A quantum-mechanical study of the chain-length dependent stability of the extended and 310-helix conformations in dehydroalanine oligopeptides

Summary A quantum-chemical study of the chain-length dependent stability of the extended, 2₇-ribbon and 3₁₀-helix conformations in dehydroalanine (Ala) oligopeptides has been performed by using both semiempirical AM1 and ab initio 4–31G methodologies. The validity of both methods in the study of the conformational properties of Ala oligopeptides was tested first on the dipeptide. The results of this test showed that 4–31G and AM1 calculations are in good agreement with 6–31G^* calculations and experimental data. In order to monitor the conformational conversions, Ala oligopeptides comprising two to six residues were constructed. Molecular geometries were fully optimized using AM1, and the final conformations were verified to be minima by analysis of the corresponding second-derivative matrices. Conformational studies revealed that the 3₁₀-helix is stabilized with respect to the 2₇-ribbon when the number of residues is three or four, at the AM1 and ab initio 4–31G level respectively, while the extended form is the most stable in all the calculations performed. On the other hand, if a linear behaviour is assumed for longer chains, our calculations show a trend that would predict a conversion from extended form to 3₁₀-helix in oligopeptides with around six (ab initio 4–31G) or eight (AM1) Ala residues. In order to explain these conformational changes, the cooperative effects for the different conformers were investigated. Large cooperative energy effects were found for the 3₁₀-helix conformation.     

氨基酸功能化磷钨酸盐的制备及其催化氧化脱硫性能

以L-丙氨酸和磷钨酸为原料,合成氨基酸功能化磷钨杂多酸盐([Ala]3PW),并采用XRD、FT-IR对其结构进行表征。以[Ala]3PW为催化剂,过氧化氢作为氧化剂,甲基咪唑四氟硼酸盐([HMIM]BF4)为萃取剂氧化萃取一体法脱除模拟油中的二苯并噻吩(DBT)。考察了反应温度、催化剂加入量、O/S物质的量比、萃取剂加入量、硫化物类型等因素对脱硫效率的影响。结果表明,在模拟油为10mL、[Ala]3PW=0.04g、O和S的物质的量比为6、V([HMIM]BF4)/V(oil)=0.6、反应温度50℃、反应时间180min的条件下,DBT的转化率可达到98.2%。催化剂循环使用4次活性没有明显的降低。     

Towards understanding the tandem mass spectra of protonated oligopeptides. 1: Mechanism of amide bond cleavage

The mechanism of the cleavage of protonated amide bonds of oligopeptides is discussed in detail exploring the major energetic, kinetic, and entropy factors that determine the accessibility of the b(x)-y(z) (Paizs, B.; Suhai, S. Rapid Commun. Mass Spectrom. 2002, 16, 375) and "diketopiperazine" (Cordero, M. M.; Houser, J. J.; Wesdemiotis, C. Anal. Chem. 1993, 65, 1594) pathways. General considerations indicate that under low-energy collision conditions the majority of the sequence ions of protonated oligopeptides are formed on the b(x)-y(z) pathways which are energetically, kinetically, and entropically accessible. This is due to the facts that (1).the corresponding reactive configurations (amide N protonated species) can easily be formed during ion excitation, (2). most of the protonated nitrogens are stabilized by nearby amide oxygens making the spatial arrangement of the two amide bonds (the protonated and its N-terminal neighbor) involved in oxazolone formation entropically favored. On the other hand, formation of y ions on the diketopiperazine pathways is either kinetically or energetically or entropically controlled. The energetic control is due to the significant ring strain of small cyclic peptides that are co-formed with y ions (truncated protonated peptides) similar in size to the original peptide. The entropy control precludes formation of y ions much smaller than the original peptide since the attacking N-terminal amino group can rarely get close to the protonated amide bond buried by amide oxygens. Modeling the b(x)-y(z) pathways of protonated pentaalanine leads for the first time to semi-quantitative understanding of the tandem mass spectra of a protonated oligopeptide. Both the amide nitrogen protonated structures (reactive configurations for the amide bond cleavage) and the corresponding b(x)-y(z) transition structures are energetically more favored if protonation occurs closer to the C-terminus, e.g., considering these points the Ala(4)-Ala(5) amide bond is more favored than Ala(3)-Ala(4), and Ala(3)-Ala(4) is more favored than Ala(2)-Ala(3). This fact explains the increasing ion abundances observed for the b(2)/y(3), b(3)/y(2), and b(4)/y(1) ion pairs in the metastable ion and low-energy collision induced mass spectra (Yalcin, T.; Csizmadia, I. G.; Peterson, M. B.; Harrison, A. G. J. Am. Soc. Mass Spectrom. 1996, 7, 233) of protonated pentaalanine. A linear free-energy relationship is used to approximate the ratio of the b(x) and y(z) ions on the particular b(x)-y(z) pathways. Applying the necessary proton affinities such considerations satisfactorily explain for example dominance of the b(4) ion over y(1) and the similar b(3) and y(2) ion intensities observed for the metastable ion and low-energy collision induced mass spectra.     

Folded structures of L-leucylglycine oligopeptides and their aggregational behavior in aqueous solution: Raman scattering spectra and proton NMR spin-lattice relaxation studies

The aggregational behavior of three L-leucylglycine oligopeptides (residue numbers of glycine are 3, 4, and 5) in aqueous solution was investigated by the use of Raman scattering and 1H NMR spin-lattice relaxation methods. The results indicate that their oligopeptides take up a folded structure to form dimeric aggregates above their critical aggregation concentration. The application of one-dimensional aggregate theory to these systems provides the following prediction. Elongation up to 6 glycine residues makes it possible to form dimeric aggregates, but further elongation (up to 7 glycine residues) makes the aggregates very unstable, and up to 8 or 9 glycine residues makes the formation of dimeric aggregates very difficult. The one-dimensional aggregate theory may be used to predict the existence of peptide aggregates through intermolecular hydrogen bonding.     

Density estimated physicochemical properties of alanine-based ionic liquid [C7mim][Ala] and its application in selective transesterification of soybean oil

Amino acid ionic liquid (AAIL) based on alanine, 1-n-heptyl-3-methylimidazolium alanine ([C7mim][Ala]), has been prepared and characterized. Since the IL can form strong hydrogen bonds with water, trace amount of water is a problematic impurity in the IL. Using the standard addition method (SAM), the densities were measured in the temperature range from 293.15 to 343.15±0.05 K. On the basis of the experimental data of density, the surface tension , molar volume, and the molecular volume Vm, molar enthalpy of vaporization lgHm0, and the thermal expansion coefficients , for [C7mim][Ala] were estimated using semi-empirical methods. Also the interstice model has been verified with good accordance. Then the [C7mim][Ala] was taken as catalyst in the transesterification reaction with fatty acid, where soybean oil was used as raw material and methanol as reactant. The amount of catalyst, alcohol consumption, reaction time, temperature and other factors of the reaction were investigated. Using GC determination, the conversions were calculated by the internal standard method. The main ingredients of the products were identified by GC-MS as palm methyl ester and linoleic acid methyl ester only, which showed high selectivity in palmitic acid and linoleic acid.     

Peptide synthesis using pentafluorophenyl diphenylphosphate (FDP) as coupling reagent

Comparison of the reaction speed and yield with its analogues and some conventional peptide coupling reagents, pentafluorophenyl diphenylphosphate (FDP) was shown to be a more preferable "active ester" type reagent for the peptide synthesis. The synthesis of oligopeptides using FDP was achieved with high yields. The influences of several reaction parameters such as solvent, base, additive and temperature on the coupling reaction were studied using HPLC method. The degree of racemization with FDP determined by HPLC or Young test was shown to be lower than that of DCCI. Octapeptide Gly-Cys(Bzl)-Ser-Gly-Lys-Leu-Ile-Cys(Bzl)-OH, corresponding to the amino acid sequence of gp41 of HIV-1, was successfully synthesized by 5+3 approach using FDP with high yield.     

Electrolyte and additive effects on enantiomer separation of peptides by nonaqueous ion-pair capillary electrophoresis using tert.-butylcarbamoylquinine as chiral counterion

Nonaqueous ion-pair capillary electrophoresis separations of N-protected (all-R)/(all-S) alanine peptide enantiomers with up to six amino acid residues using tert.-butylcarbamoylquinine as selector and employing the partial filling technique are presented. The effects of various conditional parameters on separation were studied, namely chemical nature of the capillary wall, solvent composition of the background electrolyte (BGE), acid-base-ratio (equivalent to apparent pH), ionic strength and selector concentration. The influence of the solvent composition (methanol-ethanol ratios) on resolution turned out to be rather complex. The separation of the peptide enantiomers was strongly altered by small changes in pH and ionic strength. An increase of the selector concentration was found to offer an easy way for enhancing enantioselectivity, although some drawbacks, e.g., elongation of run times, have to be considered. A method was developed that allowed the separation of N-3,5-dinitrobenzoyl oligoalanine enantiomers containing 1-6 amino acid residues in one run. Like in a recent high-performance liquid chromatography (HPLC) study, separation selectivity thereby decreased from 1.541 (Ala), 1.340 (Ala(2)), 1.054 (Ala(3)), 1.029 (Ala(4)), 1.024 (Ala(5)) to 1.020 (Ala(6)). In addition, all four stereoisomers of N-2,4-dinitrophenyl- and N-3,5-dinitrobenzyloxycarbonyl-protected alanylalanine could be baseline-resolved.     

Effectiveness of the suzuki-miyaura cross-coupling reaction for solid-phase peptide modification

The Suzuki-Miyaura (SM) cross-coupling reaction has recently become one of the most efficient methods for C-C bond construction opening a wide range of opportunities in organic synthesis. This study focused on the evaluation of the use of the SM reaction to modify peptides using a solid-phase synthesis approach, an avenue that was still not investigated intensively. We used as a peptide model [Ala (1,2,3), Leu (8)]Enk linked to a polystyrene support on which it was previously assembled. The aromatic residues Tyr (4) and Phe (7) of [Ala (1,2,3), Leu (8)]Enk were respectively substituted with p-iodo-Phe, and an SM-related strategy was developed. Results indicated that the reaction conditions involving K 3PO 4 or Na 2CO 3 (base), DMF (solvent), Pd(PPh 3) 4 (catalyst), and temperatures ranging from 50 to 80 degrees C during 20 h were found as optimal. Finally applying those optimal conditions, a series of [Ala (1,2,3), Leu (8)]Enk analogs modified at Tyr (4) or Phe (7) positions was synthesized using diverse boronic acid derivatives.     

Mn(III)/Cu(II)-mediated oxidative radical cyclization of alpha-(Methylthio)acetamides leading to erythrinanes

Treatment of N-[2-(3,4-dimethoxyphenyl)ethyl]-alpha-(methylthio)acetamide 3 with Mn(OAc)3 in the presence of Cu(OAc)2 gave tetrahydroindol-2-one 4, which then cyclized with Mn(OAc)3 to give 4-acetoxyerythrinane 5. A similar reaction of the 3,4-methylenedioxyphenyl congener 8 also gave tetrahydroindol-2-one 9, which, however, gave only a trace amount of the Mn(OAc)3-mediated cyclization product 11 and afforded the oxidation product 10. On the basis of these results, formation of 5 from 4 was thought to proceed via nucleophilic attack of the pyrrole ring on the cation-radical lX, generated by a single electron-transfer reaction of the acetoxy-substituted intermediate V. Treatment of compound 16 with Mn(OAc)3/Cu(OAc)2 gave no erythrinane derivative with recovery of the starting material, indicating that the presence of a methylthio group of 4 is essential for effecting the formation of erythrinane 5. On the other hand, treatment of 3 with Mn(OAc)3 using Cu(OTf)2 as an additive in place of Cu(OAc)2 gave another erythrinane 17. This method was applied to a formal synthesis of 3-demethoxyerythratidinone (20), a naturally occurring Erythrina alkaloid.     

Lewis acid-catalyzed benzannulation via unprecedented [4+2] cycloaddition of o-alkynyl(oxo)benzenes and enynals with alkynes

The reaction of o-alkynyl(oxo)benzenes 1 with alkynes 2 in the presence of a catalytic amount of AuCl(3) in (CH(2)Cl)(2) at 80 degrees C gave the [4+2] benzannulation products, naphthyl ketone derivatives 3 and 4, in high yields. When the reaction was carried out using AuBr(3) instead of AuCl(3), the reaction speed was enhanced and the chemical yield was increased. On the other hand, when the reaction was carried out in the presence of a catalytic amount of Cu(OTf)(2) and 1 equiv of a Br?nsted acid, such as CF(2)HCO(2)H, in (CH(2)Cl)(2) at 100 degrees C, the decarbonylated naphthalene products 5 were obtained in high yields. Similarly, the Cu(OTf)(2)-H(2)O-promoted reaction of the enynals 7 with an alkyne 2 afforded the corresponding [4+2] benzannulation products, decarbonylated benzene derivatives 8, in good yields. Both AuX(3)- and Cu(OTf)(2)-catalyzed benzannulations proceed most probably through the formation of the benzo[c]pyrylium ate complex 10, the Diels-Alder addition of alkynes 2 to the ate complex, and the resulting bicyclic pyrylium ion intermediate 12. The mechanistic difference between the AuX(3) and Cu(OTf)(2)-HA system is discussed.     

Lewis acid-catalyzed [4 + 2] benzannulation between enynal units and enols or enol ethers: novel synthetic tools for polysubstituted aromatic compounds including indole and benzofuran derivatives

The reaction of enynals 1, including o-(alkynyl)benzaldehydes, and carbonyl compounds 2, such as aldehydes and ketones, in the presence of a catalytic amount of AuBr3 in 1,4-dioxane at 100 degrees C gave the functionalized aromatic compounds 3 in high yields. Similarly, the AuBr3-catalyzed reactions of 1 with acetal compounds 5 afforded the corresponding aromatic compounds 3 in good yields. On the other hand, when the reaction was carried out in the presence of a catalytic amount of Cu(NTf2)2 and 1 equiv of H2O in (CH2Cl)2 at 100 degrees C, the decarbonylated naphthalene products 4 were obtained selectively over 3. Benzofused heteroaromatic compounds, such as indole derivatives 13 and benzofuran derivatives 15, were also synthesized by using the present benzannulation methodology.     

Oligopeptides and copeptides of homochiral sequence, via beta-sheets, from mixtures of racemic alpha-amino acids, in a one-pot reaction in water; relevance to biochirogenesis

As part of our studies on the biochirogenesis of peptides of homochiral sequence during early evolution, the formation of oligopeptides composed of 14-24 residues of the same handedness in the polymerization of dl-leucine (Leu), dl-phenylalanine (Phe), and dl-valine (Val) in aqueous solutions, by activation with N, N'-carbonyldiimidazole and then initiation with a primary amine, in a one-pot reaction, was demonstrated by MALDI-TOF MS using deuterium enantio-labeled alpha-amino acids. The formation of long isotactic peptides is rationalized by the following steps occurring in tandem: (i) creation of a library of short diasteroisomeric oligopeptides containing isotactic peptides in excess in comparison to a binomial kinetics, as a result of an asymmetric induction exerted by the N-terminal residue of a given handedness; (ii) precipitation of the less soluble racemic isotactic penta- and hexapeptides in the form of beta-sheets that are delineated by homochiral rims; (iii) regio-enantiospecific chain elongation occurring heterogeneously at the beta-sheets/solution interface. Polymerization of l-Leu with l-isoleucine (Ile) or l-Phe with l- (1) N-Me-histidine yielded mixtures of copeptides containing both residues. In contrast, in the polymerization of the corresponding mixtures of l- + d-alpha-amino acids, the long oligopeptides were composed mainly from oligo- l-Leu and oligo- d-Ile in the first system and oligo- d-Phe in the second. Furthermore, in the polymerization of mixtures of hydrophobic racemic alpha-amino acids dl-Leu, dl-Val, and dl-Phe and with added racemic dl-alanine and dl-tyrosine, copeptides of homochiral sequences are most dominantly represented. Possible routes for a spontaneous "mirror-symmetry breaking" process of the racemic mixtures of homochiral peptides are presented.     

Total syntheses of zaragozic acids A and C by a carbonyl ylide cycloaddition strategy

A carbonyl ylide cycloaddition approach to the squalene synthase inhibitors zaragozic acids A and C is described. The carbonyl ylide precursor 8 was synthesized starting from di-tert-butyl D-tartrate (47) via an eleven-step sequence involving the regioselective reduction of the mono-MPM (MPM=4-methoxybenzyl) ether 48 with LiBH4 and the diastereoselective addition of sodium tert-butyl diazoacetate to alpha-keto ester 10. The reaction of alpha-diazo ester 8 with 3-butyn-2-one (40) in the presence of a catalytic amount of [Rh2(OAc)4] gave the desired cycloadduct 59 as a single diastereomer. The dihydroxylation of enone 59 followed by sequential transformations permitted the construction of the fully functionalized 2,8-dioxabicyclo[3.2.1]octane core 5. Alkene 79 derived from 5 serves as a common precursor to zaragozic acids A (1) and C (2), since the elongation of the C1 alkyl side chain can be attained by olefin cross-metathesis, especially under the influence of Blechert's catalyst (85).     

Kinetic study of ruthenium(III)-catalyzed oxidation of <Emphasis Type="SmallCaps">l</Emphasis>-alanine by diperiodatoargentate(III) in aqueous alkaline medium

The kinetics of Ru(III)-catalyzed oxidation of l-alanine (Ala) by diperiodatoargentate(III) (DPA) in alkaline medium at 25 °C and a constant ionic strength of 0.90 mol dm⁻³ was studied spectrophotometrically. The products are acetaldehyde, Ag(I), ammonia and bicarbonate. The [Ala] to [DPA] stoichiometry is 1:1. The reaction is first order in both [Ru(III)] and [DPA] and has less than unit order in both [Ala] and [alkali]. Addition of periodate has a retarding effect on the reaction. The effects of added products, ionic strength and dielectric constant of the reaction medium have been investigated. The reaction proceeds via a Ru(III)–Ala complex, which further reacts with one molecule of monoperiodatoargentate(III) in the rate-determining step. The reaction constants were calculated at different temperatures and the activation parameters have been evaluated.     

Studies on Synthesis of a Cycloheptapeptide and Effects of Different Metal Ions on the Cyclization

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Homochiral oligopeptides via a lattice-controlled polymerisation in racemic crystals of valine N-carboxyanhydride suspended in aqueous solutions

As part of our program on the biochirogenesis of homochiral peptides, we report the formation of racemic parallel (p) beta sheets composed of alternating R and S chains of up to 14-15 repeat units of the same handedness through the polymerisation of (R,S)-valine N-carboxyanhydride (NCA) crystals suspended in aqueous solutions of a primary amine as the initiator. The occurrence of such a lattice-controlled reaction accompanied by a reduction in volume implies the operation of a mechanism that differs from that of the common solid-state polymerisation in vinyl systems. The topotacticity of the reaction is explained through the operation of a multistep nonlinear process comprising lattice control coupled with an asymmetric induction in the formation of homochiral short peptides followed by their self-assembly into racemic p beta sheets, which operate as efficient templates in the ensuing process of enantioselective chain elongation at the polymer/crystal interface. The composition of the diastereoisomeric libraries of oligopeptides was determined by MALDI-TOF and MALDI-TOF-TOF MS analyses of the products obtained from monomers enantioselectively labelled with deuterium. The structure of the p beta sheets could be determined by initiating the polymerisation reaction with water-soluble esters of enantiopure alpha-amino acids or short peptides. The same reaction performed with the monomer crystals suspended in hexane yielded a complex mixture of diastereoisomeric oligopeptides, thus highlighting the indispensable role played by water in controlling the stereoselectivity of the reaction. By contrast, polymerisation of (R,S)-leucine NCA crystals, with a different packing arrangement that presumably does not endorse the formation of periodic peptide templates, yielded, both in aqueous and hexane suspensions, libraries of peptides dominated by heterochiral diastereoisomers.     

Imidazole‐initiated polymerizations of α‐amino acid N‐carboxyanhydrides – simultaneous chain‐growth and step‐growth polymerization

The N‐carboxyanhydrides (NCAs) of sarcosine (Sar), D ,L ‐leucine (D ,L ‐Leu), D ,L ‐phenylalanine (D ,L ‐Phe), and L ‐alanine (L ‐Ala) were polymerized in dioxane. Imidazole served as initiator and the NCA/initiator ratio was varied from 1/1 to 40/1. The isolated polypeptides were characterized by ¹H NMR spectroscopy, by MALDI‐TOF mass spectrometry, by viscosity measurements, and by SEC measurements in the case of poly(sarcosine). Cyclic oligopeptides were found in all reaction products and in the case of polySar, poly(D ,L ‐Leu), and poly(D ,L ‐Phe) the cycles were the main products. In the case of poly(L ‐Ala), rapid precipitation of β‐sheet lamellaes prevented efficient cyclizations and stabilized imidazolide endgroups. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 5690–5698, 2005     

Highly enantioselective mukaiyama aldol reaction of alpha,alpha-dichloro ketene silyl acetal: an efficient synthesis of a key intermediate for diltiazem

An efficient synthesis of methyl (2R,3S)-3-(4-methoxyphenyl)glycidate (-)-2, a key intermediate for diltiazem (1), has been developed on the basis of the highly enantioselective Mukaiyama aldol reaction of p-anisaldehyde (4a) with alpha,alpha-dichloro ketene silyl acetal 5. Thus, the reaction using a stoichiometric amount of chiral oxazaborolidinone catalyst 12a proceeded to excellent yield (83%) and high enantioselectivity (96% ee), together with the chiral ligand 13a in nearly quantitative recovery. The reaction using a substoichiometric amount of 12e (20 mol %) also proceeded to excellent yield (88%), with somewhat lower enantioselectivity (77% ee). The aldol product 3a thus obtained was easily converted to (-)-2 in excellent yield (80%) and high optical purity (>99% ee). The highly enantioselective Mukaiyama aldol reaction with 5 catalyzed by 12a proved to be applicable to various aldehydes. An efficient preparation of 5 from inexpensive starting materials was also described.     

High-field 1H MAS and 15N CP-MAS NMR studies of alanine tripeptides and oligomers: distinction of antiparallel and parallel beta-sheet structures and two crystallographically independent molecules

beta-Strand peptides are known to assemble into either antiparallel (AP) or parallel (P) beta-sheet forms which are very important motifs for protein folding and fibril formations occurring in silk fibroin or amyloid proteins. Well-resolved 1H NMR signals including NH protons were observed for alanine tripeptides (Ala)3 with the AP and P structures as well as (Ala)n (n = 4-6) by high-field/fast magic-angle spinning NMR. Amide NH and amino NH3+ 1H signals of (Ala)3 with the P structure were well resonated at 7.5 and 8.9 ppm, respectively, whereas they were not resolved for the AP structure. Notably, NH 1H signals of (Ala)3 and (Ala)4 taking the P structure are resonated at higher field than those of the AP structure by 1.0 and 1.1 ppm, respectively. Further, NH 15N signals of (Ala)3 with the AP structure were resonated at lower field by 2 to 5 ppm than those of (Ala)3 with the P structure. These relative 1H and 15N hydrogen bond shifts of the P structure with respect to those of the AP structure are consistent with the relative hydrogen bond lengths of the interstrand N-H...O=C bonds. Distinction between the two crystallographically independent chains present in the AP and P structures was feasible by 15N chemical shifts but not by 1H chemical shifts because of insufficient spectral resolution in the latter. Calculated 1H and 15N shielding constants by density functional theory are generally consistent with the experimental data, although some discrepancies remain depending upon the models used.     

Controlling orientations of immobilized oligopeptides using N-terminal cysteine labels

This letter reports a strategy of using N-terminal cysteine labels for controlling the immobilization of oligopeptides on aldehyde-terminated surfaces through the formation of stable thiazolidine rings. We also study the effect of cysteine position (either N-terminal or C-terminal) and lysine residue on the immobilization of oligopeptides. On the basis of our ellipsometry and quartz crystal microbalance (QCM) results, we conclude that the proposed immobilization strategy is highly site-specific. It works only when cysteine is in the N-terminal position, and the formation of thiazolidine is much faster than the formation of imines between lysine residues and aldehydes, even in the presence of a reducing agent such as NaBH(3)CN. By labeling an oligopeptide CSNKTRIDEANNKATKML with an N-terminal cysteine, we immobilize this oligopeptide on an aldehyde-terminated surface and investigate the enzymatic activity of trypsin acting on the oligopeptide. It is found that trypsin is able to cleave the immobilized oligopeptide having a single anchoring point at the N-terminal cysteine. No cleavage is observed when the oligopeptide is immobilized through multiple anchoring points at lysine residues.