Analyzing Discrepancies in Chemical-Shift Predictions of Solid Pyridinium Fumarates
Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
20-01472S
Grantová Agentura České Republiky
PubMed
34202841
PubMed Central
PMC8270278
DOI
10.3390/molecules26133857
PII: molecules26133857
Knihovny.cz E-zdroje
- Klíčová slova
- DFT calculations, NMR spectroscopy, solids,
- Publikační typ
- časopisecké články MeSH
Highly accurate chemical-shift predictions in molecular solids are behind the success and rapid development of NMR crystallography. However, unusually large errors of predicted hydrogen and carbon chemical shifts are sometimes reported. An understanding of these deviations is crucial for the reliability of NMR crystallography. Here, recently reported large deviations of predicted hydrogen and carbon chemical shifts of a series of solid pyridinium fumarates are thoroughly analyzed. The influence of the geometry optimization protocol and of the computational level of NMR calculations on the accuracy of predicted chemical shifts is investigated. Periodic calculations with GGA, meta-GGA and hybrid functionals are employed. Furthermore, molecular corrections at the coupled-cluster singles-and-doubles (CCSD) level are calculated. The effect of nuclear delocalization on the structure and NMR shielding is also investigated. The geometry optimization with a computationally demanding hybrid functional leads to a substantial improvement in proton chemical-shift predictions.
Zobrazit více v PubMed
Hodgkinson P. NMR crystallography of molecular organics. Prog. Nucl. Magn. Reson. Spectrosc. 2020;118–119:10–53. doi: 10.1016/j.pnmrs.2020.03.001. PubMed DOI
Baias M., Widdifield C.M., Dumez J.N., Thompson H.P.G., Cooper T.G., Salager E., Bassil S., Stein R.S., Lesage A., Day G.M., et al. Powder crystallography of pharmaceutical materials by combined crystal structure prediction and solid-state 1H NMR spectroscopy. Phys. Chem. Chem. Phys. 2013;15:8069–8080. doi: 10.1039/c3cp41095a. PubMed DOI
Baias M., Dumez J.N., Svensson P.H., Schantz S., Day G.M., Emsley L. De novo determination of the crystal structure of a large drug molecule by crystal structure prediction-based powder NMR crystallography. J. Am. Chem. Soc. 2013;135:17501–17507. doi: 10.1021/ja4088874. PubMed DOI
Widdifield C.M., Robson H., Hodgkinson P. Furosemide’s one little hydrogen atom: NMR crystallography structure verification of powdered molecular organics. Chem. Commun. 2016;52:6685–6688. doi: 10.1039/C6CC02171A. PubMed DOI
Harper J.K., Grant D.M. Enhancing crystal-structure prediction with NMR tensor data. Cryst. Growth Des. 2006;6:2315–2321. doi: 10.1021/cg060244g. DOI
Widdifield C.M., Lill S.O.N., Broo A., Lindkvist M., Pettersen A., Ankarberg A.S., Aldred P., Schantz S., Emsley L. Does Z’ equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease. Phys. Chem. Chem. Phys. 2017;19:16650–16661. doi: 10.1039/C7CP02349A. PubMed DOI
Bonhomme C., Gervais C., Babonneau F., Coelho C., Pourpoint F., Azais T., Ashbrook S.E., Griffin J.M., Yates J.R., Mauri F., et al. First-principles calculation of NMR parameters using the gauge including projector augmented wave method: A chemist’s point of view. Chem. Rev. 2012;112:5733–5779. doi: 10.1021/cr300108a. PubMed DOI
Ashbrook S.E., McKay D. Combining solid-state NMR spectroscopy with first-principles calculations—A guide to NMR crystallography. Chem. Commun. 2016;52:7186–7204. doi: 10.1039/C6CC02542K. PubMed DOI
Charpentier T. The PAW/GIPAW approach for computing NMR parameters: A new dimension added to NMR study of solids. Solid State Nucl. Magn. Reson. 2011;40:1–20. doi: 10.1016/j.ssnmr.2011.04.006. PubMed DOI
Pickard C.J., Mauri F. All-electron magnetic response with pseudopotentials: NMR chemical shifts. Phys. Rev. B. 2001;6324:245101. doi: 10.1103/PhysRevB.63.245101. DOI
Perdew J.P., Burke K., Ernzerhof M. Generalized gradient approximation made simple. Phys. Rev. Lett. 1996;77:3865–3868. doi: 10.1103/PhysRevLett.77.3865. PubMed DOI
Bartók A.P., Yates J.R. Regularized SCAN functional. J. Chem. Phys. 2019;150:161101. doi: 10.1063/1.5094646. PubMed DOI
Hartman J.D., Kudla R.A., Day G.M., Mueller L.J., Beran G.J.O. Benchmark fragment-based 1H, 13C, 15N and 17O chemical shift predictions in molecular crystals. Phys. Chem. Chem. Phys. 2016;18:21686–21709. doi: 10.1039/C6CP01831A. PubMed DOI PMC
Hartman J.D., Day G.M., Beran G.J.O. Enhanced NMR discrimination of pharmaceutically relevant molecular crystal forms through fragment-based Ab lnitio chemical shift predictions. Cryst. Growth Des. 2016;16:6479–6493. doi: 10.1021/acs.cgd.6b01157. PubMed DOI PMC
Hartman J.D., Balaji A., Beran G.J.O. Improved electrostatic embedding for fragment-based chemical shift calculations in molecular crystals. J. Chem. Theory Comput. 2017;13:6043–6051. doi: 10.1021/acs.jctc.7b00677. PubMed DOI
Hartman J.D., Beran G.J.O. Accurate 13-C and 15-N molecular crystal chemical shielding tensors from fragment-based electronic structure theory. Solid State Nucl. Mag. 2018;96:10–18. doi: 10.1016/j.ssnmr.2018.09.003. PubMed DOI
Socha O., Hodgkinson P., Widdifield C.M., Yates J.R., Dračínský M. Exploring systematic discrepancies in DFT calculations of chlorine nuclear quadrupole couplings. J. Phys. Chem. A. 2017;121:4103–4113. doi: 10.1021/acs.jpca.7b02810. PubMed DOI
Corlett E.K., Blade H., Hughes L.P., Sidebottom P.J., Walker D., Walton R.I., Brown S.P. Investigating discrepancies between experimental solid-state NMR and GIPAW calculation: N=C–N 13C and OH∙∙∙O 1H chemical shifts in pyridinium fumarates and their cocrystals. Solid State Nucl. Mag. 2020;108:101662. doi: 10.1016/j.ssnmr.2020.101662. PubMed DOI
Harris R.K., Joyce S.A., Pickard C.J., Cadars S., Emsley L. Assigning carbon-13 NMR spectra to crystal structures by the INADEQUATE pulse sequence and first principles computation: A case study of two forms of testosterone. Phys. Chem. Chem. Phys. 2006;8:137–143. doi: 10.1039/B513392K. PubMed DOI
Dračínský M., Unzueta P., Beran G.J.O. Improving the accuracy of solid-state nuclear magnetic resonance chemical shift prediction with a simple molecular correction. Phys. Chem. Chem. Phys. 2019;21:14992–15000. doi: 10.1039/C9CP01666J. PubMed DOI
Dračínský M., Vícha J., Bártová K., Hodgkinson P. Towards accurate predictions of proton NMR spectroscopic parameters in molecular solids. Chemphyschem. 2020;21:2075–2083. doi: 10.1002/cphc.202000629. PubMed DOI
Dračínský M., Hodgkinson P. Effects of quantum nuclear delocalisation on NMR parameters from path integral molecular dynamics. Chem. Eur. J. 2014;20:2201–2207. doi: 10.1002/chem.201303496. PubMed DOI
Dračínský M., Bouř P., Hodgkinson P. Temperature dependence of NMR parameters calculated from path integral molecular dynamics simulations. J. Chem. Theory Comput. 2016;12:968–973. doi: 10.1021/acs.jctc.5b01131. PubMed DOI
Dračínský M., Čechová L., Hodgkinson P., Procházková E., Janeba Z. Resonance-assisted stabilisation of hydrogen bonds probed by NMR spectroscopy and path integral molecular dynamics. Chem. Commun. 2015;51:13986–13989. doi: 10.1039/C5CC05199A. PubMed DOI
Bártová K., Čechová L., Procházková E., Socha O., Janeba Z., Dračínský M. Influence of intramolecular charge transfer and nuclear quantum effects on intramolecular hydrogen bonds in azopyrimidines. J. Org. Chem. 2017;82:10350–10359. doi: 10.1021/acs.joc.7b01810. PubMed DOI
Pan Y.J., Jin Z.M., Sun C.R., Jiang C.W. Crystal structure of 2,6-dimethylpyridinium hydrogen fumarate: Hydrogen bonds of C(sp3)–H∙∙∙O, C(sp2)–H∙∙∙O and N+–H∙∙∙O−(sp3) Chem. Lett. 2001:1008–1009. doi: 10.1246/cl.2001.1008. DOI
Haynes D.A., Jones W., Motherwell W.D.S. Cocrystallisation of succinic and fumaric acids with lutidines: A systematic study. CrystEngComm. 2006;8:830–840. doi: 10.1039/b610294h. DOI
Selyani S., Dincer M. Salt and co-crystal formation from the reaction of fumaric acid with different N-heterocyclic compounds: Experimental and DFT study. Mol. Cryst. Liq. Cryst. 2018;666:65–78. doi: 10.1080/15421406.2018.1512451. DOI
Hemamalini M., Fun H.K. Bis(2-amino-5-methylpyridinium) fumarate-fumaric acid (1/1) Acta Crystallogr. E. 2010;66:o2093–o2094. doi: 10.1107/S1600536810027960. PubMed DOI PMC
Allen F.H. The Cambridge structural database: A quarter of a million crystal structures and rising. Acta Cryst. B. 2002;58:380–388. doi: 10.1107/S0108768102003890. PubMed DOI
Dračínský M., Hodgkinson P. A molecular dynamics study of the effects of fast molecular motions on solid-state NMR parameters. CrystEngComm. 2013;15:8705–8712. doi: 10.1039/c3ce40612a. DOI
Pohl R., Socha O., Slavíček P., Šála M., Hodgkinson P., Dračínský M. Proton transfer in guanine-cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations. Faraday Discuss. 2018;212:331–344. doi: 10.1039/C8FD00070K. PubMed DOI
Bernasconi D., Bordignon S., Rossi F., Priola E., Nervi C., Gobetto R., Voinovich D., Hasa D., Duong N.T., Nishiyama Y., et al. Selective synthesis of a salt and a cocrystal of the ethionamide-salicylic acid system. Cryst. Growth Des. 2020;20:906–915. doi: 10.1021/acs.cgd.9b01299. DOI
Berry D.J., Steed J.W. Pharmaceutical cocrystals, salts and multicomponent systems; intermolecular interactions and property based design. Adv. Drug Delivery Rev. 2017;117:3–24. doi: 10.1016/j.addr.2017.03.003. PubMed DOI
Kumar A., Kumar S., Nanda A. A review about regulatory status and recent patents of pharmaceutical co-crystals. Adv. Pharm. Bull. 2018;8:355–363. doi: 10.15171/apb.2018.042. PubMed DOI PMC
Garman E.F. Developments in X-ray crystallographic structure determination of biological macromolecules. Science. 2014;343:1102–1108. doi: 10.1126/science.1247829. PubMed DOI
LeBlanc L.M., Dale S.G., Taylor C.R., Becke A.D., Day G.M., Johnson E.R. Pervasive delocalisation error causes spurious proton transfer in organic acid-base co-crystals. Angew. Chem. Int. Ed. 2018;57:14906–14910. doi: 10.1002/anie.201809381. PubMed DOI
Feynman R.P., Hibbs A.R. Quantum Mechanics and Path Integrals. McGraw-Hill; New York, NY, USA: 1965.
Clark S.J., Segall M.D., Pickard C.J., Hasnip P.J., Probert M.J., Refson K., Payne M.C. First principles methods using CASTEP. Z. Kristallogr. 2005;220:567–570. doi: 10.1524/zkri.220.5.567.65075. DOI
Becke A.D. Density-functional thermochemistry 3. The role of exact exchange. J. Chem. Phys. 1993;98:5648–5652. doi: 10.1063/1.464913. DOI
Lee C.T., Yang W.T., Parr R.G. Development of the colle-salvetti correlation-energy formula into a functional of the electron-density. Phys. Rev. B. 1988;37:785–789. doi: 10.1103/PhysRevB.37.785. PubMed DOI
Monkhorst H.J., Pack J.D. Special points for brillouin-zone integrations. Phys. Rev. B. 1976;13:5188–5192. doi: 10.1103/PhysRevB.13.5188. DOI
Tkatchenko A., Scheffler M. Accurate molecular van der waals interactions from ground-state electron density and free-atom reference data. Phys. Rev. Lett. 2009;102:073005. doi: 10.1103/PhysRevLett.102.073005. PubMed DOI
Tkatchenko A., DiStasio R.A., Car R., Scheffler M. Accurate and efficient method for many-body van der waals interactions. Phys. Rev. Lett. 2012;108:236402. doi: 10.1103/PhysRevLett.108.236402. PubMed DOI
Yates J.R., Pickard C.J., Mauri F. Calculation of NMR chemical shifts for extended systems using ultrasoft pseudopotentials. Phys. Rev. B. 2007;76:024401. doi: 10.1103/PhysRevB.76.024401. DOI
Vanderbilt D. Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Phys. Rev. B. 1990;41:7892–7895. doi: 10.1103/PhysRevB.41.7892. PubMed DOI
Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Scalmani G., Barone V., Petersson G.A., Nakatsuji H., et al. Gaussian 16, Revision A.03. Gaussian, Inc.; Wallingford, CT, USA: 2016.
Bartlett R.J., Purvis G.D. Many-body perturbation-theory, coupled-pair many-electron theory, and importance of quadruple excitations for correlation problem. Int. J. Quantum Chem. 1978;14:561–581. doi: 10.1002/qua.560140504. DOI
Čížek J. On the use of the cluster expansion and the technique of diagrams in calculations of correlation effects in atoms and molecules. In: LeFebvre R., Moser C., editors. Advances in Chemical Physics, Volume 14. John Wiley & Sons, Ltd.; London, UK: 1969. pp. 35–89.
Purvis G.D., Bartlett R.J. A full coupled-cluster singles and doubles model—The inclusion of disconnected triples. J. Chem. Phys. 1982;76:1910–1918. doi: 10.1063/1.443164. DOI
Scuseria G.E., Janssen C.L., Schaefer H.F. An efficient reformulation of the closed-shell coupled cluster single and double excitation (CCSD) equations. J. Chem. Phys. 1988;89:7382–7387. doi: 10.1063/1.455269. DOI
Auer A.A., Gauss J. Triple excitation effects in coupled-cluster calculations of indirect spin-spin coupling constants. J. Chem. Phys. 2001;115:1619–1622. doi: 10.1063/1.1386698. DOI
CFOUR, Coupled-Cluster Techniques for Computational Chemistry, a Quantum-Chemical Program Package and the Integral Packages MOLECULE (J. Almlöf and P.R. Taylor), PROPS (P.R. Taylor), ABACUS (T. Helgaker, H.J. Aa. Jensen, P. Jørgensen, and J. Olsen), and ECP Routines by A. V. Mitin and C. van Wüllen. For the Current Version, See. [(accessed on 1 April 2021)]; Available online: http://www.cfour.de.