Harry
Brough
a,
Chris W.
Cook
ab,
John M.
Griffin
a and
Michael J. G.
Peach
*a
aDepartment of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK. E-mail: m.peach@lancaster.ac.uk
bThe Faraday Institution, Quad One, Didcot, OX11 0RA, UK
First published on 8th July 2025
Ab initio calculations of NMR shieldings are often used to assign spectra and help refine crystal structures in the growing field of NMR crystallography. In periodic calculations, GGA exchange–correlation functionals such as PBE and BLYP are most often used, but a “monomer correction” has recently been proposed that incorporates a “higher quality” treatment of local electronic structure into calculated shieldings. The meta-GGA functional rSCAN reportedly generates improved geometries, particularly in systems with important dispersion interactions, but has scarcely been tested for its performance in periodic shielding calculations, with or without monomer corrections. Here, the performance of rSCAN is evaluated by comparing experimental chemical shifts from 75 diverse 13C environments in 13 molecular solids, to chemical shifts calculated by rSCAN and PBE on geometries optimised by rSCAN, PBE and BLYP. We find rSCAN gives marginally improved geometries but produces less accurate chemical shifts than PBE. However, after a monomer correction is applied to the shieldings, corrected rSCAN consistently performs better than corrected PBE, indicating that rSCAN describes long-range contributions to shieldings more accurately than local effects. Monomer correction with a double-hybrid functional has previously been found to provide no additional benefit compared to correction with conventional hybrids. However, we show the double-hybrid mPW2PLYP predicts substantially improved chemical shifts when the monomer correction method is paired with an implicit solvation model, yielding better results than a correction with a cluster of molecules using a conventional hybrid functional. The method we find maximises agreement with experiment is a mPW2PLYP–CPCM correction to rSCAN periodic calculations on rSCAN-optimised geometries. When used on a larger set of organic crystals, with 132 13C environments, this method yields unprecedented accuracy, with root-mean-square error of 0.8 ppm and mean absolute error of 0.6 ppm.
The success of NMR crystallography relies on a strong correlation between theoretical chemical shifts and experimental spectra, so increasing the accuracy of calculated nuclear shieldings is highly desirable. Solid-state shieldings are normally calculated by the gauge-including projector-augmented waves (GIPAW) approach10 within Kohn–Sham density-functional theory (DFT),11,12 which can provide an effective compromise between calculation accuracy and computational cost. A practical DFT calculation relies on a choice of density-functional approximation (DFA) to the unknown exchange–correlation functional, to incorporate quantum mechanical effects. For solid-state shielding calculations, the most widely used1 is the generalised gradient approximation (GGA) by Perdew, Burke and Ernzerhof (PBE), which uses information from the local electron density and its gradient.13
To overcome this expense, a “monomer correction” approach to improve periodic shielding calculations has been proposed.14 Here, GGA shielding calculations are performed on the whole crystal (using a plane-wave approach) and on a single molecule isolated from the periodic structure. A more reliable DFA—likely a hybrid functional—is also used to calculate shieldings on this isolated molecule. These molecular calculations are performed in an atom-centered basis, usually with gauge-including atomic orbitals (GIAO).16
The periodic shieldings are then “corrected” by
σ = σcrystalGGA − σmoleculeGGA + σmoleculehigh-level | (1) |
This method, which assumes the difference in shieldings from two electronic structure methods is insensitive to the long-range geometry, has previously been shown to substantially increase agreement with experiment when correcting PBE shieldings with hybrid functionals.14,17 Corrections to PBE have also been tested with “double-hybrid” DFAs, which incorporate a contribution from second-order Møller–Plesset perturbation theory within the resolution of the identity approximation (RI-MP2), but these were found to provide no additional benefit over the less costly conventional hybrids.17
![]() | (2) |
Unlike computationally intensive (double-)hybrid functionals, mGGA functionals retain the (N3) scaling with basis functions of GGAs, making mGGAs potentially very useful for plane-wave calculations, providing they yield more accurate results.
However, an additional complication arises from incorporating τ(r). The magnetic field, B(r), is the curl of the vector potential, A(r), but since the curl of a gradient vanishes, there are many definitions of A(r) that produce the same B(r). The magnetic field and its related physical properties, are therefore said to be “gauge invariant”, and physical equations should retain this invariance. This motivates the use of the GIPAW approach for periodic shielding calculations, and the use of GIAOs for calculations in an orbital basis.19 However, the definition of τ(r) in eqn (2) is not invariant to the choice of gauge.20
Therefore, to calculate reliable shieldings using mGGAs, the form of τ(r) must be explicitly considered. The most widely used approach for dealing with this undesirable gauge-dependence was developed by Maximoff and Scuseria, τMS(r).21 However, this method has been shown to provide unphysical paramagnetic contributions to the shielding tensors of spherical atoms, and does not correctly generalise the constraint of exactness for one-electron systems to response properties.20,22 A more costly, but physically meaningful approach τD(r) developed by Dobson,23 does not suffer from these problems, and has been shown to improve both nuclear shielding and time-dependent DFT calculations.20,24
The “strongly constrained and appropriately normed” (SCAN) functional is a mGGA designed to satisfy all of the known constraints of the (unknown) exact exchange–correlation functional.25 The SCAN functional incorporates τ(r) via an “iso-orbital indicator”, α(r), which identifies the bonding environment from the relationship between τ(r), the kinetic energy density of a one-orbital system, τW(r),26 and that of the uniform electron gas, τU(r),27
![]() | (3) |
The SCAN functional has been claimed to use α(r) to account for weak interactions,25 demonstrating this ability by predicting the correct stability ordering for phases of ice—a task where PBE and the hybrid functional PBE0,28 which incorporates 25% exact exchange, fail.29
However, SCAN was found to be numerically unstable, motivating the development of a regularised functional, rSCAN.30 This new DFA was more efficient, but this came at the cost of breaking SCAN's exact constraints, leading to a large reduction in accuracy for atomisation energies.27 The authors of SCAN have recently introduced a regularised and restored functional, r2SCAN.27 This was intended to bridge the gap between accuracy and stability, restoring all but one exact constraint of the parent functional. The DFA has been reported to match or exceed the accuracy of SCAN for several molecular properties.31,32
The rSCAN functional has recently been implemented into the widely used plane-wave DFT code, CASTEP,33 but has seen few tests for its utility for NMR crystallography.34–37 To our knowledge, there has never been a systematic review of the performance of rSCAN for GIPAW 13C shielding calculations, or geometries in the context of solid-state NMR. Moreover, rSCAN has not before been tested with the monomer correction approach. Our overarching aim was therefore to assess whether the rSCAN functional could be a useful tool for NMR crystallography.
To do this, we calculated 13C chemical shifts from a set of organic crystals to compare rSCAN's geometries to those from PBE and the GGA by Becke, Lee, Yang and Parr (BLYP),38,39 and to compare rSCAN's shieldings to those from PBE. Several monomer correction approaches were subsequently tested on the periodic shielding calculations, which were performed on each set of geometries. The performance of a method was quantified by agreement of theoretical chemical shifts with experimental chemical shifts determined from 13C magic-angle spinning solid-state NMR spectra. We find that the most accurate method utilises monomer correction with the double-hybrid mPW2PLYP with a conductor-like polarisable continuum model (CPCM) solvent. Applying this correction to the rSCAN periodic shieldings, calculated from rSCAN-optimised geometries, yields highly accurate chemical shifts. On a larger test set of 132 13C environments,17 this optimal method is found to yield an unprecedented accuracy with RMSE of 0.8 ppm.
The crystal structures were optimised with the PBE, BLYP and rSCAN functionals. Relaxation of unit cell parameters risks substantial increase of cell volumes if dispersion correction is not used5 and does not incorporate the thermal expansion present at room temperature in the crystals on which solid-state NMR spectra were recorded. Therefore, unit cell parameters were fixed at their experimental values for optimisations with all three exchange–correlation functionals. This also facilitates more direct comparison to previously reported results where cell parameters were fixed.17
On the geometries computed with each of the three functionals, as well as on structures where only hydrogen atom postitions were relaxed, and on the diffraction-derived structures directly, nuclear shieldings were then calculated with PBE and rSCAN GIPAW. The BLYP functional has previously been shown to produce consistently inferior chemical shifts compared to PBE, including when monomer corrections are applied,17 so shieldings with BLYP are not considered. Shieldings were converted to chemical shifts by the widely used linear regression procedure described in Section 3.2.1.
Fig. 2 and Table 1 show that a large reduction in root-mean-square-error (RMSE) and a narrowing of the error distribution results from allowing hydrogen atom positions to relax, with little sensitivity to the underlying functional, since their positions are poorly defined by XRD.1 Fully relaxing the structures generally improves RMSE for our ambient temperature structures, but results in much higher sensitivity to the DFA used for geometry optimisation.
![]() | ||
Fig. 2 Effect of underlying geometry (bar colours) and DFA for GIPAW calculation (x-axis) on (a) root-mean-square errors and (b) error distribution, comparing calculated to experimental chemical shifts. The central line on the box and whiskers plot indicates the median error, the top and bottom of the boxes are the first and third quartiles of the error distribution and the whiskers extend to 1.5× the interquartile range. Outliers are shown beyond this point as circles and are discussed in the Section S9 of the ESI.† |
Method | RMSE | MAE | IQR | MAX |
---|---|---|---|---|
PBE GIPAW | 2.1 | 1.6 | 2.6 | 4.7 |
PBE0|PBE | 1.5 | 1.2 | 2.0 | 4.3 |
mPW2PLYP|PBE | 1.4 | 1.1 | 1.7 | 4.0 |
rSCAN GIPAW | 2.3 | 1.9 | 3.9 | 5.8 |
PBE0|rSCAN | 1.4 | 1.1 | 1.8 | 4.5 |
mPW2PLYP|rSCAN | 1.2 | 0.9 | 1.4 | 4.2 |
For both the PBE and rSCAN GIPAW calculations, the BLYP geometries produce the worst chemical shift agreement and the rSCAN structures produce the closest chemical shift agreement, although the difference between PBE and rSCAN geometries is small. This geometry sensitivity is most apparent in the rSCAN chemical shifts, which have a higher RMSE and interquartile range (IQR) than the PBE shifts. The best uncorrected results are produced by PBE GIPAW on the PBE or rSCAN geometries, with RMSEs of 2.1 ppm. The somewhat improved performance of rSCAN geometries for the rSCAN shielding calculations compared to PBE and BLYP should be taken in the context of the slightly higher computational cost for the mGGA calculations.
The apparent improvement of rSCAN for geometries—which becomes more convincing after monomer corrections are applied in Section 2.2—has been suggested to result from SCAN's incorporation of dispersion interactions using eqn (3).25 We investigated this by calculating the energy profile over the interfacial bond of a dimer of planar uracil molecules with several electronic structure methods, described in Section S6 of the ESI.† Only the SCAN family of functionals and methods incorporating non-local MP2 correlation bound the dimer. The optimal binding distance was calculated to be 3.8 Å according to the consensus of DFAs corrected with the D4 semi-empirical dispersion correction scheme,42 and the uncorrected SCAN family bound the dimer closer to this distance than non-local methods with steep (N5) scaling. This suggests that rSCAN's improvement over PBE for structures may result from the mGGA incorporating some treatment of dispersion forces.
We therefore calculated optimised geometries in CASTEP for our structures with PBE corrected with the D3 semi-empirical dispersion correction scheme43 and rSCAN, with and without relaxing unit cell parameters. Interestingly, with unfixed cell parameters, rSCAN without dispersion correction performed as well as PBE–D3, with 0.2 ppm lower RMSE compared to conventional PBE. With fixed cell parameters, PBE GIPAW calculations on the PBE, PBE–D3 and rSCAN structures all gave RMSEs of 2.1 ppm. rSCAN has been shown to resemble the hybrid B3LYP44 more closely than PBE for hydrogen bond lengths,36 but in the optimisations where only hydrogen atom positions were relaxed, there was minimal sensitivity to the choice of functional used to optimise the structures. Therefore, rSCAN's performance when producing structures for 13C NMR calculations results primarily from consideration of dispersion forces and other effects on heavy atoms.
Multiple exchange–correlation functionals were chosen for monomer corrections to the PBE and rSCAN GIPAW calculations from each rung of Perdew's “Jacob's ladder” of density-functional approximations, representing increasing computational cost and reliability.49 From the mGGA functionals, TPSS,50 SCAN and r2SCAN were tested. Functionals incorporating exact exchange included PBE0, B3LYP and the range-separated hybrid CAM-B3LYP.51 Double-hybrid functionals included the physically-motivated PBE0-DH,52 and the empirical B2PLYP and mPW2PLYP.53,54 Corrections with RI-MP2 were also calculated. The Microsoft Excel document in the (ESI†) contains detailed statistics for all correction methods tested.
In total, we consider over fifteen monomer corrections each applied to two periodic calculations, themselves each performed on three sets of periodic geometries. For brevity, we therefore introduce notation to describe the corrected shieldings, of “correction| periodic calculation||geometry”. For example, a PBE0 correction to shieldings calculated with PBE GIPAW on the rSCAN periodic geometries is denoted PBE0|PBE||rSCAN.
Fig. 3 and 4 show the effect of some of these monomer corrections to PBE and rSCAN GIPAW calculations, respectively. Corrections with mGGAs were highly sensitive to the geometry, particularly for the TPSS|rSCAN corrections, where using the rSCAN geometry lowers RMSE by 0.3 ppm compared to PBE and by 0.7 ppm compared to BLYP. Less geometry sensitivity is observed for the (double-) hybrid corrections. Here, the rSCAN and PBE geometries perform similarly for corrections to PBE GIPAW, but the rSCAN geometries are consistently better than PBE for corrections to rSCAN GIPAW. Overall, the BLYP geometries perform the worst in thirteen cases, PBE performs the worst in two cases and rSCAN performs the worst only for the PBE0-DH|PBE|| rSCAN chemical shifts.
In contrast to previous results,17 there is a small improvement in RMSE moving from corrections with PBE0 to those with mPW2PLYP for our crystals, from 1.4 to 1.2 ppm for PBE GIPAW. Moreover, the RMSE from PBE0|PBE||PBE is 1.5 ppm, 0.3 ppm higher than previously reported,17 suggesting our set of molecules may be more difficult for the electronic structure methods to describe. These results, and the asymmetric distribution of outliers, are discussed in Section 2.4.
The rSCAN shieldings are slightly worsened by correction with SCAN, which may be due to SCAN's previously reported high dependence on the integration grid.27 Corrections incorporating exact exchange substantially reduce RMSE, by at least 0.5 ppm for PBE and 0.8 ppm for rSCAN shieldings. Considering the low cost of these molecular calculations, the monomer correction method seems to be a simple and reliable strategy for NMR crystallography. Although the rSCAN geometry consistently performs well, and often slightly better than PBE, this reliability comes at a somewhat higher computational cost. There does not seem to be a benefit to using BLYP for geometries compared to PBE.
Table 1 shows the standard rSCAN GIPAW calculations benefit much more than PBE from correction, to the extent that using the (slightly) less reliable functional for GIPAW ends up a better choice if corrections are applied. This implies rSCAN's treatment of long-range effects is much better than its description of short-range effects.
Moreover, although corrected rSCAN outperforms corrected PBE, correcting PBE GIPAW with rSCAN does not improve results. This supports the hypothesis that rSCAN is picking up more long-range contributions to shieldings than PBE, but does not improve local effects. Therefore, rSCAN benefits greatly from monomer correction, where a good treatment of this local electronic structure is incorporated. rSCAN's improved long range performance may, like its geometries, result from incorporation of dispersion effects. The rSCAN functional not only incorporates dispersion into its energies, as do semi-empirical dispersion correction schemes, but also into its self-consistent electron densities, from which shieldings are calculated.
σ = σcrystalrSCAN − σmoleculerSCAN–MS + σmoleculerSCAN–D. | (4) |
The result was a notable improvement, bringing RMSE down from 2.3 to 2.1 ppm, the same as PBE GIPAW, and reducing IQR by 0.9 ppm, as shown in Table 2.
DFA | Method | RMSE | MAE | IQR | MAX |
---|---|---|---|---|---|
rSCAN | GIPAW | 2.3 | 1.9 | 3.9 | 5.8 |
−MS + D | 2.1 | 1.7 | 3.0 | 5.7 | |
r2SCAN | ±MS | 2.3 | 1.9 | 3.9 | 5.8 |
±D | 2.2 | 1.8 | 3.8 | 5.8 | |
−MS + D | 2.0 | 1.6 | 3.0 | 5.7 | |
SCAN | ±MS | 2.4 | 1.9 | 3.7 | 5.1 |
±D | 2.5 | 2.0 | 3.6 | 5.3 | |
−MS + D | 2.1 | 1.8 | 3.5 | 5.1 |
When correcting rSCAN GIPAW, a version of τ(r) must be chosen with which to calculate the molecular rSCAN shieldings. Neglecting the gauge invariance of τ(r) completely in the molecular calculations leads to very disordered results, presumably due to a higher impact of basis set incompleteness in molecular calculations compared to in plane wave calculations. Therefore, we must either choose to subtract shieldings calculated with either τMS(r) or τD(r). For the vast majority of—but not all—correction methods, subtracting τMS(r) shieldings improves results compared to subtracting τD(r) shieldings. This evidence, along with the improvement from “correcting” the rSCAN shieldings with eqn (4), suggests that the Maximoff–Scuseria scheme somehow resembles the neglect of gauge invariance in the periodic calculations more closely than the Dobson scheme. Therefore, subtraction of τMS(r) shieldings generally improves results, removing some unphysical treatment of gauge invariance.
We also considered whether its regularisation might be limiting rSCAN. Further corrections with SCAN and r2SCAN were calculated, either subtracting and adding shieldings from τMS(r) and τD(r), or by a gauge correction as in eqn (4). While correcting rSCAN GIPAW with r2SCAN–MS does not improve results, applying the gauge correction does slightly, suggesting there may be more accuracy to be gained by a GIPAW calculation of r2SCAN shieldings within the Dobson scheme. The improvement from rSCAN–D to r2SCAN–D is less substantial than the improvement from rSCAN GIPAW to rSCAN–D, indicating the exact constraints broken by the neglect of the gauge invariance of τ(r) in CASTEP may be more important for shielding calculations than the constraints broken in the rSCAN functional itself.
Despite the fact that the gauge invariance of τ(r) is less crucial in periodic calculations compared to molecular calculations, the consistent improvement from “correcting” the kinetic energy density of rSCAN motivates the implementation of the Dobson kinetic energy density, and the more constrained r2SCAN functional, into the CASTEP code.
The simplest step towards mimicking the full crystal environment may be embedding the subsystem molecule in a dielectric medium. This confines the electron density to the vicinity of the molecule, potentially enhancing the separability of long- and short-range effects, and therefore aligning effectively with the assumptions underlying monomer correction.
σ = σcrystal(m)GGA − σmolecule–CPCM(m)GGA + σmolecule–CPCMhigh-level |
Conventional hybrids do not benefit particularly in terms of RMSE, but their error distributions. A more substantial improvement in IQR and RMSE was observed in the double-hybrid mPW2PLYP, suggesting that a closer resemblance to the crystal structure environment lets this high-level electronic structure method perform closer to its full potential. For rSCAN GIPAW, mPW2PLYP–CPCM correction decreases RMSE by over 0.3 ppm compared to PBE0 correction, down to 1.1 ppm. The mean absolute error (MAE) of mPW2PLYP–CPCM correction is 0.7 ppm, and the distribution of errors is very tight, with IQR of 1.1 ppm. Apart from a few pathological environments discussed in Section 2.4, mPW2PLYP–CPCM provides extremely good agreement with experimental chemical shifts.
The highly parameterised solvation model based on electron density58 was also tested, and gave a marginally higher RMSE across GIPAW calculations and geometries. To determine the dielectric-dependence of the corrected shieldings, corrections were calculated with mPW2PLYP in an infinite dielectric constant, and CPCMs based on benzene (ε = 2.3), acetone (ε = 20.7), water (ε = 80.4), and formamide (ε = 111.4). No significant difference was observed where ε > 20, but the benzene CPCM gave a 0.1 ppm higher RMSE. The choice of dielectric therefore seems unimportant, in agreement with previously reported results which found that dielectric-dependence is largely eliminated in the process of converted shieldings to chemical shifts.59
Spectra are often assigned sequentially for NMR crystallography, so the correct ordering of calculated peaks is vital. However, conventional GIPAW calculations with PBE risk predicting the incorrect assignment for closely spaced peaks. On the rSCAN geometry of uracil, PBE GIPAW and a simple PBE0 correction predict the wrong ordering of peaks, but Fig. 5 shows that mPW2PLYP–CPCM correction gives an unambiguous and correctly ordered spectrum.
![]() | ||
Fig. 5 Experimental 13C spectrum of uracil, and theoretical spectra from PBE GIPAW on the rSCAN geometry and corrections with PBE0 and mPW2PLYP–CPCM. The experimental spectrum was recorded with 15 kHz magic-angle spinning and cross-polarisation on a spectrometer operating at 16.4 T. Simulated spectra were generated with Gaussian functions with full widths at half maximum of 0.1 ppm. The carbonyl peak, “a”, should be observed at a higher chemical shift than the C–H peak, “b”, around 152 ppm. A correction with mPW2PLYP–CPCM clearly predicts the correct ordering of these peaks, while PBE and PBE0 correction fail. The correct ordering of peaks was taken from previously reported solid-state NMR spectra of uracil.55 and is confirmed by a dipolar dephasing experiment (spectrum shown in Fig. S19 of the ESI†), which shows that the lower chemical shift resonance corresponds to a C–H carbon. |
Fig. 6 compares methods used to correct rSCAN shieldings, showing how improvements in RMSE at each stage can sum to reduce the GIPAW error by over 50%. In fact, while a full optimisation is calculated routinely, the benefit of this is small compared to using a molecular correction with PBE0, and is competitive with the improvement moving from PBE0 to mPW2PLYP–CPCM corrections. The same pattern is seen for the PBE shieldings, although the best results are found in mPW2PLYP–CPCM|rSCAN||rSCAN. We also calculated PBE0|PBE monomer corrections on the unoptimised structures directly, but this did not significantly reduce RMSE from a conventional GIPAW calculation. Some kind of geometry optimisation therefore remains necessary for predicting accurate chemical shifts for ambient temperature structures.
Considering the low cost of monomer corrections compared to full plane wave optimisations, the technique has clearly demonstrated its utility for NMR crystallography. All of the calculations with mPW2PLYP–CPCM took less than 15 minutes of computational time running on eight parallel processes, with the exception of L-ascorbic acid where the asymmetric unit consists of two molecules. Because of the formal (N5) scaling of MP2 with number of basis functions, care should be taken applying this correction approach to large molecules if computational time is limited.
σ = σcrystal(m)GGA − σcluster(m)GGA + σclusterhigh-level |
In all cases, the CPCM marginally improved RMSE. Compared to the monomer corrections, these were very expensive, with the PBE0 cluster calculations taking several hours on eight parallel processes. The computational cost is highly dependent on the crystal geometry, as some clusters like α-D-glucose require many molecules to sufficiently “cover” the central environments. The number of molecules in each cluster is shown in Table S8 (ESI†).
Table 3 shows that cluster corrections with PBE0 do not improve RMSE or MAE compared to monomer corrections, but increase maximum absolute error (MAX) and reduce IQR. This suggests that while most environments are predicted better, some outliers are predicted worse. There was no significant difference in the cluster gauge corrections compared to those on the isolated molecules. Chemical shifts from the PBE0 calculations directly on the cluster, without correcting the GIPAW calculations, were no better than PBE GIPAW, validating the molecular correction approach and highlighting how important long-range effects to shielding can be.
GIPAW | Correction | RMSE | MAE | IQR | MAX |
---|---|---|---|---|---|
PBE | None | 2.1 | 1.6 | 2.6 | 4.7 |
PBE0 | 1.5 | 1.1 | 2.0 | 4.3 | |
PBE0 cluster | 1.5 | 1.1 | 1.4 | 4.9 | |
rSCAN | None | 2.3 | 1.9 | 3.9 | 5.7 |
PBE0 | 1.4 | 1.1 | 1.5 | 4.5 | |
PBE0 cluster | 1.5 | 1.0 | 1.3 | 5.1 | |
rSCAN–D | 2.1 | 1.7 | 3.0 | 5.7 | |
rSCAN–D cluster | 2.1 | 1.7 | 3.1 | 5.7 | |
r2SCAN–D | 2.0 | 1.6 | 3.5 | 5.7 | |
r2SCAN–D cluster | 2.1 | 1.7 | 3.1 | 5.7 |
We considered that a remaining source of error may lie in the crystal geometries, which were only optimised with (m)GGA DFAs. Full optimisations on isolated molecules and clusters produced large deviations from the experimental structures, so constrained optimisations were performed on the rSCAN-optimised clusters. Here, the central molecule in each cluster was fully relaxed, but only hydrogen atoms in the other molecules were optimised. The optimisations were performed with PBE0–D4 with cc-pVTZ in an ethanol CPCM, before PBE0–CPCM shieldings were calculated.
When shieldings were corrected by
σ = σcrystalPBE − σoptimised![]() ![]() |
Overall, PBE0 cluster corrections do not come close to the 1.1 ppm RMSE from mPW2PLYP–CPCM monomer corrections, showing the importance of a high quality treatment of electronic structure in shielding calculations. These cluster corrections are also far more computationally expensive, so not recommended unless effects on chemical shifts from nearby molecules are thought to be particularly important.
To identify the most challenging environments, the lowest absolute deviation from experiment of every environment was determined, across all correction methods tested. Of the 75 environments, only seven could never achieve an absolute deviation of less than half the average line width for our experimental spectra, 0.3 ppm. In four of these seven environments, the best method was a correction to the BLYP geometry, which generally performs poorly. Three of the environments correspond to amide CO carbons, suggesting that these may be difficult for the electronic structure methods. When these seven outliers are excluded and chemical shifts are recalculated, the PBE0 correction matches the previously reported RMSE. The difference between PBE0 and mPW2PLYP correction decreases, suggesting the double-hybrid may be more useful in difficult cases, but the improvement in performance upon addition of a CPCM to mPW2PLYP remains clear, as MAE drops to an extremely low 0.6 ppm. Similar trends are observed for the other GIPAW calculations.
The charts in Section 2.2 show that chemical shifts are under-shielded for the vast majority of outliers, indicating the DFAs are overestimating the paramagnetic contribution in these environments. This contribution to shielding is reciprocal to the energy difference between the highest occupied and lowest unoccupied Kohn–Sham orbitals,19 which is often underestimated by (m)GGAs.62 In these cases, the poor performance of the GIPAW (m)GGA shieldings may not be recoverable with molecular corrections. An alternative explanation is that one of the three principal components of the shielding tensor, which are averaged to the isotropic shielding, is consistently poorly described.
To compare directly to previously reported results, we calculated chemical shifts with our best method, mPW2PLYP–CPCM|rSCAN|| rSCAN, on a previously used test set consisting of 132 13C environments, described in the Table S2 (ESI†).17 On this test set, the best previously reported RMSE was 1.1 ppm, from PBE0|PBE||PBE. Our best correction method yields a substantially lower RMSE, of 0.8 ppm, and a MAE of 0.6 ppm. This is, to our knowledge, the best agreement between theoretical and experimental 13C solid-state chemical shifts yet achieved on a large test set of structures. This confirms that our test set contains more challenging carbon environments. Since we found a small improvement by using double-hybrids for correction compared to conventional hybrids, the utility of the higher-level functionals is more pronounced for “difficult” cases.
Because these environments were so consistently badly described, we considered whether the geometry could be at fault. The structure used was from neutron diffraction at room temperature, so no poorly placed hydrogen atoms would be expected and thermal expansion is considered. The compound has also been reported to have no phase transition at ambient pressure under 440 K.63 Periodic calculations with the very high plane wave energy cut-off of 1200 eV were performed, but gave no improvement. The compound is known to have a tautomer,64 and we considered whether these could be affecting the chemical shift. A CASTEP optimisation was performed on the tautomer with rSCAN, but the final energy was around 100 kcal mol−1 higher than the original structure, giving it a negligible Boltzmann population at ambient temperature.
Despite how similar the molecules look in Fig. 7, the experimental difference in chemical shift between the “difficult” carbons was over 3 ppm. The main structural difference is in the overlying hydroxyl groups, but when these are removed from the structures, calculated chemical shifts still differ by around 3 ppm. We considered the environments could be very sensitive to the geometry, so a highly expensive B3LYP geometry optimisation in CASTEP was performed. This also produced no substantial benefit to the difficult environments.
Interestingly, L-ascorbic acid has the same conjugated, enone functionality as another organic crystal which has been reported as badly described even by monomer corrections, β-testosterone.36 This might suggest that these shielding calculations could benefit from a method where multiple electronic configurations are explicitly considered, such as coupled-cluster theory. However, due to the asymmetric distribution of outliers, we suspect that the issues with these molecules result from an issue with the GIPAW calculations, rather than the corrections. The mPW2PLYP–CPCM corrections are generally so reliable that the breakdown in accuracy for these L-ascorbic acid environments may indict the underlying (m)GGAs, rather than the choice of corrections—the (m)GGA calculations seem to be describing these few environments so poorly that they are not able to be corrected.
Spectra were recorded at room temperature with a 2.5 mm probe at a magic-angle spinning rate of between 15 and 25 kHz. Cross-polarisation was used to transfer magnetisation from 1H nuclei with contact time of between 1 and 5 ms. The cross-polarisation power was ramped linearly from 70% to 100%. 1H heteronuclear decoupling using two-pulse phase modulation65 with a pulse length of 4.8 μs and a radiofrequency field strength of 100 kHz was applied during acquisition. Spectra are the sum of between 112 and 1024 transients separated by a recycle interval of between 3 and 120 seconds. Fig. S6–S18 (ESI†) show the solid-state NMR spectra for our set of organic crystals. Structures were confirmed to be the polymorphs used for the theoretical calculations by comparing experimental powder XRD patterns to those calculated in Mercury.66
To convert from these updated shieldings to isotropic chemical shifts, the widely used linear regression method was applied.1 Here, the experimental spectra were sequentially assigned, matching the highest chemical shift with the lowest nuclear shielding calculated by PBE on the PBE geometries. A linear regression was then calculated by the least-squares algorithm in Microsoft Excel, fitting the calculated shieldings, σcalc, and experimental shifts, δexp, to
δexp = σref − mσcalc. | (5) |
This yielded the gradient, m, and reference shielding, σref. The shieldings were then converted to calculated chemical shifts by
δcalc = σref − mσcalc, | (6) |
![]() | (7) |
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This statistic is a simple mean, and does not account for the distribution of errors. In this study, the spread of the error distribution was quantified by the maximum absolute error and interquartile range. A small interquartile range indicates that shieldings are calculated consistently, but does not imply they are calculated consistently well, as the distribution may not be centered around an error of zero. Because of these limitations, a combination of error statistics was used to assess the utility of a method to calculate shieldings.
Several calculations on the l-alanine structure with plane wave kinetic energy cut-offs ranging from 200–1000 eV were performed with PBE and rSCAN to determine the convergence of the energy, forces and isotropic shieldings. For these calculations, a dense k-point spacing of 0.01 Å−1 was used via a Monkhorst–Pack grid. Calculations were then run at a 1000 eV plane wave energy cut-off with a k-point spacing ranging from 0.01–0.20 Å−1. The parameters which converged shieldings to below 0.1 ppm and root-mean-square forces below 0.01 eV Å−1 were an energy cut-off of 800 eV and k-point spacing of 0.03 Å−1. While only l-alanine was explicitly converged, these parameters are much stricter than those used in previous work on molecular corrections so were assumed to generalise to our other crystals.14,17
On diffraction-derived structures from the Cambridge Structural Database, geometry optimisations with PBE, BLYP and rSCAN with the converged energy cut-off and k-point spacing were performed. Optimisations with B3LYP were performed with an energy cut-off of 650 eV and a k-point spacing of 0.05 Å−1. The unit cell parameters were fixed at their experimental values and the Broyden–Fletcher–Goldfarb–Shanno quasi-Newton algorithm71 was used to relax the atoms in the unit cells. Optimisations were also performed where lattice parameters were allowed to relax with PBE, rSCAN and PBE–D3. Crystal structures were visualised using the VESTA program.72
On various geometries, nuclear shielding GIPAW calculations were performed with the PBE and rSCAN exchange–correlation functionals. All calculations in CASTEP were performed with an electronic energy convergence tolerance of 10−10 eV, a geometry convergence energy tolerance of 10−6 eV, and a fixed band occupancy. Increasing the geometry convergence tolerance has previously been shown to slightly increase agreement between experimental and calculated chemical shifts.73 All other parameters used were CASTEP defaults, including the Koelling–Harmon relativistic treatment of pseudopotentials.74
For the majority of the molecular corrections, the cc-pVTZ basis set was used. With this basis, molecular corrections to the PBE and rSCAN GIPAW calculations on all three sets of geometries were calculated with rSCAN, r2SCAN, SCAN, TPSS, PBE0, B3LYP, CAM-B3LYP, PBE0-DH, B2PLYP, mPW2PLYP and RI-MP2. The PBE0, B3LYP and mPW2PLYP exchange–correlation functionals were also combined with the CPCM and SMD implicit solvation models. Corrections to the rSCAN GIPAW shieldings were calculated by subtracting the Maximoff–Scuseria and Dobson schemes for the gauge invariance of the kinetic energy density. Similarly, corrections with mGGA functionals to GIPAW shieldings were calculated by adding shieldings from the Maximoff–Scuseria and Dobson schemes.
For all calculations in ORCA, “tight” self-consistent field convergence criteria were used. For calculations involving RI-MP2 including all double-hybrid calculations, core electrons were correlated and the relaxed density used. The default approximations were used in the ORCA calculations, which have been shown to increase computational speed substantially while introducing minimal loss in accuracy.46,76 The approximations include the RI-J approximation for the Coulomb interaction,77 the chain of spheres approximation for Hartree–Fock exchange,78 and the resolution of the identity approximation for MP2 and double-hybrid calculations.46 For the RI-J approximation, the default auxiliary basis set by Weigend was used,79 and for the RI-MP2 and double-hybrid calculations, the cc-pVTZ/C auxiliary basis set was used.
The coordinate scan calculation over the interfacial bond of the uracil dimer was performed with PBE, BLYP, rSCAN, r2SCAN, SCAN, PBE0, B3LYP, CAM-B3LYP, B2PLYP and mPW2PLYP, in 0.1 Å increments from 3–5 Å. The calculations were performed in the aug-cc-pVTZ basis set in ORCA, with and without the D4 semi-empirical dispersion correction scheme. For the exact exchange corrections, exchange–correlation functionals were defined based on PBE, SCAN and TPSS with the chain of spheres approximation, in line with the default implementation of hybrid functionals in ORCA.
Geometry optimisations of isolated molecules and molecular clusters were calculated with PBE0 and cc-pVTZ with a CPCM parameterised for ethanol and the D4 semi-empirical dispersion correction scheme. Corrections with geometry optimised structures were calculated both by subtracting the (m)GGA calculation on the unoptimised and optimised clusters. The corrections with implicit solvation models were determined with both the (m)GGA and high-level functional shieldings calculated in the same dielectric constant.
GaussView was used for visualisation of structures and to extract molecular geometries from the optimised crystal structures. For these extractions, the asymmetric unit was taken from the unit cell. This was always a single molecule, except in the case of the L-ascorbic acid dimer. For this structure, corrections were also calculated with the individual molecules rather than the asymmetric unit, but this did not improve RMSE.
Figures were rendered in version 1.14 of UCSF Chimera,80 ChemDraw 21 and Matplotlib.81 Simulated spectra were generated with a Python code, using Gaussian functions parameterised by full-width at half maximum.
The very low RMSE of 0.8 ppm on a large test set of crystals, from monomer corrections with mPW2PLYP–CPCM to rSCAN GIPAW calculations on rSCAN-optimised geometries, shows how important a high quality treatment of electronic structure is for shielding calculations. For small to medium-sized molecules, these corrections take a few minutes of computational time, compared to several hours required for plane wave calculations. Moreover, the GIAO shieldings can be determined in parallel with the GIPAW calculation, and are much easier to perform than methods which do not provide as much benefit, such as sampling molecular dynamics simulations to incorporate finite temperature effects. The simplicity of these corrections and low cost for most molecules promises to increase confidence in NMR crystallography experiments and facilitate derivation of new structures.
The rSCAN functional consistently generates high quality geometries. Because of the higher geometry-dependence of mGGA functionals, rSCAN GIPAW should only be used on an rSCAN geometry. It is currently a better choice to use PBE than rSCAN for uncorrected GIPAW. However, when rSCAN's ability to account for long-range effects on shielding is combined with a high quality treatment of local electronic structure by monomer correction, the mGGA becomes the better starting choice. While the difference between corrected PBE and rSCAN is small, the surprising performance of corrected rSCAN strongly motivates the implementation of the more constrained r2SCAN functional and the Dobson kinetic energy density into the CASTEP code.
Cluster corrections tighten the error distribution, and are worth considering when excellent predictions are required and computational time is not a constraint. However, the much higher cost means these cannot be recommended for routine use. The success of mPW2PLYP–CPCM indicates that more accuracy may be gained by a double-hybrid cluster correction. The poor scaling of RI-MP2 makes this intractable, but the asymptotically linear scaling “domain-based local pair natural orbital” (DLPNO) approximation82,83 produces shieldings very similar to those with RI-MP2 for our isolated molecules. This method could be applied to the clusters. Another method to increase accuracy further could be within the geometries; DLPNO-double-hybrids could be used to optimise the central molecule in a cluster, before that structure is used to correct GIPAW shieldings.
Finally, our study should be expanded to the individual components of the shielding and electric field gradient tensors, comparing calculations to solid-state NMR powder patterns,84–86 to test the success of mPW2PLYP–CPCM corrections more broadly. Likewise, this correction method should be applied to calculate chemical shifts for other relevant nuclei in NMR crystallography of molecular organics such as 15N, 17O and 1H.
Footnote |
† Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d5cp01111f |
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