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arXiv · 2412.15284

Case Studies of Using the Partial-Structure R1 and the Single-Atom R1 to Assemble Small-Molecule Crystal Structures

Xiaodong Zhang
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Abstract

This paper demonstrates how pre-knowledge of a crystal structure, including the constituent fragments, the atomic connectivity, and the approximate bond lengths, etc., can be utilized in the partial-structure R1 (pR1) and the single-atom R1 (sR1) calculations. It has been shown that taking advantage of pre-known information the calculations can proceed in an orderly and well-planned manner. Furthermore, in the case of the sR1 calculation, computer time can also be greatly reduced. Because the pR1 calculation is more time-consuming than the sR1 calculation, when there is a choice between the pR1 and the sR1, the former should be avoided. So, the usual strategy of assembling a light-atom-only structure should start with the normal sR1 method to determine a basic framework of the structure, and then uses the connectivity-guided sR1 method to complete the model. However, when the data resolution is low, the first step is necessary to use the pR1 method to assemble the known fragments. For a heavy-atom-containing structure, the correct strategy starts with the normal sR1 method to determine the heavy-atom substructure, and then uses the connectivity-guided sR1 to complete the model.

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Xiaodong Zhang. 2024-12-18. Case Studies of Using the Partial-Structure R1 and the Single-Atom R1 to Assemble Small-Molecule Crystal Structures. https://arxiv.org/abs/2412.15284

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