Electrospray ionization mass spectra of monoimidazole/polyamine conjugates

Imidazole/polyamine amides are biologically important molecules due to their specific DNA binding activity, and much attention has been attracted to the synthesis of their derivatives or analogues. In the present studies, the fragmentation of a series of synthetic monoimidazole/polyamine amides was investigated using electrospray ionization mass spectrometry (ESI-MS) combined with tandem mass spectrometry (ESI-MS/MS). All of the monoimidazole/polyamine amides produced the fragment ion m/z 183 except for the monoimidazole/ethyldiamine amide. The diamine amides produced this ion after the elimination of an alkene, the triamine amides produced it via their corresponding diamine amide fragments, and the tetraamine amide via its triamine and then diamine amide fragments. The characterization of the mass spectra for the different polyamine amides allowed identification of a specific product from the N-acylation of spermidine, and should assist further study of the polyamine amides in DNA binding action.     

Post-Assembly Photomasking of Potassium Acyltrifluoroborates (KATs) for Two-Photon 3D Patterning of PEG-Hydrogels

Chemical ligation reactions of functional groups that can be masked with two-photon labile protecting groups provide a powerful technology for the three-dimensional patterning of molecules – including proteins – onto hydrogel scaffolds. In order to utilize readily prepared hydrogels constructed by the potassium acyltrifluoroborate (KAT)-hydroxylamine amide formation ligation for two-photon patterning, we have developed a unique post-polymerization protecting group strategy through the reaction of KATs and dithiols in water and deprotection by two-photon excitation. After precise 3D spatially confined light irradiation, the unprotected KATs undergo ligations with hydroxylamine-functionalized superfolder GFP and sulforhodamine B for the composition of three-dimensional patterns.     

Preparation of triazamacrocycles containing only secondary amine functions using both tosyl and boc protecting groups

1,8,15-Triazacycloheneicosane ( 1 ); 1,9,17-triazacyclotetracosane ( 2 ) and 1,10,19-triazacycloheptacosane ( 3 ) were prepared by treating the appropriate N,N-bis(ω-bromoalkyl)toluenesulfonamide 8–10 with the appropriate N,N′-ditosyl-α,ω-diaminoalkane 11–13 in dimethylformamide using sodium hydride as the base followed by phenol and 33% hydrobromic acid in acetic acid to remove the tosyl protecting groups. 2-Allyloxymethyl-4,11,18- triazaoxacycloheneicosane ( 4 ) was prepared in two ways. First, N,N′,N″-tritosylbis(hexamemylene)triamine ( 18 ) was treated with 2-allyloxymethyl-3-oxa-1,6-hexanediol ditosylate ( 23 ) and cesium carbonate in dimethylformamide followed by sodium amalgam to remove the tosyl protecting groups. The second preparation of 4 was done by treating the tri-BOC analog of 18 with 23 followed by hydrochloric acid in isopropyl alcohol to remove the BOC protecting groups. The overall yields of 4 using these two processes were very close.     

Directional Control and Supramolecular Protection Allowing the Chemo‐ and Regioselective Transformation of a Triamine

A Zn^II‐funnel complex based on a calix[6]arene ligand decorated with three tris(imidazolyl) arms at one end of the cone and three NH₂ substituents at the other end, acts as a multipoint recognition host for polyfunctionalized guests. The selectivity is ensured by coordination to Zn^II, CH–π interaction within the calix cone, and H‐bonding at both rims of the cavity. As a result of these multiple interactions, the host can wrap and orient an unsymmetrical triamine guest with a high selectivity. Furthermore, a proton‐monitored switch between the regio‐isomeric adducts allows reversible inversion of the directionality of the system. Thanks to this directional control, the regioselective mono‐carbamoylation of the unsymmetrical triamine guest was successfully achieved on a preparative scale. This case study shows that a funnel‐like receptor can be used as a supramolecular protecting tool allowing a transformation which would be impracticable with conventional covalent chemistry.     

Traceless Staudinger ligation of glycosyl azides with triaryl phosphines: stereoselective synthesis of glycosyl amides

Alpha-glycosyl amides can be synthesized from the corresponding O-benzyl-alpha-glycosyl azides using a traceless Staudinger ligation with diphenylphosphanyl-phenyl esters 4. All the phosphines employed and their phenol precursors are stable to air at 4 degrees C for months. Fast intramolecular trapping of the reduction intermediates results in the direct formation of the amide link, which, in turn, prevents epimerisation and allows retention of configuration at the anomeric carbon. Yields and alpha-selectivity are high when the reaction is performed in polar aprotic solvents. Removal of the benzyl ether protecting groups is achieved by catalytic hydrogenation. Alpha-glycosyl amides represent a class of virtually unexplored nonhydrolyzable monosaccharide derivatives that may find a useful application as sugar mimics. Conformational studies by NMR spectroscopy confirm that deprotected alpha-glycosyl amides in the gluco, galacto, and fuco series retain the normal pyranose conformation of the monosaccharide. The reaction of phosphines 4 with tetra-O-acetyl-glycosyl azides is nonstereoconservative, and beta-glycosyl amides are obtained in good yields and with complete stereoselectivity starting from both alpha and beta azides.     

Tetrafluoroboric acid, a useful deprotecting reagent in peptide synthesis

We have found that tetrafluoroboric acid (HBF4) in trifluoroacetic acid (TFA) in the presence of thioanisole cleaves various protecting groups currently used in peptide synthesis. HBF4 in TFA cleaves an amino acid amide from 4-methylbenzhydrylamine resin more effectively than trifluoromethanesulfonic acid in TFA. Lamprey gonadotropin-releasing hormone (a 10-residue peptide amide) was synthesized using 1 M HBF4-thioanisole in TFA by both solution-phase and solid-phase methods.     

Convenient amidation of carboxyl group of carboxyphenylboronic acids

The use of catalysts in the activation of carboxyl groups towards nucleophilic attack and the protection of other functional groups by suitable protecting groups are standard and necessary procedures in amide bond formation. In contrast to the usual methods, various new compounds, amides of APTES ((3-aminopropyl)triethoxysilane, 3-triethoxysilylpropylamine) and carboxyphenylboronic acids, as well as the amides of aniline and carboxyphenylboronic acids, were obtained in good yields by a one-step synthesis under mild conditions without using any coupling reagents or additional catalysts.     

Synthesis of an eight-membered cyclic pseudo-dipeptide using ring closing metathesis

Ring closing metathesis of diallylglycine 6 provided cyclic Z-olefin 7 in 80% yield. The reaction was promoted by substitution of the amide nitrogen with the 2,4-dimethoxybenzyl group allowing for the required cis diallylglycine amide rotamer. Removal of the protecting groups provided cyclic dipeptide 2, a constrained scaffold useful in peptidomimetic research.     

Improved functional group compatibility in the palladium-catalyzed synthesis of aryl amines

[reaction: see text] The use of Pd2dba3 with bulky, electron-rich ligands 1 or 2 and LiN(TMS)2 as the base for the coupling of amines with aryl halides containing hydroxyl, amide, or enolizable keto groups is described. This protocol expands the utility of palladium-catalyzed C-N bond formation by allowing for the use of aryl halides containing these functional groups, obviating the need for protecting group manipulations.     

Selective photochemical cleavage of an α-ketoamide in a highly functionalised macrolide ascomycin

A novel photochemical amide cleavage reaction of (6S)-methoxyascomycin opening a pathway for the selective cleavage of the pipecolic acid, is described. The scope of this reaction with several analogues carrying suitable protecting groups is examined.     

Amide I infrared spectral features characteristic of some untypical conformations appearing in the structures suggested for amyloids

Amide I infrared (IR) spectral features are studied, by using the density functional theoretical method, for two untypical (but possibly rather prevalent) structures inspired from those recently suggested for amyloids: a structure consisting of loop regions in the (alpha L, alpha R) conformation stacked to form an alpha-sheet, and a structure involving some main-chain peptide groups (of any residues) and some side-chain amide groups of glutamine and asparagine residues closely located with each other. The amide I vibrational (off-diagonal) coupling constants are examined by extracting them from the calculated Cartesian-based force constants with the average partial vector method and by comparing them with those estimated on the basis of the transition dipole coupling mechanism. It is suggested that the amide I IR band characteristic of the alpha-sheet conformation in dry environment (without hydrogen bonding to solvent water molecules) is located in a high-frequency region (approximately >1670 cm(-1), somewhat higher than that of alpha-helix), because of the dependence of the diagonal (uncoupled) frequency and the off-diagonal coupling constant on the Phi and Psi dihedral angles. It is also shown that the amide I vibrations of the closely located peptide and amide groups are strongly coupled through-space with each other, and in the presence of this type of strong vibrational coupling, a noticeable change in the IR intensity upon (13)C=O substitution may occur even for a mode that arises mainly from an unsubstituted group and is not much shifted in frequency. The meaning of these results in the interpretation of observed amide I spectral profiles, especially the possible usefulness of IR spectroscopic measurements for detecting those untypical structures in the process of amyloid formation, is also discussed.     

Synthesis of (+/-)- and (-)-vibralactone and vibralactone C

Mander reductive alkylation of methyl 2-methoxybenzoate with prenyl bromide and hydrolysis of the enol ether afforded methyl 6-oxo-1-prenyl-2-cyclohexenecarboxylate. This was converted in five steps (reduction of the ketone, saponification, iodolactonization, ozonolysis, and intramolecular aldol reaction) to a spiro lactone cyclopentenal. An efficient first synthesis of (+/-)-vibralactone was completed by retro-iodolactonization with activated Zn, formation of the beta-lactone (vibralactone C), and reduction of the aldehyde. Except for the novel use of an iodolactone to protect both the prenyl double bond and carboxylic acid, no protecting groups were used. A similar sequence starting with asymmetric reductive alkylation of the (2S)-2-methoxymethoxymethylpyrrolidine amide of 2-methoxybenzoic acid with prenyl bromide afforded (-)-vibralactone confirming the absolute stereochemical assignment that was based on computational methods.     

Unusual Orthogonality in the Cleavage Process of Closely Related Chelating Protecting Groups for Carboxylic Acids by Using Different Metal Ions

Three structurally related relay protecting groups for carboxylic acids that are based on chelating amines have been developed. These protecting groups can easily be introduced by coupling the carboxylic acid and the corresponding amine in the presence of 2‐(1H‐benzotriazole‐1‐yl)‐1,1,3,3‐tetramethyluronium tetrafluoroborate (TBTU). In addition to being stable to a whole array of reaction conditions, these protecting groups are also stable under acidic and basic conditions, allowing them to be used in combination with the ester protection of carboxylic acids. The cleavage of these protecting groups is activated by the chelation of metal ions, involving an unusual coordination of the amide nitrogen. Despite their similarity, cleavage of these protecting groups is possible in both a stepwise and an orthogonal fashion by applying different metal salts.     

A New and Efficient Method for Synthesis of 5′‐Conjugates of Oligonucleotides through Amide‐Bond Formation on Solid Phase

An efficient method for synthesis of oligonucleotide 5′‐conjugates through amide‐bond formation on solid phase is described. Protected oligonucleotides containing a 5′‐carboxylic acid function were obtained by use of a novel non‐nucleosidic phosphoramidite building block, where the carboxylic acid moiety was protected by a 2‐chlorotrityl group. The protecting group is stable to the phosphoramidite coupling conditions used in solid‐phase oligonucleotide assembly, but is easily deprotected by mild acidic treatment. The protecting group may be removed also by ammonolysis. 5′‐Carboxylate‐modified oligonucleotides were efficiently conjugated on solid support under normal peptide‐coupling conditions to various amines or to the N‐termini of small peptides to yield products of high purity. The method is well‐suited in principle for the synthesis of peptide‐oligonucleotide conjugates containing an amide linkage between the 5′‐end of an oligonucleotide and the N‐terminus of a peptide.     

The chemistry of nitrogen coordinated tertiary carboxamides: a spectroscopic study on bis(picolyl)amidecopper(II) complexes

Metal coordination of the electrically neutral nitrogen atom of a tertiary carboxamide reduces the barrier to C-N-bond rotation and activates the amide towards methanolysis. X-Ray crystallographic studies indicate that this reactivity is correlated to a lifting of the amide resonance structure and concurrent pyramidalization at nitrogen. However, mechanistic data in solution have not been obtained. It became evident that structural mobility is characteristic of the complexes and the crystallographic data do not fully account for relevant reactive species. In this report we summarize IR, UV-vis, and EPR spectra of amide nitrogen coordinated bis(picolyl)amide complexes with copper(II) triflate and copper(II) chloride. A comparison between spectra sampled in the aprotic solvents dichloromethane and acetonitrile, as well as under methanolysis conditions reveals the nature of several species formed in solution. The key reactions are (I) ligand exchange involving either CH3CN or CH3OH, or, in IR experiments, bromide ions from KBr, (II) coordination-dissociation equilibria involving the urethane protecting groups of amino acid substituted ligands Boc-Xaa-bpa (Boc = tert-butoxycarbonyl, Xaa = glycine, alanine, and leucine, respectively, bpa = bis(picolyl)amine), (III) dissociation of a chloro ligand from LCuCl2 complexes and formation of square-pyramidal complex cations [LCuCl]+, and finally (IV) complete dissociation of the polydentate tertiary amide ligand to produce free copper ions in solution. Taken together, the results provide a fairly detailed qualitative picture of the processes which accompany the amide bond methanolysis.     

A Novel Synthetic Method and Potential Application of a Sulfanilic Acid-Based Surfactant

A novel synthetic method was developed to prepare a difunctional surfactant using sulfanilic acid and dodecyl bromide. In the first step, sulfanilic acid was protected by acetic anhydride. Then, Friedel–Crafts alkylation of the synthesized acetanilide with dodecyl bromide was performed in the presence of aluminum chloride. The protecting group (amide) was removed easily by acid hydrolysis. The formation of surfactant was confirmed with Fourier transform infrared and proton nuclear magnetic resonance spectroscopy. The demulsification property of this surfactant was studied using brine-fuel oil emulsion, and its result was compared with a commercially available demulsifier. The results showed that 52% of water was separated from emulsion at room temperature, but at elevated temperature 98% of water was separated from brine-fuel oil emulsion.     

Structural characterization of synthetic poly(ester amide) from sebacic acid and 4-amino-1-butanol by matrix-assisted laser desorption ionization time-of-flight/time-of-flight tandem mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS/MS) was employed to analyze a poly(ester amide) sample (PEA-Bu) from the melt condensation of sebacic acid and 4-amino-1-butanol. In particular, we investigated the fragmentation pathways, the ester/amide bond sequences and the structure of species derived from side reactions during the synthesis. MALDI-TOF/TOF-MS/MS analysis was performed on cyclic species and linear oligomers terminated by dicarboxyl groups, carboxyl and hydroxyl groups and diamino alcohol groups. The sodium adducts of these oligomers were selected as precursor ions. Different end groups do not influence the fragmentation of sodiated poly(ester amide) oligomers and similar series of product ions were observed in the MALDI-TOF/TOF-MS/MS spectra. According to the structures of the most abundant product ions identified, the main cleavages proceed through a beta-hydrogen-transfer rearrangement, leading to the selective scission of the --O--CH2-- bonds. Abundant product ions originating from --CH2--CH2-- (beta-gamma) bond cleavage in the sebacate moiety were also detected. Their formation should be promoted by the presence of an alpha,beta-unsaturated ester or amide end group. MALDI-TOF/TOF-MS/MS provided structural information concerning the ester/amide sequences in the polymer chains. In the MALDI-TOF/TOF-MS/MS spectra acquired, using argon as the collision gas, of cyclic species and linear oligomers terminated by diamino alcohol groups, product ions in the low-mass range, undetected in the mass spectra acquired using air as the collision gas, proved to be diagnostic and made it possible to establish the presence of random sequences of ester and amide bonds in the poly(ester amide) sample. Furthermore, MALDI-TOF/TOF-MS/MS provided useful information to clarify the structures of precursor ions derived from side reactions during the synthesis.     

Thiophene backbone amide linkers, a new class of easily prepared and highly acid-labile linkers for solid-phase synthesis

Solid-phase synthesis is of tremendous importance for small-molecule and biopolymer synthesis. Linkers (handles) that release amide-containing products after completion of solid-phase synthesis are widely used. Here we present a new class of highly acid-labile backbone amide linkers (BAL handles) based on 3,4-ethylenedioxythiophene (EDOT), which we have termed T-BAL. These thiophene linkers are synthesized in three convenient steps from commercially available EDOT. In the linker design, the spacer was introduced to the EDOT core either via a carbon-carbon bond or via a thioether linkage. Introduction of the spacer via a C-C bond was performed by a chemoselective Negishi coupling without transient protection of the aldehyde group to provide the T-BAL1 handle. Introduction via a thioether linkage was performed by a facile nucleophilic aromatic substitution between the brominated EDOT aldehyde and unprotected mercapto acids to provide T-BAL2 and T-BAL3 handles. The minimal use of protecting groups gave the corresponding linker molecules in few synthetic steps and in good yields. After anchoring of the linker to a polymeric support, introduction of the first amino acid was achieved by reductive amination, giving a secondary amine. A following acylation of the secondary amine with a symmetrical amino acid anhydride resulted in a backbone amide linkage between the handle and the growing substrate (e.g., peptide chain). After solid-phase synthesis, the substrates could be released from the resin by either low acid conditions using 1% TFA in CH2Cl2 or high acid conditions such as 50% TFA in CH2Cl2. Peptide thioesters could be released from the T-BAL1 handle under very mild conditions using aqueous acetic acid. Tert-butyl based protecting groups, tert-butyl esters, tert-butyl ethers, and Boc groups, as well as dimethyl acetals were relatively stable to these mild conditions for release of the peptides.     

Synthesis of well-defined poly(p-benzamide) from chain-growth polycondensation and its application to block copolymers

Poly(p-benzamide) with a defined molecular weight and a low polydispersity and block copolymers containing this well-defined aramide was synthesized. Phenyl 4-(4-octyloxybenzylamino)benzoate ( 1b ) polymerized at room temperature in the presence of base and phenyl 4-nitrobenzoate ( 2a ) as an initiator in a chain-growth polycondensation manner to give well-defined aromatic polyamides having the 4-octyloxybenzyl groups as a protecting group on nitrogen in an amide. It was confirmed by a model reaction that deprotection of this protecting group proceeded completely with trifluoroacetic acid (TFA) without breaking the amide linkage. The utility of this approach to poly(p-benzamide) with a low polydispersity was demonstrated by the synthesis of block copolymers of poly(p-benzamide) and poly(N-octyl-p-benzamide) or poly(ethylene glycol). The SEM images of the supramolecular assemblies of the former block copolymer showed μm-sized bundles and aggregates of flake structures.     

Alpha-phosphono lactone analogues of cytidine and cytosine arabinoside diphosphates: synthesis via ring closing metathesis

alpha-Phosphono lactone derivatives of the nucleosides cytidine and cytosine arabinoside have been prepared from the corresponding nucleoside aldehydes. The stereochemical outcome of allylation reactions with these aldehydes was found to be dependent upon both the choice of protecting groups for the 2'- and 3'-hydroxyl groups and, to some extent, the nature of the Lewis acid catalyst employed. Ultimately, conditions were found that favored either the 5'R or 5'S diastereomer from different cytidine aldehydes, and gave some stereoselectivity in additions to an aldehyde derivative of ara-C. The resulting homoallylic alcohols were used as substrates in attempted Knovenagel and Horner-Wadsworth-Emmons condensations, but elimination was found to predominate over lactone formation under the conditions employed. The desired alpha-phosphono lactones could be prepared through a reaction sequence that included ring-closing metathesis on acrylate esters of the homoallylic alcohols, followed by reduction of the resulting alpha,beta-unsaturated lactones and carbon-phosphorus bond formation on enolates generated from the saturated lactones.