Tilted amides in amino acid and peptide derivatives

Background: Amide bonds in peptides and proteins typically adopt planar cis or trans conformations. Conversions between cis and trans amide conformations are necessary for protein folding and for many other processes, but are difficult to achieve since they involve disruption of the planarity of the bond. As a first step to understanding cis-trans isomerization, we set out to synthesize and characterize peptides that mimic the tilted or twisted amide structures that are postulated to form the intermediate states in this process.Results: We have synthesized a model amino acid and four dipeptide derivatives containing a methyl-substituted aziridine residue. Single crystals of phenacyl (2R, 3R)-benzyloxycarbonyl-3-methyl-2-aziridinecarboxylate and phenacyl (2R, 3R)-acetyl-glycyl-3-methyl-2-aziridine-carboxylate were obtained. Using X-ray diffraction analysis, we determined that the amide nitrogens of the aziridine rings have tetrahedral sp³-like geometry with tilt angles in the range of 37–38°. The ¹³C-NMR spectra indicate that the amide carbonyl is dramatically shifted downfield as a consequence of the tilt.Conclusions: In peptides containing a substituted aziridine ring, the orbitals of the amide nitrogen are constrained into a tilted configuration. These peptides may mimic the transition state between cis and trans amide conformations. This technique thus provides a novel strategy for the study of isomerization and other biorecognition processes.     

Stereospezifische massenspektrometrische fragmentierungen von cyclohexandicarboxamiden. 34–Über massenspektrometrische untersuchungen

Two of the electron impact induced fragmentations of 1,3- and 1,4-cyclohexanedicarboxamides are very stereospecific: only the cis isomers lose CONH, whereas loss of (NH₃+CO) is more favoured in the trans isomers. In the spectra of the 1,2-isomers the differences between cis and trans are less pronounced.     

3-Aminoacetylthiazolidine-4-carboxylate esters and their l-thia-4-azaspiro[4.5]decane-3-carboxylate derivatives. Synthesis and stereochemical properties

Dimethyl thiazolidine-2,4-dicarboxylate 2 and ethyl l-thia-4-azaspiro[4.5]decane-3-carboxylates 3-5 were obtained as a diastereoisomeric mixture while their 3-aminoacetyl derivatives were isolated in only one isomeric form. These reactions of N-acylation were stereoselective, which can be explained by an interconversion of the diastereoisomers via a seco intermediate. The ¹H nmr analysis of amides 6 and 11 exhibited the presence of both cis and trans amide bond conformations, whereas only one cis conformation was observed for spiro amides 8-10 and 13-15.     

Pyranosides with 2,3‐trans Carbamate Groups: Exocyclic or Endocyclic Cleavage Reaction?

Pyranosides with 2,3‐trans carbamate groups exhibit high 1,2‐cis selectivity in glycosylation reactions. Using glycosyl donors with N‐benzyl 2,3‐trans carbamate groups, an anti‐Helicobacter pylori oligosaccharide was synthesized in an efficient manner. Moreover, pyranosides with 2,3‐trans carbamate groups readily undergo anomerization from the β to the α configuration under mild acidic conditions via endocyclic cleavage. Acyclic cations generated during the endocyclic cleavage reaction were captured using reduction and intramolecular Friedel–Crafts reaction. By exploiting this anomerization, multiply aligned 1,2‐trans glycosyl bonds can be transformed to 1,2‐cis glycosyl bonds in a single operation.     

Comparative study of the mechanical relaxation behavior of polymethacrylates containing different bulky side groups

The syntheses of poly(1,3‐dioxan‐5‐yl methacrylate), poly(cis‐2‐phenyl‐1,3‐dioxan‐5‐yl methacrylate), poly(trans‐2‐phenyl‐1,3‐dioxan‐5‐yl methacrylate), poly(cis‐2‐cyclohexyl‐1,3‐dioxan‐5‐yl methacrylate), and poly(trans‐2‐cyclohexyl‐1,3‐dioxan‐5‐yl methacrylate) are reported. The mechanical relaxation spectrum of the simplest polymer, poly(1,3‐dioxan‐5‐yl methacrylate), exhibits a prominent β relaxation centered at ?98 °C, at 1 Hz, followed in increasing order of temperature by an ostensible glass–rubber relaxation process. In addition to the β relaxation, the loss curves of poly(trans‐2‐phenyl‐1,3‐dioxan‐5‐yl methacrylate) and poly(trans‐2‐cyclohexyl‐1,3‐dioxan‐5‐yl methacrylate) display in the glassy state a high activation energy relaxation, named the β* process, that seems to be a precursor of the glass–rubber relaxation of these polymers. The mechanical spectra of poly(trans‐2‐cyclohexyl‐1,3‐dioxan‐5‐yl methacrylate) and poly(cis‐2‐cyclohexyl‐1,3‐dioxan‐5‐yl methacrylate) exhibit a low activation energy process in the low‐temperature side of the spectra, which is absent in the other polymers. The molecular origin of the mechanical activity of these polymers in the glassy state is discussed in qualitative terms. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1154–1162, 2002     

High-pressure phases in polymers. V. Crystallization studies of synthetic cis-polyisoprene

The effects of elevated pressure on the morphology and crystallization kinetics of cis-polyisoprenes containing 2–2.5% trans units have been determined. Lamellar growth rates of both α and β crystals are enhanced by elevated pressure. The degree of enhancement of α-crystal rates is much greater resulting in an effective suppression of β growth. Differences in lamellar growth rates between these polymers and cis-polyisoprene result from different preexponent values. Hedritic or axialitic growth, presumably due to low-molecular-weight fractions, is observed in shish-kebabs present in strained films. The high-pressure hexagonal phase cannot be grown in these polymers.     

Light-Responsive Oligothiophenes Incorporating Photochromic Torsional Switches

We present a quaterthiophene and sexithiophene that can reversibly change their effective π-conjugation length through photoexcitation. The reported compounds make use of light-responsive molecular actuators consisting of an azobenzene attached to a bithiophene unit by both direct and linker-assisted bonding. Upon exposure to 350 nm light, the azobenzene undergoes trans-to-cis isomerization, thus mechanically inducing the oligothiophene to assume a planar conformation (extended π-conjugation). Exposure to 254 nm wavelength promotes azobenzene cis-to-trans isomerization, forcing the thiophenic backbones to twist out of planarity (confined π-conjugation). Twisted conformations are also reached by cis-to-trans thermal relaxation at a rate that increases proportionally with the conjugation length of the oligothiophene moiety. The molecular conformations of quaterthiophene and sexithiophene were characterized by using steady-state UV-vis spectroscopy, X-ray crystallography and quantum-chemical modeling. Finally, we tested the proposed light-responsive oligothiophenes in field-effect transistors to probe the photo-induced tuning of their electronic properties.     

Stereospecific control of peptide gas‐phase ion chemistry with cis and trans cyclo ornithine residues

We report non‐chiral amino acid residues cis‐ and trans‐1,4‐diaminocyclohexane‐1‐carboxylic acid (cyclo‐ornithine, cO) that exhibit unprecedented stereospecific control of backbone dissociations of singly charged peptide cations and hydrogen‐rich cation radicals produced by electron‐transfer dissociation. Upon collision‐induced dissociation (CID) in the slow heating regime, peptide cations containing trans‐cO residues undergo facile backbone cleavages of amide bonds C‐terminal to trans‐cO. By contrast, peptides with cis‐cO residues undergo dissociations at several amide bonds along the peptide ion backbone. Diastereoisomeric cO‐containing peptides thus provide remarkably distinct tandem mass spectra. The stereospecific effect in CID of the trans‐cO residue is explained by syn‐facially directed proton transfer from the 4‐ammonium group at cO to the C‐terminal amide followed by neighboring group participation in the cleavage of the CO―NH bond, analogous to the aspartic acid and ornithine effects. Backbone dissociations of diastereoisomeric cO‐containing peptide ions generate distinct [b_n]⁺‐type fragment ions that were characterized by CID‐MS³ spectra. Stereospecific control is also reported for electron‐transfer dissociation of cis‐ and trans‐cO containing doubly charged peptide ions. The stereospecific effect upon electron transfer is related to the different conformations of doubly charged peptide ions that affect the electron attachment sites and ensuing N―C_α bond dissociations.     

Cyclic Heptapeptides Axinastatin 2, 3, and 4: Conformational analysis and evaluation of the biological potential

The conformational analysis of naturally occurring cytostatic cyclic heptapeptides axinastatin 2, 3, and 4 was carried out by two-dimensional NMR spectroscopy in combination with distance-geometry (DG) and molecular-dynamics (MD) calculations in explicit solvents. The synthesized secondary metabolites were examined in (D₆)DMSO. Axinastatin 2 was also investigated in CD₃OH. In all structures, Pro² is in the i + 1 position of a βI turn and Pro⁶ occupies the i + 2 position of a βVIa turn about the cis amide bond between residue 5 and Pro^6. In all peptides, a bifurcated H-bond occurs between residue 4 CO and the amide protons of residue 1 and 7. For axinastatin 2 and 3, an Asn I_g turn was found about Asn¹ and Pro^2. We compared these structures with conformations of cyclic heptapeptides obtained by X-ray and NMR studies. A β-bulge motif with two β turns and one bifurcated H-bond is found as the dominating backbone conformation of cyclic all-L-heptapeptides. Axinastatin 2, 3, and 4 can be characterized by six trans and one cis amide bond resulting in a β/βVI(a)-turn motif, a conformation found for many cyclic heptapeptides. Detailed biological tests of the synthetic compounds in different human cancer cell lines indicates these axinastatins to be inactive or of low activity.     

The Implications of (2S,4S)‐Hydroxyproline 4‐O‐Glycosylation for Prolyl Amide Isomerization

The conformations of peptides and proteins are often influenced by glycans O‐linked to serine (Ser) or threonine (Thr). (2S,4R)‐4‐Hydroxyproline (Hyp), together with L ‐proline (Pro), are interesting targets for O‐glycosylation because they have a unique influence on peptide and protein conformation. In previous work we found that glycosylation of Hyp does not affect the N‐terminal amide trans/cis ratios (K_trans/cis) or the rates of amide isomerization in model amides. The stereoisomer of Hyp—(2S,4S)‐4‐hydroxyproline (hyp)—is rarely found in nature, and has a different influence both on the conformation of the pyrrolidine ring and on K_trans/cis. Glycans attached to hyp would be expected to be projected from the opposite face of the prolyl side chain relative to Hyp; the impact this would have on K_trans/cis was unknown. Measurements of ³J coupling constants indicate that the glycan has little impact on the C^γ‐endo conformation produced by hyp. As a result, it was found that the D ‐galactose residue extending from a C^γ‐endo pucker affects both K_trans/cis and the rate of isomerization, which is not found to occur when it is projected from a C^γ‐exo pucker; this reflects the different environments delineated by the proline side chain. The enthalpic contributions to the stabilization of the trans amide isomer may be due to disruption of intramolecular interactions present in hyp; the change in enthalpy is balanced by a decrease in entropy incurred upon glycosylation. Because the different stereoisomers—Hyp and hyp—project the O‐linked carbohydrates in opposite spatial orientations, these glycosylated amino acids may be useful for understanding of how the projection of a glycan from the peptide or protein backbone exerts its influence.     

Bemerkung zur vorstehenden Notiz [1] von H. REMBOLD

The possible transition state conformations (chair (S), boat (W), and twist (T), respectively cross (K) forms) and methods for their determination in the thermal ortho-CLAISEN rearrangement of allyl aryl ethers are discussed. Crotyl 3,5-dimethylphenyl ether ( 11 ) gives a mixture of 2-(α-methylallyl)-3,5-dimethyl-phenol ( 12 ) and 4-crotyl-3,5-dimethyl-phenol ( 13 ) on heating in N, N-diethylaniline. Values of 3 and 31 were obtained for the ratio of 12 / 13 for trans- 11 and cis- 11 , respectively. It therefore follows that both ethers rearrange steroselectively ( > 90%) by the S or W forms of the activated complex. αMethylallyl 6-alkylphenyl ethers rearrange on heating in various solvents to a mixture of trans-and cis-2-crotyl-6-alkyl-phenols. The amount of the cis-phenols in the rearrangement products decreases with the increasing bulk of the 6-alkyl substituent. This result is only obvious if the chair form of the transition state during the rearrangement of these ethers is highly favoured. trans-Crotyl 2,6-dimethylphenyl ether (trans- 33 ) rearranges highly steroselectively (94%) on heating to trans-4-crotyl-2,6-dimethyl-phenol (trans- 34 ). In the case of the corresponding cis ether 33 , the rapid cis → trans isomerisation of this ether and the cis/trans ratio of the phenol 34 indicate that the reverse rearrangement of the intermediate ortho-dienone to the ether 33 and the further rearrangement to 4-crotyl-2,6-dimethyl-phenol ( 34 ) has little stereoselective character.     

A 13C NMR study of mesomorphic solutions of poly(p-phenylene terephthalamide)

Solutions of poly(p-phenylene terephthalamide) in fuming sulfuric acid were characterized by ¹³C NMR spectroscopy and solution viscosity measurements over the 2–28% w/w concentration range. The spectra showed the presence of two distinct amide carbonyl resonances at low concentration, tentatively assigned to cis and trans conformations. As the concentration increased, additional carbonyl lines were observed along with significant broadening. Peak area measurements showed that only the polymer molecules in the isotropic environments contributed to the ¹³C NMR spectra and a considerable amount of the polymer remained in the isotropic phase at concentrations previously considered to consist of polymer in highly anisotropic regions. Spin-lattice relaxation times were measured at six concentrations using the inversion recovery method. The aromatic carbons relaxed at a much faster rate (ca. 0.10 s) than the carbonyls (ca. 0.45 s), but the relaxation rates for both carbons were essentially constant over the concentration range, indicating that the observed isotropic phase is not affected by changes in the macroscopic solution behavior so as to alter spin-lattice relaxation mechanisms.     

Zur Lokalisierung funktioneller Gruppen in Steroiden mit Hilfe der Massenspektrometrie: XIII—Massenspektren von 3,7,17-Trihydroxyandrostanen und 7,17-Dihydroxyandrostan-3-onen

Androstanes with a trans connected A/B ring system and hydroxy groups in positions 3, 7 and 17 show in their mass spectra key ions of mass 99 and 178. The ion of mass 99 contains the carbon atoms of ring D, and the ion of mass 178 those of the A/B ring system and C-11. If the rings A and B are cis connected, the ion of mass 178 is produced with much lower abundance and the ion of mass 99 is almost absent. The α or β position of a hydroxy group in position 7 can be deduced from the spectra of corresponding trimethylsilyl derivatives: a fragment of [M ? 131] dominated by presence of a 7α-trimethylsilyl ether group and trans connection of the A/B ring system. Determination of the configuration of the hydroxy group in position 3 is very difficult. Analogous fragments are observed in the spectra of the corresponding 7, 17-dihydroxyandrostan-3-ones.     

Geometric isomers of chloro(6‐methyl‐1,4,8,11‐tetraazacyclotetradecane‐6‐amine)cobalt(III) tetrachlorozincate(II)

The crystal structures of a pair of cis and trans isomers of the macrocyclic chloro­penta­amine title complex, as their tetra­chloro­zincate(II) salts, [CoCl(C₁₁H₂₇N₅)][ZnCl₄], are re­ported. The two distinct isomeric forms lead to significant variations in the Co—N bond lengths and, furthermore, hydrogen bonding between the complex ions is influenced by the folded (cis) or planar (trans) conformations of the coordinated ligand.     

N-Ethynylation of Anilides Decreases the Double-Bond Character of Amide Bond while Retaining trans-Conformation and Planarity

Activated amide bonds have been attracting intense attention; however, most of the studied moieties have twisted amide character. To add a new strategy to activate amide bonds while maintaining its planarity, we envisioned the introduction of an alkynyl group on the amide nitrogen to disrupt amide resonance by nN→C_sp conjugation. In this context, the conformations and properties of N-ethynyl-substituted aromatic amides were investigated by DFT calculations, crystallography, and NMR spectroscopic analysis. In contrast to the cis conformational preference of N-ethyl- and vinyl-substituted acetanilides, N-ethynyl-substituted acetanilide favors the trans conformation in the crystal and in solution. It also has a decreased double bond character of the C(O)−N bond, without twisting of the amide. N-Ethynyl-substituted acetanilides undergo selective C(O)−N bond or N−C(sp) bond cleavage reactions and have potential applications as activated amides for coupling reactions or easily cleavable tethers.     

Stereoselective multigram-scale synthesis of cis- and trans-β-phenylproline derivatives

Efficient routes for the gram-scale preparation of the proline analogues that bear a phenyl substituent attached to the pyrrolidine β carbon (cis- and trans-β-phenylproline) have been developed. The cis derivative was synthesized from N-Boc-β-alanine in six steps and 78% overall yield. The generation of a vinyl triflate with full regiochemical control together with a high-yielding cross-coupling reaction and a completely stereoselective hydrogenation are at the basis of the high efficiency of the procedure. Epimerization of the cis β-phenylproline derivative with lithium bis(trimethylsilyl)amide provided access to the trans isomer.     

Structural and Conformational Aspects of Equatorial and Axial Trifluoromethyl,Difluoromethyl, and Monofluoromethyl Groups

The X‐ray crystal structures of cis‐ and trans‐1‐(indol‐3‐yl)‐4‐methyl cyclohexane and its congeners with stepwise fluorination of the methyl group are reported. The trans‐configured compounds adopted diequatorial conformations, whereas the cis analogues adopted regular cyclohexane chair conformations with the methyl group preferentially assuming the axial position, even in the case of the CF₃ group. Surprisingly, although the axial CF₃ derivative displayed distinct valence deformations in the cyclohexane moiety, the observed structural changes were relatively modest. The cis derivatives with axial mono‐ and difluorinated methyl groups exhibited conformational disorder in the crystals with significant population levels for the staggered conformations that had one fluorine atom in the endo position; their respective trans counterparts adopted unique conformations, but again with one fluorine atom in the endo position. Theoretical calculations for a series of cis‐ and trans‐1,4‐dimethyl cyclohexane model compounds with stepwise fluorination of one equatorial or axial methyl group reproduced the experimentally observed structural response patterns very well, reproduced the experimentally determined nonlinear correlation of the axial–equatorial energy difference with the degree of methyl fluorination in a satisfactory manner, and provided further insights into important conformational aspects of partially fluorinated methyl groups.     

Conformational preferences of 2-methoxypyridine from 1H and 13C NMR and from STO-3G molecular orbital calculations

Observable coupling over five formal bonds between the methoxy group protons and the ortho ring proton in 2-methoxypyridine, coupliugs between the methoxy group carbon and ring protons, and methoxy carbon spin-lattice relaxation times are all consistent with a preference for the planar cis conformer, in which conjugation is favoured and repulsions between the methyl group and the ortho hydrogen are reduced. Small-amplitude torsioas about the C-2–O bond may carry the methoxy group away from this orientation, but more distant conformations can probably be excluded. Methyl group rotation is less hindered in the cis than in the trans conformer. Molecular orbital calculations at the STO-3G level, with complete geometry optimization, support the conduskus drawn from experimental evidence.     

Stereoselective Syntheses of Benz[f]isoindoline-Derivatives by Intramolecular Cycloadditions of Styrenes to Olefins

The N-allyl-N-cinnamyl amide 10 undergoes thermal cyclization to a 2:1-mixture of the trans- and cis-benz(f)isoindolines 11a and 12a . By comparison, the thermolysis of the corresponding bis-cinnamylamide 14 proceeds in a highly stereoselective manner to give the cis-fused[4+2]-adduct 16a . Similarly, the trans-fused stereoisomeric adducts 30a and 31a were obtained with high stereochemical control on heating the N-allyl-N-diphenylallyl amide 28 . The thermal transformations 4 → 5 + 6a and 17 → 18a + 20a show the competitive formation of [2+2]-adducts. An alternative approach to (substituted) benz[f]isoindolines 16 via the all-cis-isomer 24a has been developed. The described structures have been assigned on the basis of spectral evidence, chemical correlations and by X-ray-diffraction study of the isomer 16b . These results illustrate the utility of substituent interactions in order to direct intramolecular cyclo-additions at will towards either endo- or exo-products.     

双环-HMX结构和性质的理论研究

在DFT-B3LYP/6-311G*水平上, 计算研究了高能化合物四硝基四氮杂双环辛烷(双环-HMX) α和β两种异构体的结构和性质. 比较分子对称性、分子内氢键和环张力等几何参数以及分子总能量和前线轨道能级等电子结构参数, 发现α比β稳定. 分子中N—N键较长, N—N键集居数较小, 预示该键为热解和起爆的引发键. 基于简谐振动分析求得IR谱频率和强度. 运用统计热力学方法求得200～1000 K温度的热力学性质. 以非限制性半经验PM3方法探讨其热解机理, 求得各反应通道的过渡态和活化能, 发现热解始于侧链N—NO₂键的均裂. 还从理论上预测了该化合物的密度、爆速和爆压, 有助于寻求高能量密度材料(HEDM).