TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules.

Area of Science:

• Crystallography
• Materials Science
• Chemistry

Background:

• 3D electron diffraction (3D ED), also known as microcrystal electron diffraction (MicroED), is an emerging technique for high-resolution crystal structure determination.
• This method is particularly valuable for analyzing sub-micron-sized crystals, which are often challenging for traditional X-ray diffraction.

Purpose of the Study:

• To compare the effectiveness of Independent Atom Model (IAM) and Transferable Aspherical Atom Model (TAAM) refinements using 3D ED data.
• To assess the accuracy of TAAM in representing the experimental electrostatic potential of organic crystals.
• To evaluate geometrical parameters and atomic displacement parameters (ADPs) from 3D ED refinements against simulations and published data.

Main Methods:

• Collection of high-resolution 3D ED data from L-alanine, α-glycine, and urea using an in-house TEM instrument.
• Kinematical refinement of crystal structures using both IAM and TAAM against experimental and simulated 3D ED data.
• Comparison of refinement results with periodic density functional theory (DFT) calculations and published X-ray and neutron diffraction data.

Main Results:

• TAAM refinement significantly improved model fitting statistics (R factors, residual electrostatic potential) compared to IAM for both experimental and simulated 3D ED data.
• TAAM better represents the experimental electrostatic potential of organic crystals than IAM.
• Experimental 3D ED data yielded more accurate hydrogen atom positions than IAM refinements on X-ray diffraction data.
• TAAM refinements did not improve the accuracy of non-hydrogen bond lengths, and IAM refinements on 3D ED data showed statistically insignificant differences in X-H bond lengths compared to TAAM.

Conclusions:

• TAAM is a superior model for refining 3D ED data of organic crystals, particularly for electrostatic potential and hydrogen atom positioning.
• While TAAM enhances electrostatic potential representation, it does not significantly improve non-hydrogen bond length accuracy in this study.
• Discrepancies in atomic displacement parameters suggest potential influences of unmodeled effects like radiation damage or dynamical scattering in 3D ED data.