 1,8,15,22-positions. Depending upon the basicity of the solvents, the ligand-to-metal charge transfer (LMCT) transitions on Q band envelop shift to the higher energy region in the order of pyridine>DMF>DMSO. The infrared absorption signals for C-H and metal-ligand vibrations appear to be sharper for 1,8,15,22 substituted derivatives than for 2,9,16,23 substituted ones.     

The mass spectra of N-adamantoylpeptides

The N-adamantoyl derivatives of the esters of twenty-one di-peptides and eight tri-peptides containing the amino acids glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, glutamic acid, lysine, histidine, serine, threonine, methionine, S-benzylcysteine and tyrosine were prepared and their mass spectra determined. The spectra of all compounds were suitable for amino acid sequence determination. Mixtures containing N-adamantoyl dipeptide and tripeptide methyl esters were separated by thin-layer chromatography and the components identified by high resolution mass spectrometry. The mass spectrometric features of N-adamantoyl peptide esters are discussed and compared with those of other N-acyl peptide derivatives.     

Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

A 10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are located in a stable helical region of a transmembrane peptide. The 25-residue peptide (sMTM7) used mimics the cytoplasmic proton hemichannel domain of the seventh transmembrane segment (TM7) from subunit a of H(+)-V-ATPase from Saccharomyces cerevisiae. The three-dimensional structure of peptide sMTM7 in DMSO has been previously solved by NMR spectroscopy. The radial and spatial distributions of the DMSO molecules surrounding the peptide as well as the number of hydrogen bonds between DMSO and the side chains of the amino acid residues involved are extracted from the molecular dynamics simulations. Analysis of the molecular dynamics trajectories shows that the amino acid side chains are fully embedded in DMSO. Polar and positively charged amino acid side chains have dipole-dipole interactions with the oxygen atom of DMSO and form hydrogen bonds. Apolar residues become solvated by DMSO through the formation of a hydrophobic pocket in which the methyl groups of DMSO are pointing toward the hydrophobic side chains of the residues involved. The dual solvation properties of DMSO cause it to be a good membrane-mimicking solvent for transmembrane peptides that do not unfold due to the presence of DMSO.     

Preparation of Pseudo‐Peptide Building Blocks with retro‐Thioamide Bond Mediated via Thiocarbamoyl Meldrum's Acid

An easy and efficient synthesis of pseudo‐tripeptide containing a thiomalonamide moiety was developed. Isothiocyanate derivatives of amino acids react smoothly with 2,2‐dimethyl‐1,3‐dioxane‐4,6‐dione (Meldrum's acid) to yield new thiocarbamoyl derivatives of Meldrum's acids. Thermal decomposition of these new derivatives leads to thiocarbamoyl ketenes, which acylate amino acid esters to give pseudo‐tripeptides.     

Studies on the application of the Passerini reaction and enzymatic procedures to the synthesis of tripeptide mimetics

A new, efficient method for the multicomponent synthesis of tripeptide mimetics is presented. Simple, chemoenzymatic transformations of Passerini reaction products enable the introduction of varied amino acid moieties into the tripeptide scaffold, with control of the stereochemistry. Additionally, this method allows the convenient introduction of a methyl group to the amide nitrogen, leading to derivatives of N-methylated amino acids—compounds of interest for medicinal chemistry.     

ULTRAVIOLET RESONANCE RAMAN STUDY ON PURPLE AND BLUE MEMBRANES OF Halobacterium halobium

Abstract— Two hundred and forty and 213 nm excited resonance Raman spectra of purple membrane (PM) and blue membrane (BM) of Halobacterium halobiurn were studied. Generally intense Trp scattering and a strong relative intensity of the W3 band at 1553 cm^-1 in the 240 nm spectrum of PM indicate red-shifted B_b absorptions of some Trp sidechains. A high intensity ratio of Trp doublet at 1360 and 1340 cm^-1 suggests interactions with highly hydrophobic Trp environments. These Trp are not strongly H-bonded and their N₁ sites are located in positions easily reached by solvent water molecules. Tyrosines are also in very hydrophobic environments and H-bonded. The mainchain consists of normal and distorted α-helices whose amide NH are hardly deuterated in D₂O suspension, and some NH exchangeable irregular segments on the membrane surface. Upon acidification, the ratio of Trp doublet with 240 nm excitation decreases concomitant with increase in retinal absorbance at 600 nm, and the W3 relative intensity and overall Trp scattering also decrease. These observations strongly indicate that the counterpart of Trp interactions in PM is the retinal and that the interactions partly diminish upon acidification. The Tyr environment also changes with the color. Although the 240 nm amide I intensity is greater in acid BM than in PM, the change is not related to the color change because the amide I intensity of deionized BM is practically the same as that of PM. The amide I intensity increase in acid BM is ascribable to a structural change of the surface peptides due to acid induced aggregation.     

Sulphonester podands. A new class of clathrates

The new clathrates based on di- and triethylene glycol ether of phenol sulphonic acid-4 and 1-naphtolsulphonic acid-4 are presented. The four series of p-substituted phenol esters were obtained /Fig. 1/. Generally, only the derivatives of triethylene glycol ether of naphtolsulphonic acid give complexes with benzene or toluene /Tab. I/, but not with smaller molecules of acetonitrile or nitromethane.     

Generate: a program for 3-D structure generation and conformational analysis of peptides and peptidomimetics

The program Generate, aimed at generating 3-D structures for peptides and peptidomimetics, is presented. The algorithm is based on a build-up procedure, using a library of conformations of amino acid residues. This library is built from conformational analysis of amino acids placed in a di- or tripeptide environment to mimic the surroundings of the amino acid in a true peptide, considering different positions of the residue in the peptide chain (peptidyl fragment, NH(+)(3)-terminus or COO(-)-terminus). Cis-trans isomerism in the amide bonds is taken into account by construction of rotamer libraries for different isomers. Water solvation is included through the GB/SA model. New amino acid residues can easily be added to the libraries, making it possible to generate conformations of peptidomimetics.     

Raman spectroscopy of benzenesulfonic and 4-toluenesulfonic acids dissolved in dimethylsulfoxide

Solutions of benzenesulfonic acid (BSA) and 4-toluenesulfonic acid monohydrate (PTSA) in dimethylsulfoxide (DMSO) were studied by FT-Raman spectroscopy in the concentration range 1.0-3.5 mol dm(-3) (BSA) and 1.0-4.8 mol dm(-3) (PTSA). Spectra in the region of the Raman acid complex band (C-S + C-C + SO3) stretches, at 1124 cm(-1) were analysed by band-fitting procedures in order to ascertain the degree of acid dissociation. In BSA solutions, this parameter changes from 0.78 at 1.02 M to 0.47 at 3.5M, despite the strong character of the acid. Interaction of DMSO with undissociated BSA produces a new band in the solvent nu(C-S) Raman spectral region near 671 cm(-1), displaced >15.0 cm(-1), and assigned to DMSO molecules H-bonded to BSA. In PTSA solutions, hydrogen bonds are formed with the oxonium ion (H3O+) dissociated from the acid. In this case, the displacement observed is only >10.0 cm(-1), indicating a weaker interaction. From the concentration of H-bonded DMSO, the solute/solvent coordination number and its inverse, the mean number of H-bonds participating in bonding with each solvent molecule can be calculated. This coordination number changes in BSA solutions in bimodal way, passing through a maximum and reaching a limit of 2 in the most concentrated solution. This number agrees with that found in the solid solvate BSA.2DMSO. In PTSA solutions, the general trend is similar, but low coordination numbers are obtained, in agreement with the low acidity of the oxonium ion. The bimodal behaviour observed in both acids is explained by the self-associated structure of the solvent.     

Empirical solvent correction for multiple amide group vibrational modes

Previously proposed solvent correction to the amide I peptide vibration was extended so that it can be applied to a general solvated chromophore. The combined molecular and quantum mechanics (MMQM) method is based on a linear dependence of harmonic force field and intensity tensor components of the solute on solvent electrostatic field. For N-methylacetamide, realistic solvent frequency and intensity changes as well as inhomogeneous band widths were obtained for amide A, I, II , and III modes. A rather anomalous basis set size dependence was observed for the amide A and I vibrations, when bigger basis lead to narrowing of spectral bands and lesser molecular sensibility to the environment. For a model alpha-helical peptide, a W-shape of the vibrational circular dichroism signal observed in deuterated solvent for the amide I band was reproduced correctly, unlike with previous vacuum models.     

Synthesis and characterization of new benzimidazole derivatives using 2-substituted 1,3-bis(dimethylamino)-trimethinium salts

Novel benzimidazole derivatives are synthesized by the reaction of 2-substituted 1,3-bis(dimethylamino)-trimethinium salts with 2-aminobenzimidazole in the presence of acetic acid or triethylamine in acetonitrile as the solvent. The ultraviolet spectral behavior of these compounds is examined in DMSO.