NMR of Natural Products as Potential Drugs

This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.     

Revealing the physical nature and the strength of charge‐inverted hydrogen bonds by SAPT(DFT), MP2, SCS‐MP2, MP2C,and CCSD(T) methods

The physical nature of charge‐inverted hydrogen bonds in H₃XH YH₃ (X = Si, Ge; Y = Al, Ga) dimer systems is studied by means of the SAPT(DFT)‐based decomposition of interaction energies and supermolecular interaction energies based on MP2, SCS‐MP2, MP2C, and CCSD(T) methods utilizing dimer‐centered aug‐cc‐pCVnZ (n = D, T, Q) basis sets as well as an extrapolation to the complete basis set limit. It is revealed that charge‐inverted hydrogen bonds are inductive in nature, although dispersion is also important. Computed interaction energies form the following relation: . It is confirmed that the aug‐cc‐pCVDZ basis set performs poorly and that very accurate values of interaction and dispersion energies require basis sets of at least quadrupole‐ζ quality. Considerably large binding energies suggest potential usefulness of charge‐inverted hydrogen bonds as an important structural motif in molecular binding. Terminology applying to σ‐ and π‐hole interactions as well as to triel and tetrel bonds is discussed. According to this new terminology the charge‐inverted hydrogen bond would become the first described case of a hydride‐triel bond. © 2017 Wiley Periodicals, Inc.     

Comparison of experimental and DFT‐calculated NMR chemical shifts of 2‐amino and 2‐hydroxyl substituted phenyl benzimidazoles,benzoxazoles and benzothiazoles in four solvents using the IEF‐PCM solvation model

A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2‐amino and 2‐hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd.     

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

¹⁵N 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 ¹⁵N 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.     

15N NMR study of substituted 2-(phenylamino)-5-phenyl-1,3,4-oxadiazoles

Substituted 2-(phenylamino)-5-phenyl-1,3,4-oxadiazoles were studied by 15N NMR spectroscopy. All signals were assigned on the basis of HMQC and HMBC experiments. Chemical shifts values were correlated with empirical Hammett parameters as well as with calculated electron densities and chemical shieldings.     

AlCl_3催化歧化制备二甲基二氯硅烷的DFT和MP2研究(II)

研究一甲基三氯硅烷与三甲基氯硅烷分别与三氯化铝作用并得到中间体后,中间体分别与一甲基三氯硅烷和三甲基氯硅烷作用的机理,反应的IRC(Intrinsicreactioncoordinate)曲线,各关键原子沿IRC的变化曲线及产物的理论产率.结果发现,中间体趋于与一甲基三氯硅烷作用生成二甲基二氯硅烷,且三甲基氯硅烷的转化率高于一甲基三氯硅烷.实验结果与计算结果吻合.     

Molecular structure and vibrational raman and infrared spectra of bromochlorofluoromethane and its silicon and germanium analogs: quantum-mechanical DFT and MP2 calculations

DFT(B3LYP) and MP2 calculations with the 6-311G(2d, 2p)-type basis set have been carried out for the prediction of molecular parameters (bond distances, bond angles, rotational constants, and dipole moments) and vibrational Raman and infrared spectra (harmonic wavenumbers, absolute intensities, Raman scattering activities, and depolarization ratios) of bromochlorofluoromethane (HCBrCIF) and its silicon and germanium analogs (HSiBrClF and HGeBrCIF). The predicted geometry and vibrational Raman and infrared spectra of HCBrClF agree well with the available experimental data for this molecule and their deuterated derivatives. This agreement allows one to believe that the predicted molecular parameters and vibrational spectra of HSiBrClF, HGeBrClF, and their deuterated derivatives will guide their future experimental studies.     

Prototropic tautomerism of 5‐aryloxy‐1(2)H‐tetrazoles

The structure of 5‐(2,6‐dimethylphenoxy)‐1H‐ and 2H‐tetrazoles together with those of 5‐(2,6‐diisopropyl‐phenoxy)‐1H and 2H‐tetrazoles have been theoretically studied including absolute shieldings and energies. The conclusion of these studies is that a slow tautomerism between 1H‐ and 2H‐tetrazoles cannot explain the experimental observations reported recently in the literature. Copyright © 2012 John Wiley & Sons, Ltd.     

AlCl3催化歧化制备二甲基二氯硅烷的DFT和MP2研究(II)

研究一甲基三氯硅烷与三甲基氯硅烷分别与三氯化铝作用并得到中间体后, 中间体分别与一甲基三氯硅烷和三甲基氯硅烷作用的机理, 反应的IRC (Intrinsic reaction coordinate)曲线, 各关键原子沿IRC的变化曲线及产物的理论产率. 结果发现, 中间体趋于与一甲基三氯硅烷作用生成二甲基二氯硅烷, 且三甲基氯硅烷的转化率高于一甲基三氯硅烷. 实验结果与计算结果吻合.     

The MC‐DFT approach including the SCS‐MP2 energies to the new minnesota‐type functionals

We have applied the multicoefficient density functional theory (MC‐DFT) to four recent Minnesota functionals, including M06‐2X, M08‐HX, M11, and MN12‐SX on the performance of thermochemical kinetics. The results indicated that the accuracy can be improved significantly using more than one basis set. We further included the SCS‐MP2 energies into MC‐DFT, and the resulting mean unsigned errors (MUEs) decreased by approximately 0.3 kcal/mol for the most accurate basis set combinations. The M06‐2X functional with the simple [6–311+G(d,p)/6–311+G(2d,2p)] combination gave the best performance/cost ratios for the MC‐DFT and MC‐SCS‐MP2|MC‐DFT methods with MUE of 1.58 and 1.22 kcal/mol, respectively. © 2014 Wiley Periodicals, Inc.     

Study of conformations and hydrogen bonds in the configurational isomers of pyrrole‐2‐carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis

The ¹H, ¹³C and ¹⁵N NMR studies have shown that the E and Z isomers of pyrrole‐2‐carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole‐2‐carbaldehyde oxime is stabilized by the N? H···N and N? H···O intramolecular hydrogen bonds, respectively. The N? H···N hydrogen bond in the E isomer causes the high‐frequency shift of the bridge proton signal by about 1 ppm and increase the ¹J(N, H) coupling by ～3 Hz. The bridge proton shows further deshielding and higher increase of the ¹J(N, H) coupling constant due to the strengthening of the N? H···O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by ～3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of ¹H shielding and ¹J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N? H···N and N? H···O hydrogen bondings to be estimated. The NBO analysis suggests that the N? H···N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N? H bond through the N? H···O hydrogen bond occurs in the Z isomer. Copyright © 2010 John Wiley & Sons, Ltd.     

Intramolecular hydrogen bonding of novel o-hydroxythioacetophenones and related compounds evaluated by deuterium isotope effects on 13C chemical shifts

A new class of compounds, the 2-hydroxythioacetophenones, and related compounds have recently been synthesized. The hydrogen-bond system has been characterized by NMR chemical shifts and deuterium isotope effects on these as well as by DFT calculations. Use of solid-state (13)C NMR has enabled measurements of the intrinsic deuterium isotope effects of the most abundant tautomer of beta-thioxoketones. The compounds show very interesting long-range deuterium isotope effects on the thiocarbonyl carbon. The intramolecular hydrogen bonds of o-hydroxythioacetophenones are found to be slightly stronger than those of the corresponding acetophenones. The reactivity and stability of the compounds can be related to hydrogen bonding and to the presence of electron donating substituents.     

A DFT and MP2 Study on the Molecular Structure and Vibrational Spectra of Halogenosubstituted Phosphoryl and Thiophosphoryl Compounds

The molecular geometrical parameters, rotational constants, dipole moments and vibrational infrared properties of a series of phosphoryl compounds (OPX _i Y _j Z _k , X, Y, Z = F, Cl, Br; i+ j + k = 3) and their thio analogs are predicted by density functional and MP2 calculations using the 6-311G(2d,2p) basis set. Both methods yielded similar results. The predicted molecular parameters and the vibrational Raman and infrared spectra agree well with the available experimental data. The Raman Scattering Activities (RSA) and depolarization ratios (Dep) of the molecules are obtained by DFT calculations. Considering the different substitution modes of various halogen atoms, the resultant changes in the geometrical and vibrational properties are discussed. Such studies permit detailed information to be obtained concerning unknown molecules and can define the guidelines for synthesizing molecules of particular characteristics.     

Structural investigation on phenyl‐ and pyridin‐2‐ylamino(methylene)naphthalen‐2(3H)‐one. Substituent effects on the NMR chemical shifts

Schiff bases bearing phenyl and pyridyl groups were synthesized by condensation of appropriate amines with 2‐hydroxynaphthaldehyde. These Schiff bases were obtained as colored crystalline solids. The proton NMR spectra of these compounds showed a doublet for the NH protons indicating a keto tautomer for these Schiff bases. The pyridyl‐substituted Schiff bases containing hydroxyl moiety were found to show the most downfield shift for the NH protons in DMSO solvent, and this was rationalized due to the formation of a six‐ and five‐membered ring using hydrogen bonds for these two compounds. Correspondingly, the olefinic proton of the Schiff bases is also found to be a doublet due to coupling to the amine proton. These Schiff bases exhibited thermochromic properties. Detailed NMR spectral analysis for both the phenyl‐ and pyridyl‐substituted Schiff bases is presented. Copyright © 2010 John Wiley & Sons, Ltd.     

K4[PbSe4]⋅en⋅NH3: A Non‐Oxide,Non‐Halide Inorganic Lead(IV) Compound

The first inorganic lead(IV) compound without oxygen, nitrogen or halogen ligands attached to the lead atom was obtained as the potassium salt of the tetraselenidoplumbate(IV) anion [Pb^IVSe₄]^4?. It is stable under inert conditions which may enable the transfer of the chemistry of chalcogenidogermanate(IV) or chalcogenidostannate(IV) materials, to the lead homologues.     

X-Ray, MP2 and DFT studies of the structure and vibrational spectra of homarinium chloride

The effects of hydrogen bonding, inter- and intramolecular electrostatic interactions on the structure of homarinium chloride, HOMH·Cl, in the crystal and its isolated molecule have been studied by X-ray diffraction, FT-IR, Raman, ¹H and ¹³C NMR spectroscopies, and by the MP2 and DFT theoretical methods. In the crystal, the Cl⁻ anion is connected with protonated homarine via the O–HCl⁻ hydrogen bond of the length of 2.937(4) Å, and two N⁺Cl⁻ intermolecular electrostatic interactions. In the isolated molecule, according to the MP2 and B3LYP calculations, the Cl⁻ anion is engaged in a shorter hydrogen bond (O–HCl⁻ of 2.811–2.861 Å) and in one type of intramolecular electrostatic interactions. The calculated bond lengths and bond angles at the MP2 and B3LYP levels of theory are in good agreement with the X-ray data, except the conformation of the COOH group, which is cis (syn) in the crystal and trans (anti) in the isolated molecule. The tentative assignments for the experimental solid state vibrational spectra of HOMH·Cl and HOMD·Cl have been made on the basis of the B3LYP/6-31G(d,p) calculated frequencies and intensities. The effect of quaternization of picolinic acid on the chemical shifts of the ring protons and carbons is analyzed.     

Four-component relativistic computational NMR study of ferrous,cobalt and nickel bisglycinates

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Substituent effects on (15)N and (13)C NMR chemical shifts of 5-phenyl-1,3,4-oxathiazol-2-ones: a theoretical and spectroscopic study

The synthesis and assignment of (15)N and (13)C NMR signals of the 1,3,4-oxathiazol-2-one ring in a series of para-substituted 5-phenyl derivatives are reported. DFT calculations of (15)N and (13)C chemical shifts correspond closely to observed values. Substituent effects are interpreted in terms of the Hammett correlation and calculated bond orders.