| Literature DB >> 31867497 |
Xian Wang1,2, Qun Zeng1, Jinshan Li1, Mingli Yang2.
Abstract
2,6-Diamino-3,5-dinitropyrazine-1-oxide (Entities:
Year: 2019 PMID: 31867497 PMCID: PMC6921264 DOI: 10.1021/acsomega.9b02410
Source DB: PubMed Journal: ACS Omega ISSN: 2470-1343
Figure 1(a) LLM-105 crystal structure and intermolar hydrogen bond in the crystal; the atom indexes (b) and atomic type (c) in the force field parameters.
Figure 2Overlap for molecules from DFT and FF in the gaseous phase (a); a front (b) and a lateral view (c) from the experiment and FF in the crystal form.
Structural Parameters Optimized at the DFT and FF Levels
| structural parameters | DFT | FF | Δ(FF–DFT) |
|---|---|---|---|
| B(C1–C2) | 1.419 | 1.402 | –0.018 |
| B(C2–N3) | 1.308 | 1.323 | 0.016 |
| B(C1–N12) | 1.371 | 1.391 | 0.020 |
| B(C1–N14) | 1.325 | 1.345 | 0.020 |
| B(C2–N6) | 1.459 | 1.464 | 0.005 |
| B(N14–H19) | 1.015 | 1.025 | 0.010 |
| B(N14–H18) | 1.010 | 1.022 | 0.013 |
| B(N6–O8) | 1.233 | 1.224 | –0.009 |
| B(N6–O7) | 1.206 | 1.221 | 0.015 |
| B(N12–O13) | 1.290 | 1.275 | –0.015 |
| ME | 0.006 | ||
| RMSE | 0.015 | ||
| A(H18–N14–H19) | 126.0 | 127.8 | 1.8 |
| A(C2–C1–N12) | 116.2 | 116.1 | –0.1 |
| A(C1–N12–C5) | 122.0 | 122.5 | 0.5 |
| A(N3–C2–N6) | 116.3 | 116.8 | 0.5 |
| A(C2–C1–N14) | 129.5 | 130.2 | 0.7 |
| A(C1–N14–H19) | 115.4 | 113.9 | –1.5 |
| A(C1–N14–H18) | 118.6 | 118.3 | –0.3 |
| A(C2–N3–C4) | 119.5 | 121.3 | 1.9 |
| A(N12–C1–N14) | 114.3 | 113.7 | –0.6 |
| A(C1–C2–N3) | 123.1 | 122.0 | –1.1 |
| A(O7–N6–O8) | 125.0 | 123.3 | –1.6 |
| A(C2–N6–O7) | 118.5 | 119.3 | 0.8 |
| A(C2–N6–O8) | 116.5 | 117.3 | 0.8 |
| A(C1–C2–N6) | 120.6 | 121.2 | 0.6 |
| A(C1–N12–O13) | 119.0 | 118.8 | –0.3 |
| ME | 0.1 | ||
| RMSE | 1.0 | ||
Figure 3Overlap between simulated (normal color) and experimental structures (green).
Structural Parameters, Bulk Modulus and Its Derivative of the LLM-105 Crystal from FF, DFT, and Experiments
| FF | LDA[ | PW91[ | PBE[ | PBE-D2[ | EXP[ | |
|---|---|---|---|---|---|---|
| 5.64 | 5.84 | 6.01 | 5.64 | 5.81 | 5.71–5.75 | |
| 15.55 | 15.58 | 18.28 | 15.96 | 16.05 | 15.60–15.87 | |
| 8.24 | 8.22 | 8.71 | 8.46 | 8.40 | 8.41–8.48 | |
| β (deg) | 100.96 | 99.51 | 100.75 | 100.93 | 101.01–101.22 | |
| 711.00 | 737.24 | 939.20 | 747.38 | 769.51 | 746.21–750.08 | |
| center of mass | 0.560 | 0.559 | ||||
| 0.869 | 0.867 | |||||
| 0.549 | 0.553 | |||||
| orient (deg) | 145.65 | 145.65 | ||||
| 67.38 | 67.38 | |||||
| 114.38 | 114.38 | |||||
| 13.8 | 16.5 | 12.7 | 11.19–16.2 | |||
| 11.7 | 9.4 | 9.4 | 8.30–18.54 |
Structural Parameters Optimized at the FF Levels and Experimental Values
| structural parameter | EXP | FF | Δ(FF-EXP) |
|---|---|---|---|
| B(N15–H16) | 0.860 | 0.860 | 0.000 |
| B(N15–H17) | 0.860 | 0.860 | 0.000 |
| B(N14–H18) | 0.860 | 0.860 | 0.000 |
| B(N14–H19) | 0.860 | 0.860 | 0.000 |
| B(N12–O13) | 1.321 | 1.321 | 0.000 |
| A(C1–N14–H18) | 120.01 | 120.01 | –0.01 |
| A(C1–N14–H19) | 119.98 | 119.98 | 0.00 |
| A(H18–N14–H19) | 120.01 | 120.01 | 0.01 |
| A(C5–N15–H16) | 120.00 | 120.01 | 0.00 |
| A(C5–N15–H17) | 120.02 | 120.01 | 0.00 |
| A(H16–N15–H17) | 119.98 | 119.98 | 0.00 |
| D(C1–C2–N6–O8) | 18.82 | 18.82 | 0.00 |
| D(N3–C2–N6–O8) | –159.43 | –159.43 | 0.00 |
| D(C5–C4–N9–O10) | –2.67 | –2.67 | 0.00 |
| D(N3–C4–N9–O11) | –3.48 | –3.48 | 0.00 |
Figure 4Four main dimer structures in intermolecular interaction energy: (a,b) dimers with π–π stacking; (c,d) dimers with hydrogen bonds. Estimated values are outside of parentheses, and experimental values in the parentheses.
Figure 5Pressure-dependent relative cell volumes (a) and lattice parameters (b) from the FF, experiment, and DFT.
Figure 6LLM-105 molecule and its close neighbors. The center molecule and the same color neighbor can construct the same dimer in geometry. 14 neighbors can be divided into eight groups.
Intermolecular Interaction Energies of the Neighbor Dimers and the Corresponding Energy Decomposion with CE-B3LYP (kcal/mol)
Figure 7Potential energy curves from the FF and DFT for the four main dimers: (a,b) the dimers with π–π stacking; (c,d) dimers with hydrogen bonds.