Scientific Deep Machine Learning Concepts for the Prediction of Concentration Profiles and Chemical Reaction Kinetics: Consideration of Reaction Conditions.

Emerging concepts from scientific deep machine learning such as physics-informed neural networks (PINNs) enable a data-driven approach for the study of complex kinetic problems. We present an extended framework that combines the advantages of PINNs with the detailed consideration of experimental parameter variations for the simulation and prediction of chemical reaction kinetics. The approach is based on truncated Taylor series expansions for the underlying fundamental equations, whereby the external variations can be interpreted as perturbations of the kinetic parameters. Accordingly, our method allows for an efficient consideration of experimental parameter settings and their influence on the concentration profiles and reaction kinetics. A particular advantage of our approach, in addition to the consideration of univariate and multivariate parameter variations, is the robust model-based exploration of the parameter space to determine optimal reaction conditions in combination with advanced reaction insights. The benefits of this concept are demonstrated for higher-order chemical reactions including catalytic and oscillatory systems in combination with small amounts of training data. All predicted values show a high level of accuracy, demonstrating the broad applicability and flexibility of our approach.

Comparison of different density functional theory methods for the calculation of vibrational circular dichroism spectra.

The determination of the absolute configuration (AC) of an organic molecule is still a challenging task for which the combination of spectroscopic with quantum-mechanical methods has become a promising approach. In this study, we investigated the accuracy of DFT methods (480 overall combinations of 15 functionals, 16 basis sets, and 2 solvation models) to calculate the VCD spectra of six chiral organic molecules in order to benchmark their capability to facilitate the determination of the AC.

A New Bacterial Adenosine-Derived Nucleoside as an Example of RNA Modification Damage.

The fields of RNA modification and RNA damage both exhibit a plethora of non-canonical nucleoside structures. While RNA modifications have evolved to improve RNA function, the term RNA damage implies detrimental effects. Based on stable isotope labelling and mass spectrometry, we report the identification and characterisation of 2-methylthio-1,N6-ethenoadenosine (ms2 ϵA), which is related to 1,N6-ethenoadenine, a lesion resulting from exposure of nucleic acids to alkylating chemicals in vivo. In contrast, a sophisticated isoprene labelling scheme revealed that ms2 ϵA biogenesis involves cleavage of a prenyl moiety in the known transfer RNA (tRNA) modification 2-methylthio-N6-isopentenyladenosine (ms2 i6 A). The relative abundance of ms2 ϵA in tRNAs from translating ribosomes suggests reduced function in comparison to its parent RNA modification, establishing the nature of the new structure in a newly perceived overlap of the two previously separate fields, namely an RNA modification damage.

Mimonoside D: a new triterpenoid saponin from Mimosa diplotricha Sauvalle (Fabaceae).

A new triterpenoid saponin (Mimonoside D: 3-O-α-L-arabinopyranosyl-3ß-hydroxyolean-12-en-28-oic acid 28-O-ß-D-xylopyranosyl-(1→2)-ß-D- glucopyranoside ester (1)) was isolated from the aerial parts of Mimosa diplotricha Sauvalle together with nine known compounds: 7,4'-dihydroxyflavone (2), kaempferol (3), lupeol (4), betulinic acid (5), ß-sitosterol (6), ß-sitosterol-3-O-ß-D-glucopyranoside (7), lutein (8), 5,2'-dihydroxy-7,4',5'-trimethoxyflavone (9) and vitexin (10). Their structures were elucidated on the basis of spectroscopic (1 D and 2 D nuclear magnetic resonance) and high-resolution mass spectrometric data as well as by comparison of their spectral data with those of related compounds. Compounds 2, 7 and 8 had already been isolated from M. diplotricha, while compounds 3, 4, 5 and 6 have been isolated from other Mimosa species. Compound 2 moderately inhibited Proteus mirabilis (MIC = 32 µg/mL), weakly inhibited Pseudomonas aeruginosa (MIC = 64 µg/mL) and very weakly inhibited Staphylococcus aureus (MIC = 128 µg/mL) and Enterococus faecalis (MIC = 128 µg/mL).

Hepatoprotective effects of extracts, fractions and compounds from the stem bark of Pentaclethra macrophylla Benth: Evidence from in vitro and in vivo studies.

AIM: To identify the bioactive hepatoprotective components of the ethanol extract of Pentaclethra macrophylla stem bark using in vitro and in vivo approaches. METHODS: The bioguided-fractionation of the ethanol extract was based on the substances' capacity to prevent in vitro, the lipid peroxidation of hepatocytes' membranes induced by hydrogen peroxide. For the in vivo hepatoprotective test, mice were treated orally with the ethyl acetate (EtOAc) fraction of the ethanol extract at doses of 50 and 75 mg/kg/day for one week and subjected to d-galactosamine/lipopolysaccharide (GaIN/LPS)-induced hepatotoxicity. Blood samples were collected for alanine aminotransferase (ALAT), aspartate aminotransferase (ASAT), TNF-α and IL-1ß assays. The liver was harvested for histological and biochemical (proteins, glutathione (GSH), catalase and superoxide dismutase (SOD)) analysis. RESULTS: The ethanol extract and fractions induced concentration-dependent inhibition of lipid peroxidation (IC50: 3.21-48.90 µg/mL) greater than that of silymarin (IC50: 117.4 µg/mL). The purification of the sub-fractions of EtOAc fraction yielded: (7R)-7-hydroxyhexacosanoic acid (1), (7R)-1-(7-hydroxyhexacosanoyl) glycerol (2), bergenin (3), 11-O-galloylbergenin (4), 2-hydroxymethyl-5-(2-hydroxypropan-2-yl)phenol (5), ß-sitosterol 3-O-ß-d-glucopyranosyl (6) and ß-sitosterol (7)), among which 11-O-galloylbergenin (IC50:1.8 µg/mL) was the most effective. The EtOAc fraction significantly reduced the serum level of ALAT, ASAT and TNF-α in vivo. This EtOAc fraction increased the liver protein content and protected the liver against structural damages, but did not boost the endogenous antioxidant parameters. CONCLUSION: The stem bark of Pentaclethra macrophylla possesses hepatoprotective effects that may result from its capacity to inhibit lipid peroxidation and could be attributed to its active components 3, 4 and 2.

Hantzsch Ester-Mediated Photochemical Transformations in the Ketone Series: Remote C(sp3)-H Arylation and Cyclopentene Synthesis through Strain Release.

A metal-free Hantzsch ester-mediated synthesis of cyclopentenylketones as well as γ-hetarylketones starting from ketocyclopropanes under eco-friendly conditions was developed. The versatility of the developed conditions is shown by reacting ketocyclopropanes in both a formal [3 + 2] cycloaddition with terminal alkynes (further investigated using theoretical calculations) and a radical C-C-coupling with cyanopyridines. The newly developed methodologies were later on utilized as a downstream reaction for photogenerated cyclopropanes combining UV and visible light photochemistry. Following this procedure, a UV-driven Norrish-Yang-type reaction induces the ring strain of the intermediates, which serves as activation energy for the subsequent ring transformation.

Photoredox-Catalyzed Four-Component Reaction for the Synthesis of Complex Secondary Amines.

The one-pot sulfonylation/aminoalkylation of styrene derivatives furnishing substituted γ-sulfonylamines was accomplished through a photoredox-catalyzed four-component reaction. Besides one molecule of water and the sodium counterion of the sulfinate, all atoms of the starting materials are transferred to the final product, rendering this process highly atom-efficient. The operationally simple protocol allows for the simultaneous formation of three new single bonds (C-S, C-N, and C-C) and therefore grants rapid access to structurally diverse products.

New Cysteine Protease Inhibitors: Electrophilic (Het)arenes and Unexpected Prodrug Identification for the Trypanosoma Protease Rhodesain.

Electrophilic (het)arenes can undergo reactions with nucleophiles yielding π- or Meisenheimer (σ-) complexes or the products of the SNAr addition/elimination reactions. Such building blocks have only rarely been employed for the design of enzyme inhibitors. Herein, we demonstrate the combination of a peptidic recognition sequence with such electrophilic (het)arenes to generate highly active inhibitors of disease-relevant proteases. We further elucidate an unexpected mode of action for the trypanosomal protease rhodesain using NMR spectroscopy and mass spectrometry, enzyme kinetics and various types of simulations. After hydrolysis of an ester function in the recognition sequence of a weakly active prodrug inhibitor, the liberated carboxylic acid represents a highly potent inhibitor of rhodesain (Ki = 4.0 nM). The simulations indicate that, after the cleavage of the ester, the carboxylic acid leaves the active site and re-binds to the enzyme in an orientation that allows the formation of a very stable π-complex between the catalytic dyad (Cys-25/His-162) of rhodesain and the electrophilic aromatic moiety. The reversible inhibition mode results because the SNAr reaction, which is found in an alkaline solvent containing a low molecular weight thiol, is hindered within the enzyme due to the presence of the positively charged imidazolium ring of His-162. Comparisons between measured and calculated NMR shifts support this interpretation.

Making natural products from renewable feedstocks: back to the roots?

Covering: up to mid-2019 This review highlights the utilization of biomass-derived building blocks in the total synthesis of natural products. An overview over several renewable feedstock classes, namely wood/lignin, cellulose, chitin and chitosan, fats and oils, as well as terpenes, is given, covering the time span from the initial beginning of natural product synthesis until today. The focus is put on the origin of the employed carbon atoms and on the nature of the complex structures that were assembled therefrom. The emerging trend of turning away from petrochemically derived starting materials back to bio-based resources, just as seen in the early days of total synthesis, shall be demonstrated.

A new ursane-type triterpene oxoglucopyranoside from Crossopteryx febrifuga.

A new saponin, 3-O-ß-d-3-oxo-glucopyranosyl-ursa-12,20(30)-diene-27,28-dioic acid (1), was isolated from the methanol extract of stem bark of Crossopteryx febrifuga together with the known 3ß-d-glucopyranosyl-ursa-12,20(30)-diene-27,28-dioic acid (2), shanzhiside methyl ester (3), shanzhiside (4), ß-sitosterol (5), ß-sitosterol-3-O-ß-d-glucopyranoside (6), ursa-12,20(30)-diene-27,28-dioic acid (7), hederagenin (8), and oleanolic acid (9). The structures were established by comprehensive interpretation of their spectral data 1D- (1H and 13C), 2D-NMR (1H-1H COSY, HMQC, HMBC), spectroscopic, and electrospray ionisation time-of-flight mass spectrometry analysis. The isolated compounds and extracts were screened for their antibacterial properties. Although the EtOAc and n-BuOH extracts exhibited considerable antibacterial activity against Pseudomonas aeruginosa with minimum inhibitory concentration (MIC) value of 32 µg/mL, compounds 2 and 8 showed moderate activity against Enterococcus faecalis with MIC values of 256 and 128 µg/mL, respectively. The new compound (1) exhibited a moderate antibacterial activity against Staphylococcus aureus with an MIC value of 512 µg/mL.

Visible Light-Induced Sulfonylation/Arylation of Styrenes in a Double Radical Three-Component Photoredox Reaction.

Simultaneous sulfonylation/arylation of styrene derivatives is achieved in a photoredox-catalyzed three-component reaction using visible light. A broad variety of difunctionalized products is accessible in mostly excellent yields and high diastereoselectivity. The developed reaction is scalable and suitable for the modification of styrene-functionalized biomolecules. Mechanistic investigations suggest the transformation to be operating through a designed sequence of radical formation and radical combination.