The detailed chemical composition of crude oil in subsurface reservoirs provides important information about reservoir connectivity and can potentially play a very important role for the understanding of recovery processes. Relying on studying produced oil samples alone to understand the rock-fluid and fluid-fluid interactions is insufficient as the heavier polar components may be retained by tight reservoirs and not produced. These heavy and polar compounds that constitute the resin and asphaltene fractions of crude oil are typically present in low concentrations and yet are determining for the physical-chemical properties of the oil because of their polarity. In order to obtain a fingerprint analysis of oils including polar compounds from different wells, the oil content of drill cores has been extracted and analyzed. Infrared spectroscopy has been used to perform chemical fingerprinting of the oil extracted from drill cores sampled in different geographical locations of the Danish North Sea. Statistical analysis has been employed to identify the chemical differences within the sample set and explore the link between chemical composition and geographic location of the sample. A principal component analysis, based on spectral peak fitting in the 1800-1400 cm(-1) range, has allowed for statistical grouping of the samples and identified the primary chemical feature characteristic of these groups. Statistically significant differences in the quantities of polar oxygen- and nitrogen-containing compounds were found between the oil wells. The results of this analysis have been used as guidelines and reference to establish an express statistical approach based on the full-range infrared spectra for a further expansion of the sample set. The chemical information presented in this work is discussed in relation to oil fingerprinting and geochemical analysis.

This Chapter concerns a new method of backcalculating RDCs is outlined and shown to work very well for small molecules. The capability of the method to correctly estimate conformational spaces of small organic molecules is investigated.

This Chapter includes theory on how to obtain 3D structural information from NMR spectroscopy. Focus is on residual dipolar coupling constants (RDCs) which may be used to correlate internuclear vectors, independent of where the vectors are situated a given structure.

This book explores novel nuclear magnetic resonance (NMR) spectroscopy approaches for spatial structural elucidation of organic and natural compounds. It outlines novel NMR experimental methods to determine the stereochemistry and 3D structural space of potential anti-cancer agents in solution

In this Chapter new chiral polymers are utilized as alignment media, in order to investigate whether enantiomers may be discriminated by RDCs.

This Chapter serves as a very brief introduction to the history of NMR spectroscopy.

This Chapter includes theory on how to obtain 3D structural information from NMR spectroscopy. Focus is on two NMR observables which are useful in elucidations and calculations of 3D structures, namely nuclear Overhauser effect correlations (NOEs) (dipolar relaxation, through space) and J-coupling constants (indirect dipole-dipole couplings, through bonds).

This Chapter concerns the work on two novel NMR experiments, S3 HMBC and S3 HMBC hetero, which may be used to extract long range coupling constants (homo- and heteronuclear, respectively) for small organic molecules.

This Chapter concerns the extraction of long-range RDCs to increase the number of internuclear vectors available for RDC calculations of small molecules. To be able to do this is especially important for small molecules, due to an inherent lack of short-range internuclear vectors to include in calculations. The S3 HMBC experiment is used to extract the RDCs.

Throughout this Chapter, the structural spaces that a multitude of structures inhibits are determined from NOE’s and J-coupling constants. This allow for the elucidation of relative stereochemistry of natural compounds and investigation of 3D structures of synthetic and natural origin.

The use of molecular dynamics (MD) calculations to derive relative populations of conformers is highly sensitive to both timescale and parameterisation of the MD. Where these calculations are coupled with NOE data to determine the dynamics of a molecular system, this can present issues if these populations are thus relied upon. We present an approach that refines the highly accurate PANIC NMR methodology combined with clustering approaches to generate conformers, but without restraining the simulations or considering the relative population distributions generated by MD. Combining this structural sampling with NOE fitting, we demonstrate, for S-adenosylmethionine (aqueous solution at pH 7.0), significant improvements are made to the fit of populations to the experimental data, revealing a strong overall preference for the syn conformation of the adenosyl group relative to the ribose ring, but with less discrimination for the conformation of the ribose ring itself.

Marine algae from the genus Karlodinium are known to be involved in fish-killing events worldwide. Here we report for the first time the chemistry and bioactivity of a natural product from the newly described mixotrophic dinoflagellate Karlodinium armiger. Our work describes the isolation and structural characterization of a new polyhydroxy-polyene named karmitoxin. The structure elucidation work was facilitated by use of 13C enrichment and high-field 2D NMR spectroscopy, where 1H-13C long-range correlations turned out to be very informative. Karmitoxin is structurally related to amphidinols and karlotoxins; however it differs by containing the longest carbon-carbon backbone discovered for this class of compounds, as well as a primary amino group. Karmitoxin showed potent nanomolar cytotoxic activity in an RTgill-W1 cell assay as well as rapid immobilization and eventual mortality of the copepod Acartia tonsa, a natural grazer of K. armiger.

Dereplication of the secondary metabolite profile from the filamentous fungus Aspergillus brasiliensis, by High Performance Liquid Chromatography coupled with Diode Array Detection and High Resolution Mass Spectrometry, [1] lead to the discovery of a novel biomarker having a unique UV spectrum and elemental composition. Structural elucidation based on Nuclear Magnetic Resonance spectroscopy of the pure compound revealed an apolar polyketide or fatty acid derived secondary metabolite, possibly assembled from two entities, a C8 and a C12 chain, fused via a Claisen-like condensation and subsequent cyclisation to form a core lactone ring structure. The compound has been named brasenol. To our knowledge, only two other compunds contain a similar ring structure; namely alternaric acid from Alternaria solani and fujikurin D found in Fusarium fujikuroi [2,3]. Despite the apolar nature of the compound initial bioassay investigation have demonstrated antibacterial activity (MIC = 28.44 µg/mL) against methicillin-resistant Staphylococcus aureus MB5393. We are currently investigating whether other closely related black Aspergilli in section nigri could also be identified as brasenol producers. This will be followed by comparative bioinformatics analysis of their already sequenced genomes, setting the scene for construction of knock out mutants of potential candidate genes involved using CRISPR/Cas9 in A. brasiliensis [4]. This poster will summarize our efforts towards characterization of the biosynthetic pathway of this new compound.

A novel method, Spin-State-Selective (S3) HMBC hetero, for accurate measurement of heteronuclear coupling constants is introduced. The method extends the S3 HMBC technique for measurement of homonuclear coupling constants by appending a pulse sequence element that interchanges the polarization in 13C-1H methine pairs. This amounts to converting the spin-state selectivity from 1H spin states to 13C spin states in the spectra of long-range coupled 1H spins, allowing convenient measurement of heteronuclear coupling constants similar to other S3 or E.COSY-type methods. As usual in this type of techniques, the accuracy of coupling constant measurement is independent of the size of the coupling constant of interest. The merits of the new method are demonstrated by application to vinyl acetate, the alkaloid strychnine, and the carbohydrate methyl β-maltoside.

The identification of pairs of small peptides that recognize each other in water exclusively through electrostatic interactions is reported. The target peptide and a structure-biased combinatorial ligand library consisting of ≈78 125 compounds were synthesized on different sized beads. Peptide-peptide interactions could conveniently be observed by clustering of the small, fluorescently labeled target beads on the surface of larger ligand-containing beads. Sequences of isolated hits were determined by MS/MS. The interactions of the complex showing the highest affinity were investigated by a novel single-bead binding assay and by 2D NMR spectroscopy. Molecular dynamics (MD) studies revealed a putative mode of interaction for this unusual electrostatic binding event. High binding specificity occurred through a combination of topological matching and electrostatic and hydrogen-bond complementarities. From MD simulations binding also seemed to involve three tightly bound water molecules in the interface between the binding partners. Binding constants in the submicromolar range, useful for biomolecular adhesion and in nanostructure design, were measured.

A novel method, Spin-State-Selective (S(3)) HMBC, for accurate measurement of homonuclear coupling constants is introduced. As characteristic for S(3) techniques, S(3) HMBC yields independent subspectra corresponding to particular passive spin states and thus allows determination of coupling constants between detected spins and homonuclear coupling partners along with relative signs. In the presented S(3) HMBC experiment, spin-state selection occurs via large one-bond coupling constants ensuring high editing accuracy and unequivocal sign determination of the homonuclear long-range relative to the associated one-bond coupling constant. The sensitivity of the new experiment is comparable to that of regular edited HMBC and the accuracy of the J/RDC measurement is as usual for E.COSY and S(3)-type experiments independent of the size of the homonuclear coupling constant of interest. The merits of the method are demonstrated by an application to strychnine where thirteen J(HH) coupling constants not previously reported could be measured.

Investigation of the chemical profile of the industrially important black filamentous fungus Aspergillus aculeatus by UHPLC-DAD-HRMS and subsequent dereplication has led to the discovery of several novel compounds. Isolation and extensive 1D and 2D NMR spectroscopic analyses allowed for structural elucidation of a dioxomorpholine, a unique okaramine, an aflavinine and three novel structures of mixed biosynthetic origin, which we have named aculenes A–C. Moreover, known analogues of calbistrins, okaramines and secalonic acids were detected. All novel compounds were tested for antifungal activity against Candida albicans, however all showed only weak or no activity. Aspergillus aculeatus IBT 21030 was additionally shown to be capable of producing sclerotia. Examination of the sclerotia revealed a highly regulated production of metabolites in these morphological structures.

Natural, nonribosomal cyclotetrapeptides have traditionally been a rich source of inspiration for design of potent histone deacetylase (HDAC) inhibitors. We recently disclosed the total synthesis and full HDAC profiling of the naturally occurring azumamides ( J. Med. Chem. 2013 , 56 , 6512 ). In this work, we investigate the structural requirements for potent HDAC inhibition by macrocyclic peptides using the azumamides along with a series of unnatural analogues obtained through chemical synthesis. By solving solution NMR structures of selected macrocycles and combining these findings with molecular modeling, we pinpoint crucial enzyme-ligand interactions required for potent inhibition of HDAC3. Docking of additional natural products confirmed these features to be generally important. Combined with the structural conservation across HDACs 1-3, this suggests that while cyclotetrapeptides have provided potent and class-selective HDAC inhibitors, it will be challenging to distinguish between the three major class I deacetylases using these chemotypes.