Comparison of various density functional methods for distinguishing stereoisomers based on computed (1)H or (13)C NMR chemical shifts using diastereomeric penam beta-lactams as a test set

Optoelectronic Response to the Fluor Ion Bond on 4-(4,4,5,5-Tetramethyl-1,3,2-dioxoborolan-2-yl)benzaldehyde

Boronate esters are a class of compounds containing a boron atom bonded to two oxygen atoms in an ester group, often being used as precursors in the synthesis of other materials. The characterization of the structure and properties of esters is usually carried out by UV-visible, infrared, and nuclear magnetic resonance (NMR) spectroscopic techniques. With the aim to better understand our experimental data, in this article, the density functional theory (DFT) is used to analyze the UV-visible and infrared spectra, as well as the isotropic shielding and chemical shifts of the hydrogen atoms 1H, carbon 13C and boron 11B in the compound 4-(4,4,5,5-tetramethyl-1,3,2-dioxoborolan-2-yl)benzaldehyde. Furthermore, this study considers the change in its electronic and spectroscopic properties of this particular ester, when its boron atom is coordinated with a fluoride anion. The calculations were carried out using the LSDA and B3LYP functionals in Gaussian-16, and PBE in CASTEP. The results show that the B3LYP functional gives the best approximation to the experimental data. The formation of a coordinated covalent B-F bond highlights the remarkable sensitivity of the NMR chemical shifts of carbon, oxygen, and boron atoms and their surroundings. Furthermore, this bond also highlights the changes in the electron transitions bands n → π* and π → π* during the absorption and emission of a photon in the UV-vis, and in the stretching bands of the C=C bonds, and bending of BO2 in the infrared spectrum. This study not only contributes to the understanding of the properties of boronate esters but also provides important information on the interactions and responses optoelectronic of the compound when is bonded to a fluorine atom.

An automated framework for high-throughput predictions of NMR chemical shifts within liquid solutions

Identifying stable speciation in multi-component liquid solutions is fundamentally important to areas from electrochemistry to organic chemistry and biomolecular systems. Here we introduce a fully automated, high-throughput computational framework for the accurate prediction of stable species in liquid solutions by computing the nuclear magnetic resonance (NMR) chemical shifts. The framework automatically extracts and categorizes hundreds of thousands of atomic clusters from classical molecular dynamics simulations, identifies the most stable species in solution and calculates their NMR chemical shifts via density functional theory calculations. Additionally, the framework creates a database of computed chemical shifts for liquid solutions across a wide chemical and parameter space. We compare our computational results to experimental measurements for magnesium bis(trifluoromethanesulfonyl)imide Mg(TFSI)2 salt in dimethoxyethane solvent. Our analysis of the Mg2+ solvation structural evolutions reveals key factors that influence the accuracy of NMR chemical shift predictions in liquid solutions. Furthermore, we show how the framework reduces the performance of over 300 13C and 600 1H density functional theory chemical shift predictions to a single submission procedure.

Crystal and geometry-optimized structure of an anthracene-based Diels–Alder adduct

Computational calculations of an anthracene-based Diels–Alder adduct, namely, 17-ethyl-1-hydroxymethyl-17-azapentacyclo[6.6.5.02,7.09,14.015,19]nonadeca-2,4,6,9,11,13-hexaene-16,18-dione, C21H19NO3, predicting density functional theory (DFT) optimized geometries in the gas phase are compared in terms of accuracy relative to the solid-state crystal structure and computational cost. Crystal structure determination and Hirshfeld surface analysis of the racemic product reveal that the molecules are linked by O—H...O=C hydrogen bonds between the hydroxy and carbonyl groups, accounting for 9.5% of the intermolecular contacts, while H...H contacts represent 56.9% of the total. Boltzmann population analysis of computed relative rotamer abundances in the gas phase are based on lower-level geometry optimization and thermochemical corrections coupled with higher-level electronic energy calculations using the B2PLYP double-hybrid functional. As expected, the choice of density functional has a greater effect than the basis set on accuracy for all levels of theory. For any given functional, increasing the basis set size did not always correlate with increasingly accurate structures. The hybrid functional B3LYP without dispersion correction routinely gave the closest approximations to the crystal structure where the B3LYP/aug-cc-pVDZ combination afforded the best structure (r.m.s. deviation = 0.1314 Å). However, the B3LYP/6-31+G(d,p) level of theory represents the best compromise between accuracy (r.m.s. deviation = 0.1388 Å) and cost as it yielded appreciably accurate results in a fraction of the time compared to other method combinations.

Spirocyclic lactams and curvulinic acid derivatives from the endophytic fungus Curvularia lunata and their antibacterial and antifungal activities

Curvularia lunata, isolated from the capitula of Paepalanthus chiquitensis (Eriocaulaceae), was cultured in potato dextrose broth (PDB) medium. The ethyl acetate extract yielded two new spirocyclic γ-lactams (3 and 4), and five known compounds, namely: triticones E (1) and F (2), 5-O-methylcurvulinic acid (5), curvulinic acid (6) and curvulin (7). Their structures were elucidated by spectroscopic analysis and by the comparison with literature data. Besides, a computational study was used to elucidate the absolute configuration of the C - 3' in the compounds (3) and (4). The extract and the compounds (1 and 2), (6) and (7) were assayed against gram-positive and gram-negative bacteria and fluconazole-resistant yeast. The triticones (1) and (2) showed good antibacterial activity for Escherichia coli, with a minimum inhibitory concentration of 62.5 μg/mL.

Computational studies, NMR, Raman and infrared spectral analysis of centrosymmetric (2Z,4Z)-Hexa-2,4-dienedinitrile

The Raman (50–3500[Formula: see text]cm[Formula: see text]) and infrared (200–3500[Formula: see text]cm[Formula: see text]) spectra of (2Z,4Z)-Hexa-2,4-dienedinitrile (C6H4N2; cis,cis-HDDN) have been recorded. Initially, three conformers were proposed based on following point groups: C2h, C2v and [Formula: see text] (gauche). For comparison purposes, M05-2X, M06-2X method were used in addition to B3LYP, MP2[Formula: see text]full and MP4[Formula: see text]full quantum mechanical calculations employing 6-31G(d) and 6-311+G(d,p) basis sets using Gaussian 09 program. Aided by potential energy surface scan, the C2h conformer is verified as a global minimum and the gauche ([Formula: see text]) being a local minimum with an energy barrier of 2.82[Formula: see text]kcal/mol. The energy difference ranged from 4.87 to 13.70[Formula: see text]kcal/mol favors the C2h conformer in good agreement with Raman and infrared spectral analysis. These results were also supported by the observed [Formula: see text] value (H9-H[Formula: see text]) at 10.8[Formula: see text]Hz which is consistent to 10.19[Formula: see text]Hz estimated for centrosymmetric conformer (C2h) rather than 4.81[Formula: see text]Hz predicted for gauche ([Formula: see text]). Complete vibrational assignments are proposed herein based on normal coordinate analysis (NCA) and potential energy distributions (PEDs) combined with theoretical vibrational frequencies and force constants in internal coordinates. It is crucial that NCA using VEDA 4 program with mixing shows large deviations from ours due to neglecting symmetry elements while mixing molecular vibrational motions. The results of these spectroscopic and theoretical studies are reported herein and compared with similar molecules whenever appropriate.

A concise Friedländer/Buchwald–Hartwig approach to the total synthesis of quindoline, a bioactive natural indoloquinoline alkaloid, and toward the unnatural 10-methylquindoline

Friedländer and Buchwald–Hartwig reactions were used to achieve an efficient total synthesis of quindoline and a new synthesis of the unnatural 10-methylquindoline. DFT calculations were employed to explain the outcome of a failed key transformation.

Computationally-inspired discovery of an unsymmetrical porous organic cage

A completely unsymmetrical porous organic cage was synthesised from a C_2v symmetrical building block that was identified by a computational screen. The cage was formed through a 12-fold imine condensation of a tritopic C_2v symmetric trialdehyde with a ditopic C₂ symmetric diamine in a [4 + 6] reaction. The cage was rigid and microporous, as predicted by the simulations, with an apparent Brunauer-Emmett-Teller surface area of 578 m² g^-1. The reduced symmetry of the tritopic building block relative to its topicity meant there were 36 possible structural isomers of the cage. Experimental characterisation suggests a single isomer with 12 unique imine environments, but techniques such as NMR could not conclusively identify the isomer. Computational structural and electronic analysis of the possible isomers was used to identify the most likely candidates, and hence to construct a 3-dimensional model of the amorphous solid. The rational design of unsymmetrical cages using building blocks with reduced symmetry offers new possibilities in controlling the degree of crystallinity, porosity, and solubility, of self-assembled materials.

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.

Recent Advances in Multinuclear NMR Spectroscopy for Chiral Recognition of Organic Compounds

Nuclear magnetic resonance (NMR) is a powerful tool for the elucidation of chemical structure and chiral recognition. In the last decade, the number of probes, media, and experiments to analyze chiral environments has rapidly increased. The evaluation of chiral molecules and systems has become a routine task in almost all NMR laboratories, allowing for the determination of molecular connectivities and the construction of spatial relationships. Among the features that improve the chiral recognition abilities by NMR is the application of different nuclei. The simplicity of the multinuclear NMR spectra relative to ¹H, the minimal influence of the experimental conditions, and the larger shift dispersion make these nuclei especially suitable for NMR analysis. Herein, the recent advances in multinuclear (¹⁹F, ³¹P, ¹³C, and ⁷⁷Se) NMR spectroscopy for chiral recognition of organic compounds are presented. The review describes new chiral derivatizing agents and chiral solvating agents used for stereodiscrimination and the assignment of the absolute configuration of small organic compounds.

A Benefit of Using the IDSCRF- over UFF-Radii Cavities and Why Joint Correlations of NMR Chemical Shifts Can Be Advantageous: Condensed Pyridines as an IEF-PCM/GIAO/DFT Case Study

Herein, an advantage of the use of IDSCRF- over UFF-radii-based solute cavities in GIAO/DFT calculations is presented for the ¹³C and especially ¹⁵N NMR chemical shifts made for several bicyclic aromatic nitrogen heterocycles in CDCl₃ solution treated within the classical IEF-PCM solvation scheme. Successful application of the IDSCRF-radii in the non 1:1 joint multinuclear ¹H/¹³C and particularly ¹H/¹³C/¹⁵N correlations of the measured δ_H,C(,N) values to those obtained theoretically is also documented for a series of test systems (-268 ≤ δ_N ≤ -72 ppm). The experimentally yet unknown δ_N's were found in this way for the title compounds via a trinuclear eq 1 determined for an optimally chosen value of the multiplication factor of initial raw δ_H data (m_H = 10). Such a simultaneous analysis of the δ_H,C(,N) data is proposed as a novel method to study the solution structure of the other similar conformationally homogeneous (bio)organic compounds. The issue of small spurious imaginary vibrational frequencies computed for a few molecular systems using the Gaussian 09 default UFF-radii is briefly considered as well.

Molecular structure, vibrational and 13C NMR spectra of two ent-kaurenes spirolactone type diterpenoids rabdosinate and rabdosin B: a combined experimental and density functional methods

The title compounds, rabdosinate and rabdosin B, were isolated from the leaves of Isodon japonica, and characterized by IR-NMR spectroscopy. The molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO-13C) chemical shift values of the title compounds have been calculated by using DFT/B3LYP method with 6-311++G(d,p) basis set. In addition, obtained results were related to the linear regression of experimental 13C NMR chemical shifts values. The integral equation formalism polarized continuum model (IEFPCM) was used in treating chloroform solvation effects on optimized structural parameters and 13C chemical shifts. Besides, molecular electrostatic potential (MEP), HOMO-LUMO analysis were performed by the B3LYP method.

Synthesis, characterization, and DFT studies of a new chiral ionic liquid from (S)-1-phenylethylamine

A new chiral ionic liquid was synthesized from (S)-1-phenylethylamine and it was studied by IR, Raman, polarimetry, NMR and X-ray crystal diffraction. Its vibrational spectral bands are precisely ascribed to the studied structure with the aid of DFT theoretical calculations. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from IR and Raman spectra are assigned based on the results of the theoretical calculations by the DFT-B3LYP method at 6-311G(d,p) level. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies.The vibrational modes assignments were performed by using the animation option of GaussView5.0 graphical interface for Gaussian program.

Isolation, identification and characterization of related substances in furbenicillin

Furbenicillin is a broad-spectrum semisynthetic penicillin with strong antibacterial activity against Gram-negative bacteria. In this study, three impurities in furbenicillin, including an unknown epimer, were determined. On the basis of a complete analysis of the spectrum (MS, (1)H,(13)C, 2D NMR and CD) and the results of chemical methods, the unknown epimer impurity was identified as 10-epi-furbenicillin (impurity 1). Isolation and structure elucidation of impurity 1 was also reported here for the first time.

A guide to small-molecule structure assignment through computation of (¹H and ¹³C) NMR chemical shifts

This protocol is intended to provide chemists who discover or make new organic compounds with a valuable tool for validating the structural assignments of those new chemical entities. Experimental ¹H and/or ¹³C NMR spectral data and its proper interpretation for the compound of interest is required as a starting point. The approach involves the following steps: (i) using molecular mechanics calculations (with, e.g., MacroModel) to generate a library of conformers; (ii) using density functional theory (DFT) calculations (with, e.g., Gaussian 09) to determine optimal geometry, free energies and chemical shifts for each conformer; (iii) determining Boltzmann-weighted proton and carbon chemical shifts; and (iv) comparing the computed chemical shifts for two or more candidate structures with experimental data to determine the best fit. For a typical structure assignment of a small organic molecule (e.g., fewer than ∼10 non-H atoms or up to ∼180 a.m.u. and ∼20 conformers), this protocol can be completed in ∼2 h of active effort over a 2-d period; for more complex molecules (e.g., fewer than ∼30 non-H atoms or up to ∼500 a.m.u. and ∼50 conformers), the protocol requires ∼3-6 h of active effort over a 2-week period. To demonstrate the method, we have chosen the analysis of the cis- versus the trans-diastereoisomers of 3-methylcyclohexanol (1-cis versus 1-trans). The protocol is written in a manner that makes the computation of chemical shifts tractable for chemists who may otherwise have only rudimentary computational experience.

Analysis of seven-membered lactones by computational NMR methods: proton NMR chemical shift data are more discriminating than carbon

We report an NMR chemical shift study of conformationally challenging seven-membered lactones (1-11); computed and experimental data sets are compared. The computations involved full conformational analysis of each lactone, Boltzmann-weighted averaging of the chemical shifts across all conformers, and linear correction of the computed chemical shifts. DFT geometry optimizations [M06-2X/6-31+G(d,p)] and GIAO NMR chemical shift calculations [B3LYP/6-311+G(2d,p)] provided the computed chemical shifts. The corrected mean absolute error (CMAE), the average of the differences between the computed and experimental chemical shifts for each of the 11 lactones, is encouragingly small (0.02-0.08 ppm for (1)H or 0.8-2.2 ppm for (13)C). Three pairs of cis versus trans diastereomeric lactones were used to assess the ability of the method to distinguish between stereoisomers. The experimental shifts were compared with the computed shifts for each of the two possible isomers. We introduce the use of a "match ratio"--the ratio of the larger CMAE (worse fit) to the smaller CMAE (better fit). A greater match ratio value indicates better distinguishing ability. The match ratios are larger for proton data [2.4-4.0 (av = 3.2)] than for carbon [1.1-2.3 (av = 1.6)], indicating that the former provide a better basis for discriminating these diastereomers.

Molecular structure and vibrational bands and 13C chemical shift assignments of both enmein-type diterpenoids by DFT study

We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules.

13C NMR as a general tool for the assignment of absolute configuration

(13)C NMR, alone or in combination with (1)H NMR, allows the assignment of the absolute configuration of chiral alcohols, amines, carboxylic acids, thiols, cyanohydrins, sec,sec-diols and sec,sec-aminoalcohols, derivatized with appropriate chiral auxiliaries. This extends the assignment possibilities of NMR to fully deuterated and to nonproton containing compounds.

GIAO DFT 13C/15N chemical shifts in regioisomeric structure determination of fused pyrazoles

The combined use of two-dimensional NMR correlation experiments and gauge including atomic orbital density functional theory in (13)C NMR chemical shift (CS) calculations allowed reliable and simple structural determination of regioisomeric heterocyclic systems that originate from the reactions of acylquinolinones with substituted hydrazines. Moreover, the results of differential analysis between the calculated (15)N NMR CSs for hypothetical structures and the experimental data of the title azaheterocyclic systems were even more advantageous with respect to (13)C because there was no need for correlational analysis: structures of the regioisomeric compounds could be determined just by direct comparison.

Empirical and DFT GIAO quantum-mechanical methods of (13)C chemical shifts prediction: competitors or collaborators?

The accuracy of (13)C chemical shift prediction by both DFT GIAO quantum-mechanical (QM) and empirical methods was compared using 205 structures for which experimental and QM-calculated chemical shifts were published in the literature. For these structures, (13)C chemical shifts were calculated using HOSE code and neural network (NN) algorithms developed within our laboratory. In total, 2531 chemical shifts were analyzed and statistically processed. It has been shown that, in general, QM methods are capable of providing similar but inferior accuracy to the empirical approaches, but quite frequently they give larger mean average error values. For the structural set examined in this work, the following mean absolute errors (MAEs) were found: MAE(HOSE) = 1.58 ppm, MAE(NN) = 1.91 ppm and MAE(QM) = 3.29 ppm. A strategy of combined application of both the empirical and DFT GIAO approaches is suggested. The strategy could provide a synergistic effect if the advantages intrinsic to each method are exploited.

Calculating accurate proton chemical shifts of organic molecules with density functional methods and modest basis sets

The purpose of this paper is to convince practitioners of (1)H NMR spectroscopy to consider simple quantum chemical calculations as a viable option to aid them in the assignment of their spectra. To this end, it is demonstrated, on a test set of 80 conformationally stable molecules of various kinds carrying different functional groups, that, in contrast to what is claimed in the literature, large basis sets are not needed to obtain rather accurate predictions of (1)H NMR chemical shifts by quantum chemical calculations. On the other hand, modeling the solvent by an SCRF-type calculation may improve certain predictions significantly. The best accuracy/cost ratio is provided by GIAO calculations in chloroform as a solvent with the specially parametrized WP04 functional of Cramer et al. using the cc-pVDZ or 6-31G** basis set, closely followed by similar calculations with the ubiquitious B3LYP functional (both predict (1)H chemical shifts with an average deviation of ca. 0.12 ppm, if the results are scaled linearly). A slightly higher accuracy can be attained by adding diffuse functions to the basis set, but going to the triple-zeta basis sets which have invariably been used hitherto in calculations of chemical shifts does not lead to any improvement. The popular increment schemes such as those implemented in the ChemDraw or ACD programs do not do nearly as well and are often incapable of correctly distinguishing stereoisomers.

First-Principles Determination of Molecular Conformations of Indolizidine (-)-235B' in Solution

Indolizidine (-)-235B' is a particularly interesting natural product, as it is the currently known, most potent and subtype-selective open-channel blocker of the alpha4beta2 nicotinic acetylcholine receptor (nAChR). In the current study, extensive first-principles electronic structure calculations have been carried out in order to determine the stable molecular conformations and their relative free energies of the protonated and deprotonated states of (-)-235B' in the gas phase, in chloroform, and in aqueous solution. The (1)H and (13)C NMR chemical shifts calculated using the computationally determined dominant molecular conformation of the deprotonated state are all consistent with available experimental NMR spectra of (-)-235B' in chloroform, which suggests that the computationally determined molecular conformations are reasonable. Our computational results reveal for the first time that two geminal H atoms on carbon-3 (C3) of (-)-235B' have remarkably different chemical shifts (i.e. 3.24 and 2.03 ppm). The computational results help one to better understand and analyze the experimental (1)H NMR spectra of (-)-235B'. The finding of remarkably different chemical shifts of two C3 geminal H atoms in a certain molecular conformation of (-)-235B' may also be valuable in analysis of NMR spectra of other related ring-containing compounds. In addition, the pK(a) of (-)-235B' in aqueous solution is predicted to be ~9.7. All of the computational results provide a solid basis for future studies of the microscopic and phenomenological binding of various receptor proteins with the protonated and deprotonated structures of this unique open-channel blocker of alpha4beta2 nAChRs. This computational study also demonstrates how one can appropriately use computational modeling and spectroscopic analysis to address the structural and spectroscopic problems that cannot be addressed by experiments alone.

DFT-GIAO 1H and 13C NMR prediction of chemical shifts for the configurational assignment of 6beta-hydroxyhyoscyamine diastereoisomers

(1)H and (13)C NMR chemical shift calculations using the density functional theory-gauge including/invariant atomic orbitals (DFT-GIAO) approximation at the B3LYP/6-311G++(d,p) level of theory have been used to assign both natural diastereoisomers of 6beta-hydroxyhyoscyamine. The theoretical chemical shifts of the (1)H and (13)C atoms in both isomers were calculated using a previously determined conformational distribution, and the theoretical and experimental values were cross-compared. For protons, the obtained average absolute differences and root mean square (rms) errors for each comparison showed that the experimental chemical shifts of dextrorotatory and levorotatory 6beta-hydroxyhyoscyamines correlated well with the theoretical values calculated for the (3R,6R,2'S) and (3S,6S,2'S) configurations, respectively, whereas for (13)C atoms the calculations were unable to differentiate between isomers. The nature of the relatively large chemical shift differences observed in nuclei that share similar chemical environments between isomers was asserted from the same calculations. It is shown that the anisotropic effect of the phenyl group in the tropic ester moiety, positioned under the tropane ring, has a larger shielding effect over one ring side than over the other one.

Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate

We present an experimental and quantum chemical NMR study of the mononucleotide cyclic uridine monophosphate in water. Spectral parameters ((1)H and (13)C chemical shifts and (1)H--(1)H, (13)C--(1)H, (31)P--(13)C and (31)P--(1)H spin-spin coupling constants) have been carefully obtained experimentally and calculated using DFT methods including the solvent effect and the conformational flexibility of the solute. This study confirms that the (1)H and (13)C spectra of polar, flexible molecules in aqueous solution can be predicted with a high level of accuracy, comparable to that obtained for less complex systems.