Computational Modeling of a Stereoselective Epoxidation: Reaction of Carene with Peroxyformic Acid

Catalytic Enantioselective Sulfoxidation of Functionalized Thioethers Mediated by Aspartic Acid-Containing Peptides

A peptide-catalyzed enantioselective oxidation of sulfides to yield pharmaceutically relevant chiral sulfoxides is reported. Experimental evidence suggesting that a hydrogen bond-donating moiety must be present in the substrate to achieve high levels of enantioinduction is supported by computational modeling of transition states. These models also indicate that dual points of contact between the peptidic catalyst and substrate are likely responsible for the formation of one desired sulfoxide in 94:6 er.

A molecular electron density theory study of the mechanism, chemo- and stereoselectivity of the epoxidation reaction of R-carvone with peracetic acid

The epoxidation reaction of R-carvone 8 with peracetic acid 9 has been studied within the molecular electron density theory at the B3LYP/6-311(d,p) computational level. The chemo- and stereoisomeric reaction paths involving the two C-C double bonds of R-carvone 8 have been studied. DFT calculations account for the high chemoselectivity involving the C-C double bond of the isopropenyl group and the low diastereoselectivity, in complete agreement with the experimental outcomes. The Baeyer-Villiger reaction involving the carbonyl group of R-carvone 8 has also been analysed. A bonding evolution theory analysis of the epoxidation reaction shows the complexity of the bonding changes taking place along this reaction. Formation of the oxirane ring takes place asynchronously at the end of the reaction by attack of anionic oxygen on the two carbons of the isopropenyl C-C double bond.

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.

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

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

Multi-conformer molecules in solutions: an NMR-based DFT/MP2 conformational study of two glucopyranosides of a vitamin E model compound

Overall geometries of both glucosyl derivatives of PMC were found on the basis of their NMR spectra in CDCl₃and relatedδ_H,C/ⁿJ_HHIEF-PCM(UFF,CHCl₃)/DFT calculational results.

Density functional theory study of (13)C NMR chemical shift of chlorinated compounds

The use of the standard density functional theory (DFT) leads to an overestimation of the paramagnetic contribution and underestimation of the shielding constants, especially for chlorinated carbon nuclei. For that reason, the predictions of chlorinated compounds often yield too high chemical shift values. In this study, the WC04 functional is shown to be capable of reducing the overestimation of the chemical shift of Cl-bonded carbons in standard DFT functionals and to show a good performance in the prediction of (13)C NMR chemical shifts of chlorinated organic compounds. The capability is attributed to the minimization of the contributions that intensively increase the chemical shift in the WC04. Extensive computations and analyses were performed to search for the optimal procedure for WC04. The B3LYP and mPW1PW91 standard functionals were also used to evaluate the performance. Through detailed comparisons between the basis set effects and the solvent effects on the results, the gas-phase GIAO/WC04/6-311+G(2d,p)//B3LYP/6-31+G(d,p) was found to be specifically suitable for the prediction of (13)C NMR chemical shifts of chlorides in both chlorinated and non-chlorinated carbons. Further tests with eight molecules in the probe set sufficiently confirmed that WC04 was undoubtedly effective for accurately predicting (13) C NMR chemical shifts of chlorinated organic compounds.

Assigning stereochemistry to single diastereoisomers by GIAO NMR calculation: the DP4 probability

GIAO NMR shift calculation has been applied to the challenging task of reliably assigning stereochemistry with quantifiable confidence when only one set of experimental data are available. We have compared several approaches for assigning a probability to each candidate structure and have tested the ability of these methods to distinguish up to 64 possible diastereoisomers of 117 different molecules, using NMR shifts obtained in rapid and computationally inexpensive single-point calculations on molecular mechanics geometries without time-consuming ab initio geometry optimization. We show that a probability analysis based on the errors in each (13)C or (1)H shift is significantly more successful at making correct assignments with high confidence than are probabilities based on the correlation coefficient and mean absolute error parameters. Our new probability measure, which we have termed DP4, complements the probabilities obtained from our previously developed CP3 parameter, which applies to the case of assigning a pair of diastereoisomers when one has both experimental data sets. We illustrate the application of DP4 to assigning the stereochemistry or structure of 21 natural products that were originally misassigned in the literature or that required extensive synthesis of diastereoisomers to establish their stereochemistry.

A multi-standard approach for GIAO (13)C NMR calculations

The influence of the reference standard employed in the calculation of (13)C NMR chemical shifts was investigated over a large variety of known organic compounds, using different quantum chemistry methods and basis sets. After detailed analysis of the collected data, we found that methanol and benzene are excellent reference standards for computing NMR shifts of sp(3)- and sp-sp(2)-hybridized carbon atoms, respectively. This multi-standard approach (MSTD) performs better than TMS in terms of accuracy and precision and also displays much lower dependence on the level of theory employed. The use of mPW1PW91/6-31G(d)//mPW1PW91/6-31G(d) level is recommended for accurate (13)C NMR chemical shift prediction at low computational cost.

Assigning the stereochemistry of pairs of diastereoisomers using GIAO NMR shift calculation

GIAO NMR chemical shifts have been calculated for a set of 28 pairs of diastereoisomers in order to test the ability of NMR shift calculation to distinguish between diastereomeric structures. We compare the performance of several different parameters for quantifying the agreement between calculated and experimental shifts from the point of view of assigning structures and introduce a new parameter, CP3, based on comparing differences in calculated shift with differences in experimental shift, which is significantly more successful at making correct structure assignments with high confidence than are the currently used parameters of the mean absolute error and the correlation coefficient. Using our new parameter in conjunction with Bayes' theorem, stereostructure assignments can be made with quantifiable confidence using shifts obtained in single point calculations on molecular mechanics geometries without computationally expensive ab initio geometry optimization.