Computational prediction of 1H and 13C chemical shifts: a useful tool for natural product, mechanistic, and synthetic organic chemistry

Hyperhelianthemones A-D: Polycyclic polyprenylated benzoylphloroglucinols from Hypericum helianthemoides

Phytochemical investigation of the n-hexane-soluble fraction of the aqueous ethanol extract of the aerial parts of Hypericum helianthemoides (Spach) Boiss. (Hypericaceae), furnished four undescribed polycylic polyprenylated benzoylphloroglucinols (PPBPs) 1-4, together with phytyl formate (5) and thirteen previously reported prenylated phloroglucinol derivatives, including yezo'otogirin C (6), hyperibrins A (7) and F (8), hyperibones G (9), J (10), La (11a)/Lb (11b), 7-epi-clusianone a (12a)/7-epi-clusianone b (12b), and hypermongones A (13), C (14), E (15), G (16), H (17), and sampsonione L (18). The structures of 1-4 were established by extensive 1D and 2D NMR spectral analysis as well as HREI-MS. The absolute configurations of the stereogenic carbons in 1 were established by X-ray crystallographic analysis, while the stereochemistry of 2 was assigned by quantum chemical calculation of its 1H and 13C NMR chemical shift values using DP4+ probability analysis. The isolated compounds were assayed for antileishmanial activity on Leishmania tropica and L. major parasites. Compounds 9 and 16 displayed activities against L. tropica, with IC50 values of 17.7 and 31.5 μM, respectively. Moreover, 9 was only active against L. major, with IC50 value of 34.2 μM.

Efficient prediction of the local electronic structure of ionic liquids from low-cost calculations

Understanding and predicting ionic liquid (IL) electronic structure is crucial for their development, as local, atomic-scale electrostatic interactions control both the ion-ion and ion-dipole interactions that underpin all applications of ILs. Core-level binding energies, EB(core), from X-ray photoelectron spectroscopy (XPS) experiments capture the electrostatic potentials at nuclei, thus offering significant insight into IL local electronic structure. However, our ability to measure XPS for the many thousands of possible ILs is limited. Here we use an extensive experimental XPS dataset comprised of 44 ILs to comprehensively validate the ability of a very low-cost and technically accessible calculation method, lone-ion-SMD (solvation model based on density) density functional theory (DFT), to produce high quality EB(core) for 14 cations and 30 anions. Our method removes the need for expensive and technically challenging calculation methods to obtain EB(core), thus giving the possibility to efficiently predict local electronic structure and understand electrostatic interactions at the atomic scale. We demonstrate the ability of the lone-ion SMD method to predict the speciation of halometallate anions in ILs.

Total Synthesis and Reconfirmation of the Absolute Configuration of (3R,4S)-6-Acetyl-3-hydroxy-7-methoxy-2,2-dimethylchroman-4-yl(Z)-2-methylbut-2-enoate Isolated from Ageratina grandifolia

Herein, we report the first total synthesis and confirmation of the absolute stereochemical configuration of a natural product isolated from Ageratina grandifolia as (3R,4S)-6-acetyl-3-hydroxy-7-methoxy-2,2-dimethylchroman-4-yl(Z)-2-methylbut-2-enoate. We have used readily available resorcinol as a starting material and well-established Jacobson's asymmetric epoxidation in achieving the total synthesis. During this process, we prepared its enantiomers and positional isomers, which may be useful for biological studies.

A Tricyclo[4.3.1]decane Diterpenoid Skeleton from Croton laui: Isolation and 1H NMR-Based Metabolomic Profiling

Lauicyclone A (1), a new skeletal diterpenoid characterized by an unprecedented carbon skeleton, represents the first reported natural product featuring a complex tricyclo[4.3.1]decane framework. Along with Lauicyclones B-E (2-5), all five compounds were isolated from Croton laui. Comprehensive spectroscopic analyses, quantum-chemical calculations, and X-ray diffractions were used to identify their structures. The antitumor mechanism of compound 1 was investigated using 1H NMR-based metabolomics.

NMR Crystallography Structure Determinations with 1H Chemical Shifts. GIPAW DFT Calculation Quality Can Be Substantially Degraded, but Nearly Identical Outputs Relative to Benchmark Computations Are Obtained: Why and So What?

Nuclear magnetic resonance (NMR) crystallography may be used in various solid-state structural characterization tasks. For organic compounds in this context, proton isotropic chemical shifts [δiso(1H)] are routinely used. It is typical to pair experimentally measured proton δiso values with δiso values that were computationally generated from crystal structure models. This can yield a δiso(1H) root-mean-squared deviation (RMSD) value for each crystal structure model. In this study, we monitor the way in which gauge including projector augmented wave (GIPAW) density functional theory (DFT) computations of 1H δiso values can be influenced by the quality of the computational input parameters. We consider 126 computationally generated (using crystal structure prediction, CSP) crystal structures for three molecules: cocaine (30 structures), flutamide (21 structures), and ampicillin (75 structures). The quality parameters selected are the plane wave energy cutoff (Ecut), and the k-point grid used to sample reciprocal (i.e., momentum) space. We also probe the utility of performing one-parameter and two-parameter linear mappings for transforming computed hydrogen isotropic magnetic shielding values (σiso) into computed δiso(1H) values. We find that both Ecut and the k-point grid can be degraded substantially (e.g., Ecut ∼ 25 Ry) and yet still produce very similar computed δiso(1H) values. We consider the mechanisms under GIPAW DFT that contribute to computed hydrogen σiso values to help understand this robustness: many contributions are zero or cancel out when converting σiso values to δiso(1H) values via the linear mapping. The robust nature of computed δiso(1H) values leads to consistent estimates of δiso(1H) RMSD values. It is then demonstrated using cocaine and flutamide that when δiso(1H) RMSD values are used in NMR crystallography tasks such as structure selection/determination, the quality of the GIPAW DFT computation can be severely degraded and still produce identical outcomes to those that used a more computationally intensive protocol. Ampicillin is selected as a practical example to probe how our findings might reasonably be applied in the structure determination of a complex organic molecule. We propose that relatively modest quality GIPAW DFT computations (i.e., Ecut = 35 Ry and a 1 × 1 × 1 k-point grid) may be used to first filter out obviously poor structure candidates. Subsequently, slightly higher quality GIPAW DFT computations can be used for structure selection/determination. Our findings indicate that it should be possible to, on average, reduce the computational resources required in such NMR crystallography tasks by approximately a factor of 3-4 in terms of CPU time.

Analytically Unsupervised Metabolomic Profile of the Premium Malgasy Pepper Voatsipérifery (Piper borbonense): Identification of Marker Components

The berries of Piper borbonense (Miq.) C. DC., a wild vine native to Madagascar, are prized for their distinctive aroma and flavor, considered superior to the ones of the domesticated peppers (P. nigrum L., P. longum L.). The scarcity of studies on P. borbonense, locally known as voatsipérifery, makes it difficult to secure the identity of its berries and complement its sensory analysis. This supports the need for a comprehensive phytochemical investigation utilizing complementary analytical techniques. Headspace gas chromatography highlighted differences in the "volatilome" of P. borbonense and P. nigrum, while an untargeted metabolomic analysis, based on the LC-MS2-based feature-based molecular networking tool, annotated different classes of compounds (monoterpenoids, sesquiterpenoids, monolignols, lignans, and piperamides). This analysis next guided the isolation of 40 fully characterized compounds, including two new natural products [the sesquiterpene lactone 4-hydroxyisogelehomanolide (29) and the hydroxycinnamate ester borbonensin (38)]. The phytochemical profile of voatsipérifery is remarkable for the presence of the nonvolatile monoterpene p-menth-5-en-1,2-diol (23), of sesquiterpene lactones, and of large amounts of sesamin (34), a marker trait that clearly distinguishes it from those of the cultivated peppers of commerce and was confirmed with a parallel investigation of P. nigrum. Overall, our study underlines the relevance of advanced metabolomic approaches to characterize the phytochemical profile of spices and identify specific marker compounds.

Miliseol A-D: new lanostane triterpenoids from Miliusa sessilis and their wound-healing activity

Investigation of the Miliusa sessilis hexane extract led to four novel lanostane triterpenoids, miliseol A-D (1-4) and five known compounds (5-9). Through extensive spectroscopic analyses, the new compounds were identified as (3β,23S)-23-methoxy-24-methylene-29-nor-5α-lanost-9(11)-en-3-ol (1), (3β,23S)-23-methoxy-24-methylene-5α-lanost-9(11)-en-3-ol (2), (3β,16β)-24-methylene-5α-lanost-9(11)-ene-3,16-diol (3), and (3β,24S)-24,241-epoxy-5α-lanost-9(11)-en-3-ol (4). The density functional theory (DFT) computations combined with a statistical procedure (DP4+) were used to identify the stereochemistry of compound 4. The X-ray crystallographic data was utilised to confirm the absolute configurations of compounds 1 and 3. The known compounds were isolated and elucidated as (+)-spathulenol (5), phytol (6), T-muurolol (7), β-sitosterol (8), and β-sitosterol-3-O-β-d-glucopyranoside (9) through spectroscopic analyses and comparison with the literature. Biological activity screening indicated that compound 1 promoted cell migration in the HaCaT cell line, with minimal cytotoxicity at the tested concentrations. This finding suggests its potential as an enhancing agent for skin wound healing.

Lignans with anti-inflammatory activity and protective effect on ATDC5 chondrocytes isolated from fresh Sambucus adnata Wall

Three previously unreported compounds (1-3), including two monoepoxidelignans (1-2) and one bisepoxylignan (3), together with nineteen known lignans (4-22), of which, fourteen compounds (7-17 and 20-22) were first reported from the genus Sambucus L. Their structures were comprehensively elucidated through spectroscopic methods, and their configurations were established by ECD calculations. Among the compounds, 3, 4, 5, 8, 9 and 15 could significantly reduce the contents of NO in IL-1β-stimulated ATDC5 chondrocytes. In addition, the IL-6 mRNA expression levels with 3, 4, 5, 8, 9, 13, 15, 16 and 18 were significantly reduced. Moreover, 15 displayed inhibitory activity against the catabolism of ATDC5 chondrocytes, and promoted the synthesis of COL II in IL-1β-stimulated ATDC5 chondrocytes, indicated that there were protective effects on ATDC5 chondrocytes. The binding sites were predicted by molecular docking. The aforementioned results indicated that these compounds may be the active substances in S. adnata wall. That exert anti-osteoarthritis effects.

Diverse Sesquiterpenoids From Michelia alba and Their Cytotoxic and Nitric Oxide Inhibitory Activities

Two previously undescribed sesquiterpenoids, including one germacrane sesquiterpenoid (1) and one guaiane sesquiterpenoid (2), were isolated and characterized from the branches and leaves of Michelia alba DC., along with 11 known sesquiterpenoids (3-13). The structures of the new compounds were elucidated using comprehensive high-resolution electrospray ionization mass spectroscopy, infrared, ultraviolet, and nuclear magnetic resonance analyses, with the absolute configurations being determined through single-crystal X-ray diffraction analysis and electronic circular dichroism calculations. Furthermore, this study also presented the proton and carbon-13 nuclear magnetic resonance data for 3 for the first time. All isolated compounds were evaluated for their cytotoxic effects against HL-60, A549, HepG2, MDA-MB-231, and SW480 cancer cell lines using the 3-(4,5-dimethylthiazol-2-yl)-5(3-carboxymethoxyphenyl)-2-(4-sulfopheny)-2H-tetrazolium bromide assay, as well as their ability to inhibit lipopolysaccharide-induced nitric oxide (NO) production in RAW264.7 macrophages. Notably, compound 7 showed remarkable cytotoxic activity against HL-60, HepG2, MDA-MB-231, and SW480 cancer cell lines, with half-maximal inhibitory concentration (IC50) values of 3.44 ± 0.19, 8.13 ± 0.43, 3.69 ± 0.14, and 3.50 ± 0.21 µM, respectively. Additionally, compounds 4, 7, and 13 demonstrated notable NO inhibitory activities, with IC50 values of 3.26 ± 0.04, 1.48 ± 0.07, and 8.54 ± 0.37 µM, respectively.

Novel monoterpene indole alkaloids from the fruits of Bousigonia mekongensis and their antiproliferative effects on HepG2 cells

Three new monoterpene indole alkaloids (1-3) together with eight known alkaloids (4-11) were isolated from the fruits of Bousigonia mekongensis. Compounds 1 and 2 were the first examples of akuammicine-Aspidosperma type bisindole alkaloids. Their structures were elucidated by NNR spectra, MS data and electronic circular dichroism (ECD) spectra. All compounds were evaluated for their cytotoxic activity against HepG2 liver cancer cells in vitro. Compounds 1, 4, 9 and 11 showed antiproliferative activity with IC50 values of 15.74 ± 1.37, 8.55 ± 0.97, 9.23 ± 1.11, and 0.80 ± 0.44 μM, respectively (0.51 ± 0.14 μM for the control, doxorubicin).

Six new compounds with neuroprotective activity from the leaves of Paeonia lactiflora Pall

Twenty constituents, three new terpenes named Paeoniterpene A-C (1-3), and three new fatty glycosides named Paeoniglycoside A-C (4-6) were isolated from the leaves of Paeonia lactiflora Pall. The structures of compounds 1-6 were identified using extensive spectroscopic methods, such as NMR, MS, CD, IR, and UV. Compounds 4-6 were characterized through quantum chemical calculations and DP4+ probability analysis, and ECD definitively confirmed their structures. Additionally, all compounds were assessed for their neuroprotective effects against H2O2-induced damage in PC 12 cells. Compounds 1-3, 7, 8, 11, and 12 could significantly improve H2O2-induced PC 12 injury.

IMPRESSION generation 2 - accurate, fast and generalised neural network model for predicting NMR parameters in place of DFT

Predicting 3D-aware Nuclear Magnetic Resonance (NMR) properties is critical for determining the 3D structure and dynamics, both stereochemical and conformational, of molecules in solution. Existing tools for such predictions are limited, being either relatively slow quantum chemical methods such as Density Functional Theory (DFT), or niche parameterised empirical or machine learning methods that only predict a single parameter type, often across only a limited chemical space. We present here IMPRESSION-Generation 2 (G2), a transformer-based neural network which can be used as a much faster alternative to high level DFT calculations in computational workflows of multiple classes of NMR parameter simultaneously, with time-savings of several orders of magnitude. IMPRESSION-G2 is the first system that simultaneously predicts all NMR chemical shifts, as well as scalar couplings for 1H, 13C, 15N and 19F nuclei up to 4 bonds apart, in a single prediction event starting from a 3D molecular structure. Rapid NMR predictions take <50 ms to predict on average ∼5000 chemical shifts and scalar couplings per molecule, which is approximately 106-times faster than DFT-based NMR predictions starting from a 3D structure. When combined with fast GFN2-xTB geometry optimisations to generate the 3D input structures themselves in just a few seconds, a complete workflow for NMR predictions on a new molecule is 103-104 times faster than a wholly DFT-based workflow for this. The accuracy of this multi-parameter predictor in reproducing DFT-quality results for a wide chemical space of organic molecules up to ∼1000 g mol-1 containing C, H, N, O, F, Si, P, S, Cl, Br exceeds that of existing state-of-the-art empirical or machine learning systems (∼0.07 ppm for 1H chemical shifts, ∼0.8 ppm for 13C chemical shifts, <0.15 Hz for 3 J HH scalar coupling constants) and, critically, it also demonstrates generalisability when tested against molecules from sources that are completely independent of its own training data. When compared to experimental NMR data for ∼5000 compounds, IMPRESSION-G2 gives results in minutes on a standard laptop which are almost indistinguishable from DFT results that took days on a large scale High Performance Computing system. This accuracy and speed of IMPRESSION-G2 coupled to GFN-xTB shows that it can be used to simply replace DFT for predicting 3D-aware NMR parameters inside the wide chemical space of its training data.

Unlocking Enol-Ugi-Derived Conformationally Restricted Peptidomimetic Motifs

The enol-Ugi condensation, a versatile multicomponent reaction, provides a rapid and efficient route to enamine peptidomimetics. In this study, we investigated the factors influencing the conformational behavior of three enol-Ugi adducts with distinct structural features. Through DFT calculations and NCI analysis, we identified that noncovalent interactions, including hydrogen bonds and π-π interactions, play a pivotal role in restricting conformational flexibility. While six-membered cyclic enamines 6 and 7 exhibited varying degrees of rotational freedom, the indanone-derived enamine 8 displayed a locked conformation resembling a retropeptidic turn. These findings highlight the potential of tailoring enol-Ugi adducts to mimic biologically relevant peptidic motifs, opening new avenues for drug discovery and design.

3,4-seco-Prenyllabdane sesterterpenoids and 3,4-seco-labdane diterpenoids with Zika virus inhibitory potential from Callicarpa nudiflora

Two rearranged prenyllabdane sesterterpenoids nudiflorawus A-B (1-2) with a previously unreported carbon skeleton, and five undescribed 3,4-seco-labdane diterpenoids, nudiflorawus C-G (3-7), along with two known diterpenoids (8-9), were isolated from the leaves of Callicarpa nudiflora. Compounds 1-2 exhibited the first example of 3,4-seco-prenyllabdane sesterterpenoids with a unique six-membered ring in the side chain. Their structures were established via various spectroscopic methods. NMR calculations with DP4+ analysis and ECD were further adopted to confirm their relative and absolute configurations. Compound 6 showed significant Zika virus (ZIKV) inhibitory activity with an EC50 value of 25.35 ± 0.742 μM. Western blot, quantitative real-time PCR, and immunofluorescence results further indicated that compound 6 could block ZIKV infection and replication by inhibiting the expression of ZIKV-envelope protein.

Structure Elucidation, Biosynthetic Gene Cluster Distribution, and Biological Activities of Ketomemicin Analogs in Salinispora

Pseudopeptides are attractive agents for protease inhibition due to their structural similarities to the natural substrates of these enzymes, as well as their enhanced stability and resistance to enzymatic degradation. We report three new ketomemicin pseudopeptides (1-3) from extracts of the marine actinomycete Salinispora pacifica strain CNY-498. Their constitution and relative configuration were elucidated using NMR, mass spectrometry, and quantum chemical calculations. Using GNPS molecular networking and publicly available Salinispora LCMS datasets, five additional ketomemicin analogs (4-8) were identified with ketomemicin production detected broadly across Salinispora species. The ketomemicin biosynthetic gene cluster (ktm) is highly conserved in Salinispora, occurring in 79 of 118 public genome sequences, including eight of the nine named species. Outside Salinispora, ktm homologs were detected in various genera of the phylum Actinomycetota that might encode novel ketomemicin analogs. Ketomemicins 1-3 were tested against a panel of eleven proteases, with 2 displaying moderate inhibitory activity. This study describes the first report of ketomemicin production by Salinispora cultures, the distribution of the corresponding biosynthetic gene cluster, and the protease inhibitory activity of new ketomemicin derivatives.

Renewable Thiophene Synthesis from Biomass Derived Methyl Levulinate and Elemental Sulfur

Heterocyclic compounds are pivotal building blocks in petrochemical and renewable fine chemical synthesis. The production of bio-based heterocyclic compounds is limited to furans and pyrroles, while thiophenes are rarely prepared from bio-based feedstock in a real renewable method. Current research on the "pseudo-renewable" thiophene synthesis strongly relies on unwieldy Lawesson's Reagent, which makes the process unsustainable. The present work describes for the first time that, two thiophene diesters were synthesized from biomass-derived methyl levulinate and elemental sulfur, a cheap, surplus by-product of the fossil industry that is causing potential pollution. The condensation and sulfurization steps in this process all involved multiple reaction pathways, leading to a much more intricate mechanism than previous research in its type. The footprint of sulfur in this system was tracked throughout the process, and the chemistry of this multi-step reaction provided a new orientation for the real sustainable thiophene synthesis based on elemental sulfur.

On the Use of Strong Proton Donors as a Tool for Overcoming Line Broadening in NMR: A Comment

Overcoming line broadening of labile protons and achieving high-resolution NMR spectra is crucial for the structural and conformational analysis of organic molecules. Recently, Ma et al. (Magn. Reson. Chem. 2024, 62, 198-207) demonstrated the effectiveness of 2,2,2-trifluoroacetic acid (TFA) in sharpening NMR signals for nitrogen-containing compounds which exhibit prototropic tautomerization or conformational isomerism using high molar ratio of [acids]/[solute] ~ 5 to 200. In this commentary, we provide an overview of earlier publications and highlight the extensive applications of TFA in enhancing NMR resolution across a variety of organic functional groups, with the use of very small ratios of [acids]/[solute] ~ 10-3 to 10-2. The prospects for the unequivocal structure analysis using labile protons as the starting point will be analyzed.

DFT Calculations of 1H and 13C NMR Chemical Shifts of Hydroxy Secondary Oxidation Products of Geometric Isomers of Conjugated Linoleic Acid Methyl Esters: Structures in Solution and Revision of NMR Assignments

Detailed DFT studies of 1H and 13C NMR chemical shifts of hydroxy secondary oxidation products of various geometric isomers of conjugated linolenic acids methyl esters are presented. Several low energy conformers were identified for model compounds of the central dienenol OH moiety, which were found to be practically independent on the various functionals and basis sets used. This greatly facilitated the minimization process of the geometric isomers of conjugated linolenic acids methyl esters. Several regularities of the literature experimental 1H and 13C chemical shifts were reproduced very accurately with the computational chemical shifts of the Gibbs low energy DFT optimized conformers, after a Boltzmann analysis. δ(13C) and δ(1H) of the methine CH-OH group are highly diagnostic for the trans/trans and cis/trans geometric isomerism of the adjacent double bond. δ(13C) of the -CH2- group adjacent to the terminal double bond of the conjugated system strongly depend on the cis/trans geometric isomerism of this bond and, thus, could be of importance in structural analysis. Ambiguities in the reported literature resonance assignments of olefinic carbons had been resolved. Computational δ(1H) and δ(13C) can be utilized for the identification of geometric isomerism and structural and conformational elucidation of hydroxy derivatives of conjugated linoleic acids and their ester derivatives.

SpectroIBIS: Automated Data Processing for Multiconformer Quantum Chemical Spectroscopic Calculations

Quantum chemical spectroscopic calculations have grown increasingly popular in natural products research for aiding the elucidation of chemical structures, especially their stereochemical configurations. These calculations have become faster with modern computational speeds, but subsequent data handling, inspection, and presentation remain key bottlenecks for many researchers. In this article, we introduce the SpectroIBIS computer program as a user-friendly tool to automate tedious tasks commonly encountered in this workflow. Through a simple graphical user interface, researchers can drag and drop Gaussian or ORCA output files to produce Boltzmann-averaged ECD, VCD, UV-vis and IR data, optical rotations, and/or 1H and 13C NMR chemical shifts in seconds. Also produced are formatted, publication-quality supplementary data tables containing conformer energies and atomic coordinates, saved to a DOCX file compatible with Microsoft Word and LibreOffice. Importantly, SpectroIBIS can assist researchers in finding common calculation issues by automatically checking for redundant conformers and imaginary frequencies. Additional useful features include recognition of conformer energy recalculations at a higher theory level, and automated generation of input files for quantum chemistry programs with optional exclusion of high-energy conformers. Lastly, we demonstrate the applicability of SpectroIBIS with spectroscopic calculations for five natural products. SpectroIBIS is open-source software available as a free desktop application (https://github.com/bbulcock/SpectroIBIS).

Cytotoxic Stilbenoids, Hetero- and Homodimers of Homoisoflavonoids from Prospero autumnale

An activity-guided isolation study on the EtOH extract prepared from the bulbs of Prospero autumnale yielded four new phenolic compounds, including a new stilbenoid (1), a new homoisoflavonoid derivative (8), a new homoisoflavonoid dimer (9), and an unprecedented homoisoflavone-stilbene heterodimer (10), together with six known (2-7) analogs. Their chemical structures were elucidated by spectroscopic analysis and theoretical NMR and ECD calculations. Compounds 9 and 10 are unique in their scaffolds. The in vitro cytotoxic activity of purified compounds was evaluated against eight tumor cell lines (HCT116, LoVo, DU145, PC3, HEP3B, HEPG2, MCF7, and MDA-MB-231) and one nontumor cell line (L929) by the MTS assay. Compounds 1, 2, 4, and 10 exhibited inhibition with IC50 values ranging from 8.2 to 37.6 μM. Cytotoxic cell death mechanisms were further investigated, indicating variability in apoptosis, necrosis, or cell cycle arrest.

TransPeakNet for solvent-aware 2D NMR prediction via multi-task pre-training and unsupervised learning

Nuclear Magnetic Resonance (NMR) spectroscopy is essential for revealing molecular structure, electronic environment, and dynamics. Accurate NMR shift prediction allows researchers to validate structures by comparing predicted and observed shifts. While Machine Learning (ML) has improved one-dimensional (1D) NMR shift prediction, predicting 2D NMR remains challenging due to limited annotated data. To address this, we introduce an unsupervised training framework for predicting cross-peaks in 2D NMR, specifically Heteronuclear Single Quantum Coherence (HSQC). Our approach pretrains an ML model on an annotated 1D dataset of 1H and 13C shifts, then finetunes it in an unsupervised manner using unlabeled HSQC data, which simultaneously generates cross-peak annotations. Our model also adjusts for solvent effects. Evaluation on 479 expert-annotated HSQC spectra demonstrates our model's superiority over traditional methods (ChemDraw and Mestrenova), achieving Mean Absolute Errors (MAEs) of 2.05 ppm and 0.165 ppm for 13C shifts and 1H shifts respectively. Our algorithmic annotations show a 95.21% concordance with experts' assignments, underscoring the approach's potential for structural elucidation in fields like organic chemistry, pharmaceuticals, and natural products.

Genomics-Driven Discovery of Plantariitin A, a New Lipopeptide in Burkholderia plantarii DSM9509

A significant number of silent biosynthetic gene clusters (BGCs) within the Burkholderia genome remain uncharacterized, representing a valuable opportunity for the discovery of new natural products. In this research, the recombineering system ETh1h2e_yi23, which facilitates recombination in Burkholderia and was developed in our previous study, was used for mining the BGCs of B. plantarii DSM9509. By using this recombineering system, the constitutive promoter was precisely inserted into the genome, resulting in the activation of the silent pla BGC, which led to the production of a new lipopeptide named plantariitin A. A distinctive characteristic of this lipopeptide is the incorporation of a non-proteinogenic amino acid residue, i.e., amino-1,2,3,6-tetrahydro-2,6-dioxo-4-pyrimidinepropanoic acid (ATDPP), which has not been identified in other natural products. A biological activity assay demonstrated that plantariitin A exhibits anti-inflammatory activity. This study further substantiates the notion that the in situ activation of silent BGCs is a crucial strategy for the discovery of new natural products within the genus Burkholderia. With the increasing availability of genomic data and the development of bioinformatics tools, Burkholderia is poised to emerge as a prominent source for the development of new lipopeptides.

Batrachopolyenes: Volatile Norsteroids from Femoral Scent Glands of Frogs

Steroid hormones are C18-C21-sterane derivatives, featuring the typical 6-6-6-5 ring system. Here we report on a novel C18-steroid ring system named batrachane with a contracted A-ring resulting in a 5-6-6-5 ring arrangement. The isolation, structural elucidation, and total synthesis of three members of the novel batrachopolyene family occurring in the tropical frog genus Odontobatrachus is reported. The batrachopolyenes represent an entirely new collection of volatile steroidal natural products produced by anuran amphibians. Alongside the contracted A-ring, each member contains a Δ16-17 double bond but differs in the central belt of the steroidal structure. To create these atypical structural features, syntheses featuring a combination of Breslow radical chain relay chlorination, Favorskii ring contraction, and Clemmensen reduction proved successful. The occurrence of such compounds in another distal anuran group, the Mantellinae, suggests a more widespread distribution of the batrachane-type compounds among frogs. The new structural steroid type raises questions concerning steroid biosynthesis and reception, as well as distribution in frogs in general and the structures of their hormones.

Two new compounds from the roots of Paeonia lactiflora Pall. and their anti-inflammatory effects

Two new compounds (1-2), together with six known ones (3-8), were isolated from the roots of Paeonia lactiflora Pall. The structures of two new compounds were elucidated based on HR-ESI-MS, UV, and NMR spectroscopic data analysis. Moreover, the anti-inflammatory activities of compounds 1-8 were determined using LPS-induced RAW 264.7 cells. Compounds 2, 6, and 8 showed the most potent inhibitory activities on NO production with IC50 values of 17.34 ± 1.5, 27.22 ± 1.3, and 14.79 ± 1.7 μM, respectively. Compounds 4 and 7 showed moderate inhibitory activities. Compounds 3 and 5 showed relatively weak inhibitory activities.

Bioactivity-guided isolation of potent inflammasome and mitochondria damage inhibitory diterpenoids from Orthosiphon wulfenioides

Orthosiphon wulfenioides is a medicinal plant to treat arthritis, vascular inflammation, edema, and dyspepsia. To explore the anti-inflammatory components and their mechanism of action, 12 previously undescribed highly oxidized diterpenes, wulfenioidones L-W (1-12), were isolated from O. wulfenioides by bioactivity orientation. Their structures were elucidated using HRESIMS, NMR, specific rotation, single-crystal X-ray diffraction, and ECD spectra analysis. Compounds 1-4 exhibited significant inhibition on LDH release by preventing macrophage J774A.1 pyroptosis. Compound 1 showed the most potent inhibitory effect with an IC50 value of 5.81 μM. It was revealed in the Western blot experiment that compound 1 not only significantly and dose-dependently decreased the activation of CASP1 and IL-1β, but also prevented GSDMD-FL from splitting into GSDMD-NT, the membrane pore-forming protein to release inflammatory factors, thus blocking the extracellular release of IL-1β. More interestingly, compound 1 not only blocked the activation of NLRP3 inflammasome, but also strikingly enhanced the orange fluorescence of JC-1 aggregates, thus showing the activity of maintaining mitochondrial membrane potential and reversing mitochondria damage.

DP4+-Based Stereochemical Reassignment and Total Synthesis of Polyenic Macrolactam Muanlactam

The total synthesis of the stereoisomer of muanlactam predicted by DP4+ calculations, which differed from that reported for the natural product on the relative configuration at C19, was completed, and the structure of the polyenic macrolactam was fully confirmed. Construction of the stereocenters involved the iterative enantio- and diastereoselective Krische's allylation reaction for the formal syn-1,3-diol and the addition of a propargylic Grignard reagent to Ellman's chiral nonracemic tert-butylsulfinamide for the enantiopure amine fragment. The conjugated triene and diene units were constructed by Suzuki-Miyaura cross-coupling reactions of the corresponding alkenylboronates and alkenyl iodides. Formation of the conjugated tetraene by Horner-Wadsworth-Emmons condensation of the functionalized partners was followed by challenging macrolactamization using hexafluorophosphate azabenzotriazole tetramethyluronium and N,N-diisopropylethylamine. The NMR data of the synthetic polyenic macrolactam matched those of the natural product, thus correcting the relative configuration of muanlactam at C19, which had previously been assigned by DP4.

Benchmark of Density Functional Theory in the Prediction of 13C Chemical Shielding Anisotropies for Anisotropic Nuclear Magnetic Resonance-Based Structural Elucidation

Density functional theory (DFT) calculations have emerged as a powerful theoretical toolbox for interpreting and analyzing the experimental nuclear magnetic resonance (NMR) spectra of chemical compounds. While DFT has been extensively used and benchmarked for isotropic NMR observables, the evaluation of the full chemical shielding tensor, which is necessary for interpreting residual chemical shift anisotropy (RCSA), has received much less attention, despite its recent applications in the structural elucidation of organic molecules. In this study, we present a comprehensive benchmark of carbon shielding anisotropies based on coupled cluster reference tensors taken from the NS372 benchmark data set. Additionally, we investigate the representation of the DFT-predicted shielding tensors, such as the eigenvalues and eigenvectors. Moreover, we evaluated how various DFT methods influence the discrimination of possible relative configurations using recently published ΔΔRCSA data for a set of structurally diverse natural products. Our findings demonstrate that accurate interpretation of RCSAs for configurational and conformational analysis is possible with semilocal DFT methods, which also reduce computational demands compared to hybrid functionals such as the commonly used B3LYP.

Herbicidal and Antibacterial Secondary Metabolites Isolated from the Nicotiana tabacum-Derived Endophytic Fungus Aspergillus japonicus TE-739D

Endophytic fungi possess a unique ability to produce abundant secondary metabolites, which play an active role in the growth and development of host plants. In this study, chemical investigations on the endophytic fungus Aspergillus japonicus TE-739D derived from the cultivated tobacco (Nicotiana tabacum L.) afforded two new polyketide derivatives, namely japoniones A (1) and B (2), as well as four previously reported compounds 3-6. Their chemical structures were elucidated by detailed spectroscopic analyses and quantum chemical calculations. In the herbicidal assays on the germination and radicle growth of Amaranthus retroflexus L. and Eleusine indica seeds, compound 1 was found to inhibit the germ and radicle elongation. Notably, compound 2 showed potent herbicidal activity against A. retroflexus L. germ elongation, with an IC50 value of 43.6 μg/mL, even higher than the positive control glyphosate (IC50 = 76.0 μg/mL). Moreover, compound 4 demonstrated strong antibacterial effects against the pathogens Bacillus cereus and Bacillus subtilis, with a comparable MIC value of 16 μg/mL to the positive control chloramphenicol. These findings indicate that the endophytic fungus A. japonicus TE-739D holds significant metabolic potential to produce bioactive secondary metabolites, which are beneficial, providing survival value to the host plants.

The interplay of density functional selection and crystal structure for accurate NMR chemical shift predictions

Ab initio chemical shift prediction plays a central role in nuclear magnetic resonance (NMR) crystallography, and the accuracy with which chemical shifts can be predicted relative to experiment impacts the confidence with which structures can be assigned. For organic crystals, periodic density functional theory calculations with the gauge-including projector augmented wave (GIPAW) approximation and the PBE functional are widely used at present. Many previous studies have examined how using more advanced density functionals can increase the accuracy of predicted chemical shifts relative to experiment, but nearly all of those studies employed crystal structures that were optimized with generalized-gradient approximation (GGA) functionals. Here, we investigate how the accuracy of the predicted chemical shifts in organic crystals is affected by replacing GGA-level PBE-D3(BJ) crystal geometries with more accurate hybrid functional PBE0-D3(BJ) ones. Based on benchmark data sets containing 132 13C and 35 15N chemical shifts, plus case studies on testosterone, acetaminophen, and phenobarbital, we find that switching from GGA-level geometries and chemical shifts to hybrid-functional ones reduces 13C and 15N chemical shift errors by ∼40-60% versus experiment. However, most of the improvement stems from the use of the hybrid functional for the chemical shift calculations, rather than from the refined geometries. In addition, even with the improved geometries, we find that double-hybrid functionals still do not systematically increase chemical shift agreement with experiment beyond what hybrid functionals provide. In the end, these results suggest that the combination of GGA-level crystal structures and hybrid-functional chemical shifts represents a particularly cost-effective combination for NMR crystallography in organic systems.

Naphpyrones A-H, Antibacterial Aromatic Polyketides Isolated from the Streptomyces coelicolor A3(2)/spi1 ΔspiH3

Staphylococcus aureus, a common foodborne pathogen, has a close association with agriculture and food. With the rapid emergence and widespread dissemination of antimicrobial resistance, efforts have been directed toward developing and studying new antimicrobial compounds to inhibit the growth of S. aureus and other foodborne pathogens, thereby preventing contamination and ensuring food safety. Herein, we reported eight new aromatic polyketides, naphpyrones A-H (1-8), from the heterologous expression strain Streptomyces coelicolor A3(2)/spi1 ΔspiH3. Their structures and absolute configurations were elucidated by extensive NMR, MS, theoretical NMR calculations, DP4+ probability analysis, Mosher's method, and ECD analyses. Notably, naphpyrone A (1) featured an unprecedented 6/6/6/6/5 neocyclic skeleton. Bioactivity evaluation revealed that compounds 1 and 2 exhibited antibacterial activity against S. aureus, with MIC values of 1 μg/mL and 4 μg/mL, respectively. These findings highlight the potential for screening and developing therapeutic agents from actinomycetes-derived aromatic polyketides against food pathogens.

DFT Approach for Predicting 13C NMR Shifts of Atoms Directly Coordinated to Pt: Scopes and Limitations

In this study, comparative analysis of calculated and experimental 13C NMR shifts for a wide range of model platinum complexes showed that, on the whole, the theory reproduces the experimental data well. The chemical shifts of carbon atoms directly bonded to Pt can be calculated well only within the framework of the fully relativistic matrix Dirac-Kohn-Sham (mDKS) level (R2 = 0.9973, RMSE = 3.7 ppm); however, for carbon atoms not bonded to metal, a more simple, non-relativistic approach can be used. Effective locally dense basis set schemes were developed for practical applications. The efficiency of the protocol is demonstrated using the example of the isomeric structure determination in case of several possible coordination modes.

Photocatalytic applications of covalent organic frameworks: synthesis, characterization, and utility

Photocatalysis has emerged as an energy efficient and safe method to perform organic transformations, and many semiconductors have been studied for use as photocatalysts. Covalent organic frameworks (COFs) are an established class of crystalline, porous materials constructed from organic units that are easily tunable. COFs importantly display semiconductor properties and respectable photoelectric behaviour, making them a strong prospect as photocatalysts. In this review, we summarize the design, synthetic methods, and characterization techniques for COFs. Strategies to boost photocatalytic performance are also discussed. Then the applications of COFs as photocatalysts in a variety of reactions are detailed. Finally, a summary, challenges, and future opportunities for the development of COFs as efficient photocatalysts are entailed.

Data Science Guiding Analysis of Organic Reaction Mechanism and Prediction

Advancements in synthetic organic chemistry are closely related to understanding substrate and catalyst reactivities through detailed mechanistic studies. Traditional mechanistic investigations are labor-intensive and rely on experimental kinetic, thermodynamic, and spectroscopic data. Linear free energy relationships (LFERs), exemplified by Hammett relationships, have long facilitated reactivity prediction despite their inherent limitations when using experimental constants or incorporating comprehensive experimental data. Data-driven modeling, which integrates cheminformatics with machine learning, offers powerful tools for predicting and interpreting mechanisms and effectively handling complex reactivities through multiparameter strategies. This review explores selected examples of data-driven strategies for investigating organic reaction mechanisms. It highlights the evolution and application of computational descriptors for mechanistic inference.

molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction

The construction, management, and analysis of large in silico molecular libraries is critical in many areas of modern chemistry. Herein, we introduce the MOLecular LIibrary toolkit, "molli", which is a Python 3 cheminformatics module that provides a streamlined interface for manipulating large in silico libraries. Three-dimensional, combinatorial molecule libraries can be expanded directly from two-dimensional chemical structure fragments stored in CDXML files with high stereochemical fidelity. Geometry optimization, property calculation, and conformer generation are executed by interfacing with widely used computational chemistry programs such as OpenBabel, RDKit, ORCA, NWChem, and xTB/CREST. Conformer-dependent grid-based feature calculators provide numerical representation and interface to robust three-dimensional visualization tools that provide comprehensive images to enhance human understanding of libraries with thousands of members. The package includes a command-line interface in addition to Python classes to streamline frequently used workflows. Parallel performance is benchmarked on various hardware platforms, and common workflows are demonstrated for different tasks ranging from optimized grid-based descriptor calculation on catalyst libraries to an NMR chemical shift prediction workflow from CDXML files.

Bridging pyrimidine hemicurcumin and Cisplatin: Synthesis, coordination chemistry, and in vitro activity assessment of a novel Pt(II) complex

In the upcoming decades, the incidence and mortality rates of cancer are expected to rise globally, with colorectal and prostate cancers among the most prevalent types. Despite advancements in molecular targeted therapy, platinum-based chemotherapies remain the cornerstone of treatment, especially for colorectal and prostate cancer, with oxaliplatin and cisplatin being extremely effective due to their DNA-targeting capabilities. In our pursuit of new platinum-based chemotherapeutics that are potentially less toxic and more effective, we have explored the combination of the Pt-binding groups of the diaminocyclohexane ring used in oxaliplatin, with the stable amino-pyrimidine hemicurcumin moiety. This new derivative exhibit improved stability in physiological conditions and increased solubility in aqueous media, demonstrating promising effects on cell proliferation of both colorectal and prostate cells. We report herein the complete synthesis and chemical characterization in solution of the new derivative [(1R,2R)-N1-(3-(4-((E)-2-(2-Amino-6-methylpyrimidin-4-yl)vinyl)-2-methoxyphenoxy) propyl) cyclohexane-1,2-diamine] (MPYD). Our analysis includes an examination of its acid-base equilibria, speciation and stability in physiological conditions. The synthesis and in situ formation of Pt(II) complexes were investigated by nuclear magnetic resonance spectroscopy, while density functional theory calculations were employed to elucidate the chemical structure in solution. Results on the biological activity were obtained through cell viability assays on different colorectal and prostate cell lines (HCT116, HT29, PC3 and LNCaP).

Structure elucidation, biosynthetic gene cluster distribution, and biological activities of ketomemicin analogs in Salinispora

We report three new ketomemicin pseudopeptides (1-3) from extracts of the marine actinomycete Salinispora pacifica strain CNY-498. Their constitution and relative configuration were elucidated using NMR, mass spectrometry, and quantum chemical calculations. Using GNPS molecular networking and publicly available Salinispora LCMS datasets, five additional ketomemicin analogs (4-8) were identified with ketomemicin production detected broadly across Salinispora species. The ketomemicin biosynthetic gene cluster (ktm) is highly conserved in Salinispora, occurring in 79 of 118 public genome sequences including eight of the nine named species. Outside Salinispora, ktm homologs were detected in various genera of the phylum Actinomycetota that might encode novel ketomemicin analogs. Ketomemicins 1-3 were tested against a panel of eleven proteases, with 2 displaying moderate inhibitory activity. This study describes the first report of ketomemicin production by Salinispora cultures, the distribution of the corresponding biosynthetic gene cluster, and the protease inhibitory activity of new ketomemicin derivatives.

Triantaspirols A-C and Paraphaeolactone Cs from Paraphaeosphaeria sp. KT4192: Sensitivity of CP3 in Distinguishing Close NMR Signals

Hybridized spirobisnaphthalene derivatives, triantaspirols A-C (1-3) and paraphaeolactones C1 and C2 (4 and 5), were identified from the culture broth of the fungus Paraphaeosphaeria sp. KT4192. The NMR spectra of 2 and 3, as well as 4 and 5, closely resembled each other, indicating that these were pairs of diastereomers. Although this NMR spectral resemblance made it challenging to distinguish their relative configurations, detailed analysis of the electronic circular dichroism (ECD) spectra and NOE correlations allowed us to deduce them. The CP3 metric with the DFT-based NMR chemical shifts was found to distinguish configurations of diastereomers in a highly sensitive and accurate manner that DP4 could not account for because of the very close chemical shift differences in the experimental NMR spectra. The reliability of this method was assessed using 23 published examples which could not be distinguished by DP4 protocol.

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.

Low-Scaling, Efficient and Memory Optimized Computation of Nuclear Magnetic Resonance Shieldings within the Random Phase Approximation Using Cholesky-Decomposed Densities and an Attenuated Coulomb Metric

An efficient method for the computation of nuclear magnetic resonance (NMR) shielding tensors within the random phase approximation (RPA) is presented based on our recently introduced resolution-of-the-identity (RI) atomic orbital RPA NMR method [Drontschenko, V. J. Chem. Theory Comput. 2023, 19, 7542-7554] utilizing Cholesky decomposed density type matrices and employing an attenuated Coulomb RI metric. The introduced sparsity is efficiently exploited using sparse matrix algebra. This allows for an efficient and low-scaling computation of RPA NMR shielding tensors. Furthermore, we introduce a batching method for the computation of memory demanding intermediates that accounts for their sparsity. This extends the applicability of our method to even larger systems that would have been out of reach before, such as, e.g., a DNA strand with 260 atoms and 3408 atomic orbital basis functions.

Conformational dependence of chemical shifts in the proline rich region of TAU protein

Nuclear magnetic resonance (NMR) is an important method for structure elucidation of proteins, as it is an easily accessible and well understood method. To characterize intrinsically disordered proteins (IDPs) using computational models it is often necessary to analyze and integrate calculated observables with measurements derived from solution NMR experiments. In this case study, we investigate whether and which chemical shifts of the proline-rich region of Tau protein (residues 210-240) offer information about the conformational state to distinguish two different microscopic conformers. Using multiple computational methods, the chemical shifts of these two conformationally distinct structures are calculated. The different methods are compared regarding their ability to compute chemical shifts that are sensitive to conformational change. The analysis of the data shows significant differences between the available methods and gives suggestions for an improved pathway for ensemble reweighting. Nevertheless, the variation in the chemical shifts which are predicted for configurations that are commonly considered to belong to the same conformation is such that this obscures a comparison between distinct conformations. Conformational sensitivity is found for up to ∼26% of calculated chemical shifts. It is found to be unrelated to the atom element and has a minor relationship with the change in the corresponding ϕ dihedral angle.

Influence of Selective Deoxyfluorination on the Molecular Structure of Type-2 N-Acetyllactosamine

N-Acetyllactosamine is a common saccharide motif found in various biologically active glycans. This motif usually works as a backbone for additional modifications and thus significantly influences glycan conformational behavior and biological activity. In this work, we have investigated the type-2 N-acetyllactosamine scaffold using the complete series of its monodeoxyfluorinated analogs. These glycomimetics have been studied by molecular mechanics, quantum mechanics, X-ray crystallography, and various NMR techniques, which have provided a comprehensive and complete insight into the role of individual hydroxyl groups in the conformational behavior and lipophilicity of N-acetyllactosamine.

Isolation, Structure Elucidation, and Biological Activity of the Selective TACR2 Antagonist Tumonolide and its Aldehyde from a Marine Cyanobacterium

The macrocyclic tumonolide (1) with enamide functionality and the linear tumonolide aldehyde (2) are new interconverting natural products from a marine cyanobacterium with a peptide-polyketide skeleton, representing a hybrid of apratoxins and palmyrolides or laingolides. The planar structures were established by NMR and mass spectrometry. The relative configuration of the stereogenically-rich apratoxin-like polyketide portion was determined using J-based configuration analysis. The absolute configuration of tumonolide (1) was determined by chiral analysis of the amino acid units and computational methods, followed by NMR chemical shift and ECD spectrum prediction, indicating all-R configuration for the polyketide portion, as in palmyrolide A and contrary to the all-S configuration in apratoxins. Functional screening against a panel of 168 GPCR targets revealed tumonolide (1) as a selective antagonist of TACR2 with an IC50 of 7.0 μM, closely correlating with binding affinity. Molecular docking studies established the binding mode and rationalized the selectivity for TACR2 over TACR1 and TACR3. RNA sequencing upon treatment of HCT116 colorectal cancer cells demonstrated activation of the pulmonary fibrosis idiopathic signaling pathway and the insulin secretion signaling pathway at 20 μM, indicating its potential to modulate these pathways.

Ether-Diol Ambiguity: An Inconspicuous Issue in the Structure Elucidation of Oxygenated Natural Products

Tertiary and allylic hydroxyl groups readily eliminate water during positive ion mode mass spectrometry and may show similar NMR spectra to their corresponding ethers. In a routine structure elucidation workflow, these factors can cause researchers to incorrectly assign diol moieties as ethers or vice versa, leading to inaccurate chemical structures. After facing this problem during our work on oxygenated sesquiterpenoids from a Fusarium sp. fungal strain, we became aware of this challenging issue. We examined the literature for oxygenated natural products bearing these functional groups, and with the aid of density functional calculations of NMR chemical shifts, we now report the structures of 15 natural products that should be revised. We further establish that derivatizing sub-micromolar amounts of alcohols to their sulfates can be used to distinguish these from their corresponding ethers using liquid chromatography negative ion mode mass spectrometry. Finally, we isolated lignoren/cyclonerodiol from the Fusarium sp. culture extract and supported its revised identity as cyclonerodiol using this sulfation approach. Our results suggest that ether-diol ambiguity could be a prevalent issue affecting the structure elucidation of oxygenated natural products and highlight the importance of using complementary techniques, such as sulfation with LC-(-)-ESI-MS or density functional calculations of NMR chemical shifts.

Phytotoxic Isocassadiene-Type Diterpenoids from Tomato Fusarium Crown and Root Rot Pathogen Fusarium oxysporum f. sp. radicis-lycopersici

Fusarium crown and root rot (FCRR) has emerged as a highly destructive soil-borne disease, posing a significant threat to the safe cultivation of tomatoes in recent years. The pathogen of tomato FCRR is Fusarium oxysporum f. sp. radicis-lycopersici (Forl). To explore potential phytotoxins from Forl, eight undescribed diterpenoids namely fusariumic acids A-H (1-8) were isolated. Their structures were elucidated by using spectroscopic data analyses, quantum chemical calculations, and X-ray crystallography. Fusariumic acids A (1) and C-H (3-8) were typical isocassadiene-type diterpenoids, while fusariumic acid B (2) contained a cage-like structure with an unusual 7,8-seco-isocassadiene skeleton. A biosynthetic pathway of 2 was proposed. Fusariumic acids A (1) and C-H (3-8) were further assessed for their phytotoxic effects on tomato seedlings at 200 μg/mL. Among them, fusariumic acid F (6) exhibited the strongest inhibition against the hypocotyl and root elongation of tomato seedlings, with inhibitory rates of 61.3 and 45.3%, respectively.

Electronic and Molecular Structures of a Series of Nickel Bis-1,1-Dithiolates

A series of homoleptic Ni bis-1,1-dithiolates, [Ni(S2C2RR')2]2- (R=CN, R'=CN, CO2Et, CONH2, Ph, Ph-4-Cl, Ph-4-OMe, Ph-4-NO2, Ph-3-CF3, Ph-4-CF3, Ph-4-CN; R=NO2, R'=H; R=R'=CO2Et) have been synthesized from the reaction of the alkali metal salt of the ligand and nickel chloride, and isolated as tetraphenylphosphonium or tetrabutylammonium salts. The complexes were characterized by X-ray crystallography, high-resolution mass spectrometry, and infrared (IR), nuclear magnetic resonance (NMR) and electronic absorption spectroscopies. The molecular structures show a rigidly square planar Ni(II) center linking two four-membered chelate rings whose dimensions are constant across the series. The electronic effect of the ligand substituent is revealed in the 13C NMR and electronic spectra, and corroborated by density functional calculations. Electron withdrawing groups deshield the low-field CS2 resonance, and the signature charge transfer band in the visible region is red-shifted. These observables have been accurately reproduced computationally, and revealed the Ni contribution to the ground state diminishes with decreasing electron withdrawing capacity of the ligand substituent. In contrast to 1,2-dithiolates, the redox inactivity afforded by 1,1-dithiolates stems from the smaller chelate ring and substantially reduced sulfur content that is key to stabilizing the radical form.

Quantum chemical package Jaguar: A survey of recent developments and unique features

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.

DFT investigation of coupling constant anomalies in substituted β-lactams

β-lactams are a chemically diverse group of molecules with a wide range of biological activities. Having recently observed curious trends in 2JHH coupling values in studies on this structural class, we sought to obtain a more comprehensive understanding of these diagnostic NMR parameters, specifically interrogating 1JCH, 2JCH, and 2JHH, to differentiate 3- and 4-monosubstituted β-lactams. Further investigation using computational chemistry methods was employed to explore the geometric and electronic origins for the observed and calculated differences between the two substitution patterns.

Antimicrobial metabolites from the marine-derived fungus Aspergillus sp. ZZ1861

Fungi from the genus Aspergillus are important resources for the discovery of bioactive agents. This investigation characterized the isolation, structural elucidation, and antimicrobial evaluation of 46 metabolites produced by the marine-derived fungus Aspergillus sp. ZZ1861 in rice solid and potato dextrose broth liquid media. The structures of these isolated compounds were determined based on their HRESIMS data, NMR spectral analyses, and data from ECD, NMR, and optical rotation calculations. Emericelactones F and G, 20R,25S-preshamixanthone, 20R,25R-preshamixanthone, phthalimidinic acid A, phthalimidinic acid B, aspergilol G, and 2-hydroxyemodic amide are eight previously undescribed compounds and (S)-2-(5-hydroxymethyl-2-formylpyrrol-1-yl) propionic acid lactone is reported from a natural resource for the first time. It is also the first report of the configurations of 25S-O-methylarugosin A, 25R-O-methylarugosin A, 5R-(+)-9-hydroxymicroperfuranone, and 5R-(+)-microperfuranone. Phthalimidinic acid A, phthalimidinic acid B, aspergilol G, and 2-hydroxyemodic amide have antifungal activity against Candida albicans with MIC values of 1.56, 3.12, 1.56, and 12.5 μg/mL, respectively, 20R,25S-preshamixanthone (MIC 25 μg/mL) shows antibacterial activity against Escherichia coli, and 20R,25R-preshamixanthone exhibits antimicrobial activity against all three tested pathogens of methicillin-resistant Staphylococcus aureus, E. coli, and C. albicans with MIC values of 50, 25, 25 μg/mL, respectively.

Phenolic Constituents with Glucose Uptake and GLUT4 Translocation Bioactivities from the Fruits of Cordia dichotoma

From the fruits of Cordia dichotoma, 11 new phenolic compounds, dichotomins A-K, were isolated, together with 19 known compounds. Through the analysis of detailed NMR data and HRESIMS data, the planar structures of all compounds were confirmed. Using NMR calculations, the absolute configuration of dichotomins A-K was elucidated by comparing their observed and computed electronic circular dichroism (ECD) spectra. Dichotomin H (8) and dichotomin I (9) were determined as two pairs of enantiomers. The enantiomers of compounds 8 and 9 were separated using chiral-phase high-performance liquid chromatography (HPLC), and the stereostructure of each enantiomer was determined by similarly calculating the ECD. Compounds 3, 5, 7, 17, 18, 23-25, and 27-30 increased glucose uptake by 1.04- to 2.85-folds at concentrations of 30 μg/mL. Further studies revealed that compounds 3 and 5 had a moderate effect on glucose transporter 4 (GLUT4) translocation activity in L6 cells. At 30 μg/mL, compound 3 significantly enhanced AMPK phosphorylation and GLUT4 expression. As a whole, compound 3 has the potential to be a drug candidate for the treatment of type 2 diabetes mellitus (T2DM).

Azaphilone pigments from the marine-derived Penicillium sclerotium UJNMF 0503 and their neuroprotective potential against H2O2-induced cell apoptosis through modulating PI3K/Akt pathway

Azaphilones represent a particular group of fascinating pigments from fungal source, with easier industrialization and lower cost than the traditional plant-derived pigments, and they also display a wide range of pharmacological activities. Herein, 28 azaphilone analogs, including 12 new ones, were obtained from the fermentation culture of a marine fungus Penicillium sclerotium UJNMF 0503. Their structures were elucidated by MS, NMR and ECD analyses, together with NMR and ECD calculations and biogenetic considerations. Among them, compounds 1 and 2 feature an unusual natural benzo[d][1,3]dioxepine ring embedded with an orthoformate unit, while 3 and 4 represent the first azaphilone examples incorporating a novel rearranged 5/6 bicyclic core and a tetrahydropyran ring on the side chain, respectively. Our bioassays revealed that half of the isolates exhibited neuroprotective potential against H2O2-induced injury on RSC96 cells, while compound 13 displayed the best rescuing capacity toward the cell viability by blocking cellular apoptosis, which was likely achieved by upregulating the PI3K/Akt signaling pathway.