The effects of including (a) implicit solvent in geometry optimizations, (b) conformationally flexible molecules in test sets, and (c) empirical dispersion D3(BJ) on scaling factors for predicting1H and13C NMR chemical shifts were explored. Scaling factors with optimizations performed in the gas phase and with a Polarizable Continuum Model (PCM) solvent model were obtained for 12 organic solvents, including 2,2,2‐trifluroethanol and chlorobenzene, for which scaling factors have been developed for the first time. Scaling factors for aromatic solvents were split into primary and secondary scaling factors to account for CH–π effects. Including empirical dispersion D3(BJ) did not lead to significant improvement.
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.
more » « less- Award ID(s):
- 2116395
- NSF-PAR ID:
- 10531787
- Publisher / Repository:
- MPDI
- Date Published:
- Journal Name:
- Molecules
- Volume:
- 28
- Issue:
- 6
- ISSN:
- 1420-3049
- Page Range / eLocation ID:
- 2449
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract -
Nuclear magnetic resonance (NMR) is one of the primary techniques used to elucidate the chemical structure, bonding, stereochemistry, and conformation of organic compounds. The distinct chemical shifts in an NMR spectrum depend upon each atom's local chemical environment and are influenced by both through-bond and through-space interactions with other atoms and functional groups. The in silico prediction of NMR chemical shifts using quantum mechanical (QM) calculations is now commonplace in aiding organic structural assignment since spectra can be computed for several candidate structures and then compared with experimental values to find the best possible match. However, the computational demands of calculating multiple structural- and stereo-isomers, each of which may typically exist as an ensemble of rapidly-interconverting conformations, are expensive. Additionally, the QM predictions themselves may lack sufficient accuracy to identify a correct structure. In this work, we address both of these shortcomings by developing a rapid machine learning (ML) protocol to predict 1 H and 13 C chemical shifts through an efficient graph neural network (GNN) using 3D structures as input. Transfer learning with experimental data is used to improve the final prediction accuracy of a model trained using QM calculations. When tested on the CHESHIRE dataset, the proposed model predicts observed 13 C chemical shifts with comparable accuracy to the best-performing DFT functionals (1.5 ppm) in around 1/6000 of the CPU time. An automated prediction webserver and graphical interface are accessible online at http://nova.chem.colostate.edu/cascade/. We further demonstrate the model in three applications: first, we use the model to decide the correct organic structure from candidates through experimental spectra, including complex stereoisomers; second, we automatically detect and revise incorrect chemical shift assignments in a popular NMR database, the NMRShiftDB; and third, we use NMR chemical shifts as descriptors for determination of the sites of electrophilic aromatic substitution.more » « less
-
Overhauser dynamic nuclear polarization (ODNP) NMR of solutions at high fields is usually mediated by scalar couplings that polarize the nuclei of heavier, electron-rich atoms. This leaves 1H-detected NMR outside the realm of such studies. This study presents experiments that deliver 1H-detected NMR experiments on relatively large liquid volumes (60 ∼ 100 μL) and at high fields (14.1 T), while relying on ODNP enhancements. To this end 13C NMR polarizations were first enhanced by relying on a mechanism that utilizes e--13C scalar coupling interactions; the nuclear spin alignment thus achieved was then passed on to neighboring 1H for observation, by a reverse INEPT scheme relying on one-bond JCH-couplings. Such 13C 1H polarization transfer ported the 13C ODNP gains into the 1H, permitting detection at higher frequencies and with higher potential sensitivities. For a model solution of labeled 13CHCl3 comixed with a nitroxide-based TEMPO derivative as polarizing agent, an ODNP enhancement factor of ca. 5x could thus be imparted to the 1H signal. When applied to bigger organic molecules like 2-13C-phenylacetylene and 13C8-indole, ODNP enhancements in the 1.2-3x range were obtained. Thus, although handicapped by the lower γ of the 13C, enhancements could be imparted on the 1H thermal acquisitions in all cases. We also find that conventional 1H–13C nuclear Overhauser enhancements (NOEs) are largely absent in these solutions due to the presence of co-dissolved radicals, adding negligible gains and playing negligible roles on the scalar e-→13C ODNP transfer. Potential rationalizations of these effects as well as extensions of these experiments, are briefly discussed.more » « less
-
The correlation consistent Composite Approach for transition metals (ccCA-TM) and density functional theory (DFT) computations have been applied to investigate the fluxional mechanisms of cyclooctatetraene tricarbonyl chromium ((COT)Cr(CO)3) and 1,3,5,7-tetramethylcyclooctatetraene tricarbonyl chromium, molybdenum, and tungsten ((TMCOT)M(CO)3 (M = Cr, Mo, and W)) complexes. The geometries of (COT)Cr(CO)3 were fully characterized with the PBEPBE, PBE0, B3LYP, and B97-1 functionals with various basis set/ECP combinations, while all investigated (TMCOT)M(CO)3 complexes were fully characterized with the PBEPBE, PBE0, and B3LYP methods. The energetics of the fluxional dynamics of (COT)Cr(CO)3 were examined using the correlation consistent Composite Approach for transition metals (ccCA-TM) to provide reliable energy benchmarks for corresponding DFT results. The PBE0/BS1 results are in semiquantitative agreement with the ccCA-TM results. Various transition states were identified for the fluxional processes of (COT)Cr(CO)3. The PBEPBE/BS1 energetics indicate that the 1,2-shift is the lowest energy fluxional process, while the B3LYP/BS1 energetics (where BS1 = H, C, O: 6-31G(d′); M: mod-LANL2DZ(f)-ECP) indicate the 1,3-shift having a lower electronic energy of activation than the 1,2-shift by 2.9 kcal mol−1. Notably, PBE0/BS1 describes the (CO)3 rotation to be the lowest energy process, followed by the 1,3-shift. Six transition states have been identified in the fluxional processes of each of the (TMCOT)M(CO)3 complexes (except for (TMCOT)W(CO)3), two of which are 1,2-shift transition states. The lowest-energy fluxional process of each (TMCOT)M(CO)3 complex (computed with the PBE0 functional) has a ΔG‡ of 12.6, 12.8, and 13.2 kcal mol−1 for Cr, Mo, and W complexes, respectively. Good agreement was observed between the experimental and computed 1H-NMR and 13C-NMR chemical shifts for (TMCOT)Cr(CO)3 and (TMCOT)Mo(CO)3 at three different temperature regimes, with coalescence of chemically equivalent groups at higher temperatures.more » « less
-
A fast, straightforward method for computing NMR chemical shieldings of crystalline solids is proposed. The method combines the advantages of both conventional approaches: periodic calculations using plane-wave basis sets and molecular computational approaches. The periodic calculations capture the periodic nature of crystalline solids, but the computational level of the electronic structure calculation is limited to general-gradient-approximation (GGA) density functionals. It is demonstrated that a correction to the GGA result calculated on an isolated molecule at a higher level of theory significantly improves the correlations between experimental and calculated chemical shifts while adding almost no additional computational cost. Corrections calculated with a hybrid density functional improved the accuracy of 13C, 15N and 17O chemical shift predictions significantly and allowed identifying errors in previously published experimental data. Applications of the approach to crystalline isocytosine, methacrylamide, and testosterone are presented.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/molecules28062449
