| Literature DB >> 35695111 |
Thammarat Aree1, Charles J McMonagle2, Adam A L Michalchuk3, Dmitry Chernyshov2.
Abstract
Highly anharmonic thermal vibrations may serve as a source of structural instabilities resulting in phase transitions, chemical reactions and even the mechanical disintegration of a material. Ab initio calculations model thermal motion within a harmonic or sometimes quasi-harmonic approximation and must be complimented by experimental data on temperature-dependent vibrational frequencies. Here multi-temperature atomic displacement parameters (ADPs), derived from a single-crystal synchrotron diffraction experiment, are used to characterize low-frequency lattice vibrations in the α-FOX-7 layered structure. It is shown that despite the limited quality of the data, the extracted frequencies are reasonably close to those derived from inelastic scattering, Raman measurements and density functional theory (DFT) calculations. Vibrational anharmonicity is parameterized by the Grüneisen parameters, which are found to be very different for in-layer and out-of-layer vibrations. open access.Entities:
Keywords: ADPs; anisotropic atomic displacement parameters; crystal dynamics; normal mode analysis; α-FOX-7
Year: 2022 PMID: 35695111 PMCID: PMC9254589 DOI: 10.1107/S2052520622002700
Source DB: PubMed Journal: Acta Crystallogr B Struct Sci Cryst Eng Mater ISSN: 2052-5192
Refinement statistics for α-FOX-7 from spherical (XL) and nonspherical (NoSpherA2) refinements
| Temp(K) | No. of reflections [all, >2σ(I)] |
|
| Δρ XL (e Å−3) | Δρ NoSpherA2 (e Å−3) | ||
|---|---|---|---|---|---|---|---|
| 80 | 1536, 1414 | 0.0364 | 0.0267 | 0.427 | −0.400 | 0.256 | −0.268 |
| 100 | 1536, 1400 | 0.0368 | 0.0261 | 0.481 | −0.335 | 0.216 | −0.206 |
| 120 | 1539, 1394 | 0.0381 | 0.0279 | 0.445 | −0.340 | 0.213 | −0.224 |
| 140 | 1540, 1389 | 0.0401 | 0.0299 | 0.426 | −0.331 | 0.227 | −0.222 |
| 164 | 1542, 1375 | 0.0400 | 0.0309 | 0.362 | −0.339 | 0.228 | −0.265 |
| 200 | 1560, 1363 | 0.0435 | 0.0334 | 0.343 | −0.304 | 0.180 | −0.186 |
| 240 | 1577, 1340 | 0.0502 | 0.0387 | 0.335 | −0.386 | 0.207 | −0.215 |
| 280 | 1576, 1222 | 0.0692 | 0.0574 | 0.616 | −0.452 | 0.486 | −0.318 |
| 320 | 1592, 1124 | 0.0849 | 0.0774 | 0.755 | −0.472 | 0.709 | −0.426 |
| 360 | 1607, 1029 | 0.0995 | 0.0949 | 0.710 | −0.504 | 0.681 | −0.501 |
Note: (a) R 1(F) = Σ||F o| – |F c||/Σ|F o|.
Figure 1(a) Displacement ellipsoid plots of α-FOX-7 at 80, 164, 280 and 360 K (50% probability level). (b) Four molecules in the monoclinic unit cell (P21/n) of α-FOX-7 at 80 K. (c) The wave-shaped layer-type packing of α-FOX-7 at 80 K with the interplanar angle of adjacent molecules, θ = 140.10 (2)°, viewed along the a axis. (d) Intra- and intermolecular O—H⋯O hydrogen bonds stabilizing the layer-type structure of α-FOX-7 at 80 K (magenta connecting lines). Note that atoms O21 and O22 having fewer interactions are oriented out of the mean molecular plane.
Figure 2Unit-cell parameters of α-FOX-7 in the temperature range 80–360 K.
Figure 3Multi-temperature ADPs of α-FOX-7 for atoms (a) C1, (b) N21 and (c) O11 from XL and NoSpherA2 refinements. The standard uncertainties are 3 × 10−4 Å2, or ca the line thickness. The displacement ellipsoid plot (50% probability level) with atom numbering is shown for α-FOX-7 at 80 K.
Figure 4The average absolute deviations of ADPs for each atom type in α-FOX-7, with for the i atoms of each type. Values are shown as absolute deviations between the ADPs from the harmonic simulation and the diffraction experiment at each temperature.
Comparison of internal vibrational frequencies (cm−1) of α-FOX-7 from calculations and Raman measurement
| DFT
| MP2
| p-DFT
| p-DFT
| Exp.
| Assignment
|
|---|---|---|---|---|---|
| 57 | 58 | 119 | 123 | NO2 twist | |
| 92 | 108 | 151 | 194 | NO2 twist | |
| 115 | 131 | 193 | 233 | C—NH2 wag | |
| 203 | 155 | 270 | 253 | 246 | NO2 rock, NH2 wag |
| 280 | 276 | 317 | 316 | 318 | NO2 rock, NH2 twist |
| 299 | 311 | 324 | 331 | NH2, NO2 rock | |
| 320 | 387 | 378 | 397 | 400 | NH2 rock |
| 369 | 395 | 441 | 448 | 457 | NH2, NO2 rock |
| 378 | 437 | 443 | 477 | 472 | NH2 rock, NO2 twist, C—C st |
| 432 | 459 | 469 | 490 | 481 | NH2 twist, C—C st, NO2 sci |
| 454 | 481 | 598 | 634 | NH2 twist | |
| 454 | 491 | 610 | 646 | NH2 wag | |
| 590 | 593 | 633 | 676 | 622 | NH2 sci, twist |
| 605 | 618 | 658 | 681 | NH2 twist | |
| 666 | 625 | 668 | 695 | NH2 wag | |
| 704 | 690 | 715 | 723 | C—NO2 umb, NH2 twist | |
| 732 | 726 | 735 | 741 | 737 | C—NO2 umb, NH2 twist |
| 753 | 738 | 766 | 775 | 749 | NH2 rock, NO2 sci |
| 783 | 794 | 797 | 821 | 789 | NH2 twist |
| 841 | 862 | 833 | 843 | 856 | NO2 sci, C—C st, NH2 rock |
| 1041 | 1104 | 1006 | 1063 | 1024 | NH2 rock |
| 1049 | 1127 | 1050 | 1084 | 1070 | NH2 rock |
| 1106 | 1178 | 1106 | 1119 | 1142 | NH2 rock, NO2 st (sym) |
| 1172 | 1251 | 1141 | 1156 | 1165 | NH2 rock, C–C st |
| 1220 | 1378 | 1190 | 1201 | 1208 | C—NO2 st (asym), NH2 sci |
| 1287 | 1423 | 1300 | 1315 | 1311 | C—NO2 st (sym), NH2 rock |
| 1403 | 1538 | 1321 | 1339 | 1343 | NH2 sci, NO2 st (asym) |
| 1471 | 1588 | 1398 | 1411 | 1386 | NH2 rock, C—C st, NO2 st (asym) |
| 1505 | 1677 | 1480 | 1493 | 1506 | NH2 sci, C—C st |
| 1530 | 1714 | 1497 | 1519 | 1528 | NH2 sci, C—C rock |
| 1560 | 1752 | 1562 | 1599 | 1606 | NH2 sci, C—C st |
| 1581 | 1770 | 1603 | 1624 | 1630 | NH2 sci, C—C rock |
| 3341 | 3599 | 3288 | 3293 | 3299 | NH2 st (sym) |
| 3354 | 3609 | 3321 | 3334 | 3333 | NH2 st (sym) |
| 3544 | 3776 | 3418 | 3424 | 3405 | NH2 st (asym) |
| 3546 | 3776 | 3433 | 3450 | 3425 | NH2 st (asym) |
Notes: (a) DFT/B3LYP/6-311+G(2d,p) calculation in a vacuum; frequencies are scaled by a factor of 0.965 (this work). (b) MP2/6-31G(d,p) calculation in a vacuum; frequencies are scaled by a factor of 0.937 (Sorescu et al., 2001 ▸). (c)/(d) Periodic-DFT (p-DFT) calculation (Averkiev et al., 2014 ▸; Su et al., 2019 ▸) using CASTEP (Clark et al., 2005 ▸). (e) Raman measurement from solid sample with vibrational assignment: twist = twisting, wag = wagging, rock = rocking, scissor = scissoring, umb = umbrella, st = stretching, sym = symmetric and asym = asymmetric (Dreger et al., 2014 ▸).
Normal mode analysis of multi-temperature ADPs of α-FOX-7
| Frequency ν (cm−1) and eigenvector | Grüneisen | ɛ (× 10−4)
| GOF
|
| |||||
|---|---|---|---|---|---|---|---|---|---|
|
| |||||||||
|
|
|
| 2.5 (2) | Non-H-atoms | 3.19 | 9.30 | |||
|
|
|
| 2.5 (2) | −9 (3) | 0 (1) | −3 (1) | |||
|
| −3 (3) | 3 (1) | Obs: 840 | ||||||
| 25 (3) | Restr: 64 | ||||||||
|
| −0.607 (641) | 0.702 (524) | −0.011 (105) | Param: 88 | |||||
|
| −0.317 (142) | 0.054 (356) | 0.306 (57) | ||||||
|
| −0.060 (120) | 0.007 (75) | −0.947 (14) | H atoms | |||||
|
| −0.739 (14) | −0.624 (14) | 0.253 (22) | 63 | 0 | 0 | |||
|
| 0.667 (14) | −0.731 (12) | 0.143 (22) | 174 | 0 | ||||
|
| 0.096 (26) | 0.274 (14) | 0.957 (5) | 369 | |||||
|
| −0.407 (565) | −0.602 (337) | 0.034 (57) | ||||||
|
| 0.492 (473) | 0.375 (387) | 0.041 (63) | ||||||
|
| 0.345 (90) | 0.042 (610) | 0.080 (59) | ||||||
|
| |||||||||
|
|
|
| 2.4 (2) | 3.16 | 9.19 | ||||
|
|
|
| 2.4 (2) | 840/50/78 | |||||
|
| |||||||||
|
|
|
| 2.50 | 7.23 | |||||
| 4.3 (8) | 2.8 (4) | 4.5 (10) | 840/45/78 | ||||||
|
|
|
| |||||||
| 0.7 (4) | 8.8 (3) | 1.1 (3) | |||||||
|
| |||||||||
|
|
|
| 2.1 (4) | 6.24 | 18.4 | ||||
|
|
|
| 2.1 (4) | 840/50/60 | |||||
|
| |||||||||
|
|
|
| 2.3 (5) | 5.06 | 15.2 | ||||
|
|
|
| 2.3 (5) | 640/50/60 | |||||
Notes: (a) the H-atom epsilons are restrained to the values from DFT calculations. (b) The diagonal elements of epsilon for non-H atoms from DFT calculations are 13, 19, 13 × 10−1 Å2. (c) Goodness-of-fit (GOF) based on numbers of observations (Obs), restraints (Restr) and parameters (Param). (d) wR 2 = [Σw(U obs − U calc)2/ΣwU obs 2]1/2.
Figure 5PEANUT plots showing the difference displacement parameters 3 × (U obs – U cal) of α-FOX-7 from synchrotron diffraction (80–360 K); positive and negative differences are shown with respective solid and dashed lines. Axes shown are the molecular coordinate system for normal mode analysis; see text for more details. The r.m.s. values of Σ(ΔU/σobs) = ∼3–4 for non-H and ∼1 for H atoms.
Comparison of the lattice vibrational frequencies (cm−1) from ADP analysis, Γ-point simulation, DFT calculation, INS and Raman measurements
| DFT-D
| INS
| Raman
| Γ-point
| ADP_Nosph
|
|---|---|---|---|---|
| 29.3 | 27 | 25 | 35.7 | 39.4 |
| 48.1 | 46 | 46 | 48.6, 49.8 | 44.6 |
| 57.9 | 53 | 54 | 56.6, 57.1 | 56.6 |
| 60.1 | 58 | 63 | ||
| 67.3 | 64 | 64 | 66.6 | |
| 76.3 | 69 | |||
| 77.1 | 72 | 71 | 78.0 | |
| 81.5 | 79 | 77 | 81.4, 83.1 | 76.5 |
| 86.5 | 85 | 86.7, 87.4 | 85.2 | |
| 91.7 | 88 | 90 | ||
| 93.4 | 95 | 98 | 93.9 | |
| 97.3 | 97 | 97.8, 98.6 | 97.5 | |
| 100.1 | 103 | 107 | 104.2 | |
| 109.3 | 112 | 111.5–118.4 | ||
|
|
| |||
|
|
| |||
|
|
| |||
| 124.4 | 145 | 139 | 125.8–139.2 | |
| 128.9 | 148 | 151 | 149.3 | 145.5 |
|
|
| 159 | 154.0, 156.8 | |
|
|
| 162 | 161.4 | |
|
|
| 167.4, 168.8 | ||
|
|
| |||
|
|
|
Notes: (a) dispersion-corrected density functional theory (DFT-D) calculations and inelastic neutron scattering (INS) (Hunter et al., 2015 ▸). (b) Raman spectroscopy under ambient conditions (room temperature and 1 atm) (Dreger et al., 2014 ▸). (c) Deformational vibrations from CN2 wagging and NO2 twisting. (d) Deformational vibrations from NO2 twisting. (e) Simulated Γ-point of the α-FOX-7 unit cell (this work). (f) Normal mode analysis of nonspherical ADPs and model rbeg+3b+1f (this work).