Relativistic Force Field: Parametrization of 13C–1H Nuclear Spin–Spin Coupling Constants

Conformational Sampling in Computational Studies of Natural Products: Why Is It Important?

Conformational sampling is a vital component of a reliable computational chemistry investigation. With the aim of illustrating the importance of conformational sampling, and building awareness among new practitioners, we present a series of case studies that show how the quality and reliability of computational studies depend on undertaking a thorough conformer search. The examples are drawn from the most common types of research questions in natural products chemistry, but the fundamental principles apply more generally to computational studies of molecular structure and behavior in any field of chemistry.

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.

Peculiar Reaction Products and Mechanisms Revisited with Machine Learning-Augmented Computational NMR

DU8ML, a fast and accurate machine learning-augmented density functional theory (DFT) method for computing nuclear magnetic resonance (NMR) spectra, proved effective for high-throughput revision of misassigned natural products. In this paper, we disclose another important aspect of its application: correction of unusual reaction mechanisms originally proposed because of incorrect product structures.

DU8ML: Machine Learning-Augmented Density Functional Theory Nuclear Magnetic Resonance Computations for High-Throughput In Silico Solution Structure Validation and Revision of Complex Alkaloids

Machine learning (ML) profoundly improves the accuracy of the fast DU8+ hybrid density functional theory/parametric computations of nuclear magnetic resonance spectra, allowing for high throughput in silico validation and revision of complex alkaloids and other natural products. Of nearly 170 alkaloids surveyed, 35 structures are revised with the next-generation ML-augmented DU8 method, termed DU8ML.

Maximizing Step-Normalized Increases in Molecular Complexity: Formal [4+2+2+2] Photoinduced Cyclization Cascade to Access Polyheterocycles Possessing Privileged Substructures

A new complexity building photoinduced cascade which amounts to an unprecedented formal [4+2+2+2] cycloaddition topology is developed to access complex nitrogen polyheterocycles. This photocascade is initiated by the excited state intramolecular proton transfer (ESIPT) in aromatic amino ketones with tethered dual unsaturated pendants, i.e. pyrrole and alkenic moieties, resulting in the formation of four σ-bonds and setting six new stereogenic centers in a single experimentally simple photochemical step with up to 220 mcbit complexity increases.

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.

Karplus relationships of the 2 JHNα and 3 JΗΝβ couplings in organic azides

Density functional theory (DFT) and second-order polarization propagator approximation (SOPPA) computations in model organic azides revealed a Karplus-like dependence not only of the vicinal ³ J_H-C-Nα-Nβ coupling but also of the geminal ² J_H-C-Nα one, with the H-C-N_α N_β dihedral angle. Karplus equations were derived from the DFT computations on the isopropylazide model system. In light of these stablished relationships, natural abundance ¹ H-¹⁵ N couplings obtained for the azide group of the zidovudine antiviral helped to probe its conformation around the C-N_α bond as being of the synclinal type.

Structural characterisation of natural products by means of quantum chemical calculations of NMR parameters: new insights

In this review, we focus in all aspects of NMR simulation of natural products, from the fundamentals to the new computational toolboxes available, combining advanced quantum chemical calculations with upstream data processing and machine learning.

Quantum mechanical NMR full spin analysis in pharmaceutical identity testing and quality control

Issues related to pharmaceutical quality are arising at an alarming rate. Pharmaceutical quality concerns both the Active Pharmaceutical Ingredients (APIs) and the Finished Drug Product/ Formulation. Recently, there has been a significant increase in the number of reports of harmful impurities in marketed drug formulations. Impurities range from solvents, reactants, adulterants, and catalysts to synthetic byproducts. Quality concerns in commercial preparations may also arise due to shelf life stability. Furthermore, a number of falsified and substandard drug cases have been reported. Most of the techniques which are currently in place can, at best, detect the impurities, but cannot identify them unless they are already known and can be compared to a standard. On the other hand, ¹H NMR spectroscopy detects all the hydrogen containing species, typically provides information to elucidate structures partially or even completely, and through its absolute quantitative capabilities even can detect the presence hydrogen-free species indirectly. The structural properties that produce ¹H NMR signals as characteristic representations of a given molecule are the chemical shifts (δ in ppm) and coupling constants (J in Hz). Along with the line widths (ω_1/2 in Hz), these parameters are bound to both the molecule and the NMR experimental conditions by quantum mechanical (QM) principles. This means that the ¹H NMR spectra of APIs can be precisely calculated and compared to the experimental data. This review explains how ¹H NMR spectroscopy coupled with Full Spin Analysis can contribute towards the quality control of pharmaceuticals by improving structural dereplication and achieving simultaneous quantification of both APIs and their contaminants.

EBC-232 and 323: A Structural Conundrum Necessitating Unification of Five In Silico Prediction and Elucidation Methods

Structurally unique halimanes EBC-232 and EBC-323, isolated from the Australian rainforest plant Croton insularis, proved considerably difficult to elucidate. The two diastereomers, which consist an unusual oxo-6,7-spiro ring system fused to a dihydrofuran, were solved by unification and consultation of five in silico NMR elucidation and prediction methods [i.e., ACDLabs, olefin strain energy (OSE), DP4, DU8+ and TD DFT CD]. Structure elucidation challenges of this nature are prime test case examples for empowering future AI learning in structure elucidation.

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.

DFT computational schemes for 1 H and 13 C NMR chemical shifts of natural products, exemplified by strychnine

A number of computational schemes based on different Density Functional Theory (DFT) functionals in combination with a number of basis sets were tested in the calculation of ¹ H and ¹³ C NMR chemical shifts of strychnine, as a typical representative of the vitally important natural products, and used as a challenging benchmark and a rigorous test for such calculations. It was found that the most accurate computational scheme, as compared with experiment, was PBE0/pcSseg-4//pcseg-3 characterized by a mean absolute error of 0.07 ppm for the range of about 7 ppm for ¹ H NMR chemical shifts and that of only 1.13 ppm for ¹³ C NMR chemical shifts spread over the range of about 150 ppm. For more practical purposes, including investigation of larger molecules from this series, a much more economical computational scheme, PBE0/pcSseg-2//pcseg-2, characterized by almost the same accuracy and much less computational demand, was recommended.

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.

Characterization by Empirical and Computational Methods of Dictyospiromide, an Intriguing Antioxidant Alkaloid from the Marine Alga Dictyota coriacea

The challenging structural motif of dictyospiromide (1), a spirosuccinimide alkaloid with antioxidant properties that are associated with activation of the Nrf2/ARE signaling pathway, was assigned using contemporary NMR experiments complemented with anisotropic NMR, chiroptical, and computational methodologies. Anisotropic NMR parameters provided critical orthogonal verification of the configuration of the difficult to assign spiro carbon and the other stereogenic centers in 1.

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.

Photoinitiated Cascade for Rapid Access to Pyrroloquinazolinone Core of Vasicinone, Luotonins, and Related Alkaloids

Furylimines of aromatic o-nitro aldehydes undergo a photoinduced cascade transformation offering rapid atom- and step-economical access to complex polyheterocyclic scaffolds possessing a privileged pyrroloquinazolinone core.

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

Enhancing the utility of 1JCH coupling constants in structural studies through optimized DFT analysis

High accuracy for DFT-predicted ¹J_CH-couplings can be achieved without ad hoc corrections or empirical scaling by careful selection of the DFT method utilized for geometry optimization and J-coupling calculations.

Long-range heteronuclear J-coupling constants in esters: Implications for 13C metabolic MRI by side-arm parahydrogen-induced polarization

Side-arm parahydrogen induced polarization (PHIP-SAH) presents a cost-effective method for hyperpolarization of ¹³C metabolites (e.g. acetate, pyruvate) for metabolic MRI. The timing and efficiency of typical spin order transfer methods including magnetic field cycling and tailored RF pulse sequences crucially depends on the heteronuclear J coupling network between nascent parahydrogen protons and ¹³C, post-parahydrogenation of the target compound. In this work, heteronuclear ⁿJ_HC (1 < n ≤ 5) couplings of acetate and pyruvate esters pertinent for PHIP-SAH were investigated experimentally using selective HSQMBC-based pulse sequences and numerically using DFT simulations. The CLIP-HSQMBC technique was used to quantify 2/3-bond J_HC couplings, and 4/5-bond J_HC ≲ 0.5 Hz were estimated by the sel-HSQMBC-TOCSY approach. Experimental and numerical (DFT-simulated) ⁿJ_HC couplings were strongly correlated (P < 0.001). Implications for ¹³C hyperpolarization by magnetic field cycling, and PH-INEPT and ESOTHERIC type spin order transfer methods for PHIP-SAH were assessed, and the influence of direct nascent parahydrogen proton to ¹³C coupling when compared with indirect homonuclear TOCSY-type transfer through intermediate (non-nascent parahydrogen) protons was studied by the density matrix approach.

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.

NMR and experimental reinvestigation of the condensation reaction between γ-methylene-α,β-unsaturated aldehydes and propargyl aldehydes

An experimental and computational study of the reaction between γ-methylene enals and propargyl aldehydes uncovered a deconjugative aldol condensation.

Structural revision of two unusual rhamnofolane diterpenes, curcusones I and J, by means of DFT calculations of NMR shifts and coupling constants

The structures of two unusual rhamnofolane diterpenes, curcusones I and J, have been revised using quantum calculations of NMR shifts.

Step-Economical Photoassisted Diversity-Oriented Synthesis: Sustaining Cascade Photoreactions in Oxalyl Anilides to Access Complex Polyheterocyclic Molecular Architectures

Atom- and step-economy in photoassisted diversity-oriented synthesis (DOS) is achieved with a versatile oxalyl linker offering rapid access to complex alkaloid mimics in very few experimentally simple steps: (i) it allows for fast tethering of the photoactive core to the unsaturated pendants, especially important in the case of (hetero)aromatic amines-essentially a one-pot reaction with no isolation of intermediates; (ii) the α-dicarbonyl tether acts as a chromophore enhancer, extending the conjugation chain and facilitating the "harvest" of the lower energy photons for the primary and secondary photoreactions; (iii) it enhances the quantum yield of intersystem crossing (ISC), i.e., it is capable of sensitizing secondary photochemical processes in the cascade; and (iv) the tether forms an additional heterocyclic moiety, imidazolidine-4,5-dione, a known pharmacophore. The overall photoassisted cascade is an efficient complexity-building process as quantified by computed step-normalized complexity indices, leading to extended polyheterocyclic molecular architectures comparable in complexity to natural products such as paclitaxel while requiring only 2-4 simple synthetic steps from readily available chemical feedstock.

Highly resolved HSQC experiments for the fast and accurate measurement of homonuclear and heteronuclear coupling constants

A number of J-upscaled NMR experiments are currently available to measure coupling constants along the indirect F1 dimension of a 2D spectrum. A major drawback is the limited F1 digital resolution that requires long acquisition times in order to achieve reasonably accurate measures. Here is shown how high levels of F1 digital resolution in a multiple-purpose HSQC experiment can be easily achieved by implementing a general J/δ-scaling strategy. In particular, a set of new J-resolved HSQC experiments is presented for a faster and much more accurate J determination in small molecules. Several options and practical aspects are discussed and exemplified by measuring the magnitude and/or the sign of several homo- and heteronuclear coupling constants in one shot.

Structure Determination and Mechanism of Formation of a seco-Moreliane Derivative Supported by Computational Analysis

Basic hydrolysis of a dichloromethane extract of Stevia lucida yielded (4R,5S,7R,9R,10R,11R)-7,9-dihydroxylongipin-2-en-1-one (1), which was oxidized and subjected to acidic conditions to generate the new seco-moreliane derivative 3. The structure of 3 was established based on NMR data interpretation and confirmed computationally. A plausible mechanism for the carbocationic rearrangement of the trione 2 to the seco-moreliane 3 was supported by DFT computations.

Revision of the Structure of Acremine P from a Marine-Derived Strain of Acremonium persicinum

The previously published structure of the fungal metabolite acremine P is revised by re-evaluation of chemical shift values and NOESY data, and by DFT calculations.

High-Throughput in Silico Structure Validation and Revision of Halogenated Natural Products Is Enabled by Parametric Corrections to DFT-Computed 13C NMR Chemical Shifts and Spin-Spin Coupling Constants

Halogenated natural products constitute diverse and promising feedstock for molecular pharmaceuticals. However, their solution-structure elucidation by NMR presents several challenges, including the lack of fast methods to compute ¹³C chemical shifts for carbons bearing heavy atoms. We show that parametric corrections to DFT-computed chemical shifts in conjunction with rff-computed spin-spin coupling constants allow for fast and reliable screening of a large number of reported halogenated natural products, resulting in expedient structure validation or revision. In this paper, we examine more than 100 structures of halogenated terpenoids and other natural products with the new parametric approach and demonstrate that the accuracy of the combined method is sufficient to identify misassignments and suggest revisions in most cases (16 structures are revised). As the 1D ¹H and ¹³C NMR data are ubiquitous and most routinely used in solution structure elucidation, this fast and efficient two-criterion method (nuclear spin-spin coupling and ¹³C chemical shifts) which we term DU8+ is recommended as the first essential step in structure assignment and validation.

Doubling the power of DP4 for computational structure elucidation

Improvements to the DP4 computational structure elucidation method have led to a 2-fold reduction in structural uncertainty and 7-fold improvement of statistical confidence.

A novel withanolide with an unprecedented carbon skeleton from Physalis angulata

Aromaphysalin A (1), possessing an exceptional C(11)–C(15) bond and a rearranged 4,9-cyclized aromatic ring, is isolated from of Physalis angulata.

State of the art and perspectives in the application of quantum chemical prediction of 1 H and 13 C chemical shifts and scalar couplings for structural elucidation of organic compounds

Quantum mechanical prediction of chemical shifts and scalar couplings involving ¹ H and ¹³ C nuclei is now a popular tool in structural elucidation of organic compounds. Here, we summarize the current state of the art and present to the reader present limitations and problems, mostly related to treatment of conformational flexibility, as well as future perspectives and potential applications in the field.

Investigation of two- and three-bond carbon-hydrogen coupling constants in cinnamic acid based compounds

Two- and three-bond coupling constants (² J_HC and ³ J_HC ) were determined for a series of 12 substituted cinnamic acids using a selective 2D inphase/antiphase (IPAP)-single quantum multiple bond correlation (HSQMBC) and 1D proton coupled ¹³ C NMR experiments. The coupling constants from two methods were compared and found to give very similar values. The results showed coupling constant values ranging from 1.7 to 9.7 Hz and 1.0 to 9.6 Hz for the IPAP-HSQMBC and the direct ¹³ C NMR experiments, respectively. The experimental values of the coupling constants were compared with discrete density functional theory (DFT) calculated values and were found to be in good agreement for the ³ J_HC . However, the DFT method under estimated the ² J_HC coupling constants. Knowing the limitations of the measurement and calculation of these multibond coupling constants will add confidence to the assignment of conformation or stereochemical aspects of complex molecules like natural products. Copyright © 2016 John Wiley & Sons, Ltd.

Photoassisted access to complex polyheterocycles containing a β-lactam moiety

Intramolecular cycloadditions of aza-o-xylylenes generated via excited state intramolecular proton transfer (ESIPT) to furanacetic acid-based unsaturated pendants was shown to overcome the unfavorable energetics of the azetidinone ring formation, offering rapid access to β-lactams as primary photoproducts. These 2,3- and 3,4-dihydrofuran-containing reactive intermediates are suitable for a broad spectrum of postphotochemical transformations yielding complex polyheterocyclic molecular architectures possessing the β-lactam moiety.