Theoretical and experimental study of 15N NMR protonation shifts

Exploring the pH dependence of an improved PETase

Enzymatic recycling of plastic and especially of polyethylene terephthalate (PET) has shown great potential to reduce its negative impact on our society. PET hydrolases (PETases) have been optimized using rational design and machine learning, but the mechanistic details of the PET depolymerization process remain unclear. Belonging to the carboxylic-ester hydrolase family with a canonical Ser-His-Asp catalytic triad, their observed alkaline pH optimum is generally thought to be related to the protonation state of the catalytic His. Here, we explore this aspect in the context of LCCICCG, an optimized PETase, derived from the leaf-branch compost cutinase enzyme. We use NMR to identify the dominant tautomeric structure of the six histidines. Five show surprisingly low pKa values below 4.0, whereas the catalytic H242 in the active enzyme displays a pKa value that varies from 4.9 to 4.7 when temperatures increase from 30°C to 50°C. Whereas the hydrolytic activity of the enzyme toward a soluble substrate can be modeled by the corresponding protonation/deprotonation curve, an important discrepancy is found when the substrate is the solid plastic. This opens the way to further mechanistic understanding of the PETase activity and underscores the importance of studying the enzyme at the liquid-solid interface.

Catalytic Upgrading of Acetaldehyde to Acetoin Using a Supported N-Heterocyclic Carbene Catalyst

We report the catalytic synthesis of 3-hydroxy-2-butanon (acetoin) from acetaldehyde as a key step in the synthesis of C4-molecules from ethanol. Facile C-C bond formation at the α-carbon of the C2 building block is achieved using an N-heterocyclic carbene (NHC) catalyst. The immobilization of the catalyst on a Merrifield's peptide resin and its spectroscopic characterisation using solid-state Nuclear Magnetic Resonance (NMR) is described herein. The immobilization of the NHC catalyst allows for process intensification steps and the reported catalytic system was subjected to batch recycling as well as continuous flow experiments. The robustness of the catalytic system was shown over a maximum of 10 h time-on-stream. Overall, high selectivity S>90 % was observed. The observed deactivation of the catalyst with increasing time-on-stream is explained by ex-situ 1H solution-state, as well as 13C and 15N solid-state NMR spectra allowing us to develop a deeper understanding of the underlying decomposition mechanism of the catalyst.

In-Silico Aided Screening and Characterization Results in Stability Enhanced Novel Roxadustat Co-Crystal

Roxadustat (RXD) is an approved drug substances for the treatment of renal anemia. It has poor aqueous solubility and photochemical stability. This study employs a comprehensive approach to enhance the stability and physicochemical properties RXD through coformer selection and characterization. The investigation integrates delta pKa analysis, molecular complementary assessment, molecular electrostatic potential surface analysis, and machine learning techniques to predict potential co-crystal formation and binding interactions between drug molecules and coformers. The co-crystal screening which lead to in a novel RXD-nicotinamide co-crystal (RXD-NA). Experimental characterization underscores the physical and chemical stability of the co-crystals. To elucidate the supramolecular synthons and understand the intermolecular interactions in the RXD-NA co-crystal, Hirshfeld surfaces analysis, quantum theory of atoms in molecules (QTAIM) analysis and non-covalent interaction (NCI) analysis were performed. Computational analysis of photo-isomer formation aligns with experimental observations, further enhancing our understanding of RXD-coformer interactions. RXD-NA co-crystal was found photo-chemically stable as compared to free base API drug substance. This integrated methodology provides a systematic framework for informed co-crystal design, holding promise for optimizing RXD formulations based on molecular interactions and stability considerations. Consequently, this study contributes valuable insights to the field of rational drug design and formulation optimization.

Estimations of OH·N hydrogen bond length from positions and intensities of IR bands

In this computational work applicability of IR spectral parameters for evaluations of OH···N hydrogen bond length is discussed. For a set of 124 complexes with OH···N hydrogen bond formed by combinations of methanol/acetic acid and pyridine (and their fluorine substituted versions) geometries, energies and IR parameters were calculated at MP2/def2-TZVP level of theory. For a number of IR parameters (the shift of proton donor group stretching vibration Δν_s, increase of its intensity I, the low-frequency hydrogen bond stretching vibration ν_σ, bending in-plane δ and out-of-plane γ vibrations) equations linking them with interatomic distances are proposed, the robustness and accuracy of such equations are discussed. The enthalpy of OH···N hydrogen bond formation ΔH was also linked with electron density parameters in (3; -1) critical point.

Discovery, Biosynthetic Origin, and Heterologous Production of Massinidine, an Antiplasmodial Alkaloid

Bacteria of the genus Massilia represent an underexplored source of bioactive natural products. Here, we report the discovery of massinidine (1), a guanidine alkaloid with antiplasmodial activity, from these microbes. The unusual scaffold of massinidine is shown to originate from l-phenylalanine, acetate, and l-arginine. Massinidine biosynthesis genes were identified in the native producer and validated through heterologous expression in Myxococcus xanthus. Bioinformatic analyses indicate that the potential for massinidine biosynthesis is distributed in various proteobacteria.

Insights into the κ-P,N Coordination of 1,3,5-Triaza-7-phosphaadamantane and Derivatives: κ-P,N-Heterometallic Complexes and a 15N Nuclear Magnetic Resonance Survey

Complexes {[(PTA)₂CpRu-μ-CN-1κC:2κ²N-RuCp(PTA)₂-ZnCl₃]}·2DMSO (13) {[ZnCl₂(H₂O)]-(PTA-1κP:2κ²N)(PTA)CpRu-μ-CN-1κC:2κ²N-RuCp(PTA)(PTA-1κP:2κ²N)-[ZnCl₂(H₂O)]}Cl (14), [RuCp(HdmoPTA)(PPh₃)(PTA)](CF₃SO₃)₂ (20), [RuCp(HdmoPTA)(HPTA)(PPh₃)](CF₃SO₃)₃ (21), and [RuCp(dmoPTA)(PPh₃)(PTA)](CF₃SO₃) (22) were obtained and characterized, and their crystal structure together with that of the previously published complex 18 is reported. The behavior of the 1,3,5-triaza-7-phosphatricyclo[3.3.1.13,7]decane (PTA) and 3,7-dimethyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane (dmoPTA) ligands against protonation and κN-coordination is discussed, on the basis of ¹⁵N nuclear magnetic resonance data collected on 22 different compounds, including PTA (1), HdmoPTA (7H), and some common derivatives as free ligands (2–6 and 8), along with mono- and polymetallic complexes containing PTA and/or HdmoPTA (9–22). ¹⁵N detection via ¹H–¹⁵N heteronuclear multiple bond correlation allowed the construction of a small library of ¹⁵N chemical shifts that shed light on important features regarding κN-coordination in PTA and its derivatives.

To shed light on the behavior of the triazaphosphines 1,3,5-triaza-7-phosphatricyclo[3.3.1.13,7]decane (PTA) and 3,7-dimethyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane (dmoPTA) upon κN coordination and N protonation, the ¹⁵N chemical shifts of 22 compounds, including PTA and a representative variety of its derivatives, piano-stool complexes, were collected by ¹H−¹⁵N heteronuclear multiple bond correlation nuclear magnetic resonance. New heterometallic complexes containing PTA were also synthesized and fully characterized.

Single-Crystal X-ray and Solid-State NMR Characterisation of AND-1184 and Its Hydrochloride Form

In this study, we report on a structural investigation of AND-1184, with the chemical name N-[3-[4-(6-fluoro-1,2-benzoxazol-3-yl)piperidin-1-yl]propyl]-3-methylbenzenesulfonamide (MBS), and its hydrochloride form (MBS^HCl); AND-1184 is a potential API for the treatment of dementia. The single-crystal X-ray investigation of both forms results in monoclinic crystal systems with P2₁/c and C2/c symmetry for MBS and MBS^HCl, respectively. This solid-state NMR study, combined with quantum-chemical calculations, allowed us to assign all ¹³C and most ¹H signals. The MBS structure was defined as a completely rigid system without significant dynamic behaviours, whereas MBS^HCl exhibited limited dynamic motion of the aromatic part of the molecule.

Photoinduced Generation of the π-Conjugated Zwitterionic State in the ESIPT Fluorophore of 2,4-Bisimidazolylphenol

We demonstrate that 2,4-bis(4,5-diphenyl-1H-imidazol-2-yl)phenol (2,4-bImP) undergoes photoinduced conversion into the so-called "π-conjugated zwitterion" after causing an excited-state intramolecular proton transfer (ESIPT) reaction. The powder sample of 2,4-bImP exhibits largely Stokes-shifted fluorescence characteristics to ESIPT fluorophores. On the other hand, its originally colorless solutions become colored when exposed to UV light for several minutes, whose color depends on the type of solvent. In particular, the CHCl₃ solution rapidly turns dark green with the absorption maximum around 700 nm, and the colored solution is nearly restored to original by alternating addition of acid and base. To explain such drastic and reversible color changes, we hypothesized that the occurrence of ESIPT (i.e., deprotonation of the phenol and protonation of the imidazolyl group at its 2-position) triggered the charge-separated structure between the negatively charged phenolate and the positively charged imidazoliumyl group at its 4-position, which allowed resonance with the neutral p-quinoid structure. The formation of this π-conjugated zwitterion was strongly supported by the results of ¹H and ¹⁵N NMR and Raman measurements.

Deconvolution of fast exchange equilibrium states in NMR spectroscopy using virtual reference standards and probability theory

A methodology for deconvolution of fast exchange equilibrium states in NMR spectroscopy (DFEQNMR) was developed based on DFT-GIAO NMR chemical shift prediction and a probability theory algorithm. Proof-of-concept studies were performed to estimate the protonation state of N-containing organic molecules involving fast proton exchange equilibrium and evaluate the solution tautomerism of a purine derivative. DFT-GIAO calculations were optimized to achieve good accuracy in ¹³C, ¹H and ¹⁵N chemical shift prediction for protonated species. The probability theory algorithm enabled the determination of solution species ratios and yielded 95% confidence regions by comparing experimental and simulated chemical shift data sets. The calculation showed good accuracy for model partial salts with various functionalities and application in structure elucidation of complex natural product partial salts was also demonstrated. This method showed promising potential in acquisition of important insight into fast exchange equilibrium systems with only one experimental NMR chemical shift data set.

Incarnatapeptins A and B, Nonribosomal Peptides Discovered Using Genome Mining and 1H/15N HSQC-TOCSY

Methods for the focused isolation of low-abundance natural products with specific chemical substructures could expand known bioactive chemical diversity for drug discovery. Here we report the combined use of genome mining and an ¹⁵N NMR-based screening method for the targeted isolation of the low-abundance piperazic-acid-containing peptides incarnatapeptins A (1) and B (3). Incarnatapeptin B (3) shows in vitro cytotoxicity to LNCaP prostate cancer cells.

Calculation of 15N NMR Chemical Shifts in a Diversity of Nitrogen-Containing Compounds Using Composite Method Approximation at the DFT, MP2, and CCSD Levels

Computations of ¹⁵N NMR chemical shifts in 93 diverse nitrogen-containing compounds representing almost all known classes are performed at the density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2), and coupled cluster singles and doubles (CCSD) levels using the composite method approximation (CMA) in comparison with experimental results. It is shown that the CMA-DFT and CMA-CCSD methods provided the best performance characterized by a normalized mean absolute error of 1.1-1.3% as compared to 2.3% for the CMA-MP2 results. Taking into account solvent effects within the conductor-like polarizable continuum model decreased the normalized mean absolute error by 0.4% for the CMA-DFT and by 0.2% for the CMA-CCSD calculations.

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.

A theoretical elucidation of the mechanism of tuneable fluorescence in a full-colour emissive ESIPT dye

We reinvestigate with ab initio tools the origin of the diverse colours in a complex multi-ESIPT dye, and we propose a new assignment for the blue fluorescence.

Succinyl-β-cyclodextrin: Influence of the substitution degree on albendazole inclusion complexes probed by NMR

Succinyl-β-CD derivatives were obtained by green synthesis with degrees of substitution (DS) 1.3 and 2.9. The spray-drying technique was used to obtain albendazole (ABZ):succinyl-β-CD inclusion complexes. Phase solubility diagrams indicated that both succinyl-β-CD derivatives formed 1:1 molar ratio ABZ complexes, but the complex with DS 2.9 has a lower formation constant. The presence of stable inclusion complexes in aqueous solution was confirmed by NMR. For both complexes the aromatic moiety is encapsulated into the host cavity. In the solid-state, ¹³C and ¹⁵N NMR spectral differences between ABZ and ABZ included in spray-dried systems showed that strong structural changes occurred in the systems. At least two different ABZ amorphous species were identified based on DS. ABZ species were stable over more than six months based on spectral data. Finally, the influence of DS in the number and type of the inclusion complexes was elucidated.

GIAO-DFT calculation of 15 N NMR chemical shifts of Schiff bases: Accuracy factors and protonation effects

¹⁵ N NMR chemical shifts in the representative series of Schiff bases together with their protonated forms have been calculated at the density functional theory level in comparison with available experiment. A number of functionals and basis sets have been tested in terms of a better agreement with experiment. Complimentary to gas phase results, 2 solvation models, namely, a classical Tomasi's polarizable continuum model (PCM) and that in combination with an explicit inclusion of one molecule of solvent into calculation space to form supermolecule 1:1 (SM + PCM), were examined. Best results are achieved with PCM and SM + PCM models resulting in mean absolute errors of calculated ¹⁵ N NMR chemical shifts in the whole series of neutral and protonated Schiff bases of accordingly 5.2 and 5.8 ppm as compared with 15.2 ppm in gas phase for the range of about 200 ppm. Noticeable protonation effects (exceeding 100 ppm) in protonated Schiff bases are rationalized in terms of a general natural bond orbital approach.

Substitution effects in the 15 N NMR chemical shifts of heterocyclic azines evaluated at the GIAO-DFT level

A systematic study of the accuracy factors for the computation of ¹⁵ N NMR chemical shifts in comparison with available experiment in the series of 72 diverse heterocyclic azines substituted with a classical series of substituents (CH₃ , F, Cl, Br, NH₂ , OCH₃ , SCH₃ , COCH₃ , CONH₂ , COOH, and CN) providing marked electronic σ- and π-electronic effects and strongly affecting ¹⁵ N NMR chemical shifts is performed. The best computational scheme for heterocyclic azines at the DFT level was found to be KT3/pcS-3//pc-2 (IEF-PCM). A vast amount of unknown ¹⁵ N NMR chemical shifts was predicted using the best computational protocol for substituted heterocyclic azines, especially for trizine, tetrazine, and pentazine where experimental ¹⁵ N NMR chemical shifts are almost totally unknown throughout the series. It was found that substitution effects in the classical series of substituents providing typical σ- and π-electronic effects followed the expected trends, as derived from the correlations of experimental and calculated ¹⁵ N NMR chemical shifts with Swain-Lupton's F and R constants.

On the long-range relativistic effects in the 15 N NMR chemical shifts of halogenated azines

Long-range β- and γ-relativistic effects of halogens in ¹⁵ N NMR chemical shifts of 20 halogenated azines (pyridines, pyrimidines, pyrazines, and 1,3,5-triazines) are shown to be unessential for fluoro-, chloro-, and bromo-derivatives (1-2 ppm in average). However, for iodocontaining compounds, β- and γ-relativistic effects are important contributors to the accuracy of the ¹⁵ N calculation. Taking into account long-range relativistic effects slightly improves the agreement of calculation with experiment. Thus, mean average errors (MAE) of ¹⁵ N NMR chemical shifts of the title compounds calculated at the non-relativistic and full 4-component relativistic levels in gas phase are accordingly 7.8 and 5.5 ppm for the range of about 150 ppm. Taking into account solvent effects within the polarizable continuum model scheme marginally improves agreement of computational results with experiment decreasing MAEs from 7.8 to 7.4 ppm and from 5.5 to 5.3 ppm at the non-relativistic and relativistic levels, respectively. The best result (MAE: 5.3 ppm) is achieved at the 4-component relativistic level using Keal and Tozer's KT3 functional used in combination with Dyall's relativistic basis set dyall.av3z with taking into account solvent effects within the polarizable continuum solvation model. The long-range relativistic effects play a major role (of up to dozen of parts per million) in ¹⁵ N NMR chemical shifts of halogenated nitrogen-containing heterocycles, which is especially crucial for iodine derivatives. This effect should apparently be taken into account for practical purposes.

On the accuracy factors and computational cost of the GIAO-DFT calculation of 15 N NMR chemical shifts of amides

The main factors affecting the accuracy and computational cost of Gauge-independent Atomic Orbital-density functional theory (GIAO-DFT) calculation of ¹⁵ N NMR chemical shifts in the benchmark series of 16 amides are considered. Among those are the choice of the DFT functional and basis set, solvent effects, internal reference conversion factor and applicability of the locally dense basis set (LDBS) scheme. Solvent effects are treated within the polarizable continuum model (PCM) scheme as well as at supermolecular level with solvent molecules considered in explicit way. The best result is found for Keal and Tozer's KT3 functional used in combination with Jensen's pcS-3 basis set with taking into account solvent effects within the polarizable continuum model. The proposed LDBS scheme implies pcS-3 on nitrogen and pc-2 elsewhere in the molecule. The resulting mean average error for the calculated ¹⁵ N NMR chemical shifts is about 6 ppm. The application of the LDBS approach tested in a series of 16 amides results in a dramatic decrease in computational cost (more than an order of magnitude in time scale) with insignificant loss of accuracy.

Calculation of 15N NMR chemical shifts: Recent advances and perspectives

Recent advances in computation of ¹⁵N NMR chemical shifts are reviewed, concentrating mainly on practical aspects of computational protocols and accuracy factors. The review includes the discussion of the level of theory, the choice of density functionals and basis sets together with taking into account solvent effects, rovibrational corrections and relativistic effects. Computational aspects of ¹⁵N NMR are illustrated for the series of neutral and protonated open-chain nitrogen-containing compounds and nitrogen heterocycles, coordination and intermolecular complexes.

Mapping the Binding Modes of Hemilabile Pincer-Crown Ether Ligands in Solution Using Diamagnetic Anisotropic Effects on NMR Chemical Shift

A protocol for identifying ligand binding modes in a series of iridium pincer complexes bearing hemilabile aza-crown ether ligands has been developed using readily accessible NMR methods. The approach was tested on a collection of 13 structurally diverse pincer-crown ether complexes that include several newly characterized species. New synthetic routes enable facile interconversion of coordination modes and supporting ligands. Detailed structural assignments of five complexes reveal that the difference in chemical shift (Δδ) between geminal protons in the crown ether is influenced by diamagnetic anisotropy arising from halides and other ligands in the primary coordination sphere. The average difference in chemical shift between diastereotopic geminal protons in the crown ether macrocycle (Δδ_avg), as determined through a single ¹H-¹³C HSQC experiment, provides information on the pincer ligand binding mode by establishing whether the macrocycle is in close proximity to the metal center. The Δδ_avg values for binding modes that involve chelating ether(s) bound to iridium are roughly 2-fold larger than those for tridentate complexes with no Ir-O bonds.

Systematic investigation of DFT-GIAO 15N NMR chemical shift prediction using B3LYP/cc-pVDZ: application to studies of regioisomers, tautomers, protonation states and N-oxides

The calculation of ¹⁵N NMR chemical shifts has been systematically investigated using density functional theory-gauge including/invariant atomic orbitals (DFT-GIAO) approximation at the B3LYP/cc-pVDZ level of theory. General linear regression terms for ¹⁵N chemical shift predictions were calculated for nitromethane and liquid ammonia references in DMSO. Both aliphatic and aromatic nitrogens were studied using a diverse set of molecular scaffolds. Statistical error analysis between experiment and prediction revealed that, with the exception of primary amines, 95% of linear scaled N-15 chemical shifts are within a ±9.56 ppm range. Comparison of the ¹⁵N calculated isotropic chemical shifts with the experimentally determined chemical shifts provided accurate assignment of the correct structure in cases where experimental data was ambiguous or inconclusive. Application of ¹⁵N prediction proved to be highly effective in identifying the correct regio-isomer, oxidation state, protonation state and preferred tautomer in solution.

(15)N NMR Spectroscopy, X-ray and Neutron Diffraction, Quantum-Chemical Calculations, and UV/vis-Spectrophotometric Titrations as Complementary Techniques for the Analysis of Pyridine-Supported Bicyclic Guanidine Superbases

Pyridine substituted with one and two bicyclic guanidine groups has been studied as a potential source of superbases. 2-{hpp}C5H4N (I) and 2,6-{hpp}2C5H3N (II) (hppH = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine) were protonated using [HNEt3][BPh4] to afford [I-H][BPh4] (1a), [II-H][BPh4] (2), and [II-H2][BPh4]2 (3). Solution-state (1)H and (15)N NMR spectroscopy shows a symmetrical cation in 2, indicating a facile proton-exchange process in solution. Solid-state (15)N NMR data differentiates between the two groups, indicating a mixed guanidine/guanidinium. X-ray diffraction data are consistent with protonation at the imine nitrogen, confirmed for 1a by single-crystal neutron diffraction. The crystal structure of 1a shows association of two [I-H](+) cations within a cage of [BPh4](-) anions. Computational analysis performed in the gas phase and in MeCN solution shows that the free energy barrier to transfer a proton between imino centers in [II-H](+) is 1 order of magnitude lower in MeCN than in the gas phase. The results provide evidence that linking hpp groups with the pyridyl group stabilizes the protonation center, thereby increasing the intrinsic basicity in the gas phase, while the bulk prevents efficient cation solvation, resulting in diminished pKa(MeCN) values. Spectrophotometrically measured pKa values are in excellent agreement with calculated values and confirm that I and II are superbases in solution.

Theoretical and experimental (15)N NMR study of enamine-imine tautomerism of 4-trifluoromethyl[b]benzo-1,4-diazepine system

The tautomeric structure of 4-trifluoromethyl[b]benzo-1,4-diazepine system in solution has been evaluated by means of the calculation of (15)N NMR chemical shifts of individual tautomers in comparison with the averaged experimental shifts to show that the enamine-imine equilibrium is entirely shifted toward the imine form. The adequacy of the theoretical level used for the computation of (15)N NMR chemical shifts in this case has been verified based on the benchmark calculations in the series of the push-pull and captodative enamines together with related azomethynes, which demonstrated a good to excellent agreement with experiment.