Hybrid Density Functional Methods Empirically Optimized for the Computation of (13)C and (1)H Chemical Shifts in Chloroform Solution

A DFT/MRCI Hamiltonian parameterized using only ab initio data: I. valence excited states

A new combined density functional theory and multi-reference configuration interaction (DFT/MRCI) Hamiltonian parameterized solely using the benchmark ab initio vertical excitation energies obtained from the QUEST databases is presented. This new formulation differs from all previous versions of the method in that the choice of the underlying exchange-correlation (XC) functional employed to construct the one-particle (orbital) basis is considered, and a new XC functional, QTP17, is chosen for its ability to generate a balanced description of core and valence vertical excitation energies. The ability of the new DFT/MRCI Hamiltonian, termed QE8, to furnish accurate excitation energies is confirmed using benchmark quantum chemistry computations, and a mean absolute error of 0.16 eV is determined for the wide range of electronic excitations included in the validation dataset. In particular, the QE8 Hamiltonian dramatically improves the performance of DFT/MRCI for doubly excited states. The performance of fast approximate DFT/MRCI methods, p-DFT/MRCI and DFT/MRCI(2), is also evaluated using the QE8 Hamiltonian, and they are found to yield excitation energies in quantitative agreement with the parent DFT/MRCI method, with the two methods exhibiting a mean difference of 0.01 eV with respect to DFT/MRCI over the entire benchmark set.

NMR detection of the strained metallacycles in organolithiums: theoretical study

For the first time through quantum chemistry methods, the effective use of 1JCLi spin-spin coupling constants as descriptors for assessing the formation of strained metallacycles is demonstrated. Both acyclic organolithiums and 3- to 7-membered metallacycles are examined. 80 organolithium compounds, including both monomeric and dimeric species, with ligands containing fluorine, nitrogen, oxygen, and carbon (in the form of carbanions), are tested. In general, the 1JCLi values below 12 Hz for monomeric species and below 6 Hz for dimeric species serve as clear indicators of strained monomeric metallacycle formation (for 6Li nuclei). The primary contributor to the overall 1JCLi value is the Fermi-contact term, which correlates directly with the carbon-lithium interatomic distance and allows to distinguish between dimers and monomers.

Experimental and Computational Investigation of the Oxime Bond Stereochemistry in c-Jun N-terminal Kinase 3 Inhibitors 11H-Indeno[1,2-b]quinoxalin-11-one Oxime and Tryptanthrin-6-oxime

11H-Indeno[1,2-b]quinoxalin-11-one oxime (IQ-1) and tryptanthrin-6-oxime are potent c-Jun N-terminal kinase 3 (JNK-3) inhibitors demonstrating neuroprotective, anti-inflammatory and anti-arthritic activity. However, the stereochemical configuration of the oxime carbon-nitrogen double bond (E- or Z-) in these compounds was so far unknown. In this contribution, we report the results of the determination of the double bond configuration in the solid state by single crystal X-ray diffraction and in solution by 1D and 2D NMR techniques and DFT calculations. It was found that both in the solid state and in solution, IQ-1 adopts the E-configuration stabilized by intermolecular hydrogen bonds, in contrast to previously assumed Z-configuration that could be stabilized only by an intramolecular hydrogen bond.

Structure Elucidation of Secondary Metabolites: Current Frontiers and Lingering Pitfalls

Analytical methods allow for the structure determination of submilligram quantities of complex secondary metabolites. This has been driven in large part by advances in NMR spectroscopic capabilities, including access to high-field magnets equipped with cryogenic probes. Experimental NMR spectroscopy may now be complemented by remarkably accurate carbon-13 NMR calculations using state-of-the-art DFT software packages. Additionally, microED analysis stands to have a profound effect on structure elucidation by providing X-ray-like images of microcrystalline samples of analytes. Nonetheless, lingering pitfalls in structure elucidation remain, particularly for isolates that are unstable or highly oxidized. In this Account, we discuss three projects from our laboratory that highlight nonoverlapping challenges to the field, with implications for chemical, synthetic, and mechanism of action studies. We first discuss the lomaiviticins, complex unsaturated polyketide natural products disclosed in 2001. The original structures were derived from NMR, HRMS, UV-vis, and IR analysis. Owing to the synthetic challenges presented by their structures and the absence of X-ray crystallographic data, the structure assignments remained untested for nearly two decades. In 2021, the Nelson group at Caltech carried out microED analysis of (-)-lomaiviticin C, leading to the startling discovery that the original structure assignment of the lomaiviticins was incorrect. Acquisition of higher-field (800 MHz 1H, cold probe) NMR data as well as DFT calculations provided insights into the basis for the original misassignment and lent further support to the new structure identified by microED. Reanalysis of the 2001 data set reveals that the two structure assignments are nearly indistinguishable, underscoring the limitations of NMR-based characterization. We then discuss the structure elucidation of colibactin, a complex, nonisolable microbiome metabolite implicated in colorectal cancer. The colibactin biosynthetic gene cluster was detected in 2006, but owing to colibactin's instability and low levels of production, it could not be isolated or characterized. We used a combination of chemical synthesis, mechanism of action studies, and biosynthetic analysis to identify the substructures in colibactin. These studies, coupled with isotope labeling and tandem MS analysis of colibactin-derived DNA interstrand cross-links, ultimately led to a structure assignment for the metabolite. We then discuss the ocimicides, plant secondary metabolites that were studied as agents against drug-resistant P. falciparum. We synthesized the core structure of the ocimicides and found significant discrepancies between our experimental NMR spectroscopic data and that reported for the natural products. We determined the theoretical carbon-13 NMR shifts for 32 diastereomers of the ocimicides. These studies indicated that a revision of the connectivity of the metabolites is likely needed. We end with some thoughts on the frontiers of secondary metabolite structure determination. As modern NMR computational methods are straightforward to execute, we advocate for their systematic use in validating the assignments of novel secondary metabolites.

Anomalous 1 H NMR chemical shift behavior of substituted benzoic acid esters

Benzoic acid esters represent key building blocks for many drug discovery and development programs and have been advanced as potent PDE4 inhibitors for inhaled administration for treatment of respiratory diseases. This class of compounds has also been employed in myriad industrial processes and as common food preservatives. Recent work directed toward the synthesis of intermediates for a proprietary medicinal chemistry program led us to observe that the ¹ H NMR chemical shifts of substituents ortho to the benzoic acid ester moiety defied conventional iterative chemical shift prediction protocols. To explore these unexpected results, we initiated a detailed computational study employing density functional theory (DFT) calculations to better understand the unexpectedly large variance in expected versus experimental NMR chemical shifts.

DELTA50: A Highly Accurate Database of Experimental 1H and 13C NMR Chemical Shifts Applied to DFT Benchmarking

Density functional theory (DFT) benchmark studies of ¹H and ¹³C NMR chemical shifts often yield differing conclusions, likely due to non-optimal test molecules and non-standardized data acquisition. To address this issue, we carefully selected and measured ¹H and ¹³C NMR chemical shifts for 50 structurally diverse small organic molecules containing atoms from only the first two rows of the periodic table. Our NMR dataset, DELTA50, was used to calculate linear scaling factors and to evaluate the accuracy of 73 density functionals, 40 basis sets, 3 solvent models, and 3 gauge-referencing schemes. The best performing DFT methodologies for ¹H and ¹³C NMR chemical shift predictions were WP04/6-311++G(2d,p) and ωB97X-D/def2-SVP, respectively, when combined with the polarizable continuum solvent model (PCM) and gauge-independent atomic orbital (GIAO) method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions of 20 organic compounds and natural products from a separate probe set had root-mean-square deviations (RMSD) of 0.07 to 0.19 for ¹H and 0.5 to 2.9 for ¹³C. Maximum deviations were less than 0.5 and 6.5 ppm for ¹H and ¹³C, respectively.

Cis-trans isomerization of dimethyl 2,3-dibromofumarate

The isomerization of dimethyl 2,3-dibromofumarate in chloroform solutions was investigated by the combination of nuclear magnetic resonance (NMR) and density functional theory (DFT) calculations. The bromination of dimethyl acetylenedicarboxylate leading to dimethyl 2,3-dibromofumarate produces the trans isomer initially, which however converts into the more stable cis isomer. The conversion from trans to cis is spontaneous and greatly accelerated by light.

DFT calculations of 1H- and 13C-NMR chemical shifts of 3-methyl-1-phenyl-4-(phenyldiazenyl)-1H-pyrazol-5-amine in solution

Geometries of the 3-methyl-1-phenyl-4-(phenyldiazenyl)-1H-pyrazol-5-amine azo-dye compound and its tautomer were optimized using B3LYP and M06-2X functionals in coupling with TZVP and 6-311 + G(d,p) basis sets. The ¹H- and ¹³C-NMR chemical shifts of all species were predicted using 13 density functional theory (DFT) approaches in coupling with TZVP and 6-311 + G(d,p) basis sets at the different optimized geometries by applying the using GIAO method using the eight geometries. The selected functionals are characterized by having different amount of Hartree-Fock exchange. The selected DFT methods were B3LYP, M06-2X, BP86, B97XD, TPSSTPSS, PBE1PBE, CAM-B3LYP, wB97XD, LSDA, HSEH1PBE, PW91PW91, LC-WPBE, and B3PW91. The results obtained were compared with the available experimental data using different statistical descriptors such as root mean square error (RMSE) and maximum absolute error (MAE). Results revealed that the prediction of the ¹H-NMR chemical shifts has more significant dependence on the applied geometry than that of the prediction of the ¹³C-NMR chemical shifts. Among all the examined functionals, B97D and TPSSTPSS functionals were found to be the most accurate ones, while the M06-2X functional is the least accurate one. Results also revealed that the prediction of NMR chemical shifts using TZVP basis sets results is more accurate results than 6-311 + G(2d,p) basis set.

Density functional theory calculations of δ(13 C) and δ(1 H) chemical shifts and 3 J(13 COO1 H) coupling constants as structural and analytical tools in hydroperoxides: Prospects and limitations of 1 H13 C heteronuclear multiple bond correlation experiments

Density functional theory (DFT) calculations of δ(¹³ C) and δ(¹ H) chemical shifts and ³ J(¹³ COO¹ H) coupling constants of three model hydroperoxides of the naturally occurring cis-11-OOH and trans-9-OOH isomers of oleate and 9-cis, 11-trans-16-OOH endo hydroperoxide of methyl linolenate are reported. The computational δ(OOH) for various functionals and basis sets were found to be nearly identical for the cis/trans geometric isomers. The chemical shifts of the methine CHOOH protons and carbons, on the contrary, are highly diagnostic for the identification of cis/trans geometric isomerism. The chemical shifts of the olefinic protons and carbons strongly depend on the orientation of the hydroperoxide unit relative to the double bond and, thus, of importance in conformational analysis. The results are in very good agreement with the available experimental data. For the various diastereomeric pairs of the model endo-hydroperoxide, the strongly deshielded OOH resonances, due to the presence of an intramolecular hydrogen bond between the hydroperoxide proton and an oxygen of the endo-peroxide ring, along with the δ(CHOOH), are highly diagnostic for identification and structure elucidation of complex erythro- and threo- diastereomeric pairs of endo-hydroperoxides; the computational results are in very good agreement with the available experimental data. The ³ J(¹³ COO¹ H) coupling constants were found to be <  2  Hz for the cis-trans geometric models and <  0.5  Hz for the endo-hydroperoxide and, thus, unimportant in stereochemical analysis. Sharp resonances of the hydroperoxide protons, with Δν_1/2  < 3 Hz, are required for the successful implementation of the ¹ H¹³ C heteronuclear multiple bond correlation (HMBC) technique.

Choice of computational protocol for carbon-lithium spin-spin coupling constants 1 JCLi

In this work, we tested various computational schemes for calculations of ¹ J_CLi constants with a high accuracy. On the example of six organolithium reagents (phenyllithium monomer and dimer, monomer s-butyllithium, monomers of 1- and 2-lithionaphthalenes, and a methyllithium tetramer), the following aspects are discussed: (i) the role of a model system geometry, (ii) influence of solvent effects, and (iii) the choice of a functional and basis set. Practical recommendations for calculation of ¹ J_CLi with an accuracy ±2 Hz are formulated.

An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts

The majority of primary and secondary metabolites in nature have yet to be identified, representing a major challenge for metabolomics studies that currently require reference libraries from analyses of authentic compounds. Using currently available analytical methods, complete chemical characterization of metabolomes is infeasible for both technical and economic reasons. For example, unambiguous identification of metabolites is limited by the availability of authentic chemical standards, which, for the majority of molecules, do not exist. Computationally predicted or calculated data are a viable solution to expand the currently limited metabolite reference libraries, if such methods are shown to be sufficiently accurate. For example, determining nuclear magnetic resonance (NMR) spectroscopy spectra in silico has shown promise in the identification and delineation of metabolite structures. Many researchers have been taking advantage of density functional theory (DFT), a computationally inexpensive yet reputable method for the prediction of carbon and proton NMR spectra of metabolites. However, such methods are expected to have some error in predicted 13C and 1H NMR spectra with respect to experimentally measured values. This leads us to the question-what accuracy is required in predicted 13C and 1H NMR chemical shifts for confident metabolite identification? Using the set of 11,716 small molecules found in the Human Metabolome Database (HMDB), we simulated both experimental and theoretical NMR chemical shift databases. We investigated the level of accuracy required for identification of metabolites in simulated pure and impure samples by matching predicted chemical shifts to experimental data. We found 90% or more of molecules in simulated pure samples can be successfully identified when errors of 1H and 13C chemical shifts in water are below 0.6 and 7.1 ppm, respectively, and below 0.5 and 4.6 ppm in chloroform solvation, respectively. In simulated complex mixtures, as the complexity of the mixture increased, greater accuracy of the calculated chemical shifts was required, as expected. However, if the number of molecules in the mixture is known, e.g., when NMR is combined with MS and sample complexity is low, the likelihood of confident molecular identification increased by 90%.

Towards Elucidating Structure–Spectra Relationships in Rhamnogalacturonan II: Computational Protocols for Accurate 13C and 1H Shifts for Apiose and Its Borate Esters

Apiose is a naturally occurring, uncommon branched-chain pentose found in plant cell walls as part of the complex polysaccharide Rhamnogalacturonan II (RG-II). The structural elucidation of the three-dimensional structure of RG-II by nuclear magnetic resonance (NMR) spectroscopy is significantly complicated by the ability of apiose to cross-link via borate ester linkages to form RG-II dimers. Here, we developed a computational approach to gain insight into the structure–spectra relationships of apio–borate complexes in an effort to complement experimental assignments of NMR signals in RG-II. Our protocol involved structure optimizations using density functional theory (DFT) followed by isotropic magnetic shielding constant calculations using the gauge-invariant atomic orbital (GIAO) approach to predict chemical shifts. We evaluated the accuracy of 23 different functional–basis set (FBS) combinations with and without implicit solvation for predicting the experimental 1H and 13C shifts of a methyl apioside and its three borate derivatives. The computed NMR predictions were evaluated on the basis of the overall shift accuracy, relative shift ordering, and the ability to distinguish between dimers and monomers. We demonstrate that the consideration of implicit solvation during geometry optimizations in addition to the magnetic shielding constant calculations greatly increases the accuracy of NMR chemical shift predictions and can correctly reproduce the ordering of the 13C shifts and yield predictions that are, on average, within 1.50 ppm for 13C and 0.12 ppm for 1H shifts for apio–borate compounds.

On the molecular basis of H2O/DMSO eutectic mixtures by using phenol compounds as molecular sensors: a combined NMR and DFT study

NMR and DFT studies of phenol compounds as molecular sensors were carried out to investigate H₂O/DMSO eutectic mixtures at a molecular level. The experimental ¹H NMR chemical shifts of the OH groups, δ_exp(OH), of phenol, paracoumaric acid, and vanillic acid show maximum deshielding and, thus, hydrogen bond interactions in the range of mole fractions 0.20 < χ(DMSO) < 0.33. In the mole fractions χ(DMSO) < 0.2, a progressive decrease in δ_exp(OH) was observed which demonstrates a decrease in hydrogen bond interactions at infinite dilution in H₂O, despite the increase in the number of available hydrogen bond acceptor and donor sites. DFT calculated δ_calc(OH) of minimum energy solvation clusters were shown to be in reasonable agreement with the pattern in experimental δ_exp(OH) data. The chemical shift deshielding and, thus, increased hydrogen bond interactions in the natural product + DMSO + nH₂O (n = 2, 3) solvation clusters, relative to complexes in DMSO or H₂O solutions, cannot be attributed to a single structural parameter of the cooperative interactions between H₂O and DMSO molecules with the phenol OH groups of the natural products. The minimum energy conformers of phenol compounds + 2H₂O + DMSO complexes are in excellent agreement with a recent low temperature neutron diffraction experiment of 3D₂O + DMSO and demonstrate a general structural motif of solvation complexes. The combined use of ¹H NMR and DFT studies with emphasis on δ(OH) of phenol compounds, as molecular sensors, can provide an effective method for the study of solute-solvent interactions at the atomic level.

Revving up 13C NMR shielding predictions across chemical space: benchmarks for atoms-in-molecules kernel machine learning with new data for 134 kilo molecules

The requirement for accelerated and quantitatively accurate screening of nuclear magnetic resonance spectra across the small molecules chemical compound space is two-fold: (1) a robust ‘local’ machine learning (ML) strategy capturing the effect of the neighborhood on an atom’s ‘near-sighted’ property—chemical shielding; (2) an accurate reference dataset generated with a state-of-the-art first-principles method for training. Herein we report the QM9-NMR dataset comprising isotropic shielding of over 0.8 million C atoms in 134k molecules of the QM9 dataset in gas and five common solvent phases. Using these data for training, we present benchmark results for the prediction transferability of kernel-ridge regression models with popular local descriptors. Our best model, trained on 100k samples, accurately predicts isotropic shielding of 50k ‘hold-out’ atoms with a mean error of less than 1.9 ppm. For the rapid prediction of new query molecules, the models were trained on geometries from an inexpensive theory. Furthermore, by using a Δ-ML strategy, we quench the error below 1.4 ppm. Finally, we test the transferability on non-trivial benchmark sets that include benchmark molecules comprising 10–17 heavy atoms and drugs.

Folding-controlled assembly of ortho-phenylene-based macrocycles

The self-assembly of foldamers into macrocycles is a simple approach to non-biological higher-order structure. Previous work on the co-assembly of ortho-phenylene foldamers with rod-shaped linkers has shown that folding and self-assembly affect each other; that is, the combination leads to new emergent behavior, such as access to otherwise unfavorable folding states. To this point this relationship has been passive. Here, we demonstrate control of self-assembly by manipulating the foldamers' conformational energy surfaces. A series of o-phenylene decamers and octamers have been assembled into macrocycles using imine condensation. Product distributions were analyzed by gel-permeation chromatography and molecular geometries extracted from a combination of NMR spectroscopy and computational chemistry. The assembly of o-phenylene decamers functionalized with alkoxy groups or hydrogens gives both [2 + 2] and [3 + 3] macrocycles. The mixture results from a subtle balance of entropic and enthalpic effects in these systems: the smaller [2 + 2] macrocycles are entropically favored but require the oligomer to misfold, whereas a perfectly folded decamer fits well within the larger [3 + 3] macrocycle that is entropically disfavored. Changing the substituents to fluoro groups, however, shifts assembly quantitatively to the [3 + 3] macrocycle products, even though the structural changes are well-removed from the functional groups directly participating in bond formation. The electron-withdrawing groups favor folding in these systems by strengthening arene–arene stacking interactions, increasing the enthalpic penalty to misfolding. The architectural changes are substantial even though the chemical perturbation is small: analogous o-phenylene octamers do not fit within macrocycles when perfectly folded, and quantitatively misfold to give small macrocycles regardless of substitution. Taken together, these results represent both a high level of structural control in structurally complex foldamer systems and the demonstration of large-amplitude structural changes as a consequence of a small structural effects.

The folding propensity of ortho-phenylene foldamers dictates the outcome of their self-assembly into macrocycles.

Electrochemically driven desaturation of carbonyl compounds

Electrochemical techniques have long been heralded for their innate sustainability as efficient methods to achieve redox reactions. Carbonyl desaturation, as a fundamental organic oxidation, is an oft-employed transformation to unlock adjacent reactivity through the formal removal of two hydrogen atoms. To date, the most reliable methods to achieve this seemingly trivial reaction rely on transition metals (Pd or Cu) or stoichiometric reagents based on I, Br, Se or S. Here we report an operationally simple pathway to access such structures from enol silanes and phosphates using electrons as the primary reagent. This electrochemically driven desaturation exhibits a broad scope across an array of carbonyl derivatives, is easily scalable (1-100 g) and can be predictably implemented into synthetic pathways using experimentally or computationally derived NMR shifts. Systematic comparisons to state-of-the-art techniques reveal that this method can uniquely desaturate a wide array of carbonyl groups. Mechanistic interrogation suggests a radical-based reaction pathway.

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.

A metal-free blue chromophore derived from plant pigments

Blue natural pigments are rare, especially among plants. However, flowering species that evolved to attract Hymenoptera pollinators are colored by blue anthocyanin-metal complexes. Plants lacking anthocyanins are pigmented by betalains but are unable to produce blue hues. By extending the π-system of betalains, we designed a photostable and metal-free blue dye named BeetBlue that did not show toxicity to human hepatic and retinal pigment epithelial cells and does not affect zebrafish embryonal development. This chiral dye can be conveniently synthesized from betalamic acid obtained from hydrolyzed red beetroot juice or by enzymatic oxidation of l-dopa. BeetBlue is blue in the solid form and in solution of acidified polar molecular solvents, including water. Its capacity to dye natural matrices makes BeetBlue the prototype of a new class of low-cost bioinspired chromophores suitable for a myriad of applications requiring a blue hue.

The one-electron self-interaction error in 74 density functional approximations: a case study on hydrogenic mono- and dinuclear systems

The self-interaction error (SIE), i.e. unphysical interactions of electrons with themselves, has plagued developers and users of Density Functional Approximations (DFAs) since the inception of Density Functional Theory (DFT). Formally, it can be separated into the one-electron and many-electron SIE; herein we present one of the most comprehensive studies of the first. While we focus mostly on the total SIE, we also make use of two different decompositions. The first is a separation into functional and density-driven errors as championed by Sim, Burke and co-workers [J. Phys. Chem. Lett., 2018, 9, 6385-6392]; the second separates the error into exchange, correlation, and one-electron components, with the latter being a density error that has not been discussed in this form before. After investigating the familiar hydrogen atom and dihydrogen cation, we establish a relationship between the SIE and the nuclear charge with the help of a series of heavier hydrogenic analogues. For the mononuclear systems and the diatomics at the dissociation limit, this relationship is linear in nature with prominent exceptions, mostly belonging to the Minnesota and range-separated (double-)hybrid DFAs. For the first time, we also show how the magnitude of the SIE depends on the underlying atomic-orbital basis set and how DFAs that rely on a popular van-der-Waals DFT type London-dispersion term exhibit "self-dispersion". We find that range separation is not a panacea for solving the one-electron SIE. DFAs that have been developed to be one-electron SIE free for one system, such as the hydrogen atom, show larger errors for heavier hydrogenic systems. Often, one-electron SIE-free DFAs rely on fortuitous error cancellation between their exchange and correlation components. An analysis of the most robust methods for general applications to date reveals that they suffer moderately from the one-electron SIE, while DFAs that are nearly SIE-free do not perform well in applications. Implicit in the continued existence of the one-electron SIE is that well-performing DFAs continue to suffer insufficiencies at their fundamental levels that are being compensated for by the SIE. Our analysis includes more than 250 000 datapoints, resulting in multiple insights that may drive future developments of new DFAs or SIE corrections.

Polyketides from Marine-Derived Aspergillus porosus: Challenges and Opportunities for Determining Absolute Configuration

Fungal natural products have inspired and enabled countless modern therapeutics. During a survey of the secondary metabolites of endophytic fungi, we found that Aspergillus porosus produces new polyketides with interesting structural features named porosuphenols A-D (1, 2, 3a, and 3b). The structural elucidation of these metabolites was performed with 1D and 2D NMR techniques, Mosher ester analysis, J-based conformational analysis, and isotope exchange studies. The absolute configuration of these compounds was determined using typical approaches including comparative analysis of experimental NMR and electronic circular dichroism spectra with DFT calculations. However, these efforts did not provide conclusive results for porosuphenol A (1). To resolve this issue, we applied a strategy in which NMR data guide the conformer search. Herein are presented the structure elucidation of porosuphenols A-D as a case study in the challenges and opportunities for determination of absolute configuration. Lastly, bioassay-guided fractionation of cytotoxic fractions resulted in the additional isolation of pimarane diterpenes, sphaeropsidin A (4), and aspergiloid E (5).

Macrocycles of higher ortho-phenylenes: assembly and folding

The sizes and geometries of macrocycles assembled from ortho-phenylenes are predicted by the stabilities and bite angles of possible conformers.

Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended ortho-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic ¹H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an o-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the o-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3 + 3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2 + 2] macrocycles to be formed as the predominant species. In these systems, the o-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex folds.

Density functional theory, molecular docking and bioassay studies on (S)-2-hydroxy-N-(2S,3S,4R,E)-1,3,4 trihydroxyicos-16-en-2-yl)tricosanamide

A novel indigoferamide-A, earlier isolated from the seeds of Indigofera heterantha Wall was characterized using density functional theory, molecular docking and bioassays studies. Density functional theory calculations were performed at B3LYP/6-31G(d,p) to gain geometric insight of the compound. Conformational analyses have been performed around three important dihedral angles to explore the lowest energy structure and conformer. The simulated vibrational spectrum of the compound at B3LYP/6-31G(d,p) was scaled with two scaling factors, and the scaled harmonic vibrations shows nice correlation with the experimental values. 1H and 13C NMR chemical shifts were calculated using Cramer's re-parameterized function W04 at 6- 31G(d,p) basis set. Several conformers lying within 2 kcal mol-1 of the minimum energy conformer were considered; however, the chemical shifts were not significantly different among these conformers. The Gaussian averaged theoretical 1H and 13C chemical shifts correlate nicely with the experimental data. Electronic properties such as band gap, ionization potential and electron affinities were also simulated for the first time, however, no comparison could be made with the experiment. The compound was also screened for urease, antiglycation activities and the theoretical explanation of the results is provided based on molecular docking simulations.

Computational Prediction of 1 H and 13 C NMR Chemical Shifts for Protonated Alkylpyrroles: Electron Correlation and Not Solvation is the Salvation

Prediction of chemical shifts in organic cations is known to be a challenge. In this article we meet this challenge for α-protonated alkylpyrroles, a class of compounds not yet studied in this context, and present a combined experimental and theoretical study of the ¹³ C and ¹ H chemical shifts in three selected pyrroles. We have investigated the importance of the solvation model, basis set, and quantum chemical method with the goal of developing a simple computational protocol, which allows prediction of ¹³ C and ¹ H chemical shifts with sufficient accuracy for identifying such compounds in mixtures. We find that density functional theory with the B3LYP functional is not sufficient for reproducing all ¹³ C chemical shifts, whereas already the simplest correlated wave function model, Møller-Plesset perturbation theory (MP2), leads to almost perfect agreement with the experimental data. Treatment of solvent effects generally improves the agreement with experiment to some extent and can in most cases be accomplished by a simple polarizable continuum model. The only exception is the NH proton, which requires inclusion of explicit solvent molecules in the calculation.

An automated framework for NMR chemical shift calculations of small organic molecules

When using nuclear magnetic resonance (NMR) to assist in chemical identification in complex samples, researchers commonly rely on databases for chemical shift spectra. However, authentic standards are typically depended upon to build libraries experimentally. Considering complex biological samples, such as blood and soil, the entirety of NMR spectra required for all possible compounds would be infeasible to ascertain due to limitations of available standards and experimental processing time. As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties—specifically NMR chemical shifts in this manuscript—via the open source, high-performance computational chemistry software, NWChem. ISiCLE calculates the NMR chemical shifts of sets of molecules using any available combination of DFT method, solvent, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Calculated NMR chemical shifts are provided to the user for each molecule, along with comparisons with respect to a number of metrics commonly used in the literature. Here, we demonstrate ISiCLE using a set of 312 molecules, ranging in size up to 90 carbon atoms. For each, calculation of NMR chemical shifts have been performed with 8 different levels of DFT theory, and with solvation effects using the implicit solvent Conductor-like Screening Model. The DFT method dependence of the calculated chemical shifts have been systematically investigated through benchmarking and subsequently compared to experimental data available in the literature. Furthermore, ISiCLE has been applied to a set of 80 methylcyclohexane conformers, combined via Boltzmann weighting and compared to experimental values. We demonstrate that our protocol shows promise in the automation of chemical shift calculations and, ultimately, the expansion of chemical shift libraries.

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.

Diagnostics of Data-Driven Models: Uncertainty Quantification of PM7 Semi-Empirical Quantum Chemical Method

We report an evaluation of a semi-empirical quantum chemical method PM7 from the perspective of uncertainty quantification. Specifically, we apply Bound-to-Bound Data Collaboration, an uncertainty quantification framework, to characterize (a) variability of PM7 model parameter values consistent with the uncertainty in the training data and (b) uncertainty propagation from the training data to the model predictions. Experimental heats of formation of a homologous series of linear alkanes are used as the property of interest. The training data are chemically accurate, i.e., they have very low uncertainty by the standards of computational chemistry. The analysis does not find evidence of PM7 consistency with the entire data set considered as no single set of parameter values is found that captures the experimental uncertainties of all training data. A set of parameter values for PM7 was able to capture the training data within ±1 kcal/mol, but not to the smaller level of uncertainty in the reported data. Nevertheless, PM7 was found to be consistent for subsets of the training data. In such cases, uncertainty propagation from the chemically accurate training data to the predicted values preserves error within bounds of chemical accuracy if predictions are made for the molecules of comparable size. Otherwise, the error grows linearly with the relative size of the molecules.

Linker-Directed Assembly of Twisted ortho-Phenylene-Based Macrocycles

o-Phenylene tetramers have been coassembled with linkers into macrocycles through imine condensation. Variation of linker connectivity and length allows both [1 + 1] and [2 + 2] macrocycles to be obtained, complementing (previously reported) [3 + 3] macrocycles. For the [1 + 1] macrocycles, linker length has a clear effect on o-phenylene geometry and macrocycle stability. For the [2 + 2] macrocycles, both homo- and heterochiral configurations are observed, suggesting limited communication of helix handedness in these systems.

Substituted troponimines: when aromatization of the conjugate acid leads to very strong neutral organic superbases

Highly basic 3,6-disubstituted troponimino-scaffolds enable the introduction of new aromatic-stabilizing neutral organic superbase groups.

Prediction of 1H NMR chemical shifts for ionic liquids: strategy and application of a relative reference standard

The computational predictions of ¹H NMR chemical shifts for ionic liquids were investigated. To calculate the chemical shifts more accurately, the approach of relative reference standard (RRS) was proposed. This straightforward computational technique uses organic compounds and ionic liquids that are similar to the studied ionic liquids as standards. The calculated chemical shifts of single ion pairs were strongly influenced by the anion type and the local environment. Using the RRS methodology, the calculated results agreed well with the experimental chemical shifts due to the cancellation of errors caused by the anion. Ionic clusters consisting of 4 ion pairs were also employed to model the ionic liquids with strongly coordinating anions. Large clusters slightly improve the accuracy by reducing systematic errors. Although the experimental ¹H NMR data of the reference ionic liquid should be used, the RRS methodology has been shown to predict ¹H NMR chemical shifts efficiently at different levels of theory.

Using an RRS method to calculate the ¹H NMR chemical shifts of ionic liquid agreed well with the experimental value.

Effect of Extended Benzannelation Orientation on Bergman and Related Cyclizations of Isomeric Quinoxalenediynes

A combined computational and experimental study was conducted to examine the effect of extended benzannelation orientation on C¹-C⁵ and C¹-C⁶ cyclization of acyclic quinoxalenediynes. Calculations (mPW1PW91/cc-pVTZ//mPW1PW91/6-31G(d,p)) on terminal and phenylethynyl-substituted 5,6-diethynylquinoxaline and 6,7-diethynylquinoxaline showed C¹-C⁶ Bergman cyclization as the favored thermodynamic reaction pathway, with larger C¹-C⁶ preference for the angular quinoxalenediynes due to gain of a new aromatic sextet. Kinetic studies, as a function of 1,4-cyclohexadiene concentration, revealed retro-Bergman ring opening predominates over hydrogen atom abstraction (k_-1 > k₂) for 6,7-diethynylquinoxaline while 5,6-diethynylquinoxaline undergoes irreversible Bergman cyclization indicative of a large retro-Bergman ring opening barrier (k₂ > k_-1). The effect of extended linear versus angular benzannelation on reaction pathway shows in the contrasting photocyclizations of phenylethynyl derivatives. While angular 5,6-diethynylquinoxalines gave exclusive C¹-C⁶ photocyclization, linear 6,7-diethynylquinoxaline afforded C¹-C⁵ fulvene products. Computed singlet-triplet gaps and biradical stabilization energies indicated weak interaction between the nitrogen lone pair and proximal radical center in angular 5,6-diethynylquinoxalines. The overall data indicates extended angular benzannelation effectively renders Bergman cyclization irreversible due to favorable aromatic stabilization energy, while extended linear benzannelation results in increased retro-Bergman ring opening, allowing C¹-C⁵ cyclization to become a competitive reaction channel.

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.

A complex stereochemical relay approach to the antimalarial alkaloid ocimicide A1. Evidence for a structural revision

The core structure of the potent antimalarial alkaloid ocimicide A₁ was prepared by a complex stereochemical relay. Computational studies suggest a structural revision of the metabolite is necessary.

Ocimicide A₁ (1) and the semisynthetic derivative ocimicide A₂ (2) are highly potent antimalarial agents efficacious against chloroquine-sensitive and -resistant Plasmodium falciparum strains with IC₅₀ values in the nanomolar and picomolar range, respectively. Members of this family have demonstrated radical cure in rhesus monkeys, without detectable toxicity, but their structure–function relationships and mechanism of action are unknown. Herein we describe a twelve-step synthesis of an advanced N-acylated pentacyclic precursor to the proposed structure of 1 (11% overall yield). Instability and poor P. falciparum growth inhibition of the corresponding free donor–acceptor cyclopropylamine, and large discrepancies between reported and both experimental and DFT-calculated ¹³C chemical shifts and coupling constants, suggest that substantial revision of the proposed structures may be necessary.