Addressing the stereochemistry of complex organic molecules by density functional theory-NMR

Highly Accurate Prediction of NMR Chemical Shifts from Low-Level Quantum Mechanics Calculations Using Machine Learning

Theoretical predictions of NMR chemical shifts from first-principles can greatly facilitate experimental interpretation and structure identification of molecules in gas, solution, and solid-state phases. However, accurate prediction of chemical shifts using the gold-standard coupled cluster with singles, doubles, and perturbative triple excitations [CCSD(T)] method with a complete basis set (CBS) can be prohibitively expensive. By contrast, machine learning (ML) methods offer inexpensive alternatives for chemical shift predictions but are hampered by generalization to molecules outside the original training set. Here, we propose several new ideas in ML of the chemical shift prediction for H, C, N, and O that first introduce a novel feature representation, based on the atomic chemical shielding tensors within a molecular environment using an inexpensive quantum mechanics (QM) method, and train it to predict NMR chemical shieldings of a high-level composite theory that approaches the accuracy of CCSD(T)/CBS. In addition, we train the ML model through a new progressive active learning workflow that reduces the total number of expensive high-level composite calculations required while allowing the model to continuously improve on unseen data. Furthermore, the algorithm provides an error estimation, signaling potential unreliability in predictions if the error is large. Finally, we introduce a novel approach to keep the rotational invariance of the features using tensor environment vectors (TEVs) that yields a ML model with the highest accuracy compared to a similar model using data augmentation. We illustrate the predictive capacity of the resulting inexpensive shift machine learning (iShiftML) models across several benchmarks, including unseen molecules in the NS372 data set, gas-phase experimental chemical shifts for small organic molecules, and much larger and more complex natural products in which we can accurately differentiate between subtle diastereomers based on chemical shift assignments.

Computational NMR spectroscopy of 205 Tl

We have investigated the NMR chemical shift of 205 Tl in several thallium compounds, ranging from small covalent Tl(I) and Tl(III) molecules to supramolecular complexes with large organic ligands and some thallium halides. NMR calculations were run at the ZORA relativistic level, with and without spin-orbit coupling using few selected GGA and hybrid functionals, namely BP86, PBE, B3LYP, and PBE0. We also tested solvent effects both at the optimization level and at the NMR calculation step. At the ZORA-SO-PBE0 (COSMO) level of theory we find a very good performance of the computational protocol that allows to discard or retain possible structures/conformations based on the agreement between the calculated chemical shift and the experimental value.

Importance of Noncovalent Interactions Involving Sulfur Atoms in Thiopeptide Antibiotics─Glycothiohexide α and Nocathiacin I

Noncovalent interactions involving sulfur atoms play essential roles in protein structure and function by significantly contributing to protein stability, folding, and biological activity. Sulfur is a highly polarizable atom that can participate in many types of noncovalent interactions including hydrogen bonding, sulfur-π interactions, and S-lone pair interactions, but the impact of these sulfur-based interactions on molecular recognition and drug design is still often underappreciated. Here, we examine, using quantum chemical calculations, the roles of sulfur-based noncovalent interactions in complex naturally occurring molecules representative of thiopeptide antibiotics: glycothiohexide α and its close structural analogue nocathiacin I. While donor-acceptor orbital interactions make only very small contributions, electrostatic and dispersion contributions are predicted to be significant in many cases. In pursuit of understanding the magnitudes and nature of these noncovalent interactions, we made potential structural modifications that could significantly expand the chemical space of effective thiopeptide antibiotics.

Computational NMR of carbohydrates: 1. Glucopyranoses

A high-level calculation of ¹ H and ¹³ C NMR chemical shifts of α- and β-d-glucopyranoses is carried out at the DFT level with taking into account their conformational composition to reveal the most effective computational protocols. A number of dedicated DFT functionals in combination with Jensen's pcS-n (n = 0-4) family of basis sets were applied to evaluate the most reliable combination. It was found that BHandHLYP/pcS-2 provided the most accurate and reliable computational protocol. Based on the performed calculations, the established computational protocol is generally recommended for the calculation of ¹ H and ¹³ C NMR chemical shifts of a wide series of carbohydrates.

Atypical Angucyclinones with Ring Expansion and Cleavage from a Marine Streptomyces sp

A unique ring C-expanded angucyclinone, oxemycin A (1), and seven new ring-cleavage derivatives (2-5 and 9-11) were isolated from the marine actinomycete Streptomyces pratensis KCB-132, together with eight known analogues (6-8 and 12-16). Their structures were elucidated by spectroscopic analyses, single-crystal X-ray diffractions, and NMR and ECD calculations. Among these atypical angucyclinones, compound 1 represented the first seven-membered ketoester in the angucyclinone family, which sheds light on the origin of fragmented angucyclinones with C-ring cleavage at C-12/C-12a in the Baeyer-Villiger hypothesis, such as 2-4, while the related "nonoxidized" analogues 5-8 seem to originate from a diverse pathway within the Grob fragmentation hypothesis. Additionally, we have succeeded in the challenging separation of elmenols E and F (12) into their four stereoisomers, which remained stable in aprotic solvents but rapidly racemized under protic conditions. Furthermore, the absolute configurations of LS1924 and its isomers (14 and 15) were assigned by ECD calculations for the first time. Surprisingly, these two bicyclic acetals are susceptible to hydrolysis in solution, resulting in fragmented derivatives 17 and 18 with C-ring cleavage between C-6a and C-7. Compared with ring C-modified angucyclinones, ring A-cleaved 11 was more active to multiple resistant "ESKAPE" pathogens with MIC values ranging from 4.7 to 37.5 μg/mL.

Activation of Vegetable Oils by Reaction with Maleic Anhydride as a Renewable Source in Chemical Processes: New Experimental and Computational NMR Evidence

Vegetable oils are bio-based and sustainable starting materials that can be used to develop chemicals for industrial processes. In this study, the functionalization of three vegetable oils (grape, hemp, and linseed) with maleic anhydride was carried out either by conventional heating or microwave activation to obtain products that, after further reactions, can enhance the water dispersion of oils for industrial applications. To identify the most abundant derivatives formed, trans-3-octene, methyl oleate, and ethyl linoleate were reacted as reference systems. A detailed NMR study, supported by computational evidence, allowed for the identification of the species formed in the reaction of trans-3-octene with maleic anhydride. The signals in the ¹H NMR spectra of the alkenyl succinic anhydride (ASA) moieties bound to the organic chains were clearly identified. The reactions achieved by conventional heating were carried out for 5 h at 200 °C, resulting in similar or lower amounts of ASA units/g of oil with respect to the reactions performed by microwave activation, which, however, induced a higher viscosity of the samples.

Reconsideration of the Structures of Stemara-13(14)-en-18-ol and Related Diterpene Natural Products: Vinylic Hydrogen Chemical Shifts Are Key

The reported synthesis of stemara-13(14)-en-18-ol, which revealed that the structure of this natural product was misassigned, prompted an investigation using density functional theory methods into the structural reassignment of this natural product and related diterpenoids extracted from Calceolaria plants. ¹H and ¹³C chemical shift predictions led to the reassignment of relative configuration, and in one case the carbon skeleton, of several diterpenoids from Calceolaria. In many of these cases, the chemical shift of the vinylic hydrogen was found to be diagnostic.

Computational 1 H and 13 C NMR in structural and stereochemical studies

Present review outlines the advances and perspectives of computational ¹ H and ¹³ C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational ¹ H and ¹³ C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.

Combined application of DP4+ and ANN-PRA to determine the relative configuration of natural products: The alpha-bisabol case study

The combination of computational methods and experimental data from Nuclear Magnetic Resonance (NMR) is a considerably valuable tool in the elucidation of new natural product structures and, also, in the structural revision of previously reported compounds. Until recently, only classical statistical parameters were used, for example, linear correlation coefficient (R² ), mean absolute error (MAE), or root mean square deviation (RMSD), as a way to statistically "validate" the structure pointed out by experimental NMR spectra. Regarding the resolution of the relative configuration of organic molecules, novel tools were available in the last few years to assist in the NMR elucidation process. The most relevant are DP4+, which is based on a Bayesian probability, and ANN-PRA, which is based on artificial neural networks. The combined application of these tools has become the most accurate and important alternative to solve structural and stereochemical problems in natural product chemistry. Therefore, herein, in this case study, we intended to promote these novel tools, exploring the strengths and limitations of each approach in resolving the relative configuration of the sesquiterpene alpha-bisabol. We also highlighted the advantages of the complementary use of H- and C-DP4+ to obtain optimal results in the differentiation of the stereoisomers, validating the proposal with ANN-PRA method.

Revisiting the structure of Heliannuol L: A computational approach

Recently, structural elucidation of natural products has undergone a revolution. The combined use of different modern spectroscopic methods has allowed obtaining a complete structural assignment of natural products using small amounts of sample. However, despite the extraordinary ongoing advances in spectroscopy, the mischaracterization of natural products has been and remains a recurrent problem, especially when the substance presents several stereogenic centers. The misinterpretation of nuclear magnetic resonance (NMR) data has resulted in frequent reports addressing structural reassignment. In this context, a great effort has been devoted to developing quantum chemical calculations that simulate NMR parameters accurately, allowing to achieve a more precise spectral interpretation. In this work, we employed a protocol for theoretical calculations of ¹ H NMR chemical shifts and coupling constants using density functional theory (DFT), followed by the application of the DP4+ method to revisit the structure of Heliannuol L, a member of the Heliannuol class, isolated from Helianthus annuus. Our results indicate that the originally proposed structure of Heliannuol L needs a stereochemical reassignment, placing the hydroxyl bonded to C10 in the opposite side of the methyl and hydroxyl groups bonded to C7 and C8, respectively.

NMR structural characterization from one-bond 13 C13 C couplings: Complete assignment of a hydrogen-poor depsidone

The connectivity, conformation, tautomeric form, and dynamics of a new depsidone (perisalazinic acid) were characterized using one-bond ¹³ C¹³ C NMR scalar couplings (¹ J_CC ) obtained from the INADEQUATE experiment. Characterization of perisalazinic acid using more conventional NMR techniques is problematic due to the extremely limited number of CH protons present. In the present study, 81 candidate structures were considered and a best fit structure was selected by comparing computed ¹ J_CC values for each candidate to 15 experimental values. Of the six flexible moieties in perisalazinic acid, three are adequately represented by a single orientation stabilized by intramolecular hydrogen bonding. The three remaining groups are present as mixtures of conformers with two sites consisting of a pair of conformations and another disordered over six orientations. This study demonstrates the feasibility of complete three-dimensional structural characterization of an unknown using only theoretical and experimental ¹ J_CC values.

One-bond 1 J(15 N─19 F) spin-spin coupling constants of cationic fluorinating reagents: Insights from DFT calculations

We have investigated, by means of density functional theory protocols, the one-bond ¹ J(¹⁵ N─¹⁹ F) spin-spin coupling constants in a series of fluorinating reagents, containing the N─F bond, recently studied experimentally. The results of the calculations show a very good linear relationship with the experimental values, even though only the M06-2X(PCM)/pcJ-2//B3LYP/6-311G(d,p) level affords a very low mean absolute error. The calculations allow to analyze the various molecular orbitals contributions to the J coupling and to rationalize the observed positive sign, corresponding to a negative sign of the reduced spin-pin coupling constant K(N─F). Moreover, of the four Ramsey contributions, only the diamagnetic spin orbit is negligible, whereas the paramagnetic spin orbit and spin dipole terms decrease the magnitude of the Fermi contact (FC) term by an amount that goes from a minimum of 35% up to more than 60% of the FC term itself. Several effects have been investigated, namely, the contribution of the long-range solvent reaction field, relativistic corrections, and conformational and vibrational effects.

The 1 H and 13 C NMR chemical shifts of Strychnos alkaloids revisited at the DFT level

The density functional theory calculation of ¹ H and ¹³ C NMR chemical shifts in a series of ten 10 classically known Strychnos alkaloids with a strychnine skeleton was performed at the PBE0/pcSseg-2//pcseg-2 level. It was found that calculated ¹ H and ¹³ C NMR chemical shifts provided a markedly good correlation with experiment characterized by a mean absolute error of 0.08 ppm in the range of 7 ppm for protons and 1.67 ppm in the range of 150 ppm for carbons, so that a mean absolute percentage error was as small as ~1% in both cases.

Synthesis and structural elucidation of a phthalide analog using NMR analysis and DFT calculations

Phtalides are secondary metabolites found in several fungi with a wide range of biological activities. A novel phthalide analog was synthesized by Diels-Alder reaction between cyclopentadiene and 3,4-dichlorofuran-2(5H)-one. Quantum mechanical calculations were used in conjunction with the spectrometric methods to determine the structure of the title compound. The calculated NMR chemical shifts for eight candidate pairs of enantiomers were compared with the experimental NMR chemical shifts applying the DP4 probability and mean absolute errors methodology. DP4 analysis using ¹ H and ¹³ C NMR chemical shifts without assignment of the signals presented 100% probability for the correct candidate structure 3d, proving the consistency of the method even without spectra interpretation. Results from theoretical calculation and NMR spectra interpretation were in agreement to the structure of rac-(3aR,4S,4aS,5R,8S,8aR,9R,9aS)-3a,9a-dichloro-3a,4,4a,5,8,8a,9,9a-octahydro-4,9:5,8-dimethanonaphtho[2,3-c]furan-1(3H)-one.

Computational NMR Spectroscopy of Ionic Liquids: [C4C1im]Cl/Water Mixtures

In this work, I have analyzed the structure of binary mixtures of 1-butyl-3-methylimidazolium chloride ionic liquid, [C₄C₁im]Cl, and water, using computational NMR spectroscopy. The structure of the complex fluid phase, where the ionic and hydrophobic nature of ionic liquids is further complicated by the addition of water, is first generated by classical Molecular Dynamics (MD) and then validated by calculating the NMR properties with DFT at the ONIOM(B3LYP/cc-pVTZ//B3LYP/3-21G) on clusters extracted during the MD trajectories. Three ionic liquid/water mixtures have been considered with the [C₄C₁im]Cl mole fraction of 1.00, 0.50, and 0.01, that is the pure ionic liquid [C₄C₁im]Cl, the equimolar [C₄C₁im]Cl/water mixture, and a diluted solution of [C₄C₁im]Cl in water. A good agreement is obtained with published experimental data that, at the same time, validates the structural features obtained from the MD and the force field used, and provides an example of the power of NMR spectroscopy applied to complex fluid phases.

Computational 1 H NMR: Part 3. Biochemical studies

This is the third and the last part of three closely interrelated reviews dealing with computation of ¹ H nuclear magnetic resonance chemical shifts and ¹ H-¹ H spin-spin coupling constants. Present review deals with the computation of these parameters in biologically active natural products, carbohydrates, and other molecules of biological origin focusing on stereochemical applications of computational ¹ H nuclear magnetic resonance to these objects.

dos Santos Junior F. Unraveling the helianane family: a complementary quantum mechanical study

Comprehensive work suggesting the amendment of helianane to the open ring curcudiol by means of computational spectroscopy and thermodynamic reasons.

Computational protocols for calculating 13C NMR chemical shifts

The most recent results dealing with the computation of ¹³C NMR chemical shifts in chemistry (small molecules, saturated, unsaturated and aromatic compounds, heterocycles, functional derivatives, coordination complexes, carbocations, and natural products) are reviewed, paying special attention to theoretical background and accuracy, the latter involving solvent effects, vibrational corrections, and relativistic effects.

Recent trends in the structural revision of natural products

Covering: 2012 to 2017 This article reviews recent reports on the structural revision of natural products. Through a critical assessment of the original and revised published structures, the article addresses why each structure was targeted for revision, discusses the techniques and key discrepancies that led to the proposal of the revised structure, and offers measures that may have been taken during the original structure determination to prevent error. With the revised structures in hand, weaknesses of original proposals are assessed, providing a better understanding on the logic behind structure determination.

The 125Te Chemical Shift of Diphenyl Ditelluride: Chasing Conformers over a Flat Energy Surface

The interest in diphenyl ditelluride (Ph₂Te₂) is related to its strict analogy to diphenyl diselenide (Ph₂Se₂), whose capacity to reduce organic peroxides is largely exploited in catalysis and green chemistry. Since the latter is also a promising candidate as an antioxidant drug and mimic of the ubiquitous enzyme glutathione peroxidase (GPx), the use of organotellurides in medicinal chemistry is gaining importance, despite the fact that tellurium has no recognized biological role and its toxicity must be cautiously pondered. Both Ph₂Se₂ and Ph₂Te₂ exhibit significant conformational freedom due to the softness of the inter-chalcogen and carbon–chalcogen bonds, preventing the existence of a unique structure in solution. Therefore, the accurate calculation of the NMR chemical shifts of these flexible molecules is not trivial. In this study, a detailed structural analysis of Ph₂Te₂ is carried out using a computational approach combining classical molecular dynamics and relativistic density functional theory methods. The goal is to establish how structural changes affect the electronic structure of diphenyl ditelluride, particularly the ¹²⁵Te chemical shift.

Theoretical calculations of carbon-hydrogen spin-spin coupling constants

Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.

Method Calibration or Data Fitting?

We investigate by explicit parameter optimization to what extent basis sets of polarized double-ζ quality can introduce compensating errors in five different density functional methods. It is shown that minor changes in the contraction coefficients of the valence functions in the basis sets can have a significant impact and allow different density functional methods to achieve very similar performances. This holds for nuclear magnetic shielding constants and for isomerization energies, barrier heights, and noncovalent interactions. It is furthermore shown that errors due to neglect of vibrational and solvent effects can be absorbed in the combined method and basis set errors. These findings hold for data sets consisting of 50-150 data points. This raises the question of whether the common practice of identifying combinations of density functional methods and basis sets that have a good performance against a selected set of reference data should be considered as data fitting in the combined parameter space spanned by the method and basis set.

Probing long-range spin-spin coupling constants in 2-halo-substituted cyclohexanones and cyclohexanethiones: The role of solvent and stereoelectronic effects

Earlier studies with 2-bromocyclohexanone demonstrated a measurable long-range coupling constant (⁴ J_H2,H6 ) for the equatorial conformer, although ⁴ J_H2,H4 and ⁴ J_H4,H6 were not observed; as a consequence, it is inferred that the carbonyl group plays an important role particularly due to hyperconjugative interactions σ_C2H2 →π*_C═O and σ_C6H6 →π*_C═O. In the present study, NBO analysis and coupling constant calculations were performed to cyclohexanone and cyclohexanethione alpha substituted with F, Cl, and Br, aiming to evaluate the halogen effect and acceptor character of the π* orbital on the long-range coupling pathway. The σ_C2H2 →π*_C1═Y and σ_C6H6 →π*_C1═Y (Y═O and S) hyperconjugative interactions for the equatorial conformer indeed contribute for the ⁴ J_H2,H6 transmission mechanism_. Surprisingly, the ⁴ J_H2,H6 value is higher for the carbonyl compounds, although the interactions σ_C2H2 →π*_C═Y and σ_C6H6 →π*_C═Y are more efficient for the thiocarbonyl compounds. Accordingly, the Fermi contact (FC) contribution for the thiocarbonyl compounds decays deeper than in ketones, thus reducing more the ⁴ J_H2,H6 values. Moreover, both π_C═S →σ*_C─X and π_C═S →σ*_C─H interactions seem to be stronger in thiocarbonyl than in carbonylic compounds. The implicit solvent effect (DMSO and water) on the coupling constant values was negligible when compared with the gas phase. On the other hand, an explicit solvent effect was found and ⁴ J_H2,H6 for the thiocarbonyl compounds appeared to be more sensitive than for the cyclohexanones.

Prediction of 19F NMR Chemical Shifts for Fluorinated Aromatic Compounds

Scaling factors are reported for use in predicting ¹⁹F NMR chemical shifts for fluorinated (hetero)aromatic compounds with relatively low levels of theory. Our recommended scaling factors were developed using a curated data set of 52 compounds, with 100 individual ¹⁹F shifts spanning a range of 153 ppm. With a maximum deviation of 6.5 ppm between experimental and computed shifts, or 4% of the range tested, these scaling factors allow for the assignment of chemical shifts to specific fluorines in multifluorinated aromatics. The utility of this approach is highlighted by several structural reassignments.

Ion pairing in 1-butyl-3-methylpyridinium halide ionic liquids studied using NMR and DFT calculations

Experimental and calculated ¹H, ¹³C and ¹⁵N NMR data of bulk 1-butyl-3-methylimidazolium halides ionic liquids provide key insights on their ion pairing.

A permutation approach to the assignment of the configuration to diastereomeric tetrads by comparison of experimental and ab initio calculated differences in NMR data

Scoring permutations of experimental chemical shift deviations and DFT/GIAO calculated deviations of isotropic shieldings for sets of four diastereomers can help to assign their relative configurations. This method was exercised on a set of diastereomeric Cinchona alkaloid derivatives, where ¹³C NMR data always identified the proper configuration. The presented approach is also an attempt to quantify the assignment by exclusion.

Evaluation of the Factors Impacting the Accuracy of 13C NMR Chemical Shift Predictions using Density Functional Theory-The Advantage of Long-Range Corrected Functionals

The various factors influencing the accuracy of ¹³C NMR calculations using density functional theory (DFT), including the basis set, exchange-correlation (XC) functional, and isotropic shielding calculation method, are evaluated. A wide selection of XC functionals (over 70) were considered, and it was found that long-range corrected functionals offer a significant improvement over the other classes of functionals. Based on a thorough study, it is recommended that for calculating NMR chemical shifts (δ) one should use the CSGT method, the COSMO solvation model, and the LC-TPSSTPSS exchange-correlation functional in conjunction with the cc-pVTZ basis set. A selection of problems in natural product identification are considered in light of the newly recommended level of theory.

Application of Computational Chemical Shift Prediction Techniques to the Cereoanhydride Structure Problem-Carboxylate Complications

Despite the vast array of techniques available to modern-day chemists, structural misassignments still occur. These misassignments are often only realized upon attempted synthesis, when the spectra of synthesized products do not match previously reported spectra. This was the case with marine natural product cereoanhydride. The originally proposed 7-membered ring anhydride (1) was shown to be incorrect, although a likely precursor to the correct structure (2) in both its laboratory synthesis and biosynthesis. Herein, in addition to showing how NMR computations could have been used to arrive at the correct structure, we show that the conversion of 1 to 2 is indeed energetically viable, and we highlight complications in predicting NMR chemical shifts for molecules with acidic protons.

Characterization of novel isobenzofuranones by DFT calculations and 2D NMR analysis

Phthalides are frequently found in naturally occurring substances and exhibit a broad spectrum of biological activities. In the search for compounds with insecticidal activity, phthalides have been used as versatile building blocks for the syntheses of novel potential agrochemicals. In our work, the Diels-Alder reaction between furan-2(5H)-one and cyclopentadiene was used successfully to obtain (3aR,4S,7R,7aS)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aS,4R,7S,7aR)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one (2) and (3aS,4S,7R,7aR)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aR,4R,7S,7aS)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one (3). The endo adduct (2) was brominated to afford (3aR,4R,5R,7R,7aS,8R)-5,8-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aS,4S,5S,7S,7aR,8S)-5,8-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one (4) and (3aS,4R,5R,6S,7S,7aR)-5,6-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aR,4S,5S,6R,7R,7aS)-5,6-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one (5). Following the initial analysis of the NMR spectra and the proposed two novel unforeseen products, we have decided to fully analyze the classical and non-classical assay structures with the aid of computational calculations. Computation to predict the (13) C and (1) H chemical shifts for mean absolute error analyses have been carried out by gauge-including atomic orbital method at M06-2X/6-31+G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for all viable conformers. Characterization of the novel unforeseen compounds (4) and (5) were not possible by employing only the experimental NMR data; however, a more conclusive structural identification was performed by comparing the experimental and theoretical (1) H and (13) C chemical shifts by mean absolute error and DP4 probability analyses. Copyright © 2016 John Wiley & Sons, Ltd.

Accurate prediction of the optical rotation and NMR properties for highly flexible chiral natural products

Despite advances in electronic structure theory the theoretical prediction of spectroscopic properties remains a computational challenge.

Beyond DP4: an Improved Probability for the Stereochemical Assignment of Isomeric Compounds using Quantum Chemical Calculations of NMR Shifts

The DP4 probability is one of the most sophisticated and popular approaches for the stereochemical assignment of organic molecules using GIAO NMR chemical shift calculations when only one set of experimental data is available. In order to improve the performance of the method, we have developed a modified probability (DP4+), whose main differences from the original DP4 are the inclusion of unscaled data and the use of higher levels of theory for the NMR calculation procedure. With these modifications, a significant improvement in the overall performance was achieved, providing accurate and confident results in establishing the stereochemistry of 48 challenging isomeric compounds.

Absolute Configuration of (-)-Centratherin, a Sesquiterpenoid Lactone, Defined by Means of Chiroptical Spectroscopy

(-)-Centratherin is a bioactive sesquiterpenoid lactone, whose absolute configuration (AC) was not established, but has been proposed based on those of germacrane precursors. To verify this proposal, the experimental electronic circular dichroism (ECD), electronic dissymmetry factor (EDF), optical rotatory dispersion (ORD), vibrational circular dichroism (VCD), and vibrational dissymmetry factor (VDF) spectra of (-)-centratherin have been analyzed with the corresponding density functional theoretical predictions. These analyses suggest the AC of naturally occurring (-)-centratherin to be (6R,7R,8S,10R,2'Z).

Advanced Structural Determination of Diterpene Esters Using Molecular Modeling and NMR Spectroscopy

Three new jatrophane esters (1-3) were isolated from Euphorbia amygdaloides ssp. semiperfoliata, including an unprecedented macrocyclic jatrophane ester bearing a hemiketal substructure, named jatrohemiketal (3). The chemical structures of compounds 1-3 and their relative configurations were determined by spectroscopic analysis. The absolute configuration of compound 3 was determined unambiguously through an original strategy combining NMR spectroscopy and molecular modeling. Conformational search calculations were performed for the four possible diastereomers 3a-3d differing in their C-6 and C-9 stereocenters, and the lowest energy conformer was used as input structure for geometry optimization. The prediction of NMR parameters ((1)H and (13)C chemical shifts and (1)H-(1)H coupling constants) by density functional theory (DFT) calculations allowed identifying the most plausible diastereomer. Finally, the stereostructure of 3 was solved by comparison of the structural features obtained by molecular modeling for 3a-3d with NMR-derived data (the values of dihedral angles deduced from the vicinal proton-proton coupling constants ((3)JHH) and interproton distances determined by ROESY). The methodology described herein provides an efficient way to solve or confirm structural elucidation of new macrocyclic diterpene esters, in particular when no crystal structure is available.