Unexpected Formation of 6-(1H-Benzo[d]imidazol-2-yl)-1-phenyl-hexan-1-one and Its Structure in Solution and Solid State Analyzed in the Context of Tautomerism Ryszard B. Nazarski, Małgorzata Domagała Crystals, 2024 The structure of the title compound (4d), unexpectedly obtained in the reaction between o-phenylenediamine and 2-benzoylcyclohexanone instead of the target 3H-benzo[b][1,4]diazepine derivative 3d, was determined spectroscopically in solution and by a single-crystal X-ray diffraction (XRD) study. It involves two enantiomeric rotamers, called forms D and U, of which the structure was elucidated based on NMR spectra measured and predicted in DFT-GIAO calculations. An averaging of δCs for all tautomeric positions in the benzimidazole part of the 4d hydrate studied in wet (probably slightly acidic) CDCl3 unambiguously indicates tautomeric exchange in its imidazole unit. An XRD analysis of this material confirms the existence of only one tautomer in the solid phase. The non-covalent interactions forming between molecules of water and benzimidazole derivative are shorter than the sum of van der Waals radii and create an infinite-chain hydrogen bond motif along the b-axis. A possible mechanism for the observed cyclocondensation is also proposed.
Ambient temperature 1H/13C NMR spectra of sodium 3-(trimethylsilyl)propane-1-sulfonate (DSS) in D2O referenced to external TMS: A discussion of these and closely related results. Corrections for the bulk magnetic susceptibility effect for aqueous NMR samples Ryszard B. Nazarski Magnetic Resonance in Chemistry, 2024 This study aimed to obtain the title spectra and verify the temperature dependence of δDSS of the HOD signal from D2O of the NMR sample. However, the analysis of the collected δX data, extended by the results of other closely related measurements reported in the literature, provided important guidelines for performing routine 1H/13C NMR spectra in aqueous solvents externally referenced to neat liquid TMS contained in a coaxial capillary. Therefore, it is recommended that the previously proposed correction of δX data thus determined, which is mainly due to the difference in volume magnetic susceptibility χv between the sample and the external standard used, usually called the bulk magnetic susceptibility (BMS) correction, has been increased by +0.05 ppm (7%). The new value of this correction, +0.73 ppm, based on NMR experiments carried out at a standard temperature of 25°C, was confirmed in a classical approach using critically reviewed χm, χM, and ρ data for TMS, D2O, and H2O. The BMS correction for H2O solutions is +0.75 ppm. Important issues concerning magnetic susceptibility measurements for D2O and H2O, coaxial bulb‐ended inserts, and the geometry of two‐tube NMR cells (shape factor αav) are also critically discussed here, partly from a historical perspective.
On the Use of Deuterated Organic Solvents without TMS to Report 1H/13C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues Ryszard B. Nazarski Molecules, 2023 The quite popular, simple but imperfect method of referencing NMR spectra to residual 1H and 13C signals of TMS-free deuterated organic solvents (referred to as Method A) is critically discussed for six commonly used NMR solvents with respect to their δH and δC values that exist in the literature. Taking into account the most reliable data, it was possible to recommend ‘best’ δX values for such secondary internal standards. The position of these reference points on the δ scale strongly depends on the concentration and type of analyte under study and the solvent medium used. For some solvents, chemically induced shifts (CISs) of residual 1H lines were considered, also taking into account the formation of 1:1 molecular complexes (for CDCl3). Typical potential errors that can occur as a result of improper application of Method A are considered in detail. An overview of all found δX values adopted by users of this method revealed a discrepancy of up to 1.9 ppm in δC reported for CDCl3, most likely caused by the CIS mentioned above. The drawbacks of Method A are discussed in relation to the classical use of an internal standard (Method B), two ‘instrumental’ schemes in which Method A is often implicitly applied, that is, the default Method C using 2H lock frequencies and Method D based on Ξ values, recommended by the IUPAC but only occasionally used for 1H/13C spectra, and external referencing (Method E). Analysis of current needs and opportunities for NMR spectrometers led to the conclusion that, for the most accurate application of Method A, it is necessary to (a) use dilute solutions in a single NMR solvent and (b) to report δX data applied for the reference 1H/13C signals to the nearest 0.001/0.01 ppm to ensure the precise characterization of new synthesized or isolated organic systems, especially those with complex or unexpected structures. However, the use of TMS in Method B is strongly recommended in all such cases.
1H NMR spectra, structure, and conformational exchange of S-n-alkyl-tetrahydrothiophenium cations of some ionic liquids Gerhard Hägele, Ryszard B. Nazarski, Alexa Schmitz, Shanghua Xing, Christoph Janiak Phosphorus Sulfur and Silicon and the Related Elements, 2022 S-n-alkyl-tetrahydrothiophenium cations [R-THT]+ in some iodide or tetraphenylborate ion-pairs [R-THT][X] (R = methyl to n-decyl, X−= I−, [BPh4]−, [NTf2]−) are characterized in the solid state by puckered THT rings in twist forms. In contrast, solution 1H NMR spectra of compounds [R-THT][X] indicate a rapid conformational exchange leading to dynamic [ABCD]2 spin systems due to eight protons of the THT ring. These strongly coupled spectra obtained at high magnetic fields were analyzed by iterative methods and simulated successfully. In addition, molecular modeling and gauge-including atomic orbitals (GIAOs) based calculations of proton NMR chemical shifts for two such ion-pair compounds in solution were performed at the density functional theory (DFT) level . As a result, conformational equilibrium between two different pairs of isoenergetic twist forms of the THT ring in [Me-THT][I] (global and local energy minima) was found to exist. These theoretical results are discussed in view of experimental 1H NMR spectral data. Graphical Abstract
Unexpected Rearrangement of Dilithiated Isoindoline-1,3-diols into 3-Aminoindan-1-ones via N-Lithioaminoarylcarbenes: A Combined Synthetic and Computational Study Magdalena Ciechańska, Andrzej Jóźwiak, Ryszard B. Nazarski, Ewa A. Skorupska Journal of Organic Chemistry, 2019 The reaction of 2-aryl-3-hydroxyisoindolin-1-ones with the s-BuLi●TMEDA system in THF at -78oC, affording a series of diastereomeric 3-aminoindan-1-ones via a novel rearrangement of the isoindolinone scaffold, is reported. It is proposed that α-elimination of LiOH from the transient N,O-dilithiated hemiaminal carbenoids leads to the formation of singlet carbenes followed by their trapping via an internal C-H insertion. An alternative explanation based on an intramolecular Mannich reaction seems to be less probable. A mechanistic-type study that combines spectroscopic data of the products and calculation results, with a special focus on the diverse lithiated intermediates that are most likely to engage in the title process (particularly those with internal Li-bonds), is presented. The MP2 approach, involving also the NPA and QTAIM data, provided insight into structures and properties of all these species. Two reaction routes A and B appeared to be possible for the postulated carbene mechanism. An unusual metamorphosis of the CCN atom triad, from a near sp 1-azaallene-type in more stable non-carbene Li enolates to a roughly sp2 type in their carbene keto tautomers, is recognized in one of these pathways (route B). Dominant forms of resonance structures for the aforementioned tautomeric systems that have seven-membered quasi rings stabilized by Li+ ions bridging the N- and carbonyl O-atoms, are indicated. Large computational difficulties arising from a huge impact of internal Li+ complexation on conformational preferences and electronic properties of carbonyl group-bearing lithium derivatives are also discussed. The new γ-keto carbene species under study belong to a subclass of acyclic amino-aryl-carbenes (AAACs).
Shortfall of B3LYP in Reproducing NMR JCH Couplings in Some Isomeric Epoxy Structures with Strong Stereoelectronic Effects: A Benchmark Study on DFT Functionals Jasper Adamson, Ryszard B. Nazarski, Jüri Jarvet, Tõnis Pehk, Riina Aav Chemphyschem, 2018 Unprecedented scatter plots of calculated versus measured NMR 2,3JCH coupling constants in six densely oxygen functionalized epoxides are found with some B3LYP protocols, an effect attributed to stereoelectronic effects. Hence, 26 other exchange‐correlation density functionals (xc DFs) are benchmarked in this work. Very good results are achieved with mPW1PW91 and PBE0 in conjunction with the pcJ‐1 basis set (BS) of moderate size. A thorough statistical analysis of 53 relationships between the predicted and observed 2,3JCH datasets is presented. The effects of some xc DFs, including their x and c parts, and BSs on the calculation results are discussed, also in the context of DFT modeling of electron‐density distributions. Moreover, related 1JCH datasets predicted with 11 different DF methods are considered and compared with the experimental data. Finally, some proposals for further improvement of existing DFs based on the available nJCH (n=1–3) values are briefly outlined, in line with recent results on the DFT electron densities.
A benefit of using the IDSCRF- over UFF-radii cavities and why joint correlations of NMR chemical shifts can be advantageous: Condensed pyridines as an IEF-PCM/GIAO/DFT case study Ryszard B. Nazarski, Katarzyna Justyna, Stanisław Leśniak, Anna Chrostowska Journal of Physical Chemistry A, 2016 Herein, an advantage of the use of IDSCRF- over UFF-radii-based solute cavities in GIAO/DFT calculations is presented for the 13C and especially 15N NMR chemical shifts made for several bicyclic aromatic nitrogen heterocycles in CDCl3 solution treated within the classical IEF-PCM solvation scheme. Successful application of the IDSCRF-radii in the non 1:1 joint multinuclear 1H/13C and particularly 1H/13C/15N correlations of the measured δH,C(,N) values to those obtained theoretically is also documented for a series of test systems (-268 ≤ δN ≤ -72 ppm). The experimentally yet unknown δN's were found in this way for the title compounds via a trinuclear eq 1 determined for an optimally chosen value of the multiplication factor of initial raw δH data (mH = 10). Such a simultaneous analysis of the δH,C(,N) data is proposed as a novel method to study the solution structure of the other similar conformationally homogeneous (bio)organic compounds. The issue of small spurious imaginary vibrational frequencies computed for a few molecular systems using the Gaussian 09 default UFF-radii is briefly considered as well.
Tetraazacyclotetradecane species as models of the polyazacrown macrocycles Tetraazacyclotetradecane Species as Models of the Polyazacrown Macrocycles, 2010
Tetraazacyclotetradecane species as models of the polyazacrown macrocycles: Molecular structure and reorganizations in aqueous media (pH 0-14) as probed by nmr spectroscopy and computational methods - problems and solutions Macrocyclic Chemistry New Research Developments, 2010
Physical image vs. structure relation. 9. Synthesis and structural study of some 2,5-bis-alkoxysubstituted 3-oxolenes and oxolanes: An experimental and theoretical approach Polish Journal of Chemistry, 2003
Physical image vs. structure relation, 4 [1]. Configuration and conformation determination of some bicyclic lactams by 1H NMR and theoretical methods Bulletin of the Polish Academy of Sciences Chemistry, 2000
Physical image vs. structure relation, 5 [1]. Multinuclear NMR structural study on some hydrazones of O,O-dialkyl 1-oxoalkanephosphonates Bulletin of the Polish Academy of Sciences Chemistry, 2000
Synthesis of 1-aminoalkanephosphonous acids bearing furan moiety and its stereochemical aspect [1] Polish Journal of Chemistry, 1999
Sterically crowded five-membered heterocyclic systems. Part 2.1 Conformation of 2,2,5,5-tetramethylpyrrolidin-3-ol from nuclear magnetic resonance spectroscopy, crystal structure, and molecular mechanics calculations Journal of the Chemical Society Perkin Transactions 2, 1985
