Zur konformation geschützter aminosäuren—I: NMR-untersuchungen von t-BOC-glycin

Z, E-Isomerism of the urethane bond of t-BOC-glycine was observed by ¹H- and ¹³C-NMR spectroscopy at various temperatures in several solvents. The special stabilization of the Z isomer at low temperatures in CDCl₃ has been explained by intra- and intermolecular H-bond forming a 7-membered ring. Thermodynamic data have been determined for the ground state (AH°= ?7 kcal/mol, Δ° = ?25 Clausius) as well asfor the barrier of interconversion (ΔG° = 15·4 kcal/mole for the deuterated title compound) in CDCl₃. The equilibrium between the Z and the E conformation is shifted towards the E conformation in more polar solvents (acetonitril-d₃, acetone-d₆, DMSO-d₆), in which cyclization of the Z conformation is not important.     

Conformational Properties of (Z,Z)-, (E,Z)-, and (E,E)-Cycloocta-1,4-dienes

Summary.  Ab initio calculations at the HF/6-31G^* level of theory for geometry optimization and the MP2/6-31G^*//HF/6-31G^* level for a single point total energy calculation are reported for (Z,Z)-, (E,Z)-, and (E,E)-cycloocta-1,4-dienes. The C ₂-symmetric twist-boat conformation of (Z,Z)-cycloocta-1,4-diene was calculated to be by 3.6 kJ·mol⁻¹ more stable than the C _S-symmetric boat-chair form; the calculated energy barrier for ring inversion of the twist-boat conformation via the C _S-symmetric boat-boat geometry is 19.1 kJ·mol⁻¹. Interconversion between twist-boat and boat-chair conformations takes place via a half-chair (C ₁) transition state which is 43.5 kJ·mol⁻¹ above the twist-boat form. The unsymmetrical twist-boat-chair conformation of (E,Z)-cycloocta-1,4-diene was calculated to be by 18.7 kJ·mol⁻¹ more stable than the unsymmetrical boat-chair form. The calculated energy barrier for the interconversion of twist-boat-chair and boat-chair is 69.5 kJ·mol⁻¹, whereas the barrier for swiveling of the trans-double bond through the bridge is 172.6 kJ·mol⁻¹. The C _S symmetric crown conformation of the parallel family of (E,E)-cycloocta-1,4-diene was calculated to be by 16.5 kJ·mol⁻¹ more stable than the C _S-symmetric boat-chair form. Interconversion of crown and boat-chair takes place via a chair (C _S) transition state which is 37.2 kJ·mol⁻¹ above the crown conformation. The axial- symmetrical twist geometry of the crossed family of (E,E)-cycloocta-1,4-diene is 5.9 kJ·mol⁻¹ less stable than the crown conformation. Corresponding author. E-mail: isayavar@yahoo.com Received March 25, 2002; accepted April 3, 2002     

Quantitative 1H NMR spectroscopic determination of the E/Z isomer ratio of the antidepressant drug fluvoxamine for use in pharmaceutical analysis

High‐resolution NMR spectroscopy is a powerful tool in the elucidation of a structure with respect to constitution, configuration and conformation. In recent years, NMR has been increasingly used in quantitative analysis. In this study, we show the ability of ¹H NMR to determine the isomeric composition of the antidepressant drug fluvoxamine. The activity of fluvoxamine resides on the E‐isomer, and the current British Pharmacopoeia limits the content of the Z‐isomer to 0.5%. The NMR method described here is able to determine the content of the Z‐isomer down to the 0.2% level on a total amount of 15 mg of the substance. Copyright © 2002 John Wiley & Sons, Ltd.     

Study of conformations and hydrogen bonds in the configurational isomers of pyrrole‐2‐carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis

The ¹H, ¹³C and ¹⁵N NMR studies have shown that the E and Z isomers of pyrrole‐2‐carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole‐2‐carbaldehyde oxime is stabilized by the N? H···N and N? H···O intramolecular hydrogen bonds, respectively. The N? H···N hydrogen bond in the E isomer causes the high‐frequency shift of the bridge proton signal by about 1 ppm and increase the ¹J(N, H) coupling by ～3 Hz. The bridge proton shows further deshielding and higher increase of the ¹J(N, H) coupling constant due to the strengthening of the N? H···O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by ～3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of ¹H shielding and ¹J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N? H···N and N? H···O hydrogen bondings to be estimated. The NBO analysis suggests that the N? H···N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N? H bond through the N? H···O hydrogen bond occurs in the Z isomer. Copyright © 2010 John Wiley & Sons, Ltd.     

Zur Chemie der Pyrrolpigmente, 63. Mitt.

Using hexamethylphosphoric acid triamide (HMPT) as solvent for bilatrienesabc and mainly for 2,3-dihydrobilatrienes-abc (which serve as the most suitable models for the biliproteid chromophores) a small hypsochromic shift and a dramatic change of the relative intensities of short and long wavelength absorption bands, as compared to solutions in CCl₄, is observed. Applying NMR-spectroscopic techniques (¹⁵N-,¹³C-,¹H-) a predominance of the (4Z,9E,15Z) diastereomer forming a 5syn-, 10anti-, 14syn-periplanar orclinal conformation is deduced. The stabilisation of this configuration and conformation arises from strong hydrogen bonds between the acidic protons of the bilins andHMPT. Interactions of this kind seem to be the main source of energy to stretch the otherwise coiled bilin chromophore of (4Z,9Z,15Z)-5sp,10sp,14sp geometry. Stretched systems of the type bilin-HMPT may serve as a valuable model for the natural biliproteides.

Herrn Prof. Dr.A. Eschenmoser zum 60. Geburtstag gewidmet.116, 1065 (1985).     

Structure of 1(5)-aryl-3-phenyl-5(1)-(2-benzothiazolyl)formazanes

1,3-Diphenyl-5-(2-benzothiazolyl)formazane exists in its crystalline state (based on x-ray crystal structure data) in the E ^1,2 Z ^2,3 Z ^3,4-conformation, which is stabilized by intramolecular hydrogen bonding (IMHB); the proton is localized on the nitrogen atom which is bound to the heterocycle. In chloroform solutions 1(5)-aryl-3-phenyl-5(1)-(2-benzothiazolyl)formazanes exist in the form of equilibrium mixtures of their chelate and open E ^1,2 Z ^2,3 Z ^3,4-forms, in which the first of these forms predominates. Based on their ¹³ C-NMR spectral data the tautomeric equilibrium involving these forms is shifted in favor of the benzothiazolylhydrazone form. The amount of tautomer containing the benzothiazolidene fragment structure increases in DMSO solution.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1268–1274, September, 1991.     

Stereochemical studies—XXXVII: Saturated heterocycles—XIII Configuration and conformation of Z- and E-N-methyl- and -N- benzyl-2-p-nitrophenyl-4,5- and -5,6-tetramethylenetetrahydro-1,3-oxazines

The configuration and conformation of Z- and E-N-methyl- and -N-benzyl-2-p-nitrophenyl-4,5-, and -5,6-tetramethylenetetrahydro-1,3-oxazines were determined by ¹H and ¹³C NMR spectroscopy. The Z isomers were proved to be conformationally homogeneous, having the heteroatom in axial and equatorial position, respectively, in the case of the 5,6- and 4,5-tetramethylene compounds. Consequently, the p-nitrophenyl group and the anellated cyclohexyl ring are all-cis arranged in the Z-5,6-tetramethylene compounds while in the case of the Z-4,5-tetramethylene isomers the p-nitrophenyl group and the cyclohexyl ring are trans arranged to the hetero ring.     

Beiträge zur Chemie der Pyrrolpigmente,LVIII Phytochrommodellstudien: Konformationsanalytische Untersuchungen an 2,3-Dihydrobilatrien-abc-Derivaten

Two 3,4-dihydropyrromethenones and two 2,3-dihydrobilatrienes-abc O-methylated at rings A and D resp. have been prepared. Their configurations were established as (Z), (E), (Z, Z, Z) and (Z, Z, Z), respectively, using¹H-NMR-techniques (NOE); they are also shown to exist predominantly in the lactam form. Within the pyrromethene fragment of the bilatrienes the pyrrolic and pyrroleninic ring type depends on the position of O-methylation. A helical all-synperiplanar conformation in solution could be established for all cases by applying the lanthanide induced shift (LIS) technique.

     

β‐1‐Acet­amido‐4‐O‐β‐d‐galacto­pyranosyl‐d‐gluco­pyran­ose dihydrate

The crystal structure of the title compound, C₁₄H₂₅NO₁₁·2H₂O, has been determined. The glucose and galactose residues are in a ⁴C₁ conformation. The N‐acetyl group has a Z‐anti conformation.     

The configuration and conformation of isogermacrone. The significance of crossed conformations in olefinic cyclisations

The 9,10-double bond of isogermacrone was assigned the Z configuration based on¹HNMR nOe measurements and the ¹³CNMR shifts of the methyl groups. An X-ray crystal structure determination verified this conclusion and the structure of isogermacrone was shown to be (2Z, 7E)-3,7-dimethyl-10(1-methylethyl-idene)-2,7-cyclodecadien-1-one (1). The molecule crystallised in an anti conformation, which according to ¹HNMR is the predominant conformation in solution at room temperature.¹H NMR spectroscopy revealed the presence of syn and anti conformers in the ratio 1:2 at about -60°. The stereochemistry of the base-induced formation of isogermacrone 1 from germacrone 2 and that of the transannular cyclisation of isogermacrone are discussed.     

Restoration of Ribozyme Tertiary Contact and Function by Using a Molecular Glue for RNA

Some RNA classes require folding into the proper higher‐order structures to exert their functions. Hammerhead ribozyme (HHR) requires a folding conformation stabilized by tertiary interaction for full activity. A rationally engineered HHR was developed that was inactive, but could be activated by a synthetic RNA‐binding ligand, naphthyridine carbamate tetramer with Z‐stilbene linker (Z‐NCTS). Binding of Z‐NCTS could induce the formation of an active folding structure and thereby restore ribozyme activity, where Z‐NCTS acts as a molecular glue to bring two isolated RNA loops into contact with each other. Next, we designed a Z‐NCTS‐responsive genetic switch using the HHR sequence inserted into the 3′ untranslated region as a cis‐acting element. We demonstrated that the rationally designed ribozyme switch enabled regulation of gene expression by Z‐NCTS and was functional in mammalian cells.     

Programmable conformational regulation of porphyrin dimers on geometric scaffold of duplex DNA

DNA-porphyrin conjugates were designed and synthesized in which free-base and Zn-coordinated porphyrins were introduced to the N⁶-position of the internal adenosine. Conformations of the porphyrin dimer in the major groove of duplex DNA were controlled by changing the orientation and the distance between the two porphyrin moieties. The porphyrin dimers formed a thermally favorable face-to-face conformation on the duplex DNA. In the disadvantageous geometry for porphyrin dimer formation on the duplex, the porphyrins induced the DNA duplex structures to the Z-form conformation. These results indicate that the interaction of the two porphyrins and the conformation of duplex DNA are controlled by the program of DNA sequences.     

Conformations of the Nine‐Membered Ring in the B‐Nor‐5,10‐secosteroids. X‐Ray and NMR Analysis

The conformations of (Z)‐ and (E)‐5‐oxo‐B‐nor‐5,10‐secocholest‐1(10)‐en‐3β‐yl acetates ( 2 and 3 , resp.) were examined by a combination of X‐ray crystallographic analysis and NMR spectroscopy, with emphasis on the geometry of the cyclononenone moiety. The ¹H‐ and ¹³C‐NMR spectra showed that the unsaturated nine‐membered ring of (E)‐isomer 3 in C₆D₆ and (D₆)acetone solution exists in a sole conformation of type B ₁ , which is similar to its solid‐state conformation. The (Z)‐isomer 2 in C₆D₆, CDCl₃, and (D₆)acetone solution, however, exists in two conformational forms of different families, with different orientation of the carbonyl group, the predominant form (85%) corresponding to the conformation of type A ₁ and the minor (15%) to the conformation A ₂ present also in the crystalline state. In this solid‐state conformations of the nine‐membered ring of both compounds, the 19‐Me and 5‐oxo groups are ‘β’‐oriented. The NMR analysis suggests that the nine‐membered ring of 4 has a conformation of type C ₁ in CDCl₃ solution.     

Ab Initio Study of Conformational Properties of ( Z, Z)-, ( E, Z)-, and ( E, E)-Cyclonona-1,5-dienes

Ab initio calculations at the HF/6-31G^* level of theory for geometry optimization and MP2/6-31G^*//HF/6-31G^* for a single point total energy calculation are reported for the important energy-minimum conformations and transition-state geometries of (Z,Z)-, (E,Z)-, and (E,E)-cyclonona-1,5-dienes. The C₂ symmetric chair conformation of (Z,Z)-cyclonona-1,5-diene is calculated to be the most stable form; the calculated energy barrier for ring inversion of the chair conformation via the C_s symmetric boat-chair geometry is 58.3kJmol^–1. Interconversion between chair and twist-boat-chair (C₁) conformations takes place via the twist (C₁) as intermediate. The unsymmetrical twist conformation of (E,Z)-cyclonona-1,5-diene is the most stable form. Ring inversion of this conformation takes place via the unsymmetrical chair and boat-chair geometries. The calculated strain energy for this process is 63.5kJmol^–1. The interconversion between twist and the boat-chair conformations can take place by swiveling of the trans double bond with respect to the cis double bond and requires 115.6kJmol^–1. The most stable conformation of (E,E)-cyclonona-1,5-diene is the C₂ symmetric twist-boat conformation of the crossed family, which is 5.3kJmol^–1 more stable than the C_s symmetric chair–chair geometry of the parallel family. Interconversion of the crossed and parallel families can take place by swiveling of one of the double bonds and requires 142.0kJmol^–1.     

Ab Initio Study of Conformational Properties of ( Z, Z)-, ( E, Z)-, and ( E, E)-Cyclonona-1,5-dienes

Summary. Ab initio calculations at the HF/6-31G^* level of theory for geometry optimization and MP2/6-31G^*//HF/6-31G^* for a single point total energy calculation are reported for the important energy-minimum conformations and transition-state geometries of (Z,Z)-, (E,Z)-, and (E,E)-cyclonona-1,5-dienes. The C₂ symmetric chair conformation of (Z,Z)-cyclonona-1,5-diene is calculated to be the most stable form; the calculated energy barrier for ring inversion of the chair conformation via the C_s symmetric boat-chair geometry is 58.3kJmol^–1. Interconversion between chair and twist-boat-chair (C₁) conformations takes place via the twist (C₁) as intermediate. The unsymmetrical twist conformation of (E,Z)-cyclonona-1,5-diene is the most stable form. Ring inversion of this conformation takes place via the unsymmetrical chair and boat-chair geometries. The calculated strain energy for this process is 63.5kJmol^–1. The interconversion between twist and the boat-chair conformations can take place by swiveling of the trans double bond with respect to the cis double bond and requires 115.6kJmol^–1. The most stable conformation of (E,E)-cyclonona-1,5-diene is the C₂ symmetric twist-boat conformation of the crossed family, which is 5.3kJmol^–1 more stable than the C_s symmetric chair–chair geometry of the parallel family. Interconversion of the crossed and parallel families can take place by swiveling of one of the double bonds and requires 142.0kJmol^–1.     

Zur Struktur der Produkte der Reaktion vonE/Z-1-Benzolsulfonyl-3-(1-pentenyl)-indol mit N-Phenylmaleinimid: Ein erster Beitrag zur Konfigurations- und Konformationsanalyse in der Vinylindol-Cycloadditionsreihe

The products2,3 of the reaction ofE/Z-1-benzenesulfonyl-3-(1-pentenyl)-indole (1) and N-phenylmaleimide were analysed by¹H-NMR spectroscopy. Exemplarily, the structure elucidation of theendo-cyclo-adduct2 b was achieved by using several NMR techniques (diff. NOE-, INDOR-measurements, decoupling experiments, spectra simulation). The¹H-NMR-spectroscopically gained prediction of relative configuration and conformation of2 b was supported on X-ray analysis. The cyclohexene ring of the new cycloadducts adopts in the liquid phase and in the crystal a slightly twisted boat conformation.

     

Zur Chemie der Pyrrolpigmente, 54. Mitt.: Phytochrommodellstudien: Ein 2,3-Dihydrobilatrien-abc-3-Cholesterylderivat

The diastereomeric 2,3-Dihydrobilatrienes-abc derivatives (4Z, 9Z, 15Z)-7 and (4Z, 9Z, 15E)-7 bearing a cholesterylacetate moiety in position 3 of the chromophore are prepared. The reaction sequence contains an isomerisation step providing quantitative enantioselective formation of the chiral center in position 3. Configurations and conformations of the diastereomers are elucidated using¹H- and¹³C-NMR spectra, NOE-difference spectra, 2D-NMR experiments (NOESY) and arguments from UV-VIS and CD data. It is concluded that the hydrophobic interactions between chromophore and cholesteryl-fragment yield a compact conformation where the two substructures are in close contact with each other. On the other hand these interactions seem to be too weak to induce significant changes in the chemistry, absorption spectra and conformational characterics of the bile pigment chromophore. Therefore hydrophobic interactions between chromophor and apolar amino acid residues of the protein in phytochrome should be of minor relevance for determining spectroscopic shifts.

     

Theoretical study of formic acid: A new look at the origin of the planar Z conformation and C–O rotational barrier

The E and Z rotamers of formic acid (HCOOH) and its barrier to internal rotation about the C–O bond were computationally explored at the HF/6-311 + G^∗∗, B3LYP/cc-pVTZ, and CCSD(T)/cc-pVTZ levels of theory. All calculations yielded similar results consistent with experimental observations. Subsequent analysis of the interaction between formate ion (HCOO⁻) and proton (H⁺) within formic acid demonstrated a direct correlation between the changes in fragment interaction energy and the total energy of formic acid upon rotation. To obtain further insights into the interaction, energy decomposition analysis based on the reactive bond orbital (RBO) method was carried out using the 6-311 + G^∗∗ basis set. The analysis showed the electrostatic effect constitutes a major component that gives rise to the interaction energy variation along the rotation path. Thus, the electrostatic environment of HCOO⁻ can be viewed as the key factor determining the Z ground state and C–O rotational barrier of formic acid. The anisotropic electrostatic environment of formate that favors planar conformations of formic acid may be due to the in-plane distribution of carbonyl lone pairs, and the larger electrostatic attraction in the Z form appears to come from a secondary electrostatic interaction between the proton and the distal oxygen. At the rotational transition state, the O–H bond was not exactly perpendicular to the molecular plane, but slightly tilted toward the E side, which can also be explained by the electrostatic hypothesis. Charge-transfer stabilization was smallest in the Z conformation, but it gradually increased upon rotation to a maximum at the E conformation. Therefore, charge - transfer does not explain the geometry of formic acid. The important role of the electrostatic effect was also observed in in-plane rotation of the O–H bond.     

NMR stereospecific long-range coupling and preferred conformations in some (E)- and (Z)-α-phenyl-β-[2-(N-methyl)nitropyrrolyl] acrylic acids

NMR data have been used to assign the stereochemistry to some new (E)- and (Z)-α-phenyl-β-[2-(N-methyl)nitropyrrolyl]acrylic acids. The (E)-molecules are biased in the s-cis conformation showing NMR spectroscopic features strictly depending on the conformation.The analysis of the NMR spectra reveals that the (Z)-isomers exist also in the s-cis conformation.