Toward the complete prediction of the 1H and 13C NMR spectra of complex organic molecules by DFT methods: application to natural substances

The NMR parameters (1H and 13C chemical shifts and coupling constants) for a series of naturally occurring molecules have been calculated mostly with DFT methods, and their spectra compared with available experimental ones. The comparison includes strychnine as a test case, as well as some examples of recently isolated natural products (corianlactone, daphnipaxinin, boletunone B) featuring unusual and/or crowded structures and, in the case of boletunone B, being the subject of a recent revision. Whenever experimental spectra were obtained in polar solvents, the calculation of NMR parameters was also carried out with the Integral Equation-Formalism Polarizable Continuum Model (IEF-PCM) continuum method. The computed results generally show a good agreement with experiment, as judged not only by statistical parameters but also by visual comparison of line spectra. The origin of the remaining discrepancies is attributed to the incomplete modeling of conformational and specific solvent effects.     

On the first polyarsenic organic compound from nature: arsenicin A from the New Caledonian marine sponge Echinochalina bargibanti

Reported here is the first polyarsenic compound ever found in nature. Denominated arsenicin A, it was isolated along a bioassay-guided fractionation of the organic extract of the poecilosclerid sponge Echinochalina bargibanti collected from the north-eastern coast of New Caledonia. In defining an adamantine-type polyarsenic structure for this compound, deceptively simple NMR spectra were complemented by extensive mass spectral analysis. However, it was only the synthesis of a model compound that provided the basis to discriminate structure 4 from other spectrally compatible structures for arsenicin A; to this end, a comparative ab initio simulation of IR spectra for the natural and the synthetic compounds was decisive. Arsenicin A is endowed with potent bactericidal and fungicidal activities on human pathogenic strains. All this may revive pharmacological interest in arsenic compounds while prompting us to rethink the arsenic cycle in nature.     

A minimalist NMR approach for the structural revision of mucoxin

In an attempt to revise the structural assignment of mucoxin, and faced with 64 diastereomeric possibilities, we resorted to the synthesis of truncated structures that contained the core stereochemical sites. Twelve stereochemical analogues were synthesized, their (1)H and (13)C NMR spectra were analyzed and four recurring stereochemical trends were distilled from the data. Applying the observed trends to the diastereomeric population pared the possible choices for the correct structure of mucoxin from 64 to 4. Synthesis of these analogues led to the identification of the correct structure of mucoxin.     

Atomic Contributions from Spin‐Orbit Coupling to 29Si NMR Chemical Shifts in Metallasilatrane Complexes

New members of a novel class of metallasilatrane complexes [X‐Si‐(μ‐mt)₄‐M‐Y], with M=Ni, Pd, Pt, X=F, Cl, Y=Cl, Br, I, and mt=2‐mercapto‐1‐methylimidazolide, have been synthesized and characterized structurally by X‐ray diffraction and by ²⁹Si solid‐state NMR. Spin‐orbit (SO) effects on the ²⁹Si chemical shifts induced by the metal, by the sulfur atoms in the ligand, and by heavy halide ligands Y=Cl, Br, I were investigated with the help of relativistic density functional calculations. Operators used in the calculations were constructed such that SO coupling can selectively be switched off for certain atoms. The unexpectedly large SO effects on the ²⁹Si shielding in the Ni complex with X=Y=Cl reported recently originate directly from the Ni atom, not from other moderately heavy atoms in the complex. With respect to Pd, SO effects are amplified for Ni owing to its smaller ligand‐field splitting, despite the smaller nuclear charge. In the X=Cl, Y=Cl, Br, I series of complexes the Y ligand strongly modulates the ²⁹Si shift by amplifying or suppressing the metal SO effects. The pronounced delocalization of the partially covalent M←Y bond plays an important role in modulating the ²⁹Si shielding. We also demonstrate an influence from the X ligand on the ²⁹Si SO shielding contributions originating at Y. The NMR spectra for [X‐Si‐(μ‐mt)₄‐M‐Y] must be interpreted mainly based on electronic and relativistic effects, rather than structural differences between the complexes. The results highlight the sometimes unintuitive role of SO coupling in NMR spectra of complexes containing heavy atoms.     

A New Metric for Evaluating DFT Calculated Proton and Carbon Chemical Shifts of Natural Products and Organic Compounds

The calculation of DFT (density functional theory) chemical shifts have become an important technique for the verification of a proposed structure. An easily calculated metric developed for proton and carbon chemical shifts of natural products and organic compounds, the calculated chemical shift index (CCSI), has been developed, which uses the deviation of each pair of calculated and experimental chemical shifts. The mean absolute deviation (MAD), which is commonly used as the goodness of fit metric for DFT calculated chemical shifts, can conceal large deviations in the calculated data. A classification strategy is also proposed for the CCSI to highlight when further assessment of the NMR data is required.     

Connecting Discrete Stereoclusters by Using DFT and NMR Spectroscopy: The Case of Nivariol

The structural determination of small organic molecules is mainly undertaken by using NMR techniques, although it is increasingly supplemented by using computational methods. NMR parameters, such as chemical shifts and coupling constants, are extremely sensitive indicators of local molecular conformation and are a source of structural evidence. However, their interpretation is fairly challenging in many circumstances, such as the case of the new polyether squalene derivative nivariol, the structure of which was elucidated by means of NMR spectroscopy and DFT calculations. The potential flexibility of this molecule and the high number of quaternary carbon atoms that it contains make its configurational assignment very difficult. Moreover, the relative configuration of four separated stereoclusters was established and subsequently connected by using NOE and J‐based analysis, as well as by a comparison of its experimental ¹³C NMR chemical shifts with the corresponding population‐weighted values, as calculated by using DFT methods. Limitations of these used approaches became apparent but were overcome by combining the two methods.     

Computational Chemistry to the Rescue: Modern Toolboxes for the Assignment of Complex Molecules by GIAO NMR Calculations

The calculations of NMR properties of molecules using quantum chemical methods have deeply impacted several branches of organic chemistry. They are particularly important in structural or stereochemical assignments of organic compounds, with implications in total synthesis, stereoselective reactions, and natural products chemistry. In studying the evolution of the strategies developed to support (or reject) a structural proposal, it becomes clear that the most effective and accurate ones involve sophisticated procedures to correlate experimental and computational data. Owing to their relatively high mathematical complexity, such calculations (CP3, DP4, ANN‐PRA) are often carried out using additional computational resources provided by the authors (such as applets or Excel files). This Minireview will cover the state‐of‐the‐art of these toolboxes in the assignment of organic molecules, including mathematical definitions, updates, and discussion of relevant examples.     

Computational NMR spectroscopy: reversing the information flow

Work on computational NMR recently carried out at our Laboratory in Padova is reviewed. We summarize our results concerning the calculation of NMR properties (chemical shifts and spin–spin coupling constants) in a variety of contexts, from the structure elucidation of complex organic molecules or molecules containing heavy atoms to weakly interacting species, such as those involved in hydrogen bonding or van der Waals CH-π interactions. We also present some original results, viz. the calculated ¹H and ¹³C spectra of the putative natural substance nimbosodione, the first examples of calculated ¹⁸¹Ta chemical shifts, spin–spin couplings in and through-space coupling constants involving ²⁰⁵Tl.     

Heteronuclear NMR Spectroscopy as a Surface‐Selective Technique: A Unique Look at the Hydroxyl Groups of γ‐Alumina.

The surface hydroxyl groups of γ‐alumina dehydroxylated at 500 °C were studied by a combination of one‐ and two‐dimensional homo‐ and heteronuclear ¹H and ²⁷Al NMR spectroscopy at high magnetic field. In particular, by harnessing ¹H–²⁷Al dipolar interactions, a high selectivity was achieved in unveiling the topology of the alumina surface. The terminal versus bridging character of the hydroxyl groups observed in the ¹H magic‐angle spinning (MAS) NMR spectrum was demonstrated thanks to ¹H–²⁷Al RESPDOR (resonance‐echo saturation‐pulse double‐resonance). In a further step the hydroxyl groups were assigned to their aluminium neighbours thanks to a {¹H}‐²⁷Al dipolar heteronuclear multiple quantum correlation (D‐HMQC), which was used to establish a first coordination map. Then, in combination with ¹H–¹H double quantum (DQ) MAS, these elements helped to reveal intimate structural features of the surface hydroxyls. Finally, the nature of a peculiar reactive hydroxyl group was demonstrated following this methodology in the case of CO₂ reactivity with alumina.     

Computational study of 19F NMR spectra of double four ring-containing Si/Ge-zeolites.

(19)F NMR chemical shifts are calculated in order to study the F(-) environment in double four ring (D4R) containing Si/Ge-zeolites. The calculations with the DFT/CSGT/B3PW91 methodology yielded an agreement within 2 ppm with respect to the experimental peaks corresponding to the D4R units containing 8Si0Ge, 7Si1Ge and 0Si8Ge of the octadecasil zeolite. The optimisation of the 7Si1Ge-, 6Si2Ge-, 5Si3Ge- and 4Si4Ge-D4R units with DFT/B3LYP methodology shows that a covalent Ge-F bond is formed and therefore a Ge atom in the D4R is pentacoordinated. The displacement of the fluoride ion towards a Ge atom in the Ge-containing D4R units locates four Si/Ge atoms in the close vicinity of the F(-) and this makes possible a rationalization of the (19)F NMR signals in groups according to the number of Si (n) and Ge (m) atoms in the nearest F(-) environment, F-Si(n)Ge(m) (where n+m=4). Thus, the calculated chemical shifts show that higher values are observed when the number of Ge atoms in the nearest F(-) environment increases.