Solution- and bound-state conformational study of N,N',N"-triacetyl chitotriose and other analogous potential inhibitors of hevamine: application of trNOESY and STD NMR spectroscopy

The solution-state conformations of N,N',N"-triacetyl chitotriose (1) and other potential chitinase inhibitors 2-4 were studied using a combination of NMR spectroscopy (NOESY) and molecular mechanics calculations. Determination solely of the global energy minimum conformation was found to be insufficient for an agreement with the NMR results. An appropriate consistency between the NMR experimental data and theoretical calculations was only reached by assessing the structures as population-weighted average conformers based on Boltzmann distributions derived from the calculated relative energies. Analogies, but also particular differences, between the synthetic compounds 2-4 and the naturally-occurring N,N',N"-triacetyl chitotriose were found. Furthermore, the conformation of compounds 1 and 2 when bound to hevamine was also studied using transferred NOESY experiments and the binding process was found to impart a level of conformational restriction on the ligands. The preferred conformation as determined for 1 in the bound state to hevamine belonged to one of the conformational families found for the compound when free in solution, although full characterisation of the bound-state conformations was impeded due to severe signal overlap. Saturation transfer difference NMR experiments were also employed to analyse the binding epitopes of the bound compounds. We thus determined that it is mainly the acetyl amido groups of the trisaccharide and the heterocyclic moiety which are in close contact with hevamine.     

NMR characterization of new 10-membered-ring macrolactones and dihydrobenzophenazine-5-one, oxidized derivatives of benzo[a]phenazines

Peroxidation of the phenazine of beta-lapachone using m-ClC6H4CO3H-CH2Cl2 furnished a macrolactone with a rigid 10-membered ring, and the corresponding N-oxide, along with a dihydrobenzophenazine-5-one. All of the new compounds were fully characterized by spectroscopic methods, with the unambiguous assignment of the hydrogens and carbon NMR signals for the N-oxide, with the aid of 2-D NMR, mainly COSY, HMQC, HSQC and HMBC. For the other two compounds some signals could not be assigned owing to their own intrinsic features.     

Stereochemistry and conformations of natural 1,2-epoxy-guaianolides based on 1D and 2D NMR data and semiempirical calculations

From detailed study of 1D and 2D NMR spectra of ten natural 1,2-epoxyguaianolides (bis-1,2:3,4-epoxyguaianolides and guaianolide-1,2-epoxychlorohydrins), we identified general spectral traits helpful for stereochemical assignment of such sesquiterpene lactones. We found that the chemical shifts of certain (1)H and (13)C nuclei are consistently dependent on the configuration of 1,2-epoxy-ring which could be used as a simple rule for establishing this configuration. Then, from 1D and 2D (COSY, NOESY, HMQC, HMBC) NMR data, applying the observed rule, the structure and stereochemistry of two new, diastereomeric guaianolide-1,2-epoxychlorohydrins, isolated from Achillea serbica, are determined. The NMR data, namely, nuclear overhauser enhancement (NOE) correlations, pointed out two conformations of guaianolide's cycloheptane ring. The semiempirical calculations (AM1 and PM3 methods), performed in order to gain additional information regarding conformations, resulted in three geometries of investigated lactones. Even so, the conformations derived from the NMR data agreed well with those calculated by semiempirical methods.     

Konformative Beweglichkeit Flexibler Ringsysteme—XIII: Untersuchungen mit Hilfe der Protonenresonanzspektroskopie die Konformation des Ungesättigten Siebenringes im Benzocyclohepten und in symmetrisch substituierten derivaten

The confromations of the unsaturated seven membered ring in 4,4,6,6-tetradeuterium-1,2-benzocycloheptene-(1) ( 1 ) and five benzocycloheptene derivatives were determined by NMR spectroscopy. For all investigated compounds at ?80°C only one conformer was present in detectable quantity. By analysis of the NMR data – molecular symmetry, coupling constants and chemical shift – it can be shown that the conformation is always the chair form. The free conformational enthalpy of both the other conformations with boat or twist form of the ring is for all six compounds more than 1.8 kcal/mole. The experimental results agree with those from model calculations: thus for benzocycloheptene, the 5,5-dimethyl derivative ( 2 ) and the 4,4,6,6-tetramethyl derivative ( 4 ) the lowest energy was found for the chair conformation; the second most stable conformations were found to be the boat for 1 and 4 , and the twist form for 2 .     

A new xanthone from Garcinia nitida

A detailed chemical study on the stem bark of Garcinia nitida has led to the isolation of five xanthones. They are 1,6-dihydroxy-5-methoxy-6,6-dimethylpyrano[2',3':2,3]-xanthone (1), inophyllin B (2), osajaxanthone (3), 3-isomangostin (4) and rubraxanthone (5). The structures of these compounds were established using mainly 1-D and 2-D NMR spectroscopy ((1)H, (13)C, DEPT, COSY, HMBC and HMQC) while molecular masses were determined via MS techniques; 1 is a new compound.     

Synthesis and conformational analysis of glycomimetic analogs of thiochitobiose

The synthesis of six analogs of N,N′-diacetylchitobiose is reported, including a novel transglycosylation reaction for the preparation of S-aryl thioglycosides. The conformations of the compounds were studied by a combination of NMR spectroscopy and molecular modeling, using force field calculations. In the case of the S-aryl thioglycosides with exclusively S-glycosidic linkages, dihedral angles of the disaccharidic S-glycosidic bonds, Φ′ and Ψ′ and of the S-arylglycoside bonds, Φ and Ψ, were found to be similar, whereas they were different in mixed glycosides and in a thiazoline derivative. An adequate correlation between the calculated H,H-distances of the local minima and the measured NOE contacts was achieved by applying population-weighted averages over participating conformers based on weighted relative energies.     

Application and Structural Analysis of Triazole‐Bridged Disulfide Mimetics in Cyclic Peptides

Ruthenium‐catalysed azide–alkyne cycloaddition (RuAAC) provides access to 1,5‐disubstituted 1,2,3‐triazole motifs in peptide engineering applications. However, investigation of this motif as a disulfide mimetic in cyclic peptides has been limited, and the structural consequences remain to be studied. We report synthetic strategies to install various triazole linkages into cyclic peptides through backbone cyclisation and RuAAC cross‐linking reactions. These linkages were evaluated in four serine protease inhibitors based on sunflower trypsin inhibitor‐1. NMR and X‐ray crystallography revealed exceptional consensus of bridging distance and backbone conformations (RMSD<0.5 Å) of the triazole linkages compared to the parent disulfide molecules. The triazole‐bridged peptides also displayed superior half‐lives in liver S9 stability assays compared to disulfide‐bridged peptides. This work establishes a foundation for the application of 1,5‐disubstituted 1,2,3‐triazoles as disulfide mimetics.     

Conformational Properties of New Thiosemicarbazone and Thiocarbohydrazone Derivatives and Their Possible Targets

The structure assignment and conformational analysis of thiosemicarbazone KKI15 and thiocarbohydrazone KKI18 were performed through homonuclear and heteronuclear 2D Nuclear Magnetic Resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-HSQC, and 2D-HMBC) and quantum mechanics (QM) calculations using Functional Density Theory (DFT). After the structure identification of the compounds, various conformations of the two compounds were calculated using DFT. The two molecules showed the most energy-favorable values when their two double bonds adopted the E configuration. These configurations were compatible with the spatial correlations observed in the 2D-NOESY spectrum. In addition, due to the various isomers that occurred, the energy of the transition states from one isomer to another was calculated. Finally, molecular binding experiments were performed to detect potential targets for KKI15 and KKI18 derived from SwissAdme. In silico molecular binding experiments showed favorable binding energy values for all four enzymes studied. The strongest binding energy was observed in the enzyme butyrylcholinesterase. ADMET calculations using the preADMET and pKCSm software showed that the two molecules appear as possible drug leads.     

A New Triterpene Saponin from Heteropappus biennis with an Unusual Carbohydrate Chain

A new saponin, O-α-D -arabinopyranosyl-(1→6)-O-[α-L -rhamnopyranosyl-(1→2)]-O-[β-D -xylopyranosyl-(1→3)]-β-D -glucopyranosyl arjunolate ( 1 ) was isolated from the flowers of Heteropappus biennis (LDB .) TAMAMSCH . The structure was established mainly by a combination of 1D selective and 2D NMR techniques like COSY, TOCSY, ROESY, HMQC, and HMBC. Molecular-modelling calculations showed that the oligosaccharide chain is rather rigid. Six minimum structures are discussed.     

Synthesis, IR-, NMR-, DFT and X-ray study of ferrocenyl heterocycles from thiosemicarbazones. Part 21: Study on ferrocenes

Cyclization reactions of the thiosemicarbazones of formyl- and acetylferrocene and their S-methyl derivatives with DMAD afforded novel ferrocenyl-hydrazono-substituted thiazolones, one-one dimethylthiazole-4,5-dicarboxylate and 1,3-thiazin-4-one, N-ferrocenylimino-pyrimidones/imidazolones, one intermediate β-adduct and via oxidative cyclization, a ferrocenyl-1,2,4-triazole. Ring isomerization of 1,3-thiazin-4-ones to a 1,3-thiazolones was detected. The structure of the new compounds was established by IR and NMR spectroscopy, including HMQC, HMBC and DEPT measurements and supported with GIAO NMR calculations and controlled also synthetically by phase-transfer methylation. For three compounds the stereostructure was also proved by X-ray diffraction.     

Water-soluble constituents of the heartwood of Streblus asper

A new lignan, (7'R,8'R)-threo-strebluslignanol-2-O-beta-D-glucopyranoside, along with 8 known compounds (2-9) were isolated from the water-soluble part of the MeOH extract of the heartwood of Streblus asper. Their structures were elucidated through various spectroscopic methods, including 1D NMR (1H NMR, 13C NMR), 2D NMR (HMQC, HMBC, and NOESY), and HRMS. The stereochemistry at the chiral centers was determined using the CD spectrum, as well as analyses of coupling constants and optical rotation data. In the preliminary bioassay, the isolated compounds did not show anti-HBV activities in vitro using the HBV transfected HepG2.2.15 cell line.     

Comprehensive structural studies of 2',3'-difluorinated nucleosides: comparison of theory, solution, and solid state

The conformations of three 2',3'-difluoro uridine nucleosides were studied by X-ray crystallography, NMR spectroscopy, and ab initio calculations in an attempt to define the roles that the two vicinal fluorine atoms play in the puckering preferences of the furanose ring. Two of the compounds examined contained fluorine atoms in either the arabino or xylo dispositions at C2' and C3' of a 2',3'-dideoxyuridine system. The third compound also incorporated fluorine atoms in the xylo configuration on the furanose ring but was substituted with a 6-azauracil base in place of uracil. A battery of NMR experiments in D 2O solution was used to identify conformational preferences primarily from coupling constant and NOE data. Both (1)H and (19)F NMR data were used to ascertain the preferred sugar pucker of the furanose ring through the use of the program PSEUROT. Compound-dependent parameters used in the PSEUROT calculations were newly derived from complete sets of conformations calculated from high-level ab initio methods. The solution and theoretical data were compared to the conformations of each molecule in the solid state. It was shown that both gauche and antiperiplanar effects may be operative to maintain a pseudodiaxial arrangement of the C2' and C3' vicinal fluorine atoms. These data, along with previously reported data by us and others concerning monofluorinated nucleoside conformations, were used to propose a model of how fluorine influences different aspects of nucleoside conformations.     

Constituents of the leaves of Woodfordia fruticosa Kurz. I. Isolation, structure, and proton and carbon-13 nuclear magnetic resonance signal assignments of woodfruticosin (woodfordin C), an inhibitor of deoxyribonucleic acid topoisomerase II

Woodfruticosin (woodfordin C), a new cyclic dimeric hydrolyzable tannin having an inhibitory activity toward deoxyribonucleic acid (DNA) topoisomerase II, has been isolated from the leaves of Woodfordia fruticosa Kurz (Lythraceae) along with three known flavonol glycosides and three known flavonol glycoside gallates. The structure of wood fruticosin (woodfordin C) was determined by the use of two-dimensional nuclear magnetic resonance (2-D NMR) spectroscopy including heteronuclear multiple quantum coherence (HMQC) and heteronuclear multiple bond connectivity (HMBC) techniques. Detailed analyses of the proton and carbon-13 NMR (1H- and 13C-NMR) spectra of six known flavonoids were performed.     

NMR Conformational Analysis and Theoretical Calculations for 2‐Aryl‐ 1,3‐dihydroxy‐4,4,5,5‐tetramethylimidazolidines

Conformational studies of 1,3‐dihydroxy‐4,4,5,5‐tetramethyl‐2‐(pyridin‐1‐yl)imidazolidine ( 1a ) and 1,3‐dihydroxy‐4,4,5,5‐tetramethyl‐2‐(pyridin‐3‐yl)imidazolidine ( 1b ), carried out by using 1D ¹H‐ and ¹³C‐NMR and 2D HMQC, HMBC, and NOESY experiments and with the aid of theoretical calculations, indicate that the OH groups are trans to the pyridinyl substituent. Because the two ¹H‐NMR signals of the Me groups are distinguishable and do not change between 290 and 380 K, it is proposed that 1a and 1b have each only one conformation in this temperature range. This behavior was not found with 1,3‐dihydroxy‐4,4,5,5‐tetramethyl‐2‐(pyridin‐2‐yl)imidazolidine ( 1c ) because its Me ¹H‐NMR signals cross over at 300 K. Hence, more than one conformation must be present, beyond those produced by simple inversions. Theoretical calculations including temperature and solvent effects were performed to provide further information on the conformational analysis and to help to assign the NMR data. The combination of NMR measurements and quantum‐chemical calculations is shown to be a very promising strategy for conformational analysis studies in solution.     

An extensive study of bromination of cis,trans,trans-1,5,9-cyclododecatriene: product structures and conformations

Bromine has been added to cis,trans,trans-1,5,9-cyclododecatriene under various reaction conditions. All expected direct addition products have been isolated, and their structures have been determined by microanalysis, NMR and X-ray crystallography. Advanced NMR techniques were used to determine solution conformations of several of the compounds, enabling comparison with the solid-state conformations obtained by crystallography.     

Rotational Phenomena on Substituent Phenyl Rings of (η5-Cyclopentadienyl)(η4-Tetraphenylcyclobutadiene)Cobalt

We used extended Hückel calculations, variable-temperature, homonuclear long-range shift-correlated 2-D ¹H NMR and dynamic NOE measurements to investigate rotational phenomena of substituent phenyl rings on (η⁵-cyclopentadienyl)(η⁴tetraphenylcyclobutadiene)cobalt (1). Two closely related compounds, (η⁵-cyclopentadienyl)(η⁴-1,3-diphenylcyclobutadiene)cobalt (A) and (η⁵-cyclopentadienyl)(η⁴-1,2-diphenylcyclobutadiene)cobalt (A′), were prepared. Energy minima appeared at conformations of which the dihedral angles between phenyl and cyclobutadiene rings are about 30° for I and 0° for A according to extended Hückel calculations. In 1, ortho protons of phenyl rings belong to one set of multiplet in ¹H NMR; meta and para protons belong to the other. It was supported by a long-range coupling 2-D ¹H NMR and NOE experiments. A sharp line due to phenyl rings was observed in the low-temperature ¹H NMR spectrum of A, which indicates that the five protons are magnetically equivalent at that temperature.     

The structure and conformational behavior of sulfonium salt glycosidase inhibitors in solution: a combined quantum mechanical NMR approach

We present the conformational analysis of an inhibitor of alpha-mannosidase, based on a novel sulfonium salt structure (1) that mimics the mannosyl cation intermediate. Because of the number of possible isomeric structures for 1, as well as its complex molecular structure, traditional conformational analysis by NMR was not applicable. Instead, a single experimentally consistent structure was obtained from finite perturbation quantum mechanical calculations of the NMR J-couplings at the B3LYP/6-311G** level. Using a full relaxation matrix analysis, we showed that the quantum-predicted NMR structure was the only isomer that was consistent with the experimental NOE intensities. The results illustrate the potential for finite perturbation calculations to be useful in the analysis of complex charged molecules.     

A conformational study of aromatic imide compounds. Part 2. Compounds containing diphenyl sulfide,diphenyl sulfone,and diphenylmethane moieties

An attempt was made to estimate the dihedral angles, φ, ψ, ω₁, and ω₂, of bis(4-hydroxyphthalimide)s (BHPI) and bis(phenylphthalimide)s (BPI) having diphenyl sulfide, diphenyl sulfone, or diphenylmethane linkages at the center of molecules using solid–state ¹³C CP/MAS NMR and ab initio nuclear shielding calculations. The TOSS and TOSS & DD pulse sequences were performed in the NMR measurements to obtain exact chemical shifts of each carbon. Total energies were calculated using the B3LYP/6-31G(d) level of theory, and shielding constants were calculated using the RHF/6-31G(d) level of theory for diphenyl sulfide, diphenyl sulfone, diphenylmethane with varying angles of φ, ψ from 0 to 180° at intervals of 10°. It was clarified that the –S– and –SO₂– linkages lead asymmetrical conformations with different ω₁ and ω₂ or with different φ and ψ for BHPIs and BPIs. In contrast, the compounds having –CH₂– linkages have symmetrical conformations. The dihedral angle of imide ring and phenylene ring (ω) are in the range of 40–90°, and the dihedral angles (φ,ψ) distribute in the stable regions of the energy surfaces ranging from 40 to 90°.     

Lectin-bound conformations and non-covalent interactions of glycomimetic analogs of thiochitobiose

The bound conformations of five S-glycoside analogs of N,N′-diacetylchitobiose as well as their non-covalent interactions with two lectins, Phytolacca americana lectin (PAL) and wheat germ agglutinin (WGA), are reported. The conformations of the ligands were examined by trNOESY experiments and compared with the free, solution-state conformations and molecular modeling data obtained by force field calculations. In the case of S-aryl, S-glycosides with exclusively S-glycosidic linkages, similar free and lectin-bound conformations and non-covalent interactions were found, whereas they differed for mixed glycosides and for a thiazoline derivative. In addition, STD (saturation transfer difference) NMR magnetization transfer efficiencies at three different temperatures were determined and assessed with respect to the structural differences of these pseudosaccharides. The binding epitopes of each substrate with PAL and WGA were also determined.     

Substituent Effect on 31P Chemical Shifts and Conformation of some Cyclic Phosphonates

Abstract

A series of 2-alkyl-2-oxo-1,2,3-dioxaphosphorinane (1) and some 2-alkyl-2-oxo-1,2,3-dioxaphosphepane (II) were synthesized and their NMR, IR as well as MS were reported. The substituent effect on ³¹P chemical shifts and conformations of these compounds were investigated by the molecule, mechanics calculations using Allinger's MM2 program.