Conformational Sampling in Computational Studies of Natural Products: Why Is It Important?

Conformational sampling is a vital component of a reliable computational chemistry investigation. With the aim of illustrating the importance of conformational sampling, and building awareness among new practitioners, we present a series of case studies that show how the quality and reliability of computational studies depend on undertaking a thorough conformer search. The examples are drawn from the most common types of research questions in natural products chemistry, but the fundamental principles apply more generally to computational studies of molecular structure and behavior in any field of chemistry.

Cryo-ultramicrotomy and Mass Spectrometry Imaging Analysis of Nudibranch Microstructures.

In this paper, we investigate the presence of latrunculin A in the outer rim of a nudibranch and show that by combining ultrathin cryosection methods with MALDI MSI we can achieve improved lateral ( and ) resolution and very high resolution in the dimension by virtue of the ultrathin 200 nm thin cryosections. We also demonstrate that a post ionization laser increases sensitivity. Recent advances in MALDI source design have improved the lateral resolution ( and ) and sensitivity during MSI.

Expanding the Repertoire of Spongian-16-One Derivatives in Australian Nudibranchs of the Genus and Evaluation of Their Anatomical Distribution.

Extracts of the mantle and viscera of the Indo-Pacific nudibranchs and sp. 1 afforded 11 new diterpenoids (-), all of which possess a tetracyclic spongian-16-one scaffold with extensive oxidation at C-6, C-7, C-11, C-12, C-13, and/or C-20. The structures and relative configuration were investigated by NMR experiments, while X-ray crystallography provided the absolute configuration of , including a 2' configuration for the 2-methylbutanoate substituent located at C-7.

Weapons or deterrents? Nudibranch molluscs use distinct ecological modes of chemical defence against predators.

Defensive chemicals are used by plants and animals to reduce the risk of predation through different mechanisms, including toxins that cause injury and harm (weapons) and unpalatable or odiferous compounds that prevent attacks (deterrents). However, whether effective defences are both toxins and deterrents, or work in just one modality is often unclear. In this study, our primary aim was to determine whether defensive compounds stored by nudibranch molluscs acted as weapons (in terms of being toxic), deterrents (in terms of being distasteful) or both.

The Validity of Brine Shrimp (Artemia Sp.) Toxicity Assays to Assess the Ecological Function of Marine Natural Products.

Many organisms employ toxic compounds for protection against predators. To understand the effectiveness of such compounds, chemoecological studies often use brine shrimp (Artemia spp.) as a model organism instead of more ecologically relevant species.

Lipidomics reveals associations between rice quality traits.

Introduction: Lipids are a diverse group of macromolecules that occur in rice grains and are known to impact rice grain properties. Identifying the relationships between specific lipids and traits of quality is important to improve varietal selection for high quality rice.

Objectives: Using untargeted lipidomics, this study aims to understand the role of lipids on different traits of quality by identifying the genotypic effect of lipids and their impact on traits of cooking and eating quality of a rice mapping population.

Dynamic NMR and Computational Studies Inform the Conformational Description of Dendrillane Terpenes from the Nudibranch .

Two new oxygenated terpenes ( and ) have been characterized from the Australian nudibranch . Broadened H NMR signals, together with the absence of individual carbon NMR signals, complicated analysis of 5,9-epoxydendrillolide A (); increasing the temperature to 323 K revealed the missing NMR signals. Low-temperature H NMR experiments provided an activation barrier of ∼15 kcal mol and, together with DFT calculations, supported interconversion of a twist chair conformer with two different chair conformers.

Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Correction for 'The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research' by James B. McAlpine et al., Nat.

Elucidation of Relative and Absolute Configurations of Highly Rearranged Diterpenoids and Evidence for a Putative Biosynthetic Intermediate from the Australian Nudibranch Goniobranchus geometricus.

A diterpene (1), previously isolated from a Japanese marine sponge, together with two undescribed (2, 3) diterpenes with highly rearranged carbon skeletons have been characterized from the Australian nudibranch species Goniobranchus geometricus. The structures and relative configuration were determined by spectroscopic analyses informed by detailed molecular modeling, as well as by DFT, DP4, and coupling constant predictions. A 13 R,14 R configuration was determined for secoshahamin (1) by chemical correlation with 12-desacetoxyshahamin C (4) and 12-desacetoxypolyrhaphin A (5); each metabolite (1, 4, and 5) was subjected to saponification and lactonization, yielding the same δ-lactone product (6).

Cytotoxic Spiroepoxide Lactone and Its Putative Biosynthetic Precursor from .

Epoxygoniolide-1 (), possessing spiroepoxide lactone, enal, and masked dialdehyde functionalities, has been characterized from the conspicuously patterned mollusc . Its relative configuration was investigated by spectroscopic analyses, molecular modeling, and density functional theory calculations. The biosynthesis of may involve rearrangement of a diterpene framework, providing a precursor to cometabolite gonioline (), followed by C-C bond cleavage (via Grob or P450 mechanism).

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

Toxicity and taste: unequal chemical defences in a mimicry ring.

Mimicry of warning signals is common, and can be mutualistic when mimetic species harbour equal levels of defence (Müllerian), or parasitic when mimics are undefended but still gain protection from their resemblance to the model (Batesian). However, whether chemically defended mimics should be similar in terms of toxicity (i.e.

Distribution of Defensive Metabolites in Nudibranch Molluscs.

Many plants and animals store toxic or unpalatable compounds in tissues that are easily encountered by predators during attack. Defensive compounds can be produced de novo, or obtained from dietary sources and stored directly without selection or modification, or can be selectively sequestered or biotransformed. Storage strategies should be optimized to produce effective defence mechanisms but also prevent autotoxicity of the host.

Antitubercular and Cytotoxic Chlorinated seco-Cyclohexenes from Uvaria alba.

Two new chlorine-containing polyoxygenated seco-cyclohexenes, albanols A (1) and B (2), along with the oxepinone metabolite grandiuvarone (3) were isolated from the endemic Philippine Annonaceae plant Uvaria alba. Both new compounds exhibited modest antitubercular activity. Compound 1 showed cytostatic activity (ranging from 1-50 μM) against HeLa cells and weak antiproliferative activity against HUVEC and K-562 cells with GI values of 106 and 81 μM, respectively.

Catalyst-Controlled Stereoselective Synthesis Secures the Structure of the Antimalarial Isocyanoterpene Pustulosaisonitrile-1.

Three new isocyanoditerpenes (5-7) have been characterized from Australian specimens of the nudibranch Phyllidiella pustulosa. The planar structure and (3R,6S,7R) absolute configuration of pustulosaisonitrile-1 were deduced by spectroscopic analyses at 900 MHz informed by molecular modeling, DFT calculations, and computational NMR chemical shift predictions and by comparison of experimental electronic circular dichroism (ECD) data with TDDFT-ECD calculations for the truncated model compound 8. A catalyst-controlled enantio- and diastereoselective total synthesis of the two most likely diastereomeric candidates for the structure of 5 solidified its (3R,6S,7R,10S,11R,14R) absolute configuration.

New sesquiterpenoid isonitriles from three species of phyllidid nudibranchs.

Chemical investigation of the two nudibranch species Phyllidiella pustulosa and Phyllidia ocellata collected in Queensland, Australia, provided new stereoisomers of 4-isocyano-9-amorphene (1) and of 10-isocyano-4-amorphene (2), respectively. A specimen of Phyllidia picta collected from Bali, Indonesia, contained the axane sesquiterpenoids pictaisonitrile-1 (3) and pictaisonitrile-2 (4). The planar structures were elucidated using 1D and 2D NMR spectroscopy, while relative configurations were established using NOESY correlations, coupling constant data, and comparison with literature data.

Quality evaluation, fatty acid analysis and untargeted profiling of volatiles in Cambodian rice.

This study provides the first investigation of the physical traits, pasting properties and volatile compounds of Cambodian rice cultivars, including traditional, improved, and improved traditional varieties, allowing for their differentiation as high and low quality rice. Analysis of the grain quality traits illustrates interesting features of traditional varieties and correlations between traits that assist with understanding texture. Untargeted profiling of volatile compounds shows that high quality fragrant varieties not only contain 2-acetyl-1-pyrroline but also several other compounds, including aldehydes, alcohols and 2-alkylfurans that contribute to overall aroma.

Stabilizing selection on individual pattern elements of aposematic signals.

Warning signal variation is ubiquitous but paradoxical: low variability should aid recognition and learning by predators. However, spatial variability in the direction and strength of selection for individual elements of the warning signal may allow phenotypic variation for some components, but not others. Variation in selection may occur if predators only learn particular colour pattern components rather than the entire signal.

Metabolomics and genomics combine to unravel the pathway for the presence of fragrance in rice.

Since it was first characterised in 1983, 2-acetyl-1-pyrroline (2AP) has been considered to be the most important aroma compound in rice. In this study, we show four other amine heterocycles: 6-methyl, 5-oxo-2,3,4,5-tetrahydropyridine (6M5OTP), 2-acetylpyrrole, pyrrole and 1-pyrroline, that correlate strongly with the production of 2AP, and are present in consistent proportions in a set of elite aromatic rice varieties from South East Asia and Australia as well as in a collection of recombinant inbred lines (RILs) derived from indica Jasmine-type varieties, Australian long grain varieties (temperate japonica) and Basmati-type rice (Grp V). These compounds were detected through untargeted metabolite profiling by two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOF-MS), and their identity were confirmed by comparison with authentic standards analysed using gas chromatography mass spectrometry (GC-MS) and High Resolution GC × GC-TOF-MS (GC × GC HRT-4D).

Taste and smell in aquatic and terrestrial environments.

Covering: up to 2017The review summarizes results up to 2017 on chemosensory cues occurring in both aquatic and terrestrial environments. The chemicals are grouped by their physicochemical properties to compare their potential mobility in the different media. In contrast to what is widely asserted in the literature, the report emphasizes that living organisms encounter and sense molecules of various degrees of solubility and volatility both on land and in aquatic environments.

Revision of the Structure of Acremine P from a Marine-Derived Strain of Acremonium persicinum.

The previously published structure of the fungal metabolite acremine P is revised by re-evaluation of chemical shift values and NOESY data, and by DFT calculations.

Volatile secondary metabolites as aposematic olfactory signals and defensive weapons in aquatic environments.

Olfaction is considered a distance sense; hence, aquatic olfaction is thought to be mediated only by molecules dissolved in water. Here, we challenge this view by showing that shrimp and fish can recognize the presence of hydrophobic olfactory cues by a "tactile" form of chemoreception. We found that odiferous furanosesquiterpenes protect both the Mediterranean octocoral and its specialist predator, the nudibranch gastropod , from potential predators.

Spongian-16-one Diterpenes and Their Anatomical Distribution in the Australian Nudibranch Goniobranchus collingwoodi.

Six new (1-6) spongian-16-one analogues have been characterized from the Australian nudibranch species Goniobranchus collingwoodi, along with four known spongian-16-one derivatives. The structures and relative configuration were suggested by spectroscopic analyses informed by molecular modeling. Dissection of animal tissue revealed that the mantle and viscera differ in their terpene composition.

The Sequestration of Oxy-Polybrominated Diphenyl Ethers in the Nudibranchs Miamira magnifica and Miamira miamirana.

A series of oxy-polybrominated diphenyl ethers (O-PBDEs) has been isolated from the extracts of and collected from Queensland, Australia. sequesters the new OH-PBDE and six known OH-PBDEs containing four to six bromines (-). also accumulates known tribromo- and tetrabromo OMe-PBDEs - in both mantle and viscera tissues.