Synthesis of cyclic peptides by ring-closing metathesis

The synthesis of a series of "amide to amide" cyclized peptides by ring-closing metathesis (RCM) as well as a convenient synthesis for the linear precursors is described. In addition, the influence of the length of the alkene substituents and the influence of the peptide sequence is investigated, leading to a set of general rules to obtain "amide to amide" cyclized peptides by RCM.     

On the origins of diastereoselectivity in the conjugate additions of the antipodes of lithium N-benzyl-(N-α-methylbenzyl)amide to enantiopure cis- and trans-dioxolane containing α,β-unsaturated esters

"Matching" and "mismatching" effects in the doubly diastereoselective conjugate additions of the antipodes of lithium N-benzyl-(N-α-methylbenzyl)amide to enantiopure cis- and trans-dioxolane containing α,β-unsaturated esters have been investigated. High levels of substrate control were established first upon conjugate addition of achiral lithium N-benzyl-N-isopropylamide to both tert-butyl (S,S,E)-4,5-O-isopropylidene-4,5-dihydroxyhex-2-enoate and tert-butyl (4R,5S,E)-4,5-O-isopropylidene-4,5-dihydroxyhex-2-enoate. However, upon conjugate addition of lithium (R)-N-benzyl-(N-α-methylbenzyl)amide and lithium (S)-N-benzyl-(N-α-methylbenzyl)amide to these substrates, neither reaction pairing reinforced the apparent sense of substrate control. These reactions do not, therefore, conform to the classical doubly diastereoselective "matching" or "mismatching" pattern usually exhibited by this class of reaction. A comparison of these reactions with the previously reported doubly diastereoselective conjugate addition reactions of lithium amide reagents to analogous substrates is also discussed.     

Synthesis of palau’amide and its diastereomers: confirmation of its stereostructure

Four diastereomers of palau’amide (1-4), a cytotoxic cyclodepsipeptide, were synthesized. The ¹H NMR spectrum of 1 was identical to that of natural palau’amide. This established the complete stereostructure of palau’amide.     

Single-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling

Single-conformation infrared spectra in the amide I and amide II regions have been recorded for a total of 34 conformations of three α-peptides, three β-peptides, four α∕β-peptides, and one γ-peptide using resonant ion-dip infrared spectroscopy of the jet-cooled, isolated molecules. Assignments based on the amide NH stretch region were in hand, with the amide I∕II data providing additional evidence in favor of the assignments. A set of 21 conformations that represent the full range of H-bonded structures were chosen to characterize the conformational dependence of the vibrational frequencies and infrared intensities of the local amide I and amide II modes and their amide I∕I and amide II∕II coupling constants. Scaled, harmonic calculations at the DFT M05-2X∕6-31+G(d) level of theory accurately reproduce the experimental frequencies and infrared intensities in both the amide I and amide II regions. In the amide I region, Hessian reconstruction was used to extract local mode frequencies and amide I∕I coupling constants for each conformation. These local amide I frequencies are in excellent agreement with those predicted by DFT calculations on the corresponding (13)C = (18)O isotopologues. In the amide II region, potential energy distribution analysis was combined with the Hessian reconstruction scheme to extract local amide II frequencies and amide II∕II coupling constants. The agreement between these local amide II frequencies and those obtained from DFT calculations on the N-D isotopologues is slightly worse than for the corresponding comparison in the amide I region. The local mode frequencies in both regions are dictated by a combination of the direct H-bonding environment and indirect, "backside" H-bonds to the same amide group. More importantly, the sign and magnitude of the inter-amide coupling constants in both the amide I and amide II regions is shown to be characteristic of the size of the H-bonded ring linking the two amide groups. These amide I∕I and amide II∕II coupling constants remain similar in size for α-, β-, and γ-peptides despite the increasing number of C-C bonds separating the amide groups. These findings provide a simple, unifying picture for future attempts to base the calculation of both nearest-neighbor and next-nearest-neighbor coupling constants on a joint footing.     

Synthesis and reactivity of dipole-stabilized but unchelated alpha-aminoorganolithiums

Two N-methyl-5-lithio-2-pyrrolidinones have been prepared by tin-lithium exchange. These two alpha-aminoorganolithium compounds that are stabilized by an amide dipole, but not by chelation to the amide carbonyl. Both constitute test cases for comparing the stability and reactivity of "dipole-stabilized" and "unstabilized" alpha-aminoorganolithiums. We find that active methylene protons interfere with the reaction, so geminal disubstitution alpha to the amide carbonyl was necessary to suppress side reactions. These species do not react as efficiently as unstabilized alpha-aminoorganolithiums, or even as well as chelated dipole-stabilized alpha-aminoorganolithiums, toward typical electrophiles. The tin-lithium exchange to form these species was also not as facile as with other alpha-aminoorganostannanes.     

Reaction of amides of 2,3-dibromopropionic and 2-bromoacrylic acids with pyridine and triphenylphosphine

By refluxing pyridine with 2,3-dibromopropionic acid amide in acetonitrile, amide of 3-bromo-2-pyridiniumbromidopropionic acid I was synthesized. The latter is inert toward the second molecule of pyridine under the used conditions. Compound I was found to react with triphenylphosphine to form a mixture of 3-triphenylphosphoniumbromidopropionitrile II and 1-triphenylphosphoniumbromido-2-pyridiniumbromidoethane III. Schemes of reactions were suggested involving attack of phosphine on the carbonyl group as the first stage. The reaction of α-bromoacrylic acid amide with triphenylphosphine was shown to yield also compound II. Evidently, this reaction proceeds through intermediate formation of enolphosphonium salt.     

Anharmonic vibrational probe for N-methylacetamide in different micro-environments

In the present study, anharmonic vibrational properties of the amide modes in N-methylacetamide (NMA), a model molecule for peptide vibrational spectroscopy, are examined by DFT calculations. The 3N-6 normal mode frequencies, diagonal and off-diagonal anharmonicities are evaluated by means of the second order vibrational perturbation theory (VPT2). Good performance of B3LYP/6-31+G** is found for predicting vibrational frequencies in comparison with gas phase experimental data. The amide vibrational modes are assigned through potential energy distribution analysis (PED). The solvation effect on the amide vibrational modes is modeled within the PCM method. From gas phase to polar solvents, red shifts are observed for both harmonic and anharmonic vibrational frequency of amide I mode while the CO bond length increases upon the solvent polarity. Cubic and quartic force constants are further calculated to evaluate the origin of the anharmonicity for the amide I mode of NMA in different micro-environments.     

Synthesis of N-alkyl substituted bioactive indolocarbazoles related to Gö6976

The syntheses of new nitrile and amide analogues of 7-keto Gö6976 are described. The amide analogue 22 was formed via the condensation with a new functionalized indoleacetic acid derivative 25 to overcome the solubility problem during the coupling reaction.     

Synthesis and antibiofilm activity of a second-generation reverse-amide oroidin library: a structure-activity relationship study

A second-generation library of 2-aminoimidazole-based derivatives incorporating a "reversed amide" (RA) motif in comparison to the marine natural product oroidin were synthesized and subsequently assayed for antibiofilm activity against the medically relevant Gram-negative proteobacteria P. aeruginosa and A. baumannii. Most notably, an in-depth activity profile is reported for the most active subclass of derivatives that bear linear aliphatic chains off the amide bond. Additionally, further structural modifications of the core template, such as removal of the amide bond or substitution with a triazole isostere, resulted in the discovery of analogues with antibiofilm activities that varied with respect to their inhibition and dispersal properties of P. aeruginosa and A. baumannii biofilms.     

Synthesis of porphyrinylamide and observation of N-methylation-induced trans–cis amide conformational alteration

We synthesized porphyrinylamide 4b and its N-methylated derivative 5b. Direct N-methylation of porphyrinylamides 4 proved unsuccessful, so 5b was obtained via N-methylation of 5-aminoporphyrin 10 with potassium hexamethyldisilazide. The secondary amide 4b exists in trans-amide form, while N-methylated amide 5b exists in the cis-amide form, both in solution and in the crystal. Thus, N-methylation of the amide bond of 4b resulted in trans to cis conformational alteration.     

A "traceless" Staudinger ligation for the chemoselective synthesis of amide bonds

[reaction: see text] Here we report a novel modification of our previously reported "Staudinger ligation" that generates an amide bond from an azide and a specifically functionalized phosphine. This method for the selective formation of an amide bond, which does not require the orthogonal protection of distal functional groups, should find general utility in synthetic and biological chemistry.     

Neighboring pyrrolidine amide participation in thioether oxidation. Methionine as a "hopping" site

Methionine residues have been shown to function as efficient "hopping" sites in long-range electron transfer in model polyprolyl peptides. We suggest that a key to this ability of methionine is stabilization of the transient sulfur radical cation by neighboring proline amide participation. That is, in a model system a neighboring pyrrolidine amide lowers the oxidation potential of the thioether by over 0.5 V by formation of a two-center three-electron SO bond.     

Preparation of Functional Polyamine Scaffolds via Mitsunobu Post‐Polymerization Modification Reactions

A Mitsunobu reaction of trifluoroacetamide (TFA amide) and alcohols is used in a post‐polymerization modification process. The reaction is conducted on polystyrene (PSt) bearing 20 mol% TFA amide groups with 4‐methyl benzyl alcohol in the presence of a N,N,N′,N′‐tetramethylazodicarboxamide and tributylphosphine as mediators. The Mitsunobu reaction on polymer proceeds efficiently, as confirmed by the obvious precipitation generation during the reaction and the conversion of TFA amide moiety reached 88.6% confirmed by ¹⁹F NMR measurement, yielding PSt bearing tertiary TFA amide moieties. The obtained polymers featuring tertiary TFA amide moieties are deprotected in the presence of tetrabutylammonium hydroxide as a base to afford corresponding polymers featuring functionalized polyamine scaffolds with 92.5% conversion. In addition, the precise structural assignment is proven by synthesis and analysis of the model monomeric compounds and the respective model polymers.

     

Twisted amide reduction under Wolff-Kishner conditions: synthesis of a benzo-1-aza-adamantane derivative

A synthesis of 4,5-benzo-1-aza-tricyclo[4.3.1.1(3,8)]undecane (1), a benzo-1-aza-adamantane derivative, is described and features a previously unknown application of the Wolff-Kishner reduction of a nonresonance stabilized or "twisted" amide. An intermediate amino ester is converted to a severely "twisted amide", which, when exposed to hydrazine in alcohol, provides the corresponding "twisted" amino hydrazone. Wolff-Kishner conditions (KOH/ethylene glycol, 200 degrees C) provide the reduced target 1 without hydrolysis to amino acid derivatives. These operations are conveniently performed in a single flask in high yield.     

Directed H-bonding inhibition in molecular recognition: an NMR case study of the H-bonding of a dicarboxylic acid with a new mixed diamide receptor having one adjacent pyridine-N-oxide

The inhibition of hydrogen bond formation in the recognition of adipic acid by a new diamide receptor 1 having a pyridine-N-oxide and a simple pyridine ring adjacent to the amide moieties is observed. NMR studies show binding by the pyridine amide group in 1, which demonstrates the discrimination in hydrogen bonding between the carboxyls and an amide adjacent to pyridine versus another adjacent to the pyridine N-oxide. This specific inhibition of hydrogen bonding to a carboxyl group by the two different amides in 1 is corroborated by the NMR binding studies of 1 with propionic acid.     

Conformational arm-wrestling: battles for stereochemical control in benzamides bearing matched and mismatched chiral 2- and 6-substituents

The orientation of a tertiary amide group adjacent to an aromatic ring may be governed by the stereochemistry of an adjacent chiral substituent. With a chiral substituent in both ortho positions, matched/mismatched pairs of isomers result. Evidence for matched stereochemistry is provided by the clean NMR spectra of single conformers, while mismatching gives poor or unexpected selectivities in the formation of chiral substituents, or mixtures of amide conformers. Attempts to use the match-mismatch effect to select for racemic pairs of enantiomeric substituents, and hence develop a "racemate-sequestering" reagent, are described, along with the use of "matching" to scavenge a single enantiomer of a diamine from material of incomplete enantiomeric purity.     

Cross-metathesis of allyl halides with olefins bearing an α-alkoxy amide group

We have examined whether the allyl halide cross-metathesis reaction tolerates α-alkoxy amide groups. Ruthenium-based catalysts I-III did not catalyze the cross-metathesis of allyl halides in the presence of an α-alkoxy N,N-dimethylamide group to any appreciable extent, but the reaction could tolerate either a bulky N,N-diisopropylamide or Weinreb amide group. In particular, the Grubbs-Hoveyda-Blechert 2nd generation catalyst (III) efficiently catalyzed the cross-metathesis of allyl halides with olefins bearing a Weinreb amide group.     

Regioselective Acylative Cleavage of Cyclic Formal of Chloramphenicol1

The amide 6 has been synthesised by reacting the amine 3 with dichloroketene in situ. This amide 6 on nitration gave formal 7, which when reacted with acetic anhydride and p-toluene sulfonic acid underwent regioselective cleavage of the dioxane ring to furnish the hemiacetal 11. This on treatment with Methanol-water-ammonia yielded chloramphenicol 2.     

Proline-based dipeptides with two amide units as organocatalyst for the asymmetric aldol reaction of cyclohexanone with aldehydes

A series of proline-based dipeptide organocatalysts with two amide units (1-16) have been developed and evaluated in the direct catalytic asymmetric aldol reactions of aldehydes with cyclohexanone. These catalysts showed good solubility in organic solvents compared with their corresponding carboxyl terminal dipeptides. The robust amide bond formation allowed structural modifications and fine tuning of catalyst properties by varying the stereo and electronic effects of the terminal amide to affect the ability of hydrogen bonding formation between the catalysts and the substrates. The reactions proceeded smoothly in high yields (up to 99%), enantioselectivities (up to 98% ee) and anti-diastereoselectivities (up to 99:1) in the presence of bifunctional organocatalyst 4 under the optimal reaction conditions.     

C3-symmetrical supramolecular architectures: fibers and organic gels from discotic trisamides and trisureas

Hydrogen bonded C(3)-symmetrical molecules that associate into supramolecular stacks are described. Structural mutation on these molecules has been performed to elucidate the contribution of the different secondary interactions (hydrogen bonding, pi-pi stacking) to the self-assembly of the disks into chiral stacks. Twelve C(3)-symmetrical molecules have been investigated, six of which contain three central amide functionalities (1a-f) and six of which contain three central urea groups (2a-f). Peripheral groups of the disks are "small", "medium", or "large", half of them being achiral and the other half being chiral, to enable investigation of the supramolecular architectures with CD spectroscopy. In all of the cases, elongated, helical stacks are formed in apolar solution, except for the "medium" amide disks 1c/d. The elongated stacks of the C(3)-symmetrical disks form gels, which are visualized by AFM and SANS, and this confirms the directionality of the interactions. For the "large" urea disk, 2f, fibers with a length of up to 2 microm are observed. Temperature dependent and "sergeants-and-soldiers" CD measurements reveal that the urea stacks are much more rigid than the corresponding amide ones. In case of the "medium" urea disks, 2c/d, a true rigid rod, is formed. Where amide disks immediately reach their thermodynamic equilibrium, kinetic factors seem to govern urea aggregation. In a number of experiments aimed at reversibility with the urea stacks, hysteresis is observed, implying that these urea disks initially form a poorly defined stack, which subsequently transforms slowly into a well-defined, chiral architecture.