NMR crystallography of amino acids.

The development of NMR crystallography methods requires a reliable database of chemical shifts measured for systems with known crystal structure. We measured and assigned carbon and hydrogen chemical shifts of twenty solid natural amino acids of known polymorphic structure, meticulously determined using powder X-ray diffraction. We then correlated the experimental data with DFT-calculated isotropic shieldings. The small size of the unit cell of most amino acids allowed for advanced computations using various families of DFT functionals, including generalized gradient approximation (GGA), meta-GGA and hybrid DFT functionals. We tested several combinations of functionals for geometry optimizations and NMR calculations. For carbon shieldings, the widely used GGA functional PBE performed very well, although an improvement could be achieved by adding shielding corrections calculated for isolated molecules using a hybrid functional. For hydrogen nuclei, we observed the best performance for NMR calculations carried out with structures optimized at the hybrid DFT level. The high fidelity of the calculations made it possible to assign additional signals that could not be assigned based on experiments alone, for example signals of two non-equivalent molecules in the unit cell of some of the amino acids.

Experimental and Theoretical Evidence of Spin-Orbit Heavy Atom on the Light Atom 1 H†NMR Chemical Shifts Induced through H⋠⋠⋠I- Hydrogen Bond.

Spin-orbit (SO) heavy-atom on the light-atom (SO-HALA) effect is the largest relativistic effect caused by a heavy atom on its light-atom neighbors, leading, for example, to unexpected NMR chemical shifts of 1 H, 13 C, and 15 N nuclei. In this study, a combined experimental and theoretical evidence for the SO-HALA effect transmitted through hydrogen bond is presented. Solid-state NMR data for a series of 4-dimethylaminopyridine salts containing I- , Br- and Cl- counter ions were obtained experimentally and by theoretical calculations. A comparison of the experimental chemical shifts with those calculated by a standard DFT methodology without the SO contribution to the chemical shifts revealed a remarkable error of the calculated proton chemical shift of a hydrogen atom that is in close contact with the iodide anion. The addition of the relativistic SO correction in the calculations significantly improves overall agreement with the experiment and confirms the propagation of the SO-HALA effect through hydrogen bonds.

Experimental and Theoretical Evidence of Spin-Orbit Heavy Atom on the Light Atom 1 H†NMR Chemical Shifts Induced through H⋠⋠⋠I- Hydrogen Bond.

Invited for the cover of this issue is the group of Michal Straka and Martin Dracínský (IOCB Prague, Czech Academy of Sciences). The image depicts a neutron star, which is used to represent the relativistic effects between a heavy element and a hydrogen atom reported in this work. Read the full text of the article at 10.1002/chem.202001532.

Towards Accurate Predictions of Proton NMR Spectroscopic Parameters in Molecular Solids.

The factors contributing to the accuracy of quantum-chemical calculations for the prediction of proton NMR chemical shifts in molecular solids are systematically investigated. Proton chemical shifts of six solid amino acids with hydrogen atoms in various bonding environments (CH, CH2 , CH3 , OH, SH and NH3 ) were determined experimentally using ultra-fast magic-angle spinning and proton-detected 2D NMR experiments. The standard DFT method commonly used for the calculations of NMR parameters of solids is shown to provide chemical shifts that deviate from experiment by up to 1.5 ppm. The effects of the computational level (hybrid DFT functional, coupled-cluster calculation, inclusion of relativistic spin-orbit coupling) are thoroughly discussed. The effect of molecular dynamics and nuclear quantum effects are investigated using path-integral molecular dynamics (PIMD) simulations. It is demonstrated that the accuracy of the calculated proton chemical shifts is significantly better when these effects are included in the calculations.

Synthesis and Biological Profiling of Pyrazolo-Fused 7-Deazapurine Nucleosides.

A series of 8-substituted 1-methyl-1,4-dihydropyrazolo[3',4':4,5]pyrrolo[2,3-d]pyrimidine (methylpyrazolo-fused 7-deazapurine) ribonucleosides have been designed and synthesized. Two synthetic approaches to the key heterocyclic aglycon 7, (i) a six-step classical heterocyclization starting from 5-chloro-1-methyl-4-nitropyrazole and (ii) a three-step cross-coupling and cyclization approach starting from the zincated 4,6-dichloropyrimidine, gave comparable total yields of 18% vs 13%. The glycosylation of 7 was attempted by three different methods but only the Vorbrüggen silyl-base protocol was efficient and stereoselective to give desired ß-anomeric nucleoside intermediate 17A. Its nucleophilic substitutions or cross-coupling reactions at position 8 and deprotection of the sugar moiety gave eight derivatives of pyrazolo-fused deazapurine ribonucleosides, some of which were weakly fluorescent. Methyl, amino, and methylsulfanyl derivatives exerted submicromolar cytotoxic effects in vitro against a panel of cancer and leukemia cell lines as well as antiviral effects against hepatitis C virus in the replicon assay.

Tandem Anionic oxy-Cope Rearrangement/Oxygenation Reactions as a Versatile Method for Approaching Diverse Scaffolds.

Tandem anionic oxy-Cope rearrangement/radical oxygenation reactions provide δ,ϵ-unsaturated α-(aminoxy) carbonyl compounds, which serve as convenient precursors to diverse compound classes. Functionalized carbocycles are accessible by very rare all-carbon 5-endo-trig cyclizations, but also common 5-exo-trig radical cyclizations, based on the persistent radical effect. The tandem reactions can be further extended by highly diastereoselective allylation or reduction steps to give complex scaffolds.

Synthesis of Dihydroxyalkynyl and Dihydroxyalkyl Nucleotides as Building Blocks or Precursors for Introduction of Diol or Aldehyde Groups to DNA for Bioconjugations.

(3,4-Dihydroxybut-1-ynyl)uracil, -cytosine and -7-deazaadenine 2'-deoxyribonucleoside triphosphates (dNTPs) were prepared by direct aqueous Sonogashira cross-coupling of halogenated dNTPs with dihydroxybut-1-yne and converted to 3,4-dihydroxybutyl dNTPs through catalytic hydrogenation. Sodium periodate oxidative cleavage of dihydroxybutyl-dUTP gave the desired aliphatic aldehyde-linked dUTP, whereas the oxidative cleavage of the corresponding deazaadenine dNTP gave a cyclic aminal. All dihydroxyalkyl or -alkynyl dNTPs and the formylethyl-dUTP were good substrates for DNA polymerases and were used for synthesis of diol- or aldehyde-linked DNA. The aldehyde linked DNA was used for the labelling or bioconjugations through hydrazone formation or reductive aminations.

Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines.

Intramolecular hydrogen bonds (IMHBs) in 5-azopyrimidines are investigated by NMR spectroscopy and DFT computations that involve nuclear quantum effects. A series of substituted 5-phenylazopyrimidines with one or two hydrogen bond donors able to form IMHBs with the azo group is prepared by azo coupling. The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is determined by variable temperature NMR spectroscopy and it is demonstrated that the barrier is significantly affected by intramolecular charge transfer. Through-hydrogen-bond scalar coupling is investigated in 15N labeled compounds and the stability of the IMHBs is correlated with experimental NMR parameters and rationalized by path integral molecular dynamics simulations that involve nuclear quantum effects. Detailed information on the hydrogen bond geometry upon hydrogen-to-deuterium isotope exchange is obtained from a comparison of experimental and calculated NMR data.

Short communication: Pasteurization as a means of inactivating staphylococcal enterotoxins A, B, and C in milk.

Our aim was to assess the effect of pasteurization temperature on inactivation of staphylococcal enterotoxins (SE). Milk samples were inoculated with log 4.38 to 5.18cfu/mL of 40 different Staphylococcus aureus strains having the ability to produce types A, B, or C SE and incubated at 37°C for 24h to develop SE. This incubation was followed by heat treatment for 15 s at 72, 85, and 92°C. Samples were analyzed for Staph. aureus count by plate method and, specifically, for SE presence. An enzyme-linked immunofluorescent assay on a MiniVIDAS analyzer (bioMérieux, Marcy l'Étoile, France) was used to detect SE, which were determined semiquantitatively based on test values. The Staph. aureus count in milk before pasteurization did not affect the amount of SE. Before pasteurization, SEB was detected in the lowest amount compared with other SE types. Staphylococcal enterotoxins were markedly reduced with pasteurization and inactivated at pasteurization temperatures to an extent depending on the amount in the sample before pasteurization. After pasteurization at 72°C, SE were detected in 87.5% of samples (35/40), after pasteurization at 85°C in 52.5% of samples (21/40), and after pasteurization at 92°C in 45.0% of samples (18/40). We determined that SE may still persist in milk even when Staph. aureus bacteria are inactivated through pasteurization. Although pasteurization may partially inactivate SE in milk, a key measure in the prevention of staphylococcal enterotoxicosis linked to pasteurized milk consumption is to avoid any cold chain disruption during milk production and processing.

Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides.

Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,ß,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,ß,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.

Unified Total Synthesis of Diverse Meroterpenoids from Ganoderma Applanatum.

A unified approach to meroterpenoids applanatumols B, V, W, X, and Y produced by the medicinal fungus Ganoderma applanatum and 2'-epi-spiroapplanatumine O is presented. The key synthetic sequence consists of a tandem anionic ketone allylation/oxy-Cope rearrangement/α-oxygenation furnishing an α-aminoxy ketone and a persistent radical effect-based 5-exo-trig cyclization leading to the trisubstituted cyclopentane core. The relative configuration of applanatumol V has to be revised. Some compounds display significant cytotoxic and antioxidant properties.

Effects of microcystin and complex cyanobacterial samples on the growth and oxidative stress parameters in green alga Pseudokirchneriella subcapitata and comparison with the model oxidative stressor--herbicide paraquat.

Oxidative stress is one of the biochemical mechanisms involved in toxicity of cyanobacterial toxins microcystins (MC), but its role in the effects of complex water blooms is elusive. The aim of this study was to investigate effects of pure MCs and different complex mixtures of cyanobacterial metabolites on the growth and biochemical markers of oxidative stress and detoxification in green alga Pseudokirchneriella subcapitata. Pure MCs at high concentrations (300 µg/L) had no effects on the growth of P. subcapitata (up to 10 day exposures) but stimulated activity of glutathione reductase (GR) after short 3 and 24 h exposures. Other biomarkers (levels of glutathione, GSH, and activities of glutathione-S-transferase, GST, and glutathione peroxidase, GPx) were not affected by pure MCs). Crude extract of the laboratory culture of cyanobacteria Microcystis aeruginosa (containing 300 µg/L of MCs) had no effects on algal growth or any of the biomarkers. Weak growth stimulations after 4-7 days were observed after exposures to the growth-spent medium of the M. aeruginosa culture, which also inhibited activities of GST after prolonged exposures. Other investigated parameters (reduced GSH and activity of GPx) were not affected by any of the cyanobacterial samples. The results were compared with effects of model oxidative stressor herbicide paraquat, which exhibited variable effects on both algal growth and biomarkers (decrease in reduced GSH, stimulations of GR). Taken together, although pure MCs induce oxidative stress in green alga, the effects of cyanobacterial mixtures, which are more relevant to the natural situation, are more complex and they differ from the pure toxin. High variability in the biochemical responses to the oxidative stress makes the interpretation of results complicated, which limits the use of these biomarkers as early warnings of toxicity under natural conditions.

Two immunoassays for the detection of 2C-B and related hallucinogenic phenethylamines.

INTRODUCTION: The use of new psychoactive substances as drugs of abuse has dramatically increased over the last years. Hallucinogenic phenethylamines gained particular popularity as they have both stimulating and psychedelic effects. Although generally perceived as safe, these illicit drugs pose a serious health risk; they have been linked to cases of severe poisoning or even deaths. Therefore, simple, cost-effective and reliable methods are needed for rapid determination of abused hallucinogens. METHODS: For this purpose, two haptens derived from 2C-H were designed, synthesized and subsequently attached to a carrier protein. Polyclonal antibodies obtained from a rabbit immunized with one of the prepared immunogens were used for the development of two immunoassays. RESULTS: In this study, a lateral flow immunoassay (LFIA) and an enzyme linked immunosorbent assay (ELISA) for the detection of 2C-B and related hallucinogenic phenethylamines in urine were developed. The presented LFIA is primarily suitable for on-site monitoring as it is simple and can provide a visual evidence of 2C-B presence within a few minutes. Its reasonable sensitivity (LODLFIA = 15 ±â€¯7 ng mL-1) allows detection of the drug presence in urine after acute exposure. For greater accuracy, highly sensitive ELISA (LODELISA = 6 ±â€¯3 pg mL-1) is proposed for toxicological quantitative analyses of positive samples captured by the LFIA. DISCUSSION: The comparison of the ELISA with the well-established UHPLC-MS-MS method shows excellent agreement of results, which confirms good potential of the ELISA to be used for routine analyses of 2C-B and related hallucinogenic phenethylamines of both main sub-families.

Determination of nucleobase-pairing free energies from rotamer equilibria of 2-(methylamino)pyrimidines.

A fast straightforward method for the determination of free energies of modified nucleobase pairing is proposed. The method is based on the nuclear magnetic resonance (NMR) spectroscopy monitoring of conformational changes of 2-(methylamino)-pyrimidines upon intermolecular binding.