| Title |
Determination of atomic radii from small-molecule crystal structures / |
| Translation of Title |
Atomų spindulių nustatymas iš mažų molekulių kristalinių struktūrų. |
| Authors |
Šidlauskaitė, Eglė |
| Full Text |
|
| Pages |
53 |
| Keywords [eng] |
atomic radii, van der Waals gap, X-ray diffraction, small molecule crystals, Crystallography Open Database, interatomic distance distribution, atomic radii table |
| Abstract [eng] |
Detailed analysis of small-molecule structures is a vital part of drug discovery. X-ray crystallography can be used to determine exact atom positions in crystal structures. Chemical bonding is usually inferred by comparing the distance between atoms to the sum of their atomic radii. However, there is no univocal method for the determination of atomic radii and commonly used radii tables are derived using data which is distributed under proprietary licenses. In this study, a methodology and an independent workflow for automatic atomic radii derivation was developed. Crystal structures from the Crystallography Open Database were analyzed to filter out structures with unusual observations and used to obtain interatomic distance data. Typical maximum intramolecular bond length was determined for each pair of elements by fitting the Gaussian mixture model to the interatomic distance distribution and identifying the location of the van der Waals gap. The results were used to generate an overdetermined system of equations that was solved using the weighted least squares algorithm. As a result, atomic radii for 84 chemical elements were calculated. Verification of the derived atomic radii table shows that it is able to detect connectivity in molecular entities comparably to other published atomic radii tables. The final atomic radii table, its comparison to other published covalent radii tables and intermediate data are freely accessible online. |
| Dissertation Institution |
Vilniaus universitetas. |
| Type |
Master thesis |
| Language |
English |
| Publication date |
2023 |
