Rotamers in Crystal Structures of Xylitol, D-Arabitol and L-Arabitol
Abstract
:1. Introduction
2. Results and Discussion
2.1. Crystal Structures of Xylitol
2.2. Geometry
2.3. Crystal Structures of L-Arabitol and D-Arabitol
2.4. Theoretical Calculations
2.5. Absolute Configuration of Xylitol
2.6. Numbering System in Deposited Compounds
3. Materials and Methods
3.1. Preparation of Crystals
- Recrystallization of xylitol (2);
- Co-crystallization of xylitol (1) and xylitol (2);
- Co-crystallization of xylitol (1) with other sugars (i.e., D-arabitol, L-arabitol, and ribitol).
3.2. Single Crystal X-ray Studies
3.3. CSD Search
3.4. Computational Studies
3.5. Powder X-ray Diffraction Studies
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Structure | Dimers | Gaussian Calculations (kJ/mol) |
---|---|---|
Rotamer 1 (1) | H12…O4(−0.5+x, 1.5−y, 1−z) O3…H15(−0.5+x, 1.5−y, 1−z) | −48.37 |
H14…O2(1−x, 0.5+y, 0.5−z) O1…H13(1−x, 0.5+y, 0.5−z) | −50.56 | |
H11…O5(−1+x, y, z) | −13.28 | |
Rotamer 2 (D) | H14…O2(−0.5+x, 0.5−y, 1−z) O3…H11(−0.5+x, 0.5−y, 1−z) | −48.47 |
H12…O4(1−x, −0.5+y, 0.5−z) O5…H13(1−x, −0.5+y, 0.5−z) | −50.56 | |
H15…O1(−1+x, y, z) | −13.26 |
Structure | Dimers | Gaussian Calculations [kJ/mol] |
---|---|---|
D-arabitol (3D) | O1A…H1B(x, 1+y, 1+z) | −15.78 |
H1A…O4B(x, y, 1+z), H4A…O1B(x, y, 1+z) | −61.74 | |
O3A…H3B | −31.56 | |
H3A…O2A(1+x, y, z), H5A…O4A(1+x, y, z) | −48.45 | |
H2A…O5A(x, 1+y, z) | −18.23 | |
O2B…H5B(−1+x, −1+y, z) | −20.48 | |
O3B…H2B(1+x, y, z), O5B…H4B(1+x, y, z) | −51.96 | |
L-arabitol (3L) | O1A…H1B(x, −1+y, −1+z) | −15.90 |
H1A…O4B(x, y, −1+z), H4A…O1B(x, y, −1+z) | −61.78 | |
O3A…H3B | −31.46 | |
H3A…O2A(−1+x, y, z), H5A…O4A(−1+x, y, z) | −48.36 | |
H2A…O5A(x, −1+y, z) | −18.34 | |
O2B…H5B(1+x, 1+y, z) | −20.67 | |
H2B…O3B(−1+x, y, z), H4B…O5B(−1+x, y, z) | −52.03 |
Crystal Data | 1 | 2 | 3L | 3D |
---|---|---|---|---|
Chemical formula | C5H12O5 | |||
Mr | 152.15 | |||
Crystal system, space group | Orthorhombic, P212121 | Triclinic, P1 | ||
Temperature (K) | 122 | 123 | 100 | 100 |
a, b, c (Å) | 8.2664(1), 8.8978(1), 8.9132(2) | 8.2707(2), 8.9022(2), 8.9217(2) | 4.8000(2), 7.6568(3), 9.6384(4), 95.910(3), 96.094(4), 106.833(4) | 4.8055(2), 7.6526(3), 9.6387(4), 95.908(3), 96.052(4), 106.862(4) |
V (Å3) | 655.59(2) | 656.88(3) | 333.80(2) | 333.99(3) |
Z | 4 | 2 | 2 | |
Radiation type | Cu Kα | |||
µ (mm−1) | 1.21 | 1.20 | 1.19 | 1.19 |
Crystal size (mm) | 0.23 × 0.17 × 0.09 | 0.18 × 0.22 × 0.35 | 0.28 × 0.09 × 0.05 | 0.17 × 0.15 × 0.12 |
Data Collection | ||||
Diffractometer | SuperNova, Dual, CuKα, and Atlas detector | |||
Tmin, Tmax | 0.837, 1.000 | 0.383, 1.000 | 0.825, 1.000 | 0.901, 1.000 |
No. of measured, independent, and observed [I > 2σ(I)] reflections | 23,329, 1325, and 1316 | 14,853, 1383, and 1370 | 11,435, 2336, and 2230 | 8367, 2449, and 2385 |
Rint | 0.026 | 0.046 | 0.027 | 0.027 |
(sin θ/λ)max (Å−1) | 0.624 | 0.631 | 0.625 | 0.624 |
Refinement | ||||
R[F2 > 2σ(F2)], wR(F2), S | 0.022, 0.057, and 1.07 | 0.028, 0.077, and 1.09 | 0.032, 0.084, and 1.05 | 0.028, 0.074, and 1.04 |
No. of reflections | 1325 | 1383 | 2336 | 2449 |
No. of parameters | 102 | 99 | 277 | 191 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement | |||
Δρmax, Δρmin (e Å−3) | 0.27, −0.15 | 0.32, −0.21 | 0.33, −0.22 | 0.30, −0.18 |
Absolute structure | Flack × determined using 525 quotients [(I+) − (I−)]/[(I+) + (I−)] [30] | Flack × determined using 550 quotients [(I+) − (I−)]/[(I+) + (I−)] [30] | Flack × determined using 995 quotients [(I+) − (I−)]/[(I+) + (I−)] [30] | Flack × determined using 1055 quotients [(I+) − (I−)]/[(I+) + (I−)] [30] |
Absolute structure parameter | 0.01(4) | 0.03(7) | −0.02(13) | 0.07(10) |
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Wanat, M.; Malinska, M.; Kucia, M.; Sicinski, R.R.; Woźniak, K. Rotamers in Crystal Structures of Xylitol, D-Arabitol and L-Arabitol. Int. J. Mol. Sci. 2022, 23, 3875. https://doi.org/10.3390/ijms23073875
Wanat M, Malinska M, Kucia M, Sicinski RR, Woźniak K. Rotamers in Crystal Structures of Xylitol, D-Arabitol and L-Arabitol. International Journal of Molecular Sciences. 2022; 23(7):3875. https://doi.org/10.3390/ijms23073875
Chicago/Turabian StyleWanat, Monika, Maura Malinska, Malgorzata Kucia, Rafal R. Sicinski, and Krzysztof Woźniak. 2022. "Rotamers in Crystal Structures of Xylitol, D-Arabitol and L-Arabitol" International Journal of Molecular Sciences 23, no. 7: 3875. https://doi.org/10.3390/ijms23073875