The use of residual dipolar coupling for conformational analysis of structurally related natural products

Determining the conformational preferences of molecules in solution remains a considerable challenge. Recently, the use of residual dipolar coupling (RDC) analysis has emerged as a key method to address this. Whilst to date the majority of the applications have focused on biomolecules including proteins and DNA, the use of RDCs for studying small molecules is gaining popularity. Having said that, the method continues to develop, and here, we describe an early case study of the quantification of conformer populations in small molecules using RDC analysis. Having been inspired to study conformational preferences by unexpected differences in the NMR spectra and the reactivity of related natural products, we showed that the use of more established techniques was unsatisfactory in explaining the experimental observations. The use of RDCs provided an improved understanding that, following use of methods to quantify conformer populations using RDCs, culminated in a rationalisation of the contrasting diastereoselectivities observed in a ketone reduction reaction. Copyright © 2015 John Wiley & Sons, Ltd.     

Current developments in homonuclear and heteronuclear J‐resolved NMR experiments

Two‐dimensional J‐resolved (Jres) NMR experiments offer a simple, user‐friendly spectral representation where the information of coupling constants and chemical shifts are separated into two orthogonal frequency axis. Since its initial proposal 40 years ago, Jres has been the focus of considerable interest both in improving the basic pulse sequence and in its successful application to a wide range of studies. Here, the latest developments in the design of novel Jres pulse schemes are reviewed, mainly focusing on obtaining pure absorption lineshapes, minimizing strong coupling artifacts, and also optimizing sensitivity and experimental measurements. A discussion of several Jres versions for the accurate measurement of a different number of homonuclear (J_HH) and heteronuclear (J_CH) coupling constants is presented, accompanied by some illustrative examples.     

Geminal 2J(29Si‐O‐29Si) couplings in oligosiloxanes and their relation to direct 1J(29Si‐13C) couplings

Absolute values of (79) geminal ²J(²⁹Si‐O‐²⁹Si) couplings were measured in an extensive series of (55) unstrained siloxanes dissolved in chloroform‐d. Signs of ²J(²⁹Si‐O‐²⁹Si) in some (9) silicon hydrides were determined relative to ¹J(²⁹Si‐¹H) which are known to be negative. It is supposed that positive sign of the ²J(²⁹Si‐O‐²⁹Si) coupling found in all studied hydrides is common to all siloxanes. Theoretical calculations for simple model compounds failed to reproduce this sign and so their predictions of bond length and angle dependences cannot be taken as reliable. Useful empirical correlations were found between the ²J(²⁹Si‐O‐²⁹Si) couplings on one side and the total number m of oxygen atoms bonded to the silicon atoms, sum of ²⁹Si chemical shifts or product of ¹J(²⁹Si‐¹³C) couplings on the other side. The significance of these correlations is briefly discussed. Copyright © 2011 John Wiley & Sons, Ltd.     

Recoupled Polarization-Transfer Methods for Solid-State H–C Heteronuclear Correlation in the Limit of Fast MAS

An in-depth account of the effects of homonuclear couplings and multiple heteronuclear couplings is given for a recently published technique for ¹H–¹³C dipolar correlation in solids under very fast MAS, where the heteronuclear dipolar coupling is recoupled by means of REDOR π-pulse trains. The method bears similarities to well-known solution-state NMR techniques, which form the framework of a heteronuclear multiple-quantum experiment. The so-called recoupled polarization-transfer (REPT) technique is versatile in that rotor-synchronized ¹H–¹³C shift correlation spectra can be recorded. In addition, weak heteronuclear dipolar coupling constants can be extracted by means of spinning sideband analysis in the indirect dimension of the experiment. These sidebands are generated by rotor encoding of the reconversion Hamiltonian. We present generalized variants of the initially described heteronuclear multiple-quantum correlation (HMQC) experiment, which are better suited for certain applications. Using these techniques, measurements on model compounds with ¹³C in natural abundance, as well as simulations, confirm the very weak effect of ¹H–¹H homonuclear couplings on the spectra recorded with spinning frequencies of 25–30 kHz. The effect of remote heteronuclear couplings on the spinning-sideband patterns of CH_n groups is discussed, and ¹³C spectral editing of rigid organic solids is shown to be practicable with these techniques.     

Total synthesis of Resolvin E1

The enantioselective total synthesis of Resolvin E1 (RvE1), a naturally occurring small molecule mediator of inflammation resolution, is reported. Two routes are presented, both modular and convergent in nature, with an excellent control of all stereocenters. The C12- and C18-hydroxy groups are derived from (S)-glycidol while the C5-hydroxy group is installed via enantioselective reduction of a ketone precursor. Both the cis-alkenes are introduced with excellent control by the reduction of a late-stage bis-alkyne intermediate. The synthetic disconnections are very amenable to analog preparation, and further modifications to the chemistry have allowed for scale-up and First in Man testing of this novel pro-resolution molecule.     

CABS‐NMR—De novo tool for rapid global fold determination from chemical shifts,residual dipolar couplings and sparse methyl‐methyl noes

Recent development of nuclear magnetic resonance (NMR) techniques provided new types of structural restraints that can be successfully used in fast and low‐cost global protein fold determination. Here, we present CABS‐NMR, an efficient protein modeling tool, which takes advantage of such structural restraints. The restraints are converted from original NMR data to fit the coarse grained protein representation of the C‐Alpha‐Beta‐Side‐group (CABS) algorithm. CABS is a Monte Carlo search algorithm that uses a knowledge‐based force field. Its versatile structure enables a variety of protein‐modeling protocols, including purely de novo folding, folding guided by restraints derived from template structures or, structure assembly based on experimental data. In particular, CABS‐NMR uses the distance and angular restraints set derived from various NMR experiments. This new modeling technique was successfully tested in structure determination of 10 globular proteins of size up to 216 residues, for which sparse NMR data were available. Additional detailed analysis was performed for a S100A1 protein. Namely, we successfully predicted Nuclear Overhauser Effect signals on the basis of low‐energy structures obtained from chemical shifts by CABS‐NMR. It has been observed that utility of chemical shifts and other types of experimental data (i.e. residual dipolar couplings and methyl‐methyl Nuclear Overhauser Effect signals) in the presented modeling pipeline depends mainly on size of a protein and complexity of its topology. In this work, we have provided tools for either post‐experiment processing of various kinds of NMR data or fast and low‐cost structural analysis in the still challenging field of new fold predictions. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Determination of Configuration and Conformation of a Reserpine Derivative with Seven Stereogenic Centers Using Molecular Dynamics with RDC-Derived Tensorial Constraints**

NMR-based determination of the configuration of complex molecules containing many stereocenters is often not possible using traditional NOE data and coupling patterns. Making use of residual dipolar couplings (RDCs), we were able to determine the relative configuration of a natural product containing seven stereocenters, including a chiral amine lacking direct RDC data. To identify the correct relative configuration out of 32 possible ones, experimental RDCs were used in three different approaches for data interpretation: by fitting experimental data based singular value decomposition (SVD) using a single alignment tensor and either (i) a single conformer or (ii) multiple conformers, or alternatively (iii) using molecular dynamics simulations with tensorial orientational constraints (MDOC). Even though in all three approaches one and the same configuration could be selected and clear discrimination between possible configurations was achieved, the experimental data was not fully satisfied by the methods based on single tensor approaches. While these two approaches are faster, only MDOC is able to fully reproduce experimental results, as the obtained conformational ensemble adequately covers the conformational space necessary to describe the molecule with inherent flexibility.     

Intramolecular cross-dehydrogenative coupling of benzaldehyde derivatives: A novel and efficient route to benzocyclic ketones

Benzocyclic ketones are not only found throughout many natural products and synthetic pharmaceutically active compounds but also used as versatile building blocks in organic synthesis. In view of their importance, many researchers have been working to explore novel and efficient synthetic routes for this class of carbonyl compounds. Recently, cross-dehydrogenative coupling reactions have emerged as one of the most versatile and powerful synthetic strategies to construct various carbon-carbon and carbon-heteroatom bonds. In this regard, direct acylation of (hetero)arenes with aldehydes through C(sp²)-H activation opened up a new page on the synthesis of the titled compounds. In this focus-review, we discuss the most representative and important reports on the synthesis of cyclic diaryl ketones through intramolecular cross-dehydrogenative coupling reactions of corresponding benzaldehydes with emphasis on the mechanistic aspects of the reactions.     

Optimized NMR Experiments for the Isolation of I=1/2 Manifold Transitions in Methyl Groups of Proteins

Optimized NMR experiments are developed for isolating magnetization belonging to the I=1/2 manifolds of ¹³CH₃ methyl groups in proteins, enabling the manipulation of the magnetization of a ¹³CH₃ moiety as if it were an AX (¹H-¹³C) spin-system. These experiments result in the same ‘simplification’ of a ¹³CH₃ spin-system that would be obtained from the production of {¹³CHD₂}-methyl-labeled protein samples. The sensitivity of I=1/2 manifold-selection experiments is a factor of approximately 2 less than that of the corresponding experiments acquired on {¹³CHD₂}-labeled methyl groups. The methodology described here is primarily intended for small-to-medium sized proteins, where the losses in sensitivity associated with the isolation of I=1/2 manifold transitions can be tolerated. Several NMR applications that benefit from simplification of the ¹³CH₃ (AX₃) spin-systems are described, with an emphasis on the measurements of methyl ¹H-¹³C residual dipolar couplings in a {¹³CH₃}-methyl-labeled deletion mutant of the human chaperone DNAJB6b, where modulation of NMR signal intensities due to evolution of methyl ¹H-¹³C scalar and dipolar couplings follows a simple cosine function characteristic of an AX (¹H-¹³C) spin-system, significantly simplifying data analysis.