Structural and conformational analysis of two native procyanidin trimers

The structure and conformation of two native procyanidin trimers in water have been determined using 2D NMR and molecular mechanics. The results show the existence of four rotameric forms, one of which is predominant (60 to 80%). These four rotamers are shown to be in slow to intermediate exchange on the NMR timescale. Both trimers, whose structures vary owing to a different substitution of one carbon atom, adopt conformations in which stacking between different phenolic rings is favored.     

Conformational study of fosinopril sodium in solution using NMR and molecular modeling

Two conformers of fosinopril sodium in methanol were unambiguously established using 2D NMR methods and variable‐temperature NMR experiments. Differences in their conformational structure were shown to be related to the rotational energy barrier about the amide bond and hydrophobic interaction. The relationship between the 3D structure and activity is discussed. It is suggested that the trans‐conformer may be more biologically active owing to its stacking structure and strong hydrophobic interaction and the cis‐conformer could be more easily hydrolyzed because of its extended structure. Copyright © 2003 John Wiley & Sons, Ltd.     

A conformational NMR analysis of methymycin aglycones: complete and unambiguous assignments of stereochemically diverse glycosylated methymycin analogs by 1D and 2D NMR techniques and molecular modeling

The ¹H and ¹³C NMR spectra of 10‐deoxymethynolide (1), 8.9‐dihydro‐10‐deoxymethynolide (2) and its glycosylated derivatives (3–9) were analyzed using gradient‐selected NMR techniques, including 1D TOCSY, gCOSY, 1D NOESY (DPFGSENOE), NOESY, gHMBC, gHSQC and gHSQC‐TOCSY. The NMR spectral parameters (chemical shifts and coupling constants) of 1–9 were determined by iterative analysis. For the first time, complete and unambiguous assignment of the ¹H NMR spectrum of 10‐deoxymethynolide (1) has been achieved in CDCl₃, CD₃OD and C₆D₆ solvents. The ¹H NMR spectrum of 8,9‐dihydro‐10‐deoxymethynolide (2) was recorded in CDCl₃, (CD₃)₂CO and CD₃OD solutions to determine the conformation. NMR‐based conformational analysis of 1 and 2 in conjugation with molecular modeling concluded that the 12‐membered ring of the macrolactones may predominantly exist in a single stable conformation in all solvents examined. In all cases, a change in solvent caused only small changes in chemical shifts and coupling constants, suggesting that all glycosylated methymycin analogs exist with similar conformations of the aglycone ring in solution. Copyright © 2013 John Wiley & Sons, Ltd.     

Conformational studies on indole alkaloids from Flustra foliacea by NMR and molecular modeling

¹H and ¹³C NMR assignments for 1a–4a and 1b–4b were obtained using HSQC, HMBC and NOESY techniques. Differences and ambiguities from literature assignments are reconciled. For the pyrrolidine C‐ring, the combined use of NMR spectroscopy and molecular mechanics calculations revealed that this ring exists in a dynamic conformational equilibrium between twist (²T₁) and envelope‐twist (¹E–¹T₂) conformations. In chloroform‐d₁, the ¹H NMR coupling constants indicate that the pyrrolidine ring is biased in favor of the envelope‐twist conformation. Steric requirements of the N‐prenyl group enhanced the envelope‐twist (¹E–¹T₂) conformation populations. Copyright © 2002 John Wiley & Sons, Ltd.     

Multinuclear magnetic resonance and molecular modeling investigations as unambiguous methods for the determination of silacycle 3D structures

An unexpected six-membered silacycle was obtained using ring-closing metathesis of diallylsilane 3. The ring size of the compound formed was derived using a 2D 13C-13C inadequate experiment. All proton and carbon-13 resonances were assigned from classical 2D NMR experiments and the proton coupling pattern was clarified. Molecular modeling calculation was then applied using NMR data as constraints, giving the 3D structure of the synthesized compound.     

Structure elucidation and 3D solution conformation of the antibiotic enduracidin determined by NMR spectroscopy and molecular dynamics

Enduracidin and ramoplanin belong to the large family of cyclodepsipeptide antibiotics, highly effective against Gram-positive bacteria. The primary and 3D solution structure of ramoplanin is already well known, and the primary structure of enduracidin has been determined by a combination of chemical and NMR spectroscopic methods. Both antibiotics share a similar peptide core of 17 amino acids and differ mainly in the length of the acyl chain and the presence of two D-mannose moieties in ramoplanin. Based on the high sequence homology with ramoplanin, the structure in solution of enduracidin is modeled as a cyclic peptide. The tertiary structure thus obtained was refined through molecular dynamics (MD) simulation, in which the interatomic NOE-derived distance restraints were imposed. MD simulations yielded a family of representative 3D structures (RMSD = 0.89), which highlighted a backbone geometry similar to that of ramoplanin in its beta-hairpin arrangement. In contrast, enduracidin displays a different arrangement of the side-chain and of the residues forming the hydrophobic core.     

NMR and x-ray conformational study of artemisiifolin and three other related germacranolides

From an acetone extract of Staehelina dubia, large quantities of the previously known germacranolide artemisiifolin were isolated. The conformations of the 10-membered germacra-1(10)E,4Z-diene ring system of this compound and those of its derivatives 11,13-dihydroartemisiifolin, isabelin and 6alpha-hydroxy-15-oxogermacra-1(10)E,4Z,11(13)-trien-12,8alpha-olide were studied by NMR spectroscopic methods. Low-energy conformations were obtained by quantum mechanical calculations. An x-ray diffraction analysis of artemisiifolin established that, in the crystalline state, it possesses a unique conformation that corresponds to the majority one existing in acetone-d6 solution.     

Structural elucidation and total assignment of the 1H and 13C NMR spectra of new chalcone dimers

Conventional 1D NMR methods and 2D shift‐correlated NMR experiments (COSY, HMQC, HMBC) were used for the structural elucidation and ¹H and ¹³C chemical shifts assignments of four new types of chalcone dimers isolated from Myracrodruon urundeuva. Copyright © 2003 John Wiley & Sons, Ltd.     

Chiral diaminopyrrolic receptors for selective recognition of mannosides, part 2: a 3D view of the recognition modes by X-ray, NMR spectroscopy, and molecular modeling

The structural features of a representative set of five complexes of octyl α- and β-mannosides with some members of a new generation of chiral tripodal diaminopyrrolic receptors, namely, (R)-5 and (S)- and (R)-7, have been investigated in solution and in the solid state by a combined X-ray, NMR spectroscopy, and molecular modeling approach. In the solid state, the binding arms of the free receptors 7 delimit a cleft in which two solvent molecules are hydrogen bonded to the pyrrolic groups and to the benzenic scaffold. In a polar solvent (CD(3)CN), chemical shift and intermolecular NOE data, assisted by molecular modeling calculations, ascertained the binding modes of the interaction between the receptor and the glycoside for these complexes. Although a single binding mode was found to adequately describe the complex of the acyclic receptor 5 with the α-mannoside, for the complexes of the cyclic receptors 7 two different binding modes were required to simultaneously fit all the experimental data. In all cases, extensive binding through hydrogen bonding and CH-π interactions is responsible for the affinities measured in the same solvent. Furthermore, the binding modes closely account for the recognition preferences observed toward the anomeric glycosides and for the peculiar enantiodiscrimination properties exhibited by the chiral receptors.     

Solution conformation by NMR and molecular modeling of three sulfide-free somatostatin octapeptide analogs compared to angiopeptin

Summary The conformation in dimethylsulfoxide of the somatostatin derivative angiopeptin and of three disulfide-free analogs was estimated by two-dimensional nuclear magnetic resonance spectroscopy at room temperature. The resulting 3D molecular graphics were compared and shown to reflect the observed differences in the inhibition of restenosis after rat aorta balloon injury by these octapeptide inhibitors. Angiopeptin and its active analog 2 displayed a relatively rigid conformation of the cyclic hexapeptide backbone due to the presence of two well-defined hydrogen bonds, further stabilized by a third hydrogen bond outside the ring. No such constraints were detected for the two biologically inactive analogs, which, compared to 2, had a two-atom longer or shorter hexapeptide ring. The well-defined structure of compound 2 may serve as an improved pharmacophore for this new class of drugs.     

A study of fire retardant blooming in HIPS by molecular modeling

The blooming process of two fire retardants: FR 1808 (by DSBG) and FR 8010 (by Albemarle) in high impact polystyrene (HIPS) was studied using experimental and computational methods. The degree of blooming was determined by accelerated aging followed by transmission electron microscopy (TEM) micrographs. Several levels of computational tools were used. On the molecular level, forced diffusion, calculations showed that the relative diffusion coefficient of FR 1808 in pure polystyrene (PS) is significantly higher than that of FR 8010. It was shown that this diffusion coefficient could be reduced by the addition of chloroprene and polychloroprene. Cohesive energy density (CED) solubility parameter and heat of mixing calculations showed that FR 1808 was compatible in PS, with an even higher compatibility in the interface of PS and butadiene in HIPS. TEM micrographs were in agreement with these findings. A three‐stage blooming mechanism was suggested: FR 1808 accumulates in the PS butadiene interface and diffuses to the surface, through the butadiene inclusions, due to FR 1808 concentration gradient. Copyright © 2010 John Wiley & Sons, Ltd.     

[60]富勒烯及其衍生物结构表征的有力工具－^3He 核磁共振谱

对[60]富勒烯衍生物的结构表征手段,特别是近年来兴起的^3He@C~n(n=60,70,78,84…)的合成及^3He核磁共振谱在结构表征中的应用进行了综述。     

Molecular recognition of aminoglycoside antibiotics by bacterial defence proteins: NMR study of the structural and conformational features of streptomycin inactivation by Bacillus subtilis aminoglycoside-6-adenyl transferase

The molecular recognition of streptomycin by Bacillus subtilis aminoglycoside-6-adenyl transferase has been analysed by a combination of NMR techniques and molecular dynamic simulations. This protein inactivates streptomycin by transferring an adenyl group to position six of the streptidine moiety. Our combined approach provides valuable information about the bioactive conformation for both the antibiotic and ATP and shows that the molecular recognition process for streptomycin involves a conformational selection phenomenon. The binding epitope for both ligands has also been analysed by 1D-STD experiments. Finally, the specificity of the recognition process with respect to the aminoglycoside and to the nucleotide has been studied.     

Isolation and structural determination of sorbinols A and B, new triterpenes from Sorbus cashmariana, by 1D and 2D NMR spectroscopy

Two new pentacyclic triterpenes, sorbinols A (1) and B (2) have been isolated from the ethyl acetate fraction of Sorbus cashmariana and their structures assigned from (1)H and (13)C NMR spectra, DEPT and by 2D COSY, NOE, HMQC and HMBC experiments. Both 1 and 2 showed moderate inhibitory potential against the enzyme lipoxygenase.     

毛冬青三萜皂甙Ilexsaponin B3糖部分的核磁共振法分析

采用1H、13C、DEPT(无畸变极化转移增益法)、1H-1H COSY(氢-氢化学位移相关谱)、1H-1HTCOSY(氢-氢化学位移全相关潜)、HSQC(异核单量子相关谱)、HMBC(异核多键相关谱)等多种NMR分析方法,首次对毛冬青三萜皂甙Ilexsaponin B3的1H和13C NMR信号进行了全归属,特别是应用1H-1H COSY和1H-1H TCOSY相结合的分析方法,对该化合物中氢谱信号严重重叠的糖部分进行了详细的分析,提出了一套对三萜皂甙糖部分信号进行全归属的核磁共振法.     

Conformational analysis of 14‐hydroxymodhephene by NMR,x‐ray diffraction and molecular modeling studies

The conformational state of the [3.3.3]propellane framework for 14‐hydroxymodhephene was determined by extensive application of one‐ and two‐dimensional ¹H and ¹³C NMR spectroscopy combined with x‐ray diffraction studies of a synthesized derivative, spectral simulation and molecular modeling. The conformational rigidity of the molecule in solution, established at room temperature, revealed the existence of envelope conformers for both cyclopentane fragments, with C‐7 puckered endo and C‐10 exo with respect to the mean plane containing the B and C rings. Copyright © 2003 John Wiley & Sons, Ltd.     

2D NMR对Sarcophine所有^1H NMR和^1^3C NMR归属的指定

从中国南海软珊瑚Sarcophyton molle中分离得到大环二萜内酯Sarcophine(1)。本文利用^1H-^1H COSY，HMQC，HMBC等二维谱手段首次对Sarcophine所有^1H NMR、^1^3C NMR的信号归属进行了完全的指定。并第一次报道了其^1^3C NMR数据。     

An NMR and molecular modeling study of carbosilane-based dendrimers functionalized with phenolic groups or titanium complexes at the periphery

Dendrimers are modified polymers whose architecture is defined by the presence of a central atom or core with multiple branches. These molecules lend themselves to a variety of architectures and uses, including drug delivery and catalysis. The study of the molecular conformations and shapes of dendritic molecules is necessary but not yet routine. Here we present an NMR and molecular modeling study of a series of carbosilane dendrimers, namely 1G-{(CH2)3[C6H3(OMe)]OH}4 (1), 2G-{(CH2)3[C6H3(OMe)]OH}8 (2), and 2G-{(CH2)3[C6H3(OMe)]O[Ti(C5H5)Cl2]}8 (3). Various two-dimensional NMR techniques were used to completely assign the 1H and 13C resonances of molecules 1-3. This information was used, in conjunction with 1H and 13C spin-lattice relaxation measurements, to assess the chain motion of the molecules. The NMR data were also compared with 1-ns molecular dynamics (MD) simulations of 1 and 2 using the MMFF94 force field. The results indicate that these dendrimers possess a core that is motionally decoupled from the rest of the dendrimer, with flexible arm segments that extend from the core. The addition of eight functionalized titanium groups to the ends of the dendrimer chains of 2 to yield molecule 3 serves to further restrict chain motion.