Dissolved Organic Matter Contains Ketones Across a Wide Range of Molecular Formulas.

The carbonyl functionality of natural organic matter (NOM) is poorly constrained. Here, we treated Suwannee River NOM (SRNOM) with ammonium acetate and sodium cyanoborohydride to convert ketone-containing compounds by reductive amination to their corresponding primary amines. The total dissolved nitrogen content increased by up to 275% after amination. Up to 30% of the molecular formulas of SRNOM contained isomers with ketone functionalities as detected by ultrahigh-resolution mass spectrometry. Most of these isomers contained one or two keto groups. At least 3.5% of the oxygen in SRNOM was bound in ketone moieties. The conversion of reacted compounds increased linearly with O/H values of molecular formulas and was predictable from the elemental composition. The mean conversion rate of reacted compounds nearly followed a log-normal distribution. This distribution and the predictability of the proportion of ketone-containing isomers solely based on the molecular formula indicated a stochastic distribution of ketones across SRNOM compounds. We obtained isotopically labeled amines by using 15N-labeled ammonium acetate, facilitating the identification of reaction products and enabling NMR spectroscopic analysis. 1H,15N HSQC NMR experiments of derivatized samples containing less than 20 µg of nitrogen confirmed the predominant formation of primary amines, as expected from the reaction pathway.

Investigation of hydrogen bonds in proton transfer complexes derived from the reaction of 2- and 4-(N,N-dimethylamino)pyridines with chloranilic acid.

New complexes of 2-(N,N-dimethylamino)pyridine with chloranilic acid (2-DMAP + CLA) and 4-(N,N-dimethylamino)pyridine with chloranilic acid (4-DMAP + CLA) were synthesized and characterized by single crystal X-ray diffraction, infrared spectroscopy, thermal analysis methods and 1H, 13C and 15N NMR spectroscopy. The NMR spectroscopies were carried out in both, DMSO solution and in the solid state (CPMAS NMR). The 2-DMAP + CLA and 4-DMAP + CLA complexes crystallize in centrosymmetric P-1 and P21/c space group, respectively. In both complexes, the phenomenon of proton transfer is observed, which results in the formation of strong N+-H···O- hydrogen bonds. Thermal decompositions of 2-DMAP + CLA and 4-DMAP + CLA complexes were studied by thermogravimetric analysis. Temperature dependent IR spectra revealed that methyl groups of 4-DMAP + CLA perform fast stochastic reorientational motion at room temperature which is slowed on cooling while in 2-DMAP + CLA reonrientational motion of CH3 groups is much slower due to steric effects.

Lessons on protein structure from interleukin-4: All disulfides are not created equal.

Interleukin-4 (IL-4) is a hematopoietic cytokine composed by a four-helix bundle stabilized by an antiparallel beta-sheet and three disulfide bonds: Cys3-Cys127, Cys24-Cys65, and Cys46-Cys99. IL-4 is involved in several immune responses associated to infection, allergy, autoimmunity, and cancer. Besides its physiological relevance, IL-4 is often used as a "model" for protein design and engineering. Hence, to understand the role of each disulfide in the structure and dynamics of IL-4, we carried out several spectroscopic analyses (circular dichroism [CD], fluorescence, nuclear magnetic resonance [NMR]), and molecular dynamics (MD) simulations on wild-type IL-4 and four IL-4 disulfide mutants. All disulfide mutants showed loss of structure, altered interhelical angles, and looser core packings, showing that all disulfides are relevant for maintaining the overall fold and stability of the four-helix bundle motif, even at very low pH. In the absence of the disulfide connecting both protein termini Cys3-Cys127, C3T-IL4 showed a less packed protein core, loss of secondary structure (~9%) and fast motions on the sub-nanosecond time scale (lower S2 order parameters and larger τc correlation time), especially at the two protein termini, loops, beginning of helix A and end of helix D. In the absence of Cys24-Cys65, C24T-IL4 presented shorter alpha-helices (14% loss in helical content), altered interhelical angles, less propensity to form the small anti-parallel beta-sheet and increased dynamics. Simultaneously deprived of two disulfides (Cys3-Cys127 and Cys24-Cys65), IL-4 formed a partially folded "molten globule" with high 8-anilino-1-naphtalenesulphonic acid-binding affinity and considerable loss of secondary structure (~50%decrease), as shown by the far UV-CD, NMR, and MD data.

On the Efficiency of the Density Functional Theory (DFT)-Based Computational Protocol for 1H and 13C Nuclear Magnetic Resonance (NMR) Chemical Shifts of Natural Products: Studying the Accuracy of the pecS-n (n = 1, 2) Basis Sets.

The basis set issue has always been one of the most important factors of accuracy in the quantum chemical calculations of NMR chemical shifts. In a previous paper, we developed new pecS-n (n = 1, 2) basis sets purposed for the calculations of the NMR chemical shifts of the nuclei of the most popular NMR-active isotopes of 1-2 row elements and successfully approbated these on the DFT calculations of chemical shifts in a limited series of small molecules. In this paper, we demonstrate the performance of the pecS-n (n = 1, 2) basis sets on the calculations of as much as 713 1H and 767 13C chemical shifts of 23 biologically active natural products with complicated stereochemical structures, carried out using the GIAO-DFT(PBE0) approach. We also proposed new alternative contraction schemes for our basis sets characterized by less contraction depth of the p-shell. New contraction coefficients have been optimized with the property-energy consistent (PEC) method. The accuracies of the pecS-n (n = 1, 2) basis sets of both the original and newly contracted forms were assessed on massive benchmark calculations of proton and carbon chemical shifts of a vast variety of natural products. It was found that less contracted pecS-n (n = 1, 2) basis sets provide no noticeable improvement in accuracy. These calculations represent the most austere test of our basis sets as applied to routine calculations of the NMR chemical shifts of real-life compounds.

Reversible Parahydrogen Induced Hyperpolarization of 15 N in Unmodified Amino Acids Unraveled at High Magnetic Field.

Amino acids (AAs) and ammonia are metabolic markers essential for nitrogen metabolism and cell regulation in both plants and humans. NMR provides interesting opportunities to investigate these metabolic pathways, yet lacks sensitivity, especially in case of 15 N. In this study, spin order embedded in p-H2 is used to produce on-demand reversible hyperpolarization in 15 N of pristine alanine and ammonia under ambient protic conditions directly in the NMR spectrometer. This is made possible by designing a mixed-ligand Ir-catalyst, selectively ligating the amino group of AA by exploiting ammonia as a strongly competitive co-ligand and preventing deactivation of Ir by bidentate ligation of AA. The stereoisomerism of the catalyst complexes is determined by hydride fingerprinting using 1 H/D scrambling of the associated N-functional groups on the catalyst (i.e., isotopological fingerprinting), and unravelled by 2D-ZQ-NMR. Monitoring the transfer of spin order from p-H2 to 15 N nuclei of ligated and free alanine and ammonia targets using SABRE-INEPT with variable exchange delays pinpoints the monodentate elucidated catalyst complexes to be most SABRE active. Also RF-spin locking (SABRE-SLIC) enables transfer of hyperpolarization to 15 N. The presented high-field approach can be a valuable alternative to SABRE-SHEATH techniques since the obtained catalytic insights (stereochemistry and kinetics) will remain valid at ultra-low magnetic fields.

Acrylamide derivatives: A dynamic nuclear magnetic resonance study.

Substituted acrylamides have found an extensive application in organic and medical chemistry; therefore, it is very important to get insight into their features such as electronic structure, spectral properties, and stereochemical transformations. A correct interpretation of the chemical behavior and biological activity of these heteroatomic systems is impossible without knowledge of the structure of stereodynamic forms and factors determining their relative stability. The structure and peculiarities of stereodynamic behavior of substituted acrylamides and their model compounds were studied by dynamic and multinuclear 1 H, 13 C, and 15 N nuclear magnetic resonance (NMR) spectroscopy in CDCl3 and DMSO-d6 solution. It has been established that acrylamides in solution are realized as Z- and E-isomers, with the E-rotamer being somewhat predominant. The obtained experimental values of the free activation energy of rotamers vary within 15-17 kcal/mol, depending on the stereochemical structure of the molecule. 15 N NMR spectroscopy is the most reliable and fastest method for determining the structural and stereochemical features of nitrogen-containing compounds.

Synthesis, characterization and computational investigation of the phosphatase activity of a dinuclear Zinc(II) complex containing a new heptadentate asymmetric ligand.

We report the synthesis of a new asymmetric heptadentate ligand based on the 1,3-diaminopropan-2-ol backbone. The ligand 3-[[3-(bis-pyridin-2-ylmethyl-amino)-2-hydroxy-propyl]-(2-carbamoyl-ethyl)-amino]-propionamide (HL1) contains two amide and two pyridine groups attached to the 1,3-diaminopropan-2-ol core. Reaction between HL1 and Zn(ClO4)2.6H2O resulted in the formation of the dinuclear [Zn2(L1)(µ-OAc)](ClO4)2 complex, characterized by single crystal X-ray diffraction, 1H, 13C and 15N NMR, ESI-(+)-MS, CHN elemental analysis as well as infrared spectroscopy. The phosphatase activity of the complex was studied in the pH range 6-11 employing pyridinium bis(2,4-dinitrophenyl)phosphate (py(BDNPP)) as substrate. The complex exhibited activity dependent on the pH, presenting an asymmetric bell shape profile with the highest activity at pH 9; at high pH ligand exchange is rate-limiting. The hydrolysis of BDNPP- at pH 9 displayed behavior characteristic of Michaelis-Menten kinetics, with kcat = 5.06 × 10-3 min-1 and Km = 5.7 ± 1.0 mM. DFT calculations map out plausible reaction pathways and identify a terminal, Zn(II)-bound hydroxide as likely nucleophile.

Molecular Rearrangement of Pyrazino[2,3-c]quinolin-5(6H)-ones during Their Reaction with Isocyanic Acid.

New tetrahydropyrazino[2,3-c]quinolin-5(6H)-ones were prepared from 3-chloroquinoline-2,4(1H,3H)-diones and ethylene diamine. In their reaction with HNCO, an unprecedented molecular rearrangement produced new types of hydantoin derivatives. All prepared compounds were characterized on the basis of their 1H, 13C, and 15N NMR and ESI mass spectra and some were authenticated by X-ray analysis of single crystalline material. A proposed mechanism for rearrangement is discussed in this essay. The CDK and ABL inhibition activity as well as in vitro cytotoxicity of the prepared compounds was also tested.

Relationship between the Crystal Structure and Tuberculostatic Activity of Some 2-Amidinothiosemicarbazone Derivatives of Pyridine.

Tuberculosis remains one of the most common diseases affecting developing countries due to difficult living conditions, the rapidly increasing resistance of M. tuberculosis strains and the small number of effective anti-tuberculosis drugs. This study concerns the relationship between molecular structure observed in a solid-state by X-ray diffraction and the 15N NMR of a group of pyridine derivatives, from which promising activity against M. tuberculosis was reported earlier. It was found that the compounds exist in two tautomeric forms: neutral and zwitterionic. The latter form forced the molecules to adopt a stable, unique, flat frame due to conjugation and the intramolecular hydrogen bond system. As the compounds exist in a zwitterionic form in the crystal state generally showing higher activity against tuberculosis, it may indicate that this geometry of molecules is the "active" form.

Convenient Synthesis of Pyrazolo[4',3':5,6]pyrano[4,3-c][1,2]oxazoles via Intramolecular Nitrile Oxide Cycloaddition.

A simple and efficient synthetic route to the novel 3a,4-dihydro-3H,7H- and 4H,7H-pyrazolo[4',3':5,6]pyrano[4,3-c][1,2]oxazole ring systems from 3-(prop-2-en-1-yloxy)- or 3-(prop-2-yn-1-yloxy)-1H-pyrazole-4-carbaldehyde oximes has been developed by employing the intramolecular nitrile oxide cycloaddition (INOC) reaction as the key step. The configuration of intermediate aldoximes was unambiguously determined using NOESY experimental data and comparison of the magnitudes of 1JCH coupling constants of the iminyl moiety, which were greater by approximately 13 Hz for the predominant syn isomer. The structures of the obtained heterocyclic products were confirmed by detailed 1H, 13C and 15N NMR spectroscopic experiments and HRMS measurements.

The omega-loop of cobra cytotoxins tolerates multiple amino acid substitutions.

Cobra cytotoxins (CTs), the three-fingered proteins, feature high amino acid sequence homology in the beta-strands and variations in the loop regions. We selected a pair of cytotoxins from Naja kaouthia crude venom to clarify the sequence-structure relationships. Using chromatography and mass spectroscopy, we separated and identified the mixture of cytotoxins 2 and 3, differentiated by the only Val 41/Ala 41 substitution. Here, using natural abundance 13C, 15N NMR-spectroscopy we performed chemical shift assignments of the signals of the both toxins in aqueous solution in the major and minor forms. Combining NOE and chemical shift data, the toxins' spatial structure was determined. Finally, we proved that the tip of the "finger"-2, or the loop-2 of cytotoxins adopts the shape of an omega-loop with a tightly-bound water molecule in its cavity. Comparison with other NMR and X-ray structures of cytotoxins possessing different amino acid sequences reveals spatial similarity in this family of proteins, including the loop-2 region, previously considered to be flexible.

15N NMR Shifts of Eumelanin Building Blocks in Water: A Combined Quantum Mechanics/Statistical Mechanics Approach.

Theoretical results for the magnetic shielding of protonated and unprotonated nitrogens of eumelanin building blocks including monomers, dimers, and tetramers in gas phase and water are presented. The magnetic property in water was determined by carrying out Monte Carlo statistical mechanics sampling combined with quantum mechanics calculations based on the gauge-including atomic orbitals approach. The results show that the environment polarization can have a marked effect on nitrogen magnetic shieldings, especially for the unprotonated nitrogens. Large contrasts of the oligomerization effect on magnetic shielding show a clear distinction between eumelanin building blocks in solution, which could be detected in nuclear magnetic resonance experiments. Calculations for a π-stacked structure defined by the dimer of a tetrameric building block indicate that unprotonated N atoms are significantly deshielded upon π stacking, whereas protonated N atoms are slightly shielded. The results stress the interest of NMR experiments for a better understanding of the eumelanin complex structure.

A multi-methodological inquiry of the behavior of cisplatin-based Pt(IV) derivatives in the presence of bioreductants with a focus on the isolated encounter complexes.

The study of Pt(IV) antitumor prodrugs able to circumvent some drawbacks of the conventional Pt(II) chemotherapeutics is the focus of a lot of attention. This paper reports a thorough study based on experimental methods (reduction kinetics, electrochemistry, tandem mass spectrometry and IR ion spectroscopy) and quantum-mechanical DFT calculations on the reduction mechanism of cisplatin-based Pt(IV) derivatives having two hydroxido (1), one hydroxido and one acetato (2), or two acetato ligands (3) in axial position. The biological reductants glutathione and ascorbic acid were taken into consideration. The presence of a hydroxido ligand resulted to play an important role in the chemical reduction with ascorbic acid, as verified by 15N-NMR kinetic analysis using 15N-enriched complexes. The reactivity trend (1 > 2 > 3) does not reflect the respective reduction peak potentials (1 < 2 < 3), an inverse relationship already documented in similar systems. Turning to a simplified environment, the Pt(IV) complexes associated with a single reductant molecule (corresponding to the encounter complex occurring along the reaction coordinate in bimolecular reactions in solution) were characterized by IR ion spectroscopy and sampled for their reactivity under collision-induced dissociation (CID) conditions. The complexes display a comparable reduction reactivity ordering as that observed in solution. DFT calculations of the free energy pathways for the observed fragmentation reactions provide theoretical support for the CID patterns and the mechanistic hypotheses on the reduction process are corroborated by the observed reaction paths. The bulk of these data offers a clue of the intricate pathways occurring in solution.Graphic abstract.

Forensic application of position-specific isotopic analysis of trinitrotoluene (TNT) by NMR to determine 13C and 15N intramolecular isotopic profiles.

2,4,6-trinitrotoluene (TNT) is a molecule which is easily identified with current instrumental techniques but it is generally impossible to distinguish between sources of the same substance (TNT). To overcome this difficulty, we present a multi stable isotope approach using isotope ratio monitoring by mass spectrometry (irm-MS) and Nuclear Magnetic Resonance spectrometry (irm-NMR). In the one hand, irm-MS provides bulk isotopic composition at natural abundance in 13C and 15N. The range of variation between samples is rather small particularly for 13C. In the other hand, irm-13C NMR and irm-15N NMR enable the determination of positional intramolecular 13C/12C ratios (δ13Ci) and 15N/14N ratios (δ15Ni) with high precision that lead to larger variation between samples. The present work reports an application of the recent methodology using irm-15N NMR to determine position-specific 15N isotope content of TNT. The interest of this methodology is compared to irm-13C NMR and irm-MS (13C and 15N) in terms of TNT samples discrimination. Thanks to the use of irm-NMR the results show a unique isotopic fingerprint for each TNT which enable origin discrimination between the samples without ambiguity.

Terminal charges modulate the pore forming activity of cationic amphipathic helices.

KIA peptides are a series of designer-made cationic amphipathic α-helical antimicrobial peptides of different lengths, based on the repetitive sequence [KIAGKIA]. They can form toroidal pores in membranes, wherein the helices are aligned in a transmembrane orientation. Solid-state 15N NMR is used here to differentiate between the surface-bound and transmembrane states. We find that the pore-forming activity increases when the peptides carry a positive charge (Lys residue) at the N-terminus, compared to a hydrophobic Ile-Ala N-terminal motif. In contrast, a positive charge at the C-terminus gives a lower membrane activity compared to C-terminal Ile-Ala. For peptides with otherwise identical sequence, a more than ten-fold difference in vesicle leakage can be observed, depending on which terminus carries the charge. This difference is attributed to a shift in the equilibrium between peptide helices oriented on the membrane surface and those inserted into the membrane in a pore-forming state. We show that the 3D hydrophobic moment can be used to predict which peptide sequence is more prone to form pores and will thereby show a higher membranolytic activity.

Crystallographic and NMR Investigation of Ergometrine and Methylergometrine, Two Alkaloids from Claviceps purpurea.

Ergometrine and methylergometrine are two alkaloids that are used as maleate salts for the prevention and control of postpartum hemorrhage. Although the two molecules have been known for a long time, few and discordant crystallographic and NMR spectroscopic data are available in the literature. With the aim of providing more conclusive data, we performed a careful NMR study for the complete assignment of the 1H, 13C, and 15N NMR signals of ergometrine, methylergometrine, and their maleate salts. This information allowed for a better definition of their conformational equilibria. In addition, the stereochemistry and the intermolecular interactions in the solid state of the two maleate salts were deeply investigated by means of single-crystal X-ray diffraction, showing the capability of these derivatives to act as both hydrogen-bond donors and acceptors, and evidencing a correlation between the number of intermolecular interactions and their different solubility.

Synthesis and Electrochemical and Spectroscopic Characterization of 4,7-diamino-1,10-phenanthrolines and Their Precursors.

New approaches to the synthesis of 4,7-dichloro-1,10-phenanthrolines and their corresponding 9H-carbazol-9-yl-, 10H-phenothiazin-10-yl- and pyrrolidin-1-yl derivatives were developed. Their properties have been characterized by a combination of several techniques: MS, HRMS, GC-MS, electronic absorption spectroscopy and multinuclear NMR in both solution and solid state including 15N CP/MAS NMR. The structures of 5-fluoro-2,9-dimethyl-4,7-di(pyrrolidin-1-yl)-1,10-phenanthroline (5d), 4,7-di(9H-carbazol-9-yl)-9-oxo-9,10-dihydro-1,10-phenanthroline-5-carbonitrile (6a) and 4,7-di(10H-phenothiazin-10-yl)-1,10-phenanthroline-5-carbonitrile (6b) were determined by single-crystal X-ray diffraction measurements. The nucleophilic substitutions of hydrogen followed by oxidation produced compounds 6a and 6b. The electrochemical properties of selected 1,10-phenanthrolines were investigated using cyclic voltammetry and compared with commercially available reference 1,10-phenanthrolin-5-amine (5l). The spatial distribution of frontier molecular orbitals of the selected compounds has been calculated by density functional theory (DFT). It was shown that potentials of reduction and oxidation were in consistence with the level of HOMO and LUMO energies.

Position-specific 15 N isotope analysis in organic molecules: A high-precision 15 N NMR method to determine the intramolecular 15 N isotope composition and fractionation at natural abundance.

The position-specific 15 N isotope content in organic molecules, at natural abundance, is for the first time determined by using a quantitative methodology based on 15 N Nuclear Magnetic Resonance (NMR) spectrometry. 15 N NMR spectra are obtained by using an adiabatic "Full-Spectrum" INEPT sequence in order to make possible 15 N NMR experiments with a high signal-to-noise ratio (>500), to reach a precision with a standard deviation below 1‰ (0.1%). This level of precision is required for observing small changes in 15 N content associated to 15 N isotope effects. As an illustration, the measurement of an isotopic enrichment factor ε for each 15 N isotopomer is presented for 1-methylimidazole induced during a separation process on a silica column. The precision expressed as the long-term repeatability of the methodology is good enough to evaluate small changes in the 15 N isotope contents for a given isotopomer. As observed for 13 C, inverse and normal 15 N isotope effects occur concomitantly, giving access to new information on the origin of the 15 N isotope effects, not detectable by other techniques such as isotope ratio measured by Mass Spectrometry for which bulk (average) values are obtained.

DFT computational schemes for 15 N NMR chemical shifts of the condensed nitrogen-containing heterocycles.

A systematic density functional theory (DFT) study of the accuracy factors (functionals, basis sets, and solvent effects) for the computation of 15 N NMR chemical shifts has been performed in the series of condensed nitrogen-containing heterocycles. The behavior of the most representative functionals was examined based on the benchmark calculations of 15 N NMR chemical shifts in the reference set of compounds. It was found that the best agreement with experiment was achieved with OLYP functional in combination with aug-pcS-3(N)//pc-2 locally dense basis set scheme providing mean absolute error of 5.2 ppm in the range of about 300 ppm. Taking into account solvent effects was performed within a general Tomasi's polarizable continuum model scheme. It was also found that computationally demanding supermolecular solvation model computations essentially improved some "difficult" cases, as was illustrated with phenanthroline dissolved in methanol. Based on the performed calculations, some 200 unknown 15 N NMR chemical shifts were predicted with a high level of confidence for about 50 real-life condensed nitrogen-containing heterocycles, which could serve as a practical guide in structural elucidation of this class of compounds.

1 H-15 N HMBC NMR as a tool for rapid identification of isomeric azaindoles: The case of 5F-MDMB-P7AICA.

The high frequency of the synthetic cannabinoid receptor agonists (SCRAs) emergence renders this group of new psychoactive compounds particularly demanding in terms of detection, identification, and responding. Without the available reference material, one of the specific problems is differentiation and structure elucidation of constitutional isomers. Herein, we report a simple and efficient flow chart diagram applicable for a rapid nuclear magnetic resonance (NMR) identification and differentiation between azaindoles, 4-, 5-, 6-, and 7-azaindole, which is a common structural motif of synthetic cannabinoids. The flow chart diagram is based on 1 H NMR and 1 H-15 N NMR spectra, and to prove the concept, it has been tested on 5F-MDMB-P7AICA (1). Spectral and analytical data including standard 1D and 2D NMR spectra, gas chromatography-mass spectrometry (GC-MS), Fourier transform infrared-attenuated total reflectant (FTIR-ATR), Raman, melting point, and combustion analysis are provided for compound 1.