Full configurational and conformational analysis of artemisinin by one-bond carbon-carbon residual dipolar couplings at natural abundance.

Configurational and conformational analysis of the biologically relevant natural product artemisinin was conducted using carbon-carbon residual dipolar couplings (D RDCs) at natural abundance. These RDCs were measured through the 2D-INADEQUATE NMR experiment using a sample aligned in a compressed poly (methyl methacrylate) (PMMA) gel swollen in CDCl. Singular value decomposition (SVD) fitting analysis of all carbon-carbon bonds, D RDCs, in relation to the full configuration/conformational space (32 diastereoisomers) of artemisinin, unambiguously identified the correct configuration of artemisinin.

Regioselective Hydroxylation of Unsymmetrical Ketones Using Cu, HO, and Imine Directing Groups via Formation of an Electrophilic Cupric Hydroperoxide Core.

Herein, we describe the regioselective functionalization of unsymmetrical ketones using imine directing groups, Cu, and HO. The C-H hydroxylation of the substrate-ligands derived from 2-substituted benzophenones occurred exclusively at the γ-position of the unsubstituted ring due to the formation of only one imine stereoisomer. Conversely, the imines derived from 4-substituted benzophenones produced / mixtures that upon reacting with Cu and HO led to two γ-C-H hydroxylation products.

Cross-Linked Poly-4-Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water.

Determination of the solution conformation of both small organic molecules and peptides in water remains a substantial hurdle in using NMR solution conformations to guide drug design due to the lack of easy to use alignment media. Herein we report the design of a flexible compressible chemically cross-linked poly-4-acrylomorpholine gel that can be used for the alignment of both small molecules and cyclic peptides in water. To test the new gel, residual dipolar couplings (RDCs) and J-coupling constants were used in the configurational analysis of strychnine hydrochloride, a molecule that has been studied extensively in organic solvents as well as a small cyclic peptide that is known to form an α-helix in water.

Reference-free NOE NMR analysis.

Nuclear Overhauser Effect (NOE) methods in NMR are an important tool for 3D structural analysis of small molecules. Quantitative NOE methods conventionally rely on reference distances, known distances that have to be spectrally separated and are not always available. Here we present a new method for evaluation and 3D structure selection that does not require a reference distance, instead utilizing structures optimized by molecular mechanics, enabling NOE evaluation even on molecules without suitable reference groups.

Deuterium Residual Quadrupolar Couplings: Crossing the Current Frontiers in the Relative Configuration Analysis of Natural Products.

The determination of the 3D structure (configuration and preferred conformation) of complex natural and synthetic organic molecules is a long-standing but still challenging task for chemists, with various implications in pharmaceutical sciences whether or not these substances have specific bioactivities. Nuclear magnetic resonance (NMR) in aligning media, either lyotropic liquid crystals (LLCs) or polymer gels, in combination with molecular modeling is a unique framework for solving complex structural problems whose analytical wealth lies in the establishment of nonlocal structural correlations. As an alternative to the already well-established anisotropic NMR parameters, such as RDCs (residual dipolar couplings) and RCSAs (residual chemical shift anisotropies), it is shown here that deuterium residual quadrupolar couplings (H-RQCs) can be extracted from H 2D-NMR spectra recorded at the natural abundance level in samples oriented in a homopolypeptide LLCs (poly-γ-benzyl-l-glutamate (PBLG)).

Controlling magnetism of Au(TBBT) nanoclusters at single electron level and implication for nonmetal to metal transition.

The transition from the discrete, excitonic state to the continuous, metallic state in thiolate-protected gold nanoclusters is of fundamental interest and has attracted significant efforts in recent research. Compared with optical and electronic transition behavior, the transition in magnetism from the atomic gold paramagnetism (Au 6s) to the band behavior is less studied. In this work, the magnetic properties of 1.

Computer-Assisted 3D Structure Elucidation (CASE-3D): The Structural Value of J in Addition to J Coupling Constants.

We present a method to use long-range CH coupling constants to derive the correct diastereoisomer from the molecular constitution of small molecules. A set of 79 J and J values collected from a single HSQMBC experiment on a sample of strychnine were used in the CASE-3D (computer-assisted 3D structure elucidation) protocol. In addition to the most commonly used J coupling constants, the subset of 32 J values alone showed an excellent degree of configuration selection.

Herpotrichones A and B, Two Intermolecular [4 + 2] Adducts with Anti-Neuroinflammatory Activity from a Species.

Herpotrichones A and B ( and ), two intermolecular [4 + 2] adducts with an unprecedented pentacyclic 6/6/6/6/3 skeleton, were isolated from sp. SF09, an isopod-associated fungus, along with a new shunt product protrichone (). Their structures were elucidated by the analysis of spectroscopic data, residual dipolar coupling (RDC)-based computer-assisted 3D structure elucidation (CASE-3D), and single-crystal X-ray diffraction in combination with electronic circular dichroism (ECD) calculations.

Effect of the solvent on the conformation of monocrotaline as determined by isotropic and anisotropic NMR parameters.

The conformation in solution of monocrotaline, a pyrrolizidine alkaloid presenting an eleven-membered macrocyclic diester ring, has been investigated using a combination of isotropic and anisotropic nuclear magnetic resonance parameters measured in four solvents of different polarity (D O, DMSO-d , CDCl , and C D ). Anisotropic nuclear magnetic resonance parameters were measured in different alignment media, based on their compatibility with the solvent of interest: cromoglycate liquid crystal solution was used for D O, whereas a poly (methyl methacrylate) polymer gel was chosen for CDCl and C D , and a poly (hydroxyethyl methacrylate) gel for DMSO-d . Whereas the pyrrolizidine ring shows an E exo-puckered conformation in all of the solvents, the macrocyclic eleven-membered ring adopts different populations of syn-parallel and anti-parallel relative orientation of the carbonyl groups according to the polarity of the solvent.

Cyclic Peptide Design Guided by Residual Dipolar Couplings, J-Couplings, and Intramolecular Hydrogen Bond Analysis.

Cyclic peptides have long tantalized drug designers with their potential ability to combine the best attributes of antibodies and small molecules. An ideal cyclic peptide drug candidate would be able to recognize a protein surface like an antibody while achieving the oral bioavailability of a small molecule. It has been hypothesized that such cyclic peptides balance permeability and solubility using their solvent-dependent conformational flexibility.

Application of anisotropic NMR parameters to the confirmation of molecular structure.

The use of anisotropic NMR data, such as residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs), has emerged as a powerful technique for structural characterization of organic small molecules. RDCs typically report the relative orientations of different H-C bonds; RCSAs report the relative orientations of different carbon chemical shielding tensors and hence are more useful for proton-deficient molecules. This information is complementary to that obtained from conventional NMR data such as J couplings, isotropic chemical shifts, and nuclear Overhauser effects (NOEs)/rotational frame nuclear Overhauser effects (ROEs).

NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.

Even though NMR has found countless applications in the field of small molecule characterization, there is no standard file format available for the NMR data relevant to structure characterization of small molecules. A new format is therefore introduced to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters, which we shall call NMReDATA (for nuclear magnetic resonance extracted data), include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates.

Design of Bivalent Nucleic Acid Ligands for Recognition of RNA-Repeated Expansion Associated with Huntington's Disease.

We report the development of a new class of nucleic acid ligands that is comprised of Janus bases and the MPγPNA backbone and is capable of binding rCAG repeats in a sequence-specific and selective manner via, inference, bivalent H-bonding interactions. Individually, the interactions between ligands and RNA are weak and transient. However, upon the installation of a C-terminal thioester and an N-terminal cystine and the reduction of disulfide bond, they undergo template-directed native chemical ligation to form concatenated oligomeric products that bind tightly to the RNA template.

Isotropic/Anisotropic NMR Editing by Resolution-Enhanced NMR Spectroscopy.

Modern resolution-enhanced NMR techniques can monitor the in situ discrimination of co-existing isotropic and anisotropic contributions of small molecules dissolved in weakly aligning PMMA/CDCl3 media. The simultaneous sign-sensitive determination of accurate Δδ ( H), Δδ ( C) and/or isotropic J and anisotropic T coupling constants (and consequently H- C residual dipolar couplings and H/ C residual chemical shift anisotropies) can be performed from spectral-aliased heteronuclear single-quantum correlation spectra.

New Stretching Method for Aligning Gels: Its Application to the Measurement Residual Chemical Shift Anisotropies (RCSAs) without the Need for Isotropic Shift Correction.

An existing gel stretching device is modified, permitting the use of organic solvents for the study of small molecules. Different from the original device, gels are stretched into 4 mm open-ended NMR tubes and then inserted into regular 5 mm NMR tubes. No open-ended tubes are inserted in the NMR probe avoiding the risk of sample leaking.

Measurement of residual chemical shift anisotropies in compressed polymethylmethacrylate gels. Automatic compensation of gel isotropic shift contribution.

Mechanical compression of polymer gels provides a simple way for the measurement of residual chemical shift anisotropies, which then can be employed, on its own, or in combination with residual dipolar couplings, for structural elucidation purposes. Residual chemical shift anisotropies measured using compression devices needed a posteriori correction to account for the increase of the polymer to solvent ratio inside the swollen gel. This correction has been cast before in terms of a single-free parameter which, as shown here, can be simultaneously optimized along with the components of the alignment tensor while still retaining discriminating power of the different relative configurations as illustrated in the stereochemical analysis of α-santonin and 10-epi-8-deoxycumambrin B.

Computer-Assisted 3D Structure Elucidation (CASE-3D) of Natural Products Combining Isotropic and Anisotropic NMR Parameters.

A computer-assisted structural elucidation (CASE-3D) strategy based on the use of isotropic and/or anisotropic NMR data is proposed to elucidate relative configuration and preferred conformation in complex natural products. The methodology involves the selection of conformational models through the use of the Akaike Information Criterion and scoring of the different configurations. As illustrative examples, the methodology furnished the correct configuration of the already known compounds artemisinin (1) and homodimericin A (2).

Shape selective bifacial recognition of double helical DNA.

An impressive array of antigene approaches has been developed for recognition of double helical DNA over the past three decades; however, few have exploited the 'Watson-Crick' base-pairing rules for establishing sequence-specific recognition. One approach employs peptide nucleic acid as a molecular reagent and strand invasion as a binding mode. However, even with integration of the latest conformationally-preorganized backbone design, such an approach is generally confined to sub-physiological conditions due to the lack of binding energy.

Highly resolved HSQC experiments for the fast and accurate measurement of homonuclear and heteronuclear coupling constants.

A number of J-upscaled NMR experiments are currently available to measure coupling constants along the indirect F1 dimension of a 2D spectrum. A major drawback is the limited F1 digital resolution that requires long acquisition times in order to achieve reasonably accurate measures. Here is shown how high levels of F1 digital resolution in a multiple-purpose HSQC experiment can be easily achieved by implementing a general J/δ-scaling strategy.

J-resolved HSQC: Exclusive determination of geminal proton-proton coupling constants.

The measurement of two-bond proton-proton coupling constants (J) in prochiral CH groups from the F2 dimension of 2D spectra is not easy due to the usual presence of complex multiplet J patterns, line broadening effects and strong coupling artifacts. These drawbacks are particularly pronounced and frequent in AB spin systems, as those normally exhibited by the pair of diastereotopic CH protons. Here, a novel J-resolved HSQC experiment for the exclusive and accurate determination of the magnitude of J from the doublet displayed along the highly-resolved indirect F1 dimension is described.

Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules.

Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest.

Computer-Assisted 3D Structure Elucidation of Natural Products using Residual Dipolar Couplings.

An enhanced computer-assisted procedure for the determination of the relative configuration of natural products, which starts from the molecular formula and uses a combination of conventional 1D and 2D NMR spectra, and residual dipolar couplings (RDCs), is reported. Having already the data acquired (1D/2D NMR and RDCs), the procedure begins with the determination of the molecular constitution using standard computer-assisted structure elucidation (CASE) and is followed by fully automated determination of relative configuration through RDC analysis. In the case of moderately flexible molecules the simplest data-explaining conformational model is selected by the use of the Akaike information criterion.

Application of Residual Dipolar Couplings and Selective Quantitative NOE to Establish the Structures of Tetranortriterpenoids from Xylocarpus rumphii.

Nine triterpenoid derivatives were isolated from the heartwood of Xylocarpus rumphii and were identified as xylorumphiins E (1), C (2), L (3), and M-R (4-9). Compounds 4-9 have a hemiacetal group in the triterpenoid side chain, making them impossible to purify. Purification was achieved after acetylation and subsequent separation of the epimeric mixtures of acetates; however differentiaition of the R and S epimers was not possible using standard NMR techniques.