Parametrizing the Spatial Dependence of 1H NMR Chemical Shifts in π-Stacked Molecular Fragments
Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
LTAUSA18011
Ministerstvo Školství, Mládeže a Tělovýchovy
PubMed
33114411
PubMed Central
PMC7662755
DOI
10.3390/ijms21217908
PII: ijms21217908
Knihovny.cz E-zdroje
- Klíčová slova
- GIAO, GIPAW, intermolecular stacking, noncovalent interactions, proton NMR,
- MeSH
- benzen chemie MeSH
- kvantová teorie MeSH
- molekulární modely MeSH
- protonová magnetická rezonanční spektroskopie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- benzen MeSH
Most recently a renewed interest in several areas has arisen in factors governing the 1H NMR chemical shift (1H CS) of protons in aromatic systems. Therefore, it is important to describe how 1H CS values are affected by π-stacking intermolecular interactions. The parametrization of radial and angular dependences of the 1H CS is proposed, which is based on conventional gauge-independent atomic orbital (GIAO) calculations of explicit molecular fragments. Such a parametrization is exemplified for a benzene dimer with intermonomer vertical and horizontal distances which are in the range of values often found in crystals of organic compounds. Results obtained by the GIAO calculations combined with B3LYP and MP2 methods were compared, and revealed qualitatively the same trends in the 1H CS data. The parametrization was found to be quantitatively correct for the T-shaped benzene dimers, and its limitations were discussed. Parametrized 1H CS surfaces should become useful for providing additional restraints in the search of site-specific information through an analysis of structurally induced 1H CS changes.
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Larive C.K., Barding G.A., Dinges M.N. NMR spectroscopy for metabolomics and metabolic profiling. Anal. Chem. 2015;87:133–146. doi: 10.1021/ac504075g. PubMed DOI
Zhang R., Mroue K.H., Sun P., Ramamoorthy A. High-Resolution Proton NMR Spectroscopy of Polymers and Biological Solids. In: Webb G.A., editor. Modern Magnetic Resonance. 2nd ed. Springer; Cham, Switzerland: 2018. pp. 521–536.
Stone A.J. The Theory of Intermolecular Forces. 1st ed. Clarendon Press; Oxford, UK: 2002. pp. 56–63.
Kudisch B., Maiuri M., Moretti L., Oviedo M.B., Wang L., Oblinsky D.G., Prud’homme R.K., Wong B.M., McGill S.A., Scholes G.D. Ring currents modulate optoelectronic properties of aromatic chromophores at 25 T. Proc. Natl. Acad. Sci. USA. 2020;117:11289–11298. doi: 10.1073/pnas.1918148117. PubMed DOI PMC
Platzer G., Mayer M., Beier A., Brüschweiler S., Fuchs J.E., Engelhardt H., Geist L., Bader G., Schörghuber J., Lichtenecker R., et al. PI by NMR: Probing CH–π Interactions in Protein–Ligand Complexes by NMR Spectroscopy. Angew. Chem. Int. Ed. 2020;59:14861–14868. doi: 10.1002/anie.202003732. PubMed DOI PMC
Rickhaus M., Jirasek M., Tejerina L., Gotfredsen H., Peeks M.D., Haver R., Jiang H.-W., Claridge T.D.W., Anderson H.L. Global aromaticity at the nanoscale. Nat. Chem. 2020;12:236–241. doi: 10.1038/s41557-019-0398-3. PubMed DOI PMC
Gabryelczyk B., Cai H., Shi X., Sun Y., Swinkels P.J.M., Salentinig S., Pervushin K., Miserez A. Hydrogen bond guidance and aromatic stacking drive liquid-liquid phase separation of intrinsically disordered histidine-rich peptides. Nat. Commun. 2019;10 doi: 10.1038/s41467-019-13469-8. PubMed DOI PMC
Chaudhari S.R., Griffin J.M., Broch K., Lesage A., Lemaur V., Dudenko D., Olivier Y., Sirringhaus H., Emsley L., Grey C.P. Donor–acceptor stacking arrangements in bulk and thin-film high-mobility conjugated polymers characterized using molecular modelling and MAS and surface-enhanced solid-state NMR spectroscopy. Chem. Sci. 2017;8:3126–3136. doi: 10.1039/C7SC00053G. PubMed DOI PMC
Bass T.M., Carr C.R., Sherbow T.J., Fettinger J.C., Berben L.A. Syntheses of Square Planar Galluim Complexes and a Proton NMR Correlation Probing Metalloaromaticity. Inor. Chem. 2020;59:13517–13523. doi: 10.1021/acs.inorgchem.0c01908. PubMed DOI
Lampkin B.J., Karadakov P.B., VanVeller B. Detailed Visualization of Aromaticity Using Isotropic Magnetic Shielding. Angew. Chem. Int. Ed. 2020;59:2–9. doi: 10.1002/anie.202008362. PubMed DOI
Kilymis D., Bartók A.P., Pickard C.J., Forse A.C., Merlet C. Efficient prediction of nucleus independent chemical shifts for polycyclic aromatic hydrocarbons. Phys. Chem. Chem. Phys. 2020;22:13746–13755. doi: 10.1039/D0CP01705A. PubMed DOI
Pöppler A.-C., Corlett E.K., Pearce H., Seymour M.P., Reid M., Montgomery M.G., Brown S.P. Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil. Acta Cryst. C. 2017;73:149–156. doi: 10.1107/S2053229617000870. PubMed DOI PMC
Schwartz E., Lim E., Gowda C.M., Liscio A., Fenwick O., Tu G., Palermo V., de Gelder R., Cornelissen J.J.L.M., Van Eck E.R.H., et al. Synthesis, Characterization, and Surface Initiated Polymerization of Carbazole Functionalized Isocyanides. Chem. Mater. 2010;8:2597–2607. doi: 10.1021/cm903664g. DOI
Gowda C.M., Vasconcelos F., Schwartz E., Van Eck E.R.H., Marsman M., Cornelissen J.J.L.M., Rowan A.E., De Wijs G.A., Kentgens A.P.M. Hydrogen bonding and chemical shifts assignments in carbazole functionalized isocyanides from solid-state NMR and first-principles calculations. Phys. Chem. Chem. Phys. 2011;13:13082–13095. doi: 10.1039/c1cp20304e. PubMed DOI
Bonhomme C., Gervais C., Babonneau F., Coelho C., Pourpoint F., Azais T., Asbrook S.E., Griffin J.M., Yates J.R., Pickard J.C. 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
Bootsma A.N., Doney A.C., Wheeler S.E. Predicting the Strength of Stacking Interactions between Heterocycles and Aromatic Amino Acid Side Chain. J. Am. Chem. Soc. 2019;141:11027–11035. doi: 10.1021/jacs.9b00936. PubMed DOI
D’Ischia M., Napolitano A., Pezzella A., Meredith P., Buehler M. Melanin biopolymers: Tailoring chemical complexity for materials design. Angew. Chem. Int. Ed. 2020;59:11196–11205. doi: 10.1002/anie.201914276. PubMed DOI
Lyu Q., Hsueh N., Chai C.L.L. Unravelling the polydopamine mystery: Is the end in sight? Polym. Chem. 2019;10:5771–5777. doi: 10.1039/C9PY01372E. DOI
Proks V., Brus J., Pop-Georgievski O., Večerníková E., Wiśniewski W., Kotek J., Urbanová M., Rypáček F. Thermal-Induced Transformation of Polydopamine Structures: An Efficient Route for the Stabilization of the Polydopamine Surfaces. Macromol. Chem. Phys. 2013;214:499–507. doi: 10.1002/macp.201200505. DOI
Circu M., Filip C. Closer to the polydopamine structure: New insights from a combined 13C/1H/2H solid-state NMR study on deuterated samples. Polym. Chem. 2018;9:3379–3387. doi: 10.1039/C8PY00633D. DOI
Loeffler J.R., Fernández-Quintero M.L., Schauperl M., Liedl K.R. STACKED – Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding. J. Chem. Inf. Model. 2020;60:2304–2313. doi: 10.1021/acs.jcim.9b01165. PubMed DOI PMC
Bartolomei M., Pirani F., Marques J.M.C. Low-energy structures of benzene clusters with a novel accurate potential surface. J. Comput. Chem. 2015;36:2291–2301. doi: 10.1002/jcc.24201. PubMed DOI
Kennedy M.R., McDonald A.R., DePrince A.E., III, Marshall M.S., Podeszwa R., Sherrill C.D. Resolving the three-body contribution to the lattice energy of crystalline benzene: Benchmark results from coupled-cluster theory. J. Chem. Phys. 2014;140 doi: 10.1063/1.4869686. PubMed DOI
Miliordos E., Apra E., Xantheas S.S. Benchmark Theoretical Study of the π−π Binding Energy in the Benzene Dimer. J. Phys. Chem. A. 2014;118:7568–7578. doi: 10.1021/jp5024235. PubMed DOI
DiStasio R.A., Jr., Von Helden G., Steele R.P., Head-Gordon M. On the T-shaped structures of the benzene dimer. Chem. Phys. Lett. 2007;437:277–283. doi: 10.1016/j.cplett.2007.02.034. DOI
Czernek J., Brus J. Exploring Accuracy Limits of Predictions of the 1H NMR Chemical Shielding Anisotropy in the Solid State. Molecules. 2019;24:1731. doi: 10.3390/molecules24091731. PubMed DOI PMC
Czernek J., Brus J. Monitoring the Site-Specific Solid-State NMR Data in Oligopeptides. Int. J. Mol. Sci. 2020;21:2700. doi: 10.3390/ijms21082700. PubMed DOI PMC
Czernek J., Brus J. Polymorphic Forms of Valinomycin Investigated by NMR Crystallography. Int. J. Mol. Sci. 2020;21:4907. doi: 10.3390/ijms21144907. PubMed DOI PMC
Řezáč J., Riley K.E., Hobza P. S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures. J. Chem. Theory Comput. 2011;7:2427–2438. doi: 10.1021/ct2002946. PubMed DOI PMC
Řezáč J., Jurečka P., Riley K.E., Černý J., Valdes H., Pluháčková K., Berka K., Řezáč T., Pitoňák M., Vondrášek J., et al. Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com. ): A Users Manual and Examples. Collect. Czech. Chem. Commun. 2008;73:1261–1270. doi: 10.1135/cccc20081261. DOI
Brown S.P. Applications of high-resolution 1H solid-state NMR. Solid State Nucl. Magn. Reson. 2012;41:1–27. doi: 10.1016/j.ssnmr.2011.11.006. PubMed DOI
Dudenko D.V., Yates J.R., Harris K.D.M., Brown S.P. An NMR crystallography DFT-D approach to analyse the role of intermolecular hydrogen bonding and π–π interactions in driving cocrystallisation of indomethacin and nicotinamide. CrystEngComm. 2013;15:8797–8807. doi: 10.1039/c3ce41240g. DOI
Dudenko D.V., Williams P.A., Hughes C.E., Antzutkin O.N., Velaga S.P., Brown S.P., Harris K.D.M. Exploiting the Synergy of Powder X-ray Diffraction and Solid-State NMR Spectroscopy in Structure Determination of Organic Molecular Solids. J. Phys. Chem. C. 2013;117:12258–12265. doi: 10.1021/jp4041106. PubMed DOI PMC
Czernek J., Brus J. The covariance of the differences between experimental and theoretical chemical shifts as an aid for assigning two-dimensional heteronuclear correlation solid-state NMR spectra. Chem. Phys. Lett. 2014;608:334–339. doi: 10.1016/j.cplett.2014.05.099. DOI
Carignani E., Borsacchi S., Bradley J.P., Brown S.P., Geppi M. Strong Intermolecular Ring Current Influence on 1H Chemical Shifts in Two Crystalline Forms of Naproxen: A Combined Solid-State NMR and DFT Study. J. Phys. Chem. C. 2013;117:17731–17740. doi: 10.1021/jp4044946. DOI
Czernek J. On the solid-state NMR spectra of naproxen. Chem. Phys. Lett. 2015;619:230–235. doi: 10.1016/j.cplett.2014.11.031. 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. Magn. Reson. 2020;108 doi: 10.1016/j.ssnmr.2020.101662. PubMed DOI
Hušák M., Jegorov A., Rohlíček J., Fitch A., Czernek J., Kobera L., Brus J. Determining the Crystal Structures of Peptide Analogs of Boronic Acid in the Absence of Single Crystals: Intricate Motifs of Ixazomib Citrate Revealed by XRPD Guided by ss-NMR. Cryst. Growth Des. 2018;18:3616–3625. doi: 10.1021/acs.cgd.8b00402. DOI
Harris R.K., Hodgkinson P., Zorin V., Dumez J.N., Elena-Herrmann B., Emsley L., Salager E., Stein R.S. Computation and NMR crystallography of terbutaline sulfate. Magn. Reson. Chem. 2010;48:S103–S112. doi: 10.1002/mrc.2636. PubMed DOI
Kerr H.E., Softley L.K., Suresh K., Nangia A., Hodgkinson P., Radosavjlevic Evans I. A furosemide–isonicotinamide cocrystal: An investigation of properties and extensive structural disorder. CrystEngComm. 2015;17:6707–6715. doi: 10.1039/C5CE01183C. DOI
Frantsuzov I., Ford S.J., Radosavjlevic Evans I., Horsewill A.J., Trommsdorff H.P., Johnson M.R. Measurement of Proton Tunneling in Short Hydrogen Bonds in Single Crystals of 3,5 Pyridinedicarboxylic Acid Using Nuclear Magnetic Resonance Spectroscopy. Phys. Rev. Lett. 2014;113 doi: 10.1103/PhysRevLett.113.018301. 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
Nishiyama Y., Malon M., Potrzebowski M.J., Paluch P., Amoreux J.P. Accurate NMR determination of C–H or N–H distances for unlabeled molecules. Solid State Nucl. Magn. Reson. 2016;73:15–21. doi: 10.1016/j.ssnmr.2015.06.005. PubMed DOI
Zhang R., Mroue K.H., Ramamoorthy A. Proton-Based Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy. Acc. Chem. Res. 2017;50:1105–1113. doi: 10.1021/acs.accounts.7b00082. PubMed DOI PMC
Li M., Lu X., Xu W., Troup G.M., McNevin M.J., Nie H., Su Y. Quantifying Pharmaceutical Formulations from Proton Detected Solid-State NMR under Ultrafast Magic Angle Spinning. J. Pharm. Sci. 2020;109:3045–3053. doi: 10.1016/j.xphs.2020.06.026. PubMed DOI
Huber R.G., Margreiter M.A., Fuchs J.E., Von Grefenstein S., Tuatermann C.S., Liedl K.R., Fox T. Heteroaromatic π-Stacking Energy Landscapes. J. Chem. Inf. Model. 2014;54:1371–1379. doi: 10.1021/ci500183u. PubMed DOI PMC
Gyevy-Nagy L., Kállay M., Nagy P.R. Integral-Direct and Parallel Implementation of the CCSD(T) Method: Algorithmic Developments and Large-Scale Applications. J. Chem. Theory Comput. 2020;16:366–384. doi: 10.1021/acs.jctc.9b00957. PubMed DOI
Bootsma A.N., Doney A.C., Wheeler S.E. Tuning Stacking Interactions between Asp–Arg Salt Bridges and Heterocyclic Drug Fragments. J. Chem. Inf. Model. 2019;59:149–158. doi: 10.1021/acs.jcim.8b00563. PubMed DOI
Brandl M., Weiss M.S., Jabs A., Sühnel J., Hilgenfeld R. C–H … π-Interaction in Proteins. J. Mol. Biol. 2001;307:357–377. doi: 10.1006/jmbi.2000.4473. PubMed DOI
Nishiyo M., Umezawa Y., Fantini J., Weiss M.S., Chakrabarti P. CH–π hydrogen bonds in biological macromolecules. Phys. Chem. Chem. Phys. 2014;16:12648–12683. doi: 10.1039/C4CP00099D. PubMed DOI
Sahakyan A.B., Vendruscolo M. Analysis of the Contributions of Ring Current and Electric Field Effects to the Chemical Shifts of RNA Bases. J. Phys. Chem. B. 2013;117:1989–1998. doi: 10.1021/jp3057306. PubMed DOI
Widdifield C.M., Farrell J.D., Cole J.C., Howard J.A.K., Hodgkinson P. Resolving alternative organic crystal structures using density functional theory and NMR chemical shifts. Chem. Sci. 2020;11:2987–2992. doi: 10.1039/C9SC04964A. PubMed DOI PMC
Ditchfield R. Self-consistent perturbation theory of diamagnetism. Mol. Phys. 1974;27:789–807. doi: 10.1080/00268977400100711. DOI
Wolinski K., Hinton J.F., Pulay P. Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations. J. Am. Chem. Soc. 1990;112:8251–8260. doi: 10.1021/ja00179a005. DOI
Boys S., Bernardi F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol. Phys. 1970;19:553–566. doi: 10.1080/00268977000101561. DOI
Chai J.-D., Head-Gordon M. Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys. Chem. Chem. Phys. 2008;10:6615–6620. doi: 10.1039/b810189b. PubMed DOI
Frish M.J., Trucks J.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Scalmani G., Barone V., Mennucci B., Petersson G.A., et al. Gaussian 09. Gaussian, Inc.; Wallingford, UK: 2013. Revision D.01.
Kresse G., Joubert D. From ultrasoft pseudopotentials to the projector augmented-wave method. Phys. Rev. B. 1999;59:1758–1775. doi: 10.1103/PhysRevB.59.1758. DOI
Segall M.D., Lindan P.J.D., Probert M.J., Pickard C.J., Hasnip P.J., Clark S.J., Payne M.C. First principles simulation: Ideas, illustrations, and the CASTEP code. J. Phys. Condens. Matter. 2002;14:2717–2744. doi: 10.1088/0953-8984/14/11/301. DOI
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
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
Pickard C.J., Mauri F. All-electron magnetic response with pseudopotentials: NMR chemical shifts. Phys. Rev. B. 2001;63 doi: 10.1103/PhysRevB.63.245101. DOI
Yates J.R., Pickard C.J., Mauri F. Calculations of NMR chemical shifts for extended systems using ultrasoft pseudopotentials. Phys. Rev. B. 2007;76 doi: 10.1103/PhysRevB.76.024401. DOI
BIOVIA Materials Studio Dassault Systèmes, Vélizy-Villacoublay: Paris, France. [(accessed on 22 September 2020)]; Available online: https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-materials-studio/
Gao S.-P., Pickard C.J., Perlov A., Milman V. Core-Level Spectroscopy Calculation and the Plane Wave Pseudopotential Method. J. Phys. Condens. Matter. 2009;21 doi: 10.1088/0953-8984/21/10/104203. PubMed DOI
Halkier A., Helgaker T., Jørgensen P., Klopper W., Koch H., Olsen J., Wilson A.K. Basis-set convergence in correlated calculations on Ne, N2, and H2O. Chem. Phys. Lett. 1998;286:243–252. doi: 10.1016/S0009-2614(98)00111-0. DOI
Patkowski K. Recent developments in symmetry-adapted perturbation theory. Wiley Interdiscip. Rev. Comput. Mol. Phys. 2019;10 doi: 10.1002/wcms.1452. DOI
Hesselmann A., Jansen G., Schütz M. Density-functional theory-symmetry-adapted intermolecular perturbation theory with density fitting: A new efficient method to study intermolecular interaction energies. J. Chem. Phys. 2005;122 doi: 10.1063/1.1824898. PubMed DOI
Hesselmann A., Jansen G., Schütz M. Interaction Energy Contributions of H-Bonded and Stacked Structures of the AT and GC DNA Base Pairs from the Combined Density Functional Theoryand Intermolecular Perturbation Theory Approach. J. Am. Chem. Soc. 2006;128:11730–11731. doi: 10.1021/ja0633363. PubMed DOI
Werner H.J., Knowles P.J., Manby F.R., Black J.A., Doll K., Hesselmann A., Kats D., Kohn A., Korona T., Kreplin D.A., et al. The Molpro quantum chemistry package. J. Chem. Phys. 2020;152 doi: 10.1063/5.0005081. PubMed DOI
A Volumetric Analysis of the 1H NMR Chemical Shielding in Supramolecular Systems