| Literature DB >> 27276509 |
Xiaozhou Li1, Lukas Tapmeyer2, Michael Bolte2, Jacco van de Streek3.
Abstract
The excellent results of dispersion-corrected density functional theory (DFT-D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT-D calculations is a target, especially for the field of molecular NMR crystallography. Four (13) C ss-NMR calibration compounds are investigated by single-crystal X-ray diffraction, molecular dynamics and DFT-D calculations. The crystal structure of 3-methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated (13) C chemical shifts of these compounds are in excellent agreement with experiment, with a root-mean-square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT-D chemical shift calculation improves the accuracy of calculated chemical shifts.Entities:
Keywords: NMR crystallography; X-ray diffraction; density functional calculations; molecular dynamics; solid-state NMR spectroscopy
Year: 2016 PMID: 27276509 PMCID: PMC5096255 DOI: 10.1002/cphc.201600398
Source DB: PubMed Journal: Chemphyschem ISSN: 1439-4235 Impact factor: 3.102
Scheme 1The chemical structures of a) adamantane, b) glycine, c) hexamethylbenzene and d) 3‐methylglutaric acid.
The cell parameters of the DFT‐D energy minimized molecular crystals.
| Compound | Lattice parameters | ||||||
|---|---|---|---|---|---|---|---|
|
|
|
| α [°] | β [°] | γ [°] | RMSCD[a] [Å] | |
| α‐Gly,[b] exp. | 5.10 | 11.95 | 5.46 | 90 | 111.78 | 90 | – |
| α‐Gly, DFT‐D | 5.06 | 11.78 | 5.47 | 90 | 112.67 | 90 | 0.089 |
| γ‐Gly, exp. | 7.04 | 7.04 | 5.48 | 90 | 90 | 120 | – |
| γ‐Gly, DFT‐D | 6.93 | 6.93 | 5.51 | 90 | 90 | 120 | 0.065 |
| 3‐MGA,[c] exp. (173 K) | 13.85 | 5.32 | 10.13 | 90 | 110.28 | 90 | – |
| 3‐MGA, DFT‐D | 13.60 | 5.30 | 9.66 | 90 | 108.29 | 90 | 0.077 |
[a] RMSCD: Root‐mean‐square Cartesian displacement (hydrogen atoms excluded). [b] Gly: glycine. [c] 3‐MGA: 3‐methylglutaric acid.
Figure 1Overlays of the DFT‐D energy‐minimized (blue) and the experimental (red) structures. Each overlay was viewed along two different axes. a) α‐Glycine, b) γ‐glycine, c) 3‐methylglutaric acid.
Calculated and room temperature experimental 13C chemical shifts for standard compounds.
| Site | Method | Calcd CS [ppm] | Exp. CS [ppm] | Deviation [ppm] |
|---|---|---|---|---|
| α‐Gly,[d] CO | DFT‐D | 179.3 | 176.5 | +2.8 |
| α‐Gly, CH2 | DFT‐D | 41.8 | 43.7 | −1.9 |
| γ‐Gly, CO | DFT‐D | 176.4 | 173.4 | +3.0 |
| γ‐Gly, CH2 | DFT‐D | 40.1 | 41.4 | −1.3 |
| ADA,[e] CH | MD | 30.9 | 29.5 | +1.4 |
| ADA, CH2 | MD | 39.4 | 38.5 | +0.9 |
| HMB,[f] CH (aromatic) | MD | 129.4 | 132.0 | −2.6 |
| HMB, CH3 (aliphatic) | MD | 16.1 | 17.2 | −1.1 |
| 3‐MGA,[g] COOH (1) | MD | 179.0 | 180.7[h] | −1.7 |
| 3‐MGA, COOH (2) | MD | 179.7 | 181.6[h] | −1.9 |
| 3‐MGA, CH2 (1) | MD | 40.0 | 38.3[h] | +1.7 |
| 3‐MGA, CH2 (2) | MD | 42.9 | 39.5[h] | +3.4 |
| 3‐MGA, CH | MD | 24.1 | 25.2[h] | −1.1 |
| 3‐MGA, CH3 | MD | 17.3 | 18.8[h] | −1.5 |
| Reference shielding [ppm] | 168.9 | |||
| MAD [ppm] | 1.9 | |||
| RMSD [ppm] | 2.0 | |||
[a] Calcd CS: calculated chemical shift. [b] Exp. CS: experimental chemical shift. [c] Deviation=Calcd CS−Exp. CS. [d] Gly: glycine. [e] ADA: adamantane. [f] HMB: hexamethylbenzene. [g] 3‐MGA: 3‐methylglutaric acid. [h] Unpublished data, provided by Dr. Sean Delaney and Prof. Dr. Eric Munson. [i] MAD: mean absolute deviation. [j] RMSD: root‐mean‐square deviation.