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 (1DCC 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 CDCl3. Singular value decomposition (SVD) fitting analysis of all carbon-carbon bonds, 1DCC 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, H2O2, 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 H2O2. 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 E/Z mixtures that upon reacting with Cu and H2O2 led to two γ-C-H hydroxylation products. Contrary to our initial hypothesis, the ratio of the hydroxylation products did not depend on the ratio of the E/Z isomers but on the electrophilicity of the reactive [LCuOOH]1+. A detailed mechanistic analysis suggests a fast isomerization of the imine substrate-ligand binding the CuOOH core before the rate-determining electrophilic aromatic hydroxylation. Varying the benzophenone substituents and/or introducing electron-donating and electron-withdrawing groups on the 4-position of pyridine of the directing group allowed for fine-tuning of the electrophilicity of the mononuclear [LCuOOH]1+ to reach remarkable regioselectivities (up to 91:9 favoring the hydroxylation of the electron-rich arene ring). Lastly, we performed the C-H hydroxylation of alkyl aryl ketones, and like in the unsymmetrical benzophenones, the regioselectivity of the transformations (sp3 vs sp2) could be controlled by varying the electronics of the substrate and/or the directing group.

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. The conformational ensembles for each molecule with the best fit to the data are reported. Identification of minor conformers in water that cannot easily be determined by conventional NOE measurements will facilitate the use of RDC experiments in structure-based drug design.

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 (D2 O, DMSO-d6 , CDCl3 , and C6 D6 ). 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 D2 O, whereas a poly (methyl methacrylate) polymer gel was chosen for CDCl3 and C6 D6 , and a poly (hydroxyethyl methacrylate) gel for DMSO-d6 . Whereas the pyrrolizidine ring shows an E6 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.

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 (2H-RQCs) can be extracted from 2H 2D-NMR spectra recorded at the natural abundance level in samples oriented in a homopolypeptide LLCs (poly-γ-benzyl-l-glutamate (PBLG)). These 2H-RQCs were successfully used to address nontrivial structural problems in organic molecules. The performance and scope of this new tool is examined for two natural chiral compounds of pharmaceutical interest (strychnine and artemisinin). This is the first report in which the 3D structure/relative configuration of complex bioactive molecules is unambiguously determined using only 2H-RQCs, which, in this case, are at 2H natural abundance.

Computer-Assisted 3D Structure Elucidation (CASE-3D): The Structural Value of 2 JCH in Addition to 3 JCH 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 2 JCH and 3 JCH 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 3 JCH coupling constants, the subset of 32 2 JCH values alone showed an excellent degree of configuration selection. The study is mainly based on comparison of DFT-calculated 2,3 JCH values with experimental ones, critical for the case of 2 JCH . But the configuration selection also works well using 3 JCH values predicted from a semi-empirical Karplus-based equation limited to H-C-C-C fragments. The robustness, shown using strychnine as a proof of concept, makes the J-based CASE-3D analysis a viable option for the application in fields such as peptide and carbohydrate research, organic synthesis, natural-product identification and analysis, as well as medicinal chemistry.

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.

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

Herpotrichones A and B (1 and 2), two intermolecular [4 + 2] adducts with an unprecedented pentacyclic 6/6/6/6/3 skeleton, were isolated from Herpotrichia sp. SF09, an isopod-associated fungus, along with a new shunt product protrichone (3). 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. Compounds 1 and 2 were assessed to be potent anti-neuroinflammatory agents in lipopolysaccharide (LPS)-induced BV-2 microglial cells with the half maximal inhibitory concentration (IC50) values of 0.41 and 0.11 µM, respectively.

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. Herein we report a conformational deconvolution NMR methodology that combines residual dipolar couplings, J-couplings, and intramolecular hydrogen bond analysis along with conformational analysis using molecular dynamics simulations and density functional theory calculations for studying cyclic peptide conformations in both low-dielectric solvent (chloroform) and high-dielectric solvent (DMSO) to experimentally study the solvent-dependent conformational change hypothesis. Taken together, the combined experimental and computational approaches can illuminate conformational ensembles of cyclic peptides in solution and help identify design opportunities for better permeability.

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 1H-13C 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). Obtaining anisotropic NMR data requires the creation of an anisotropic sample environment through an alignment medium. Here, we focus on the use of compressed or stretched polymeric gels as two different but fundamentally equivalent methods for introducing sample anisotropy. Protocols are provided for the synthesis of the chloroform-compatible poly(methyl methacrylate) and dimethyl sulfoxide (DMSO)-compatible poly(2-hydroxyethyl methacrylate) gels and sample setup with a preparation time of 2-3 d. The bond-specific RDC data and the atom-specific RCSA data are extracted as changes in 1H-13C couplings and 13C chemical shifts, respectively, between two measurements under different alignment conditions, with a total experimental time of 0.5-4 d. NMR data acquisition and important considerations are described in detail. We also provide step-by-step procedures for the density functional theory (DFT) calculations involved and data analysis using the commercial software MSpin. We use three example compounds, namely cryptospirolepine (505 Da), retrorsine (351 Da), and estrone (270 Da), to demonstrate some important aspects of the workflow, such as input data preparation, handling of structural flexibility, and RCSA data correction when necessary.

Controlling magnetism of Au133(TBBT)52 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 6s1) to the band behavior is less studied. In this work, the magnetic properties of 1.7 nm [Au133(TBBT)52]0 nanoclusters (where TBBT = 4-tert-butylbenzenethiolate) with 81 nominal "valence electrons" are investigated by electron paramagnetic resonance (EPR) spectroscopy. Quantitative EPR analysis shows that each cluster possesses one unpaired electron (spin), indicating that the electrons fill into discrete orbitals instead of a continuous band, for that one electron in the band would give a much smaller magnetic moment. Therefore, [Au133(TBBT)52]0 possesses a nonmetallic electronic structure. Furthermore, we demonstrate that the unpaired spin can be removed by oxidizing [Au133(TBBT)52]0 to [Au133(TBBT)52]+ and the nanocluster transforms from paramagnetism to diamagnetism accordingly. The UV-vis absorption spectra remain the same in the process of single-electron loss or addition. Nuclear magnetic resonance (NMR) is applied to probe the charge and magnetic states of Au133(TBBT)52, and the chemical shifts of 52 surface TBBT ligands are found to be affected by the spin in the gold core. The NMR spectrum of Au133(TBBT)52 shows a 13-fold splitting with 4-fold degeneracy of 52 TBBT ligands, which are correlated to the quasi-D 2 symmetry of the ligand shell. Overall, this work provides important insights into the electronic structure of Au133(TBBT)52 by combining EPR, optical and NMR studies, which will pave the way for further understanding of the transition behavior in metal nanoclusters.

Phytochemical Study of Senecio volckmannii Assisted by CASE-3D with Residual Dipolar Couplings and Isotropic 1H/13C NMR Chemical Shifts.

Nine new eremophilanolides, with seven known sesquiterpenoids, and 4-hydroxyacetophenone were isolated from the aerial parts of Senecio volckmannii var. volckmannii. The structures of these compounds were fully characterized using a combination of spectroscopic techniques including multinuclear and multidimensional NMR and mass spectrometry. The recently published Computer Assisted 3D Structure Elucidation (CASE-3D) protocol was applied in the configurational and conformational analysis of many of these eremophilanolides on the basis of Residual Dipolar Couplings (RDCs) and/or DFT predicted 1H/13C chemical shifts.

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. The file format is an extension of the existing Structure Data Format, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, allowing automatic verification of published results, and for assisting the constitution of highly needed open-source structural databases.

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. In the absence of an RNA target, they self-deactivate by undergoing an intramolecular reaction to form cyclic products, rendering them inactive for further binding. The work has implications for the design of ultrashort nucleic acid ligands for targeting rCAG-repeat expansion associated with Huntington's disease and a number of other related neuromuscular and neurodegenerative disorders.

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 Δδiso-aniso (1 H), Δδiso-aniso (13 C) and/or isotropic 1 JCH and anisotropic 1 TCH coupling constants (and consequently 1 H-13 C residual dipolar couplings and 1 H/13 C residual chemical shift anisotropies) can be performed from spectral-aliased heteronuclear single-quantum correlation spectra.

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). Revised structures (5 and 6), including their absolute configuration, for the recently reported curcusones I (3) and J (4) are proposed.

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. It is also shown that residual chemical shift anisotropies (RCSAs) measured with the device are free of isotropic shift interferences and corrections for them are not needed during the post-acquisition data analysis. Three internal references for chemical shift were evaluated (CCl4 , CBr4 and TMS), being CCl4 the most convenient one to measure RCSAs in CDCl3 . RCSAs measured with the modified stretching device using CCl4 as the internal chemical shift reference were enough to determine the relative configuration of three small molecules with an excellent degree of configuration discrimination.

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.

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. Here we report the use of a class of shape-selective, bifacial nucleic acid recognition elements, namely Janus bases, for targeting double helical DNA or RNA. Binding occurs in a highly sequence-specific manner under physiologically relevant conditions. The work may provide a foundation for the design of oligonucleotides for targeting the secondary and tertiary structures of nucleic acid biopolymers.

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. In particular, a set of new J-resolved HSQC experiments is presented for a faster and much more accurate J determination in small molecules. Several options and practical aspects are discussed and exemplified by measuring the magnitude and/or the sign of several homo- and heteronuclear coupling constants in one shot.