Armando Navarro-Vázquez

Residual Dipolar Couplings of Freely Rotating Groups in Small Molecules. Stereochemical Assignment and Side-Chain Conformation of 8-Phenylmenthol

A procedure for the direct use of (1)D(CH) residual dipolar couplings (RDCs) from freely rotating groups in the structural analysis of small molecules was implemented. (1)D(CH) RDCs were used to determine both the preferred conformation and the stereochemical assignment of the diastereotopic geminal methyls of 8-phenylmenthol. Furthermore, a method was also set up to fit RDC data to a set of conformations in solution on the assumption that they all have the same alignment tensor.

MSpin‐RDC. A program for the use of residual dipolar couplings for structure elucidation of small molecules

We developed a new program, MSpin‐RDC for the analysis of residual dipolar coupling data. This software, specially designed for small molecule analysis, can directly read many molecular‐modeling and popular chemistry file formats and accept RDC values as a simple free‐format table. Alignment tensor can then be computed by singular value decomposition, as well as predicted using inertia and gyration tensor‐based methodologies. Trial structures are then ranked according to their Cornilescus quality factor (Q) values. Analysis of multiconformational problems and fitting of RDC data to relative populations can be accomplished using the single‐tensor approximation. Copyright

Structural Discrimination in Small Molecules by Accurate Measurement of Long‐Range Proton–Carbon NMR Residual Dipolar Couplings

Accurate measurement of long-range CH residual dipolar couplings (RDCs) (2DCH and 3DCH) by a new selective J-scaled HSQC experiment significantly improves the structural discrimination power of RDCs in small molecules with multiple stereocenters. The extraction of the long-range couplings is clean and straightforward, and in most cases yields the sign of the RDC too. The experiment is demonstrated with 10-epi-8-deoxycumambrin B, a tricyclic natural compound with five chiral centers.

Challenge of large-scale motion for residual dipolar coupling based analysis of configuration: the case of fibrosterol sulfate A.

Fibrosterol sulfate A is a polysulfated bis-steroid with an atypical side chain. Due to the flexibility of the linker, large-scale motions that change dramatically the shape of the entire molecule are expected. Such motions pose major challenges to the structure elucidation and the correct determination of configuration. In this study, we will describe the determination of the relative configuration of fibrosterol sulfate A through a residual dipolar coupling based multiple alignment tensor analysis complemented by molecular dynamics. For completeness, we applied also the single tensor approach which is unreliable due to the large-scale motions and compare the results.

Stereochemistry Determination by Powder X‐Ray Diffraction Analysis and NMR Spectroscopy Residual Dipolar Couplings

A matter of technique: For a new steroidal lactol, jaborosalactol 24 (1), isolated from Jaborosa parviflora, NMR spectroscopy residual dipolar couplings and powder X-ray diffraction analysis independently gave the same stereochemistry at C23-C26. Conventional NMR spectroscopic techniques, such as NOE and {sup 3}J coupling-constant analysis failed to unambiguously determine this stereochemistry.

Is Enantiomer Assignment Possible by NMR Spectroscopy Using Residual Dipolar Couplings from Chiral Nonracemic Alignment Media?—A Critical Assessment

The discovery of Jean-Baptiste Biot in 1815 that optical activity is not a property bound to a certain aggregation state of matter but a property of the constituting molecules themselves, has had an enormous influence on the structural models that chemists developed at the end of the 19th century, long before the description of the chemical bond was based on quantum mechanics. Pasteur achieved the first separation of enantiomers in 1847, namely by crystallization of a racemic tartrate mixture that separated the two enantiomers into enantiomorphic crystals, solutions of which rotated the plane of linearly polarized light in opposite directions. Not until 1951, when Bijvoet used anomalous X-ray diffraction, it was possible to assign the absolute configuration to a specific enantiomer. However, anomalous X-ray diffraction has not put the problem of assigning absolute configurations to rest, because many chemical compounds cannot be crystallized. Moreover, anomalous X-ray diffraction of molecules that consist exclusively of lightweight atoms commonly lacks the needed accuracy to allow unambiguous assignment of absolute configurations. An alternative method for resolving enantiomers is to convert them to diastereoisomers, either by chemical derivatization with chiral nonracemic moieties or by intermolecular coordination with chiral nonracemic reagents. In this way it is possible to determine absolute configuration from NMR observables, most commonly chemical shifts. The use of chiroptical spectroscopies such as optical rotatory dispersion, and electronic or vibrational circular dichroism is well established, sometimes in combination with ab initio calculations. Further methods are conceivable but impractical momentarily. Yet, there is currently not a simple and universally applicable approach to determine the absolute configuration of molecules with few stereogenic centers. Two recent papers published in 2007 and 2011 have therefore created a lot of excitement in the chemistry and NMR spectroscopy communities. Their titles are: “Stereochemical Identification of (R)and (S)-Ibuprofen Using Residual Dipolar Couplings, NMR, and Modeling”, henceforth called “article 1”, and more recently: “Spin-Selective Correlation Experiment for Measurement of Long-Range J Couplings and for Assignment of (R/S) Enantiomers from the Residual Dipolar Couplings and DFT”, henceforth called “article 2”. Both articles describe the assignment of the absolute configuration of the chiral molecules, ibuprofen 1 (article 1) and 4-methyl-1,3-dioxolan-2-one 2 (article 2), using NMR spectroscopy in chiral nonracemic alignment media (Figure 1). Under chiral nonracemic conditions, the authors measured residual dipolar couplings (RDCs), a NMR parameter only visible in oriented samples, such as in liquid crystals, but not in isotropic solvents. The interaction of the enantiomers with the chiral nonracemic alignment medium gives rise to diastereomorphic associates for which reason the authors indeed found different sets of anisotropic parameters for each enantiomer, in total

Preparation and characterization of a halogen-bonded shape-persistent chiral alleno-acetylenic inclusion complex.

A chiral bidentate inclusion complex has been formed by halogen-bond interaction between the pyridyl moieties of a pyridoallenoacetylenic host and octafluorodiiodobutane. X-ray crystallography showed that the guest adopts a chiral conformation inside the molecular channels formed by stacking of the host units. A 10 ppm shielding of the (15)N NMR resonance for the pyridil units provided evidence of the formation of the halogen-bond complex in solution.

Dynamics of the glycosidic bond: conformational space of lactose.

The dynamics of the glycosidic bond of lactose was studied by a paramagnetic tagging-based NMR technique, which allowed the collection of an unusually large series of NMR data for a single compound. By the use of distance- and orientation-dependent residual dipolar couplings and pseudocontact shifts, the simultaneous fitting of the probabilities of computed conformations and the orientation of the magnetic susceptibility tensor of a series of lanthanide complexes of lactose show that its glycosidic bond samples syn/syn, anti/syn and syn/anti ϕ/ψ regions of the conformational space in water. The analysis indicates a higher reliability of pseudocontact shift data as compared to residual dipolar couplings with the presently available weakly orienting paramagnetic tagging technique. The method presented herein allows for an improved understanding of the dynamic behaviour of oligosaccharides.

Determination of Relative Configuration from Residual Chemical Shift Anisotropy

Determination of relative configuration is frequently a rate-limiting step in the characterization of small organic molecules. Solution NMR-based nuclear Overhauser effect and scalar J-coupling constants can provide useful spatial information but often fail when stereocenters are separated by more than 4-5 Å. Residual dipolar couplings (RDCs) can provide a means of assigning relative configuration without limits of distance between stereocenters. However, sensitivity limits their application. Chemical shift is the most readily measured NMR parameter, and partial molecular alignment can reveal the anisotropic component of the chemical shift tensor, manifested as residual chemical shift anisotropy (RCSA). Hence, (13)C RCSAs provide information on the relative orientations of specific structural moieties including nonprotonated carbons and can be used for stereochemical assignment. Herein, we present two robust and sensitive methods to accurately measure and apply (13)C RCSAs for stereochemical assignment. The complementary techniques are demonstrated with five molecules representing differing structural classes.

Lanthanide-Chelating Carbohydrate Conjugates Are Useful Tools To Characterize Carbohydrate Conformation in Solution and Sensitive Sensors to Detect Carbohydrate–Protein Interactions

The increasing interest in the functional versatility of glycan epitopes in cellular glycoconjugates calls for developing sensitive methods to define carbohydrate conformation in solution and to characterize protein-carbohydrate interactions. Measurements of pseudocontact shifts in the presence of a paramagnetic cation can provide such information. In this work, the energetically privileged conformation of a disaccharide (lactose as test case) was experimentally inferred by using a synthetic carbohydrate conjugate bearing a lanthanide binding tag. In addition, the binding of lactose to a biomedically relevant receptor (the human adhesion/growth-regulatory lectin galectin-3) and its consequences in structural terms were defined, using Dy(3+), Tb(3+), and Tm(3+). The described approach, complementing the previously tested protein tagging as a way to exploit paramagnetism, enables to detect binding, even weak interactions, and to characterize in detail topological aspects useful for physiological ligands and mimetics in drug design.