Argeloside A and B, two novel 14,15-secopregnane glycosides from Solenostemma argel

Argeloside A and B, two novel 14,15-secopregnane glycosides characterized by the presence of two hemiketal functions involved in two five-membered rings, were isolated from Solenostemma argel fruits. Their structures have been established by ESIMS and NMR experiments. In particular the relative configuration of the molecules has been defined by combining the available NMR data with quantum chemical calculations of the geometries and ¹³C chemical shifts.     

Attacking boron nucleophiles: NMR properties of five-membered diazaborole rings

This paper reports computed NMR spectral data for the diazaborole anion (C2H4B1N2-) and the corresponding neutral five-membered rings with B-H (C2H5B1N2, diazaborole) and B-Li (C2H4B1Li1N2, Li-diazaborole) bonds, which are the central moieties of newly synthesized nucleophilic organoboryl five-membered rings, recently reported by Segawa et al. (Science 2006, 314, 113). Both spin-spin coupling constants and chemical shifts were obtained using high-level ab initio calculations. These data are a necessary complement to the very scarce experimental information available.     

Glycolipids from sponges. 20. J-Coupling analysis for stereochemical assignments in furanosides: structure elucidation of vesparioside B, a glycosphingolipid from the marine sponge Spheciospongia vesparia

Reinvestigation of the glycosphingolipid composition of the marine sponge Spheciospongia vesparia revealed the presence of vesparioside B ( 2a), a new furanose-rich hexaglycosylated glycosphingolipid that is the most complex glycosphingolipid isolated from a marine sponge to date. The structure of the new compound was elucidated using extensive 2D NMR studies and chemical degradation. Particularly useful for structure elucidation of vesparioside B was a quantum mechanical computational study, showing that in furanosides a vicinal coupling constant <2.0 Hz (for H-1/H-2 or H-3/H-4) or <3.5 Hz (for H-2/H-3) is a proof of the trans orientation of the relevant protons. This general rule, combined with ROE data, allowed us to elucidate the relative stereochemistry (including anomeric configuration) of the three furanose five-membered rings.     

Activity difference between alpha-COOH and beta-COOH in N-phosphorylaspartic acids

N-phosphorylamino acids are chemically active species that have many biomimic activities. alpha-COOH in amino acids and peptides behaviors rather differently than beta-COOH in many biochemical processes and takes a more important role in the origin of life. Activity differences between alpha-COOH and beta-COOH in the peptide formation of phosphoryl amino acids are studied by 1D, 2D NMR techniques and by ab initio and density functional theory (DFT) calculations in this paper. Phosphoryl dipeptide is formed directly from phosphoryl aspartic acids without any coupling reagents. Only the alpha-dipeptide ester is observed by 1D (1)H, (13)C, and (31)P NMR and 2D NMR. In the ab initio and DFT calculations, the pentacoordinate phosphorane intermediates containing five-membered rings are predicted to be more favored than those with six-membered rings. Both the experimental results and the theoretical calculations suggest that only the alpha-COOH group is activated by N-phosphorylation in N-phosphorylaspartic acid under mild conditions.     

Cadmium cyclam complexes: interconversion of cis and trans configurations and fixation of CO(2)

There is current interest in the antiviral activity of metal, especially zinc, cyclam (1,4,8,11-tetraazacyclotetradecane) complexes. Their biological activity appears to be dependent on recognition of membrane proteins (viral coreceptors) and therefore on their configurations. Here, we use Cd(II) as a probe for Zn(II) on account of its useful NMR properties. We have prepared and characterized Cd(II) complexes of cyclam, Cd(cyclam)(ClO(4))(2) (1), Cd(cyclam)Cl(2) (2), and [Cd(3)(cyclam)(3)(CO(3))](ClO(4))(4).3H(2)O (3), and have identified key markers for various configurations adopted by these complexes under a variety of solution conditions using 1D and 2D (1)H, (13)C, (15)N, and (111)Cd NMR spectroscopy, including Karplus-type analyses of (1)H, (1)H and (1)H, (111)Cd coupling constants. These complexes were stable at high pH (>8.2) but dissociated completely on lowering the pH to 5.3. Two major configurations of both 1 and 2 exist in aqueous solution: trans-I (R,S,R,S at nitrogen) and cis-V (R,R,R,R). (3)J((111)Cd, (1)H) coupling constants showed that the five-membered rings of the trans-I configuration adopt the eclipsed conformation, and the six-membered rings adopt chair conformations. The X-ray crystal structure of 3 shows that the cation adopts the unusual folded cis-I configuration in which all of the N-H bonds are oriented up (or down) in a novel tri-cadmium cluster. This complex contains triply bridged carbonate fixed from atmospheric CO(2). Each Cd(II) is bound by two cis oxygen atoms from CO(3)(2-) (Cd-O bond lengths 2.373 and 2.412 A) and four nitrogen atoms from cyclam (C-N bond lengths 2.270-2.323 A). The geometry can be described as trigonal bipyramidal with the two donor oxygen atoms occupying one of the apices of the in-plane triangle. In acetonitrile solution, complex 3 gives rise to only one configuration, trans-I, with eclipsed five-membered rings, and six-membered rings with chair conformations.     

Structural elucidation of nitro-substituted five-membered aromatic heterocycles utilizing GIAO DFT calculations

The GIAO (Gauge Including Atomic Orbitals) DFT (Density Functional Theory) method is applied at the B3LYP/6-31+G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311+G (2d,p)//B3LYP/6-31+G(d) and B3LYP/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants for 25 nitro-substituted five-membered heterocycles. Difference (1D NOE) spectra in combination with long-range gHMBC experiments were used as tools for the structural elucidation of nitro-substituted five-membered heterocycles. The assigned NMR data (chemical shifts and coupling constants) for all compounds were found to be in good agreement with theoretical calculations using the GIAO DFT method. The magnitudes of one-bond (1JCH) and long-range (nJCH, n>1) coupling constants were utilized for unambiguous differentiation between regioisomers of nitro-substituted five-membered heterocycles.     

细胞毒活性化合物Glaucocalyxin A的晶体结构和DFT研究

采用单晶x射线衍射技术对化合物的晶体结构进行了研究．研究结果表明,Glaucocalyxin A分子含3个六元环和1个五元环,其中六元环均为椅式构象,五元环为扭曲信封式构象．Glaucocalyxin A晶体结构属正交晶系．采用密度函数理论和Hartree—Fock方法对该化合物晶体的键长、键角和两面角进行计算,并与X衍射测定值进行比较,结果表明理论值与实验值符合相当好．应用规范不变原子轨道,分别在不同水平上,计算了GlaucocalyxinA的^1 H和^13 C NMR化学位移,并对理论计算值的误差进行了统计分析,结果表明计算值与实验值的符合是令人满意的．通过对该分了的三维分子表面静电位的研究,提出了该分子抗癌活性的可能部位．     

Bijvoet in solution reveals unexpected stereoselectivity in a Michael addition

The absolute configuration of small crystallizable molecules can be determined with anomalous X-ray diffraction as shown by Bijvoet in 1951. For the majority of compounds that can neither be crystallized nor easily be converted into crystallizable derivatives, stereocontrolled organic synthesis is still required to establish their absolute configuration. In this contribution, a new fundamental methodology for resolving the absolute configuration will be presented that does not require crystallization. With residual dipolar coupling enhanced NMR spectroscopy, ensembles of a limited number of structures are created reflecting the correct conformations and relative configuration. Subsequently, from these ensembles, optical rotation dispersion (ORD) spectra are predicted by DFT calculations and compared to experimental results. The combination of these two steps reveals the absolute configuration of a flexible molecule in solution, which is a big challenge to chiroptical methods and DFT in the absence of NMR spectroscopy. Here the absolute stereochemistry of the product of a new Michael addition, synthesized via a niobium(V) chiral enolate, will be elucidated by using the new methodology.     

One-pot synthesis of conformationally restricted spirooxindoles

Diastereomeric three-, five- and six-membered spirocycloalkyloxindoles were successfully synthesized in a rapid and convenient manner from readily accessible starting materials in moderate to high yields using 1-methyl-3-acetonitriloxindole after a one-pot base-mediated double-alkylation strategy. It was found that the diastereoselection is dependent on the reaction conditions and the spirocycloalkyl ring size, with the 3R^∗,8R^∗ diastereomers being thermodynamically favored under the basic reaction conditions for three- and five-membered rings, and the 3R^∗,8S^∗ diastereomer in the case of six-membered rings, as predicted by DFT calculations. The relative stereochemistry was supported by 2D NMR spectra and X-ray crystal structural analysis. The conformational rigidity of the spirocycloalkyloxindoles in solution was established based on NMR experimental and theoretical DFT approaches.     

Numerical studies for a theoretical analysis of semiempirical LCAO–CI methods

A numerical investigation of Del Re and Parr's formulas [1] for the treatment of π systems has been preformed in the case of five-membered rings, using two different expressions for the core Hamiltonian and different values for the effective charges. The results obtained are discussed by analysing the three stages of the calculation: (a) a non-iterative LCAO –MO calculation; (b) the same calculation with corrections for exchange and repulsion terms arising from fluctuations of the orbital populations; (c) configuration interaction. The calculations are interesting also because they do not involve the zero differential overlap approximation; a calculation without inclusion of overlap hse been carried out for pyrrole and the results have been compared with those including S . The main conclusions hold also for σ electrons, and can serve to assess better the validity of simple σ calculations.     

Theoretical prediction and assignment of vicinal 1H-1H coupling constants of diastereomeric 3-alkoxy-6,7-epoxy-2-oxabicyclo[3.3.0]octanes

Spin-spin coupling constants between nuclei in NMR spectroscopy reflect their spatial arrangement. A number of calculation methods, applying different levels of theory, have been developed to support the stereochemical assignment of novel compounds. Nevertheless, revisions of the assignment of structures in the literature are not rare. In the present work, the reliability of the calculation methods amenable for a theoretical prediction of spin-spin coupling constants of vicinal protons to support correct stereochemical assignment of substitution at five-membered rings of 3-alkoxy-6,7-epoxy-2-oxabicyclo[3.3.0]octanes was studied. Experimental (3)J(H,H) coupling constants were compared with the coupling constants calculated for all possible diastereomers. The fully quantum chemical approach provided theoretical (3)J(H,H) coupling constants with an absolute deviation of no more than 1.1 Hz for 91% of the experimentally studied coupled spins, whereas the methods without quantum chemical geometry optimization resulted in completely unreliable predictions. Consequently, for a reliable stereochemical assignment of small and medium size molecules, the protocol for calculating the coupling constants based on the results of the quantum chemical geometry optimization is recommended.     

An alternative method for pucker determination in carbohydrates from residual dipolar couplings: a solution NMR study of the fructofuranosyl ring of sucrose

A simple solution NMR method is presented for pucker determination of five-membered rings using only residual dipolar couplings obtained in a single liquid crystalline medium, DMPC/DHPC bicelles (DMPC = dimyristoylphosphatidylcholine; DHPC = dihexanoylphosphatidylcholine). The method was applied to determine the pucker of the fructofuranosyl ring of sucrose. The results indicate a fructofuranosyl pucker phase in the 20 degrees - 70 degrees range. The pucker phases are in agreement with those from previous NMR and optical spectroscopic studies and, importantly, do not rely on empirically parametrized Karplus curves. Furthermore, the analysis implies more than one stable pucker phase and rapid ring interconversion in this range. The present results suggest that using residual dipolar couplings alone can reveal multiple conformations present in solution. Hence, when a sufficient number of residual dipolar coupling constants is measured, the outcome is a robust, reliable, and independent route for determining carbohydrate and nucleic acid structure by NMR spectroscopy.     

Ab initio study of the NMR shielding constants and spin-spin coupling constants in cyclopropene

Summary Ab initio calculations of parameters which characterize the NMR spectrum are presented for the cyclopropene molecule. The London orbitals CHF (or GIAO-CHF, Gauge-Independent Atomic Orbital Coupled Hartree-Fock) results for the shielding constants are in good agreement with the experimental data, accurately determined, and with otherab initio values. The calculations of the NMR spin-spin coupling constants have been performed using the Multiconfiguration Time-Dependent Hartree-Fock (MC TDHF) approach. Different basis sets and MC SCF wavefunctions were used to estimate the accuracy of the results. Good agreement is obtained with the coupling constants estimated using the available experimental data.Dedicated to Professor Werner Kutzelnigg on the occasion of his 60th birthday     

Diastereomer configurations from joint experimental-computational analysis

The potential of the approach combining nuclear magnetic resonance (NMR) spectroscopy, relaxed grid search (RGS), molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations for the determination of diastereomer configurations is demonstrated using four diastereomers of a trisubstituted epoxide. Since the change in configuration of the chiral center is expected to change the distribution of conformer populations (including those of side-chain rotamers), changes in NMR parameters [chemical shifts, J couplings, and nuclear Overhauser effects (NOEs)] are expected. The method therefore relies on (1) identification of possible conformations in each diastereomer using relaxed grid search analysis and MD simulations; (2) geometry optimizations of conformers selected from step (1), followed by calculations of their relative energies (populations) using QM methods; (3) calculations of averaged NMR parameters using QM methods; (4) matching calculated and experimental values of NMR parameters of diastereomers. The diastereomer configurations are considered resolved, if three NMR parameters different in nature, chemical shifts, J couplings, and NOEs, are in agreement. A further advantage of this method is that full structural and dynamics characterization of each of the diastereomers is achieved based on the joint analysis of experimental and computational data.     

Thermodynamic analysis of strain in the five-membered oxygen and nitrogen heterocyclic compounds

Cyclopentane is conventionally strained. Replacement of a carbon atom by a heteroatom obviously impacts angular strain in the five-membered ring compounds. Changes of strains in the five-membered cycles are also caused by a double bond or atttached benzene rings. We studied the thermochemical properties of Indane, 2,3-dihydrobenzofuran, indoline, N-methyl-indoline, carbazole, and N-ethyl-carbazole to obtain a better quantitative understanding of the energetics associated with these compounds containing five-membered ring units. We used combustion calorimetry, transpiration method, and high-level first-principles calculations to derive gaseous enthalpies of formation of the five-membered heterocyclic compounds. Our new values together with the selected values for parent heterocyclic compounds, available from the literature, were used for calculation of the strain energies H(S) of five-membered C-, N-, and O-containing cycles. Quantitative analysis of the resulting stabilization or destabilization of a molecule due to interaction of benzene rings with the heteroatom has been performed.     

Stemmosides C and D, two novel unusual pregnane glycosides from Solenostemma argel: structural elucidation and configurational study by a combined NMR-quantum mechanical strategy

Stemmosides C and D, two novel pregnane glycosides characterized by an unusual C-17 side chain were isolated from the pericarps of Solenostemma argel. In addition, stemmoside D displays an uncommon 14β proton configuration, apparently being the first pregnane isolated from plants known to have a 15 keto, cis CD ring junction. Their structures have been established by ESIMS and NMR experiments. The relative configuration of the molecules was determined using a strategy based on the simulation of ¹H, ¹³C, and J coupling NMR parameters. DFT calculations of ¹H and ¹³C chemical shifts, and of the ¹H homonuclear spin–spin coupling constants were performed with the mPW1PW91 functional using the 6-31G(d,p) basis set on the fully optimized geometries of all the possible stereoisomers.     

五员碳环、氮环和磷环比较的量子化学研究

用密度泛函(DFT)理论中的B3LYP和从头算(abinitio)理论中UHF,在6-31G基组水平上,对五员碳环、氮环和磷环进行几何优化计算,由所得结果讨论了分子的成键情况,对两类环(一类是C5H5、N5、P5;另一类是C5H5-、N5-和P5-)的相对稳定性分别作比较。结果表明:有机五员碳环比无机五员氮环、磷环稳定,而五员氮环与五员磷环相比,磷环更稳定。     

Application of fluorine NMR for structure identification of steroids

Fluorinated steroids were examined using 1D and 2D homo- and heteronuclear (19)F NMR, such as (19)F-(1) H and (19)F-(13)C. The utilization of fluorine NMR accounted for spectral simplification and resulted in a straightforward pathway for the determination of structures including the configuration of these compounds; these steroids present an illustrative example for other types of fluorinated compounds, which are increasingly encountered in drug discovery. The potential of (19)F NMR is elaborated on in detail for two compounds containing diastereotopic fluorines with different coupling patterns. The analysis of the coupling patterns and the through-space interactions resulted in the determination of the structure and configuration. Heteronuclear correlation experiments, i.e. (19)F-(1)H HETCOR, (19)F-(13)C HMQC and HMBC, and (19)F-(1)H HOESY, were applied to determine first the relative stereochemistry and then the molecular configuration at C4 and C5 of a steroidal compound bearing a fused three-membered ring with two fluorine substituents. These examples proved (19)F NMR to be a useful addition to the extensively used (1)H and (13)C NMR within structure elucidation and configuration determination of small molecules.     

Geminal 2JCCH spin-spin coupling constants as probes of the phi glycosidic torsion angle in oligosaccharides

Two-bond (13)C-(1)H NMR spin-spin coupling constants ((2)J(CCH)) between C2 and H1 of aldopyranosyl rings depend not only on the relative orientation of electronegative substituents on the C1-C2 fragment but also on the C-O torsions involving the same carbons. The latter dependencies were elucidated theoretically using density functional theory and appropriate model pyranosyl rings representing the four relative configurations at C1 and C2, and a 2-deoxy derivative, to probe the relationship between (2)J(C2,H1) magnitude and sign and the C1-O1 (phi, phi) and C2-O2 (alpha) torsion angles. Related calculations were also conducted for the reverse coupling pathway, (2)J(C1,H2). Computed J-couplings were validated by comparison to experimentally measured couplings. (2)J(CCH) displays a primary dependence on the C-O torsion involving the carbon bearing the coupled proton and a secondary dependence on the C-O torsion involving the coupled carbon. These dependencies appear to be caused mainly by the effects of oxygen lone pairs on the C-H and C-C bond lengths along the C-C-H coupling pathway. New parameterized equations are proposed to interpret (2)J(C1,H2) and (2)J(C2,H1) in aldopyranosyl rings. The equation for (2)J(C2,H1) has particular value as a potential NMR structure constraint for the C1-O1 torsion angle (phi) comprising the glycosidic linkages of oligosaccharides.     

Conformational energy landscapes of liquid crystal molecules

The conformational energy landscape of the prototypical nematic liquid crystal 4-pentyl-4cyanobiphenyl (5CB) is studied using first principles computer modelling. It is found that the most favourable conformation occurs when the two constituent phenyl rings are inclined at an angle of 31 with respect to each other. Also, the orientation of the alkyl chain is found to have an important influence on the ring-ring torsional potential. We fit the energy surface of these coupled torsions to yield an accurate intramolecular potential for use in empirical modelling. To test the strength of the coupling between the alkyl tail and the phenyl rings and the cyano group, we also calculate potentials for the relative orientation of the phenyl rings in biphenyl and cyanobiphenyl (0CB). Our calculations are performed using density functional theory using pseudo-potentials and the generalized gradient approximation to exchange and correlation. The molecular electronic wavefunction is expanded in terms of a plane wave basis set. We compare our results with recent NMR and Gaussian-based quantum chemistry calculations where available.