What is the form of muscimol from fly agaric mushroom (Amanita muscaria) in water? An insight from NMR experiment supported by molecular modeling

The biologically active alkaloid muscimol is present in fly agaric mushroom (Amanita muscaria), and its structure and action is related to human neurotransmitter _γ-aminobutyric acid (GABA). The current study reports on determination of muscimol form present in water solution using multinuclear ¹H and ¹³C nuclear magnetic resonance (NMR) experiments supported by density functional theory molecular modeling. The structures of three forms of free muscimol molecule both in the gas phase and in the presence of water solvent, modeled by polarized continuous model, and nuclear magnetic isotropic shieldings, the corresponding chemical shifts, and indirect spin–spin coupling constants were calculated. Several J-couplings observed in proton and carbon NMR spectra, not available before, are reported. The obtained experimental spectra, supported by theoretical calculations, favor the zwitterion form of muscimol in water. This structure differs from NH isomer, previously determined in dimethyl sulfoxide (DMSO) solution. In addition, positions of signals C3 and C5 are reversed in both solvents.     

β-Lactam antibiotics. Spectroscopy and molecular orbital (MO) calculations: Part I: IR studies of complexation in penicillin-transition metal ion systems and semi-empirical PM3 calculations on simple model compounds

IR studies were preformed to determine possible transition metal ion binding sites of penicillin. the observed changes in spectral position and shape of characteristic IR bands of cloxacillin in the presence of transition metal ions (both in solutions and in the solid state) indicate formation of M–L complexes with engagement of –COO⁻ and/or –CONH– functional groups. The small shift of ν_C=O towards higher frequencies rules out direct M–L interaction via β-lactam carbonyl. PM3 calculations on simple model compounds (substituted formamide, cyclic ketones, lactams and substituted monocyclic β-lactams) have been performed. All structures were fully optimized and the calculated bond lengths, angles, heats of formation and C=O stretching frequencies were discussed to determine the β-lactam binding sites and to explain its susceptibility towards nucleophilic attack (hydrolysis in vitro) and biological activity. The relative changes of calculated values were critically compared with available experimental data and same correlation between structural parameters and in vivo activity was shown.     

Theoretical DFT and experimental Raman and NMR studies on thiophene, 3-methylthiophene and selenophene

The results of extended MO calculations using density functional theory (DFT) approximation supported by experimental Raman, ¹H and ¹³C NMR studies on thiophene are reported. Raman spectra of liquid thiophene were re-examined and the performance of a hybrid B3PW91 density functional was compared with the ab initio restricted Hartree–Fock (RHF) method. With the basis sets of the 6-311++G^** quality, the DFT calculated bond lengths, dipole moments and harmonic vibrations were predicted in a very good agreement with available experimental data.

Additionally, the results on thiophene were extended by calculations on 3-methylthiophene and selenophene. In this case, a significant change in geometry and charge distribution in thiophene ring due to a methyl group substituent or replacement of sulphur by selene atom was observed.

A linear correlation between the predicted harmonic vibrational frequencies (scaled using SQM method) and experimental ones for thiophene, selenophene and 3-methylthiophene was shown. The theoretically calculated spectra have satisfactorily reproduced the available experimental spectra for thiophene and selenophene.     

Impact of the ΔPhe configuration on the Boc-Gly-ΔPhe-NHMe conformation: experiment and theory

Conformational propensities of N-t-butoxycarbonyl-glycine-(E/Z)-dehydrophenylalanine N′-methylamides (Boc-Gly-(E/Z)-ΔPhe-NHMe) in chloroform were investigated by NMR and IR techniques. The low-temperature crystal structure of the E isomer was determined by single crystal X-ray diffraction and the experimental data were elaborated by theoretical calculations using DFT (B3LYP, M06-2X) and MP2 approaches. The β-turn tendencies for both isomers were determined in the gas phase and in the presence of solvent. The obtained results reveal that the configuration of ΔPhe residue significantly affects the conformations of the studied dehydropeptides. The tendency to adopt β-turn conformations is significantly lower for the E isomer (Boc-Gly-(E)-ΔPhe-NHMe), both in gas phase and in chloroform solution.

     

One-bond 1J(15N,H) coupling constants at sp2-hybridized nitrogen of Schiff bases,enaminones and similar compounds: A theoretical study

¹J(¹⁵N,H) coupling constants for enaminones and NH-forms of intramolecularly hydrogen-bonded Schiff bases as model compounds for sp²-hybridized nitrogen atoms are evaluated using density functional theory (DFT) to find the optimal functionals and basis sets. Ammonia is used as a test molecule and its one-bond coupling constant is compared with experiment. A methylamine Schiff base of a truncated molecule of gossypol is used for checking the performance of selected B3LYP, O3LYP, PBE, BHandH, and APFD density functionals and standard, modified, and dedicated basis sets for coupling constants. Both in vacuum and in chloroform, modeled by the simple continuum model of solvent, the modified basis sets predict significantly better the ¹J(¹⁵N,H) value in ammonia and in the methylamine Schiff base of a truncated molecule of gossypol than the standard basis sets. This procure is then used on a broad set of intramolecularly hydrogen-bonded molecules, and a good correlation between calculated and experimental one-bond NH coupling constants is obtained. The ¹J(¹⁵N,H) couplings are slightly overestimated. The calculated data show for hydrogen-bonded NH interatomic distances that the calculated values depend on the NH bond lengths. The shorter the bond lengths, the larger the ¹J(¹⁵N,H). A useful correlation between ¹J(¹⁵N,H) and NH bond length is derived that enables realistic predictions of one-bond NH coupling constants. The calculations reproduce experimentally observed trends for the studied molecules.     

New Molecular Receptors with Cyclophosphazene Subunits: Synthesis, Reactivity, and Structure-Property Relationships

A series of hydrophopic ( 2 and 3) and new hydrophilic ( 4– 7) molecular receptors of the PNP-lariat ether with tetra-substituted cyclotriphosphazene subunits have been prepared by the complete nucleophilic substitution of chlorine atoms in the reactive PNP-crown precursor 1 with the respective sodium cation-paired oxyanions (phenoxy 2, -naphthoxy 3, and methoxytrioxyethylenoxy 4) and aliphatic amines (n-propylamine 5 aziridine 6, and pyrrolidine 7). Their structures were established by MS and ³¹P NMR spectroscopy and their metal ion complexing properties tested by a TLC method. Comparison of the complexation behaviour for ligands 1– 7 shows that the affinity for particular cations is strongly substituent-dependent and, in general, is significantly enhanced by cooperation of the side arm donor atoms (O or N) with the parent PNP-crown structure in the binding process. The remarkable affinity of some ligands for selected cations, in particular lithium, cesium, and silver ions, is interpreted in terms of structure-property relationships.     

Estimation of isotropic nuclear magnetic shieldings in the CCSD(T) and MP2 complete basis set limit using affordable correlation calculations

A linear correlation between isotropic nuclear magnetic shielding constants for seven model molecules (CH₂O, H₂O, HF, F₂, HCN, SiH₄ and H₂S) calculated with 37 methods (34 density functionals, RHF, MP2 and CCSD(T)), with affordable pcS‐2 basis set and corresponding complete basis set results, estimated from calculations with the family of polarization‐consistent pcS‐n basis sets is reported. This dependence was also supported by inspection of profiles of deviation between CBS estimated nuclear shieldings and shieldings obtained with the significantly smaller basis sets pcS‐2 and aug‐cc‐pVTZ‐J for the selected set of 37 calculation methods. It was possible to formulate a practical approach of estimating the values of isotropic nuclear magnetic shielding constants at the CCSD(T)/CBS and MP2/CBS levels from affordable CCSD(T)/pcS‐2, MP2/pcS‐2 and DFT/CBS calculations with pcS‐n basis sets. The proposed method leads to a fairly accurate estimation of nuclear magnetic shieldings and considerable saving of computational efforts. Copyright © 2013 John Wiley & Sons, Ltd.     

H2O,H2, HF,F2 and F2O nuclear magnetic shielding constants and indirect nuclear spin–spin coupling constants (SSCCs) in the BHandH/pcJ‐n and BHandH/XZP Kohn–Sham limits

Good performance of segmented contracted basis sets XZP, where X = D, T, Q and 5, for obtaining H₂O, H₂, HF, F₂ and F₂O nuclear isotropic shielding constants in the BHandH Kohn–Sham basis set limit was shown. The results of two‐ and three‐parameter complete basis set limit extrapolation schemes were compared with experimental results, earlier literature data and benchmark ab initio results. Similar convergence patterns of shieldings obtained from calculations using general purpose XZP basis sets and from polarization‐consistent basis sets pcS‐n and pcJ‐n, where n = 0, 1, 2, 3 and 4, designed to accurately predict magnetic properties were observed. On the contrary, the SSCCs were more sensitive to the XZP basis set size and generally less accurate than those estimated using pcJ‐n basis set family. The BHandH density functional markedly outperforms B3LYP method in predicting heavy atom shieldings and SSCCs values in the studied systems. Copyright © 2009 John Wiley & Sons, Ltd.     

Complete basis set prediction of methanol isotropic nuclear magnetic shieldings and indirect nuclear spin–spin coupling constants (SSCC) using polarization‐consistent and XZP basis sets and B3LYP and BHandH density functionals

Efficient B3LYP and BHandH density functionals were used to estimate methanol's nuclear magnetic isotropic shieldings and spin–spin coupling constants in the basis set limit. Polarization‐consistent pcS‐n and pcJ‐n (n = 0, 1, 2, 3 and 4), and segmented contracted XZP, where X = D, T, Q and 5, basis sets were used and the results fitted with simple mathematical formulas. The performance of the methods was assessed from comparison with experiment and higher level calculations. ¹J(CH) and ³J(HH) values were determined from very diluted solutions in deuterochloroform and compared with theoretical predictions. The agreement between complete basis set (CBS) density functional theory (DFT) predicted isotropic shieldings and spin–spin values and experiment was good. The BHandH/pcS‐n methanol shieldings obtained using structures optimized at the same level of theory are approaching the accuracy of the advanced coupled‐cluster‐singles‐doubles‐approximate triples (CCSD(T)) calculations. Copyright © 2009 John Wiley & Sons, Ltd.     

Modeling red coral (Corallium rubrum) and African snail (Helixia aspersa) shell pigments: Raman spectroscopy versus DFT studies

Pigments from red coral (Corallium rubrum) and African snail (Helixia aspersa) shell were studied non‐invasively using Raman spectroscopy with 1064‐nm laser beam. The two observed bands because of organic pigments confined in biomineralized CaCO₃ matrix at about 1500 and 1100 cm⁻¹ were assigned to ν(CC) and ν(C―C), respectively. Both signals originate from polyene(s) of largely unknown structure, containing several conjugated CC bonds. The small peak at 1016 cm⁻¹ in the Raman spectrum of coral pigment was assigned to in‐plane ―CH₃ rocking or structural deformation of polyene chain because of spatial confinement in the mineral matrix. The organic pigments in red coral and snail shell were present in inorganic matrix containing aragonite (shell) and calcite (coral). In addition, using Raman spectroscopy, it was observed that aragonite was replaced by calcite as result of healing damaged parts of snail shell. This is an important finding which indicates a great potential of nondestructive Raman spectroscopy instead of X‐ray technique, as a diagnostic tool in environmental studies. To support analysis of the observed Raman spectra detailed calculations using density functional theory (DFT with B3LYP and BLYP density functionals) on structure and vibrations of model all‐trans polyenes were undertaken. DFT calculated CC and C―C stretching frequencies for all‐trans polyenes containing from 2 to 14 CC units were compared with the observed ν(CC) and ν(C―C) band positions of the studied coral and shell. Individual correction factors were used to better match theoretical wavenumbers with observed band positions in red coral and African snail. It was concluded that all‐trans polyene pigments of red coral and dark parts of African snail shell contain 11–12 and 14 CC double bond units, respectively. However, Raman spectroscopy cannot produce any clear information on the presence and nature of the end‐chain substituents in the studied pigments. Copyright © 2016 John Wiley & Sons, Ltd.