Possible factors influencing the separation mechanism of diastereomeric amino acid derivatives obtained from s-triazine type reagents

Diastereomeric derivatives prepared from an amino acid and an amino amide using trichloro s-triazine as a coupling platform are known to produce good chromatographic diastereoselectivity for many amino acid analytes. The chromatographic diastereoselectivity of these derivatives is difficult to rationalize based on the possibility of four possible conformational isomers, which can interconvert by rotation about the C-N bonds between the amino substituents and the triazine ring. The observed diastereoselectivity implicates an unobvious but significant driving force which causes one of several conformations to be favored over the others. Several possibilities are discussed. Intramolecular hydrogen bonding between acid and amide substituents was explored using computer aided molecular modeling. While such hydrogen bonding may be geometrically possible between the amino acid and the amide substituents, it does not explain why derivatives produced from other chiral compounds which are not capable of the same hydrogen bonding interaction nevertheless exhibit substantial diastereoselectivity. Two other more general effects, steric hindrance to solvation and ion pairing, are therefore suggested as possible contributing factors to the chromatographic diastereoselectivity. Based on the conformational equilibrium behavior of related triazine compounds as reported in the literature, either one of these effects could influence the conformation of the diastereomeric derivatives even in the absence of intramolecular hydrogen bonding interactions between the two chiral substituents, and these effects may therefore be a contributing factor for the observed elution order of the diastereomers.     

Conformational behavior of peptides containing residues of 3-azetidinesulfonic (3AzeS) and 4-piperidinemethanesulfonic (4PiMS) acids

The conformational behavior of four model peptides containing residues of 3-azetidinesulfonic (3AzeS) and 4-piperidinemethane sulfonic (4PiMS) acids was studied in both a crystalline state and in solution using X-ray, NMR, and IR experiments. It was found that in the crystalline state, both of the models di- and tripeptides studied adopted extended conformations and demonstrated considerable conformational flexibility. In solution, it is likely that a flexible ensemble of conformations is adopted, including extended structures and more compact ones without persistent hydrogen bonds. One of the most interesting features of the peptides was the axial chirality observed due to the slow rotation around the amide bond formed by the endocyclic nitrogen atoms of the non-chiral 3AzeS and 4PiMS residues. It was shown for one of the derivatives that the configuration of the chiral axis had an impact on the conformation of the neighboring amino acid residue.     

Solid-phase synthesis and structural characterization of highly substituted hydroxyproline-based 2,5-diketopiperazines

Two general solid-phase methods for the synthesis of a new class of 2,5-diketopiperazines (DKPs) containing the trans-4-hydroxy-L-proline amino acid residue (Hyp) have been developed. An N-protected hydroxyproline methyl ester was linked through the hydroxyl function to the Ellman resin. The synthesis procedures were conceived to enable a sequence of Hyp alkylation, Hyp N-acylation, cyclization, and amide bond alkylation. Up to three different centers of molecular diversity were introduced around the DKP scaffold. Highly functionalized bicyclic compounds were obtained in good yield and purity. The alkylation of hydroxyproline alpha CH was performed without control of the diastereoselectivity. During the final alkylation of the backbone, amide bond epimerization at the alpha-carbon atoms of the two amino acid residues was observed. The structures of representative DKPs were elucidated with multidimensional NMR experiments. The described reaction pathways can be applied to the identification of heterocyclic molecule inhibitors to diverse enzyme targets.     

Chiral bis(amino amides) as chiral solvating agents for enantiomeric excess determination of α-hydroxy and arylpropionic acids

A family of bis(amino amides) derived from natural amino acids has been synthesized and tested for the NMR enantiodiscrimination, as chiral solvating agents, for enantiomeric excess determination of some carboxylic acids. Those bis(amino amide) receptors contain different structural modifications and the splitting of the signals of the acids, after addition of the corresponding CSAs, depends on those structural variables. The influence of aminoacid side chain and the nature of the aliphatic spacer are important parameters to obtain good chiral discriminations. The results obtained clearly show the chiral recognition abilities of these bis(amino amide) ligands and suggest their advantageous use as chiral solvating agents for carboxylic acids. The binding between bis(amino amides) and carboxylic acids has been studied by ESI-MS, NMR, DSC, and molecular modeling. The data suggest that enantiodiscrimination involves the formation of an ionic pair after proton transfer from the carboxylic substrate to the bis(amino amides).     

Atomic Polarizability Dominates the Electronic Properties of Peptide Bonds upon Thioxo or Selenoxo Substitution

The amide bond as peptide linkage plays an important role in protein structure and function. A large number of theoretical and experimental studies have focused on the specific nature of the peptide bond. Little attention, however, has been paid to their chalcogen-substituted congeners, although experimental data on thioamides revealed inconsistencies with the conventional view of amide resonance theory. Here, we employed thioxo and selenoxo substitution to determine experimentally how heavier chalcogens affect the properties of the peptide bond and adjacent atoms. NMR data revealed pronounced deshielding of heteronuclei within a three-bond distance to the chalcogen atom; this indicates an enhanced electron-withdrawing potential of the heavier chalcogens despite their lower electronegativities compared to oxygen. Interestingly, linear correlations were observed between chalcogen atomic polarizability and the chemical shift values of those neighboring heteronuclei as well as several physicochemical properties, such as electronic excitation energy, C?N rotation barrier, dipole moment and amide proton dissociation. We conclude that the chalcogen polarizability, which relates to the charge capacity, is the dominant factor that determines the electronic properties of peptide bonds substituted with heavier chalcogens.     

Complete NMR Elucidation of Two N-Protected Trishomocubane Hydantoins and the Ethyl Ester of the Corresponding Amino Acid

In an attempt to resolve a racemic mixture of a trishomocubane hydantoin, the synthesis of a pair of novel diastereomers was obtained by protecting the racemic hydantoin with chlorocarbonic acid-(–)(R)-sec-butyl ester. An achiral i-propyl ester was first used to establish the procedure. The NMR elucidation of both the chiral and achiral N-protected hydantoins is described. Some proton and carbon NMR shifts on the cage are reversed when relative small changes on the protection group are introduced. The chiral centre on the protective group induced splitting of some carbon signals in the ¹³C spectrum on the cage skeleton, but effective separation of the diastereomers could not be obtained. In a further attempt to demonstrate the potential use of the trishomocubane amino acid in peptide synthesis, the ethyl ester of the cage amino acid was synthesised. The structures of the amino acid derivatives were elucidated with 2D NMR techniques and the assignment of the NMR data is presented.     

Acceleration of amide bond rotation by encapsulation in the hydrophobic interior of a water-soluble supramolecular assembly

The hydrophobic interior cavity of a self-assembled supramolecular assembly exploits the hydrophobic effect for the encapsulation of tertiary amides. Variable-temperature (1)H NMR experiments reveal that the free energy barrier for rotation around the C-N amide bond is lowered by up to 3.6 kcal/mol upon encapsulation. The hydrophobic cavity of the assembly is able to stabilize the less polar transition state of the amide rotation process. Carbon-13 labeling studies showed that the (13)C NMR chemical shift of the carbonyl resonance increases with temperature for the encapsulated amides, which suggests that the assembly is able to favor a twisted form of the amide.     

Carbohydrates as chiral templates: asymmetric ugi-synthesis of alpha-amino acids using galactosylamines as the chiral matrices

In the presence of Lewis acid catalysts O-acetyl- (1) and O-pivaloyl- (2) protected β-D-galactopyranosylamines react with aldehydes, isocyanides and carboxylic acids in Ugi-four-component-condensations to give the corresponding N-galactosyl-amino acid amide derivatives 3,5 in almost quantitative yields. Zinc chloride is the most effective Lewis acid catalyst. At 0°C or even at room temperature the (2R,β-D)-diastereomers of the amino acid derivatives 3,5 are formed with high diastereoselectivity. If the sterically more demanding O-pivaloyl galactosylamine 2 is used at -78°C to -25°C the stereoselectivity often exeeds 20:1 favouring the (2R,β-D) diastereomers 5. After one recrystallisation pure (R)-amino acid derivatives 5 are obtained in yields of 80–95%. In addition to the high yields and stereoselectivity the amino acid synthesis discribed here has the further advantage that it neither requires organometallic reagents and intermediates nor exclusion of oxygen and moisture. Two step acid hydrolysis of the N-galactosylamino acid amide derivatives 5 delivers the enantiomerically pure (R)-amino-acids 8 in high yields.     

A new, efficient and stereoselective synthesis of tricyclic and tetracyclic compounds by samarium diiodide induced cyclisations of naphthyl-substituted arylketones--an easy access to steroid-like skeletons

In this report, we present the application of samarium diiodide induced cyclisations of naphthyl-substituted ketones towards an easy and stereoselective access to tri- and tetracyclic-functionalised compounds. Typical naphthalene derivatives were studied to investigate the scope and limitations of this novel cyclisation process. The model substrates studied demonstrate that the samarium ketyl cyclisations are essentially restricted to the formation of six-membered rings. The diastereoselectivity of these reactions is strongly influenced by the connection of the alkyl side chain to the naphthalene core. Gamma-naphth-1-yl-substituted ketones furnished cyclisation products, such as 17 or 22-26, as single diastereomers, whereas gamma-naphth-2-yl-substituted precursors gave mixtures of diastereomers--as demonstrated by the conversion of model compound 10 into tricyclic products 18 a/18 b, or that of cyclohexanone derivative 33 into tetracyclic diastereomers 34 a/34 b. Cyclic ketones as ketyl precursors furnished steroid-like tetracyclic skeletons; however, due to the cis/cis fusion of rings B/C and C/D these products have an "unnatural" bowl-like shape. Several of the cyclisation products have been identified by X-ray analyses, which not only proved the constitutions, but also the relative configurations and the preferred conformations. Steroid analogue 23 was subjected to subsequent transformations, which demonstrate that the styrene-like double bond of such compounds can be used for further structural diversification. First attempts to synthesise related azasteroids by incorporating nitrogen atoms into the ketone moiety are also reported. Thus, pyrrolidine derivatives 44 and 47 as well as piperidine derivatives 50 and 52 were subjected to samarium diiodide induced cyclisations. The expected tetracyclic products 48, 49 a/49 b, 51 and 53 a/53 b were obtained in moderate to good yields. The stereoselectivities observed follow the rules already established for the all-carbon precursors. The resulting products, bearing a nitrogen atom in ring D, are interesting azasteroid analogues with "unnatural" configuration.     

Coexistence of hydrogen-bonded loop and extended tetrapeptide conformations

The conformations of a protected tetrathiopeptide have been analysed by isotope labelling and two-dimensional infrared spectroscopy (2D-IR). It has been found that Boc-Ala-Gly(=S)-Ala-Aib-OMe in acetonitrile, as well as its oxopeptide analogue, can adopt a hydrogen-bonded loop conformation in coexistence with less restricted structures. The two types of conformations interconvert too quickly to be resolved on the nuclear magnetic resonance (NMR) timescale, but give rise to different cross peaks in two-dimensional infrared spectra. The hydrogen bond between the Boc terminal group and the amide proton of Aib can be broken by photoisomerisation of the thioamide bond.     

(+)- and (-)-2-aminocyclobutane-1-carboxylic acids and their incorporation into highly rigid beta-peptides: stereoselective synthesis and a structural study

[Chemical reaction: See text] Several derivatives of (+)- and (-)-2-aminocyclobutane-1-carboxylic acid, 1, have been prepared through enantiodivergent synthetic sequences. The stereoselective synthesis of free amino acid (+)-1 has been achieved, and this product has been fully characterized for the first time. Stereocontrolled alternative synthetic methodologies have been developed for the preparation of bis(cyclobutane) beta-dipeptides in high yields. Among them, enantio and diastereomers have been synthesized. beta,beta- and beta,delta-Dimers resulting from the coupling of a cyclobutane residue and a linear amino acid have also been prepared. The ability of the cyclobutane ring as a structure-promoting unit both in the monomers and in the dimers has been manifested. The NMR structural study and DFT theoretical calculations evidence the formation of strong intramolecular hydrogen bonds giving rise to cis-fused [4.2.0]octane structural units that confer high rigidity on these molecules both in solution and in the gas phase. The contribution of a cis-trans conformational equilibrium derived from the rotation around the carbamate N-C(O) bond has also been observed, the trans form being the major conformer. In the solid state, this equilibrium does not exist, and moreover, intermolecular hydrogen bonds are present.     

Kinetics and equilibria of cis/trans isomerization of backbone amide bonds in peptoids

The biological activities of N-substituted glycine oligomers (peptoids) have been the subject of extensive research. As compared to peptides, both the cis and trans conformations of the backbone amide bonds of peptoids can be significantly populated. Thus, peptoids are mixtures of configurational isomers, with the number of isomers increasing by a factor of 2 with each additional monomer residue. Here we report the results of a study of the kinetics and equilibria of cis/trans isomerization of the amide bonds of N-acetylated peptoid monomers, dipeptoids, and tripeptoids by NMR spectroscopy. Resonance intensities indicate the cis conformation of the backbone amide bonds of the peptoids studied is more populated than is generally the case for the analogous secondary amide bond to proline residues in acyclic peptides. Rate constants were measured by inversion-magnetization transfer techniques over a range of temperatures, and activation parameters were derived from the temperature dependence of the rate constants. The rate of cis/trans isomerization by rotation around the amide bonds in the peptoids studied is generally slower than that around amide bonds to proline residues and takes place on the NMR inversion-magnetization transfer time scale only by rotation around the amide bond to the C-terminal peptoid residue.     

Effects of internal hydrogen bonds between amide groups: protonation of alicyclic diamides

The proton affinity (PA) of cyclopentane carboxamide 1, cyclohexane carboxamide 2 and their secondary and tertiary amide derivatives S1, S2, T1 and T2, was determined by the thermokinetic method and the kinetic method [PA(1) = 888 +/- 5 kJ mol(1); PA(2) = 892 +/- 5 kJ mol(1); PA(S1) = 920 +/- 6 kJ mol(1); PA(S2) = 920 +/- 6 kJ mol(1); PA(T1) = 938 +/- 6 kJ mol(1); PA(T2) = 938 +/- 6 kJ mol(1)]. Special entropy effects are not observed. Additionally, the effects of protonation have been studied using an advanced kinetic method for all isomers 37 of cyclopentane dicarboxamides and cyclohexane dicarboxamides (with the exception of cis-cyclopentane-1,2-dicarboxamide) and their bis-tertiary derivatives T3T7 by estimating the PA and the apparent entropy of protonation Delta(DeltaS(app)). Finally, the study was extended to bicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxamide 8 and its bis-tertiary derivative T8, to all stereoisomers of bicyclo[2.2.1]heptane-2,3-dicarboxamide 9, their secondary and tertiary amide derivatives S9 and T9, and to endoendobicyclo[2.2.1]heptane-2,5-dicarboxamide 10 and the corresponding secondary and tertiary derivatives S10 and T10. Compared with 1 and 2, all alicyclic diamides exhibit a significant increase of the PA (DeltaPA) and special entropy effects on protonation. For alicyclic diamides, which can not accommodate a conformation appropriate for building a proton bridge, the values of DeltaPA and Delta(DeltaS(app)) are small to moderate. This is explained by ion / dipole interactions between the protonated and neutral amide group which stabilize the protonated species but hinder the free rotation of the amide groups. If any of the conformations of the alicyclic diamide allows formation of a proton bridge, DeltaPA and Delta(DeltaS(app)) increase considerably. A spectacular case is cis-cyclohexane-1,4-dicarboxamide 7c which is the most basic monocyclic diamide, although generation of the proton bridge requires the unfavorable boat conformation with both amide substituents at a flagpole position. A pre-orientation of the two amide groups in such a 1,4-position in 10 results in a particularly large PA of < 1000 kJ mol(1). The observation of comparable values for Delta(DeltaS(app)) for linear and monocyclic diamides indicates that a major part of the entropy effects originates from freezing the free rotation of the amide groups by formation of the proton bridge. This is corroborated by observing corresponding effects during the protonation of dicarboxamides containing the rigid bicyclo[2.2.1]heptane carbon skeleton, where the only internal movements of the molecules corresponds to rotation of the amide substituents.     

Effect of large volume injection of hydrophobic solvents on the retention of less hydrophobic pharmaceutical solutes in RP-LC

Injection of large volumes of samples in solvents other than mobile phase composition has been proved for some less hydrophobic compounds. Thus, the retention behavior of several compounds of pharmaceutical interest (isosorbide-2-nitrate, isosorbide-5-nitrate, tropicamide, pentoxifylline, and methyl p-hydroxybenzoate) was studied by using different hydrophobic solvents (n-hexane, n-heptane, or i-octane) as sample solvents. Two types of stationary phases were used: octyl and octadecyl modified silica (both of Zorbax Eclipse type). The experiments showed a linear dependence between capacity factor of each solute and sample injection volume, up to maximum volume values of about 680 microL for C8 stationary phase and 580 microL for C18 stationary phase, when the solutes are no longer retained in stationary phase. Injection of large volumes of these hydrophobic solvents is thus possible in RP-LC with a gradual reduction of retention and peak efficiency. Two major conditions are however necessary in order to apply such an injection approach: the solutes must have a proper solubility in hydrophobic solvents and meanwhile they have to be less hydrophobic than the sample solvent in order to avoid competition with solvent molecules in partitioning between mobile and stationary phases.     

Liquid chromatographic resolution of proline and pipecolic acid derivatives on chiral stationary phases based on (+)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid

Two liquid chromatographic chiral stationary phases based on (+)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid were applied to the resolution of the amide derivatives of cyclic α‐amino acids including proline and pipecolic acid. Among the five amide derivatives of proline, aniline amide was resolved best on the first chiral stationary phase, which contains two N–H tethering amide groups, with the separation factor of 1.31 and the resolution of 2.60, and on the second chiral stationary phase, which contains two N–CH₃ tethering amide groups, with the separation factor of 1.57 and the resolution of 5.50. Among the five amide derivatives of pipecolic acid, 2‐naphthyl amide was resolved best on the first chiral stationary phase with the separation factor of 1.30 and the resolution of 1.75, but 1‐naphthylmethyl amide was resolved best on the second chiral stationary phase with the separation factor of 1.30 and the resolution of 2.26. In general, the second chiral stationary phase was found to be better than the first chiral stationary phase in the resolution of the amide derivatives of cyclic α‐amino acids. In this study, the second chiral stationary phase was first demonstrated to be useful for the resolution of secondary amino compounds.     

Modulations in restricted amide rotation by steric induced conformational trapping

The rotation around the amide bond in N,N-diethyl-m-toluamide (m-DEET) has been studied extensively and often used in laboratory instructions to demonstrate the phenomenon of chemical exchange. Herein, we show that a simple modification to N,N-diethyl-o-toluamide (o-DEET) significantly alters the dynamics of the restricted rotation around the amide bond due to steric interactions between the ring methyl group and the two N-ethyl groups. This alters the classic two-site exchange due to restricted rotation around the amide bond, to a three-site exchange, with the third conformation trapped at a higher-energy state compared to the other two. This often overlooked phenomenon is elucidated using variable-temperature NMR, two-dimensional exchange spectroscopy and molecular modeling studies.     

Synthesis and structure of macrocyclic bis(hydroxynaphthoic amide)s connected by an achiral or chiral diamine

Macrocyclic bis(hydroxynaphthoic amide)s 6, connected by an achiral or chiral diamine, were synthesized by the tandem Claisen rearrangement. CD spectra, X-ray crystallographic analyses, and variable-temperature NMR measurements of the chiral bis(hydroxynaphthoic amide)s revealed that the two hydroxynaphthalene rings in these macrocycles adopt a twisted conformation both in solution and in the crystalline state because of the steric hindrance between the two hydroxynaphthalene rings and that the chirality of the twisted conformation is generated by that of the chiral linker. Theoretical calculations revealed that the chiral linker works effectively to favor energetically one conformer of the diastereomers, although a flipping process was possible and can be observed to occur on the NMR time scale in variable-temperature experiments.     

Spectroscopic,X-ray Diffraction and Density Functional Theory Study of Intra- and Intermolecular Hydrogen Bonds in Ortho-(4-tolylsulfonamido)benzamides

The conformations of the title compounds were determined in solution (NMR and UV-Vis spectroscopy) and in the solid state (FT-IR and XRD), complemented with density functional theory (DFT) in the gas phase. The nonequivalence of the amide protons of these compounds due to the hindered rotation of the C(O)–NH₂ single bond resulted in two distinct resonances of different chemical shift values in the aromatic region of their ¹H-NMR spectra. Intramolecular hydrogen bonding interactions between the carbonyl oxygen and the sulfonamide hydrogen atom were observed in the solution phase and solid state. XRD confirmed the ability of the amide moiety of this class of compounds to function as a hydrogen bond acceptor to form a six-membered hydrogen bonded ring and a donor simultaneously to form intermolecular hydrogen bonded complexes of the type N–H···O=S. The distorted tetrahedral geometry of the sulfur atom resulted in a deviation of the sulfonamide moiety from co-planarity of the anthranilamide scaffold, and this geometry enabled oxygen atoms to form hydrogen bonds in higher dimensions.     

Why are silyl ethers conformationally different from alkyl ethers? Chair-chair conformational equilibria in silyloxycyclohexanes and their dependence on the substituents on silicon. The wider roles of eclipsing, of 1,3-repulsive steric interactions, and of attractive steric interactions

An NMR study of the diaxial/diequatorial chair equilibrium in a range of silylated derivatives of trans-1,4- and trans-1,2-dihydroxycyclohexane is reported and discussed with a view to explaining unusually large populations of chair conformations with axial substituents, noted previously for some monosilyloxycyclohexanes and in some silylated sugars. X-ray diffraction studies of three bis-triphenylsilyloxycyclohexanes are reported and show both axial and equatorial silyloxy groups with the exocyclic bonds eclipsed. Eclipsing is also suggested by molecular mechanics (MM3) calculations on such derivatives. Both axial and equatorial tertiary silyl groups have 1,3-repulsive interactions with whatever substituents or hydrogen atoms are at the two adjacent equatorial positions, and these are relieved by rotation toward the eclipsed conformation of the exocyclic C-O bond. The three substituents on silicon interact attractively with the nine atoms at the 3, 4, and 5-positions of the cyclohexane ring and calculations suggest that these stabilizing interactions are significantly greater in the axial than in the equatorial conformation. An equatorial C-OSiR(3) bond with one or two equatorial neighbors has a restricted potential energy well that becomes much broader when the bond is axial without any equatorial neighbors in the alternative chair. Adjacent silyl groups in the 1,2-disubstituted series interact in a stabilizing way overall in all conformations, this being particularly marked in the diaxial conformation of the more complex ethers. These factors lead to unusually large axial populations.     

A new bicyclic dipeptide isostere with pyrrolizidinone skeleton

The synthesis of a new conformationally constrained Gly-(s-cis)Pro Turn Mimetic (GPTM) in both racemic and enantiomerically pure forms and their incorporation into peptides 18, 21, and 24 are reported. The synthetic strategy adopted to assemble the bicyclic pyrrolizidinone skeleton is based on the 1,3-dipolar cycloaddition of the cyclic nitrone 4a derived from proline and acrylamide, followed by a reductive cleavage/cyclization domino process. The enantiomerically pure GPTMs are obtained by synthesis and separation of diastereomeric intermediates containing (1R)-1-phenylethylamine as chiral auxiliary. Analysis of pseudotripeptides 18, 21, and 22 by FT-IR and NMR shows that the amide proton of GPTM derivatives 21 is intramolecularly hydrogen bonded in CDCl(3), while DMSO was shown to disrupt this hydrogen bond.