Imaging Valence-Level Electrons in an Organic Molecule!!

Just WOW!! A team from Nagoya University in Japan performing synchrotron X-ray diffraction experiments at SPring-8 were able to selectively extract an image of valence level electron density in the amino acid glycine. Did you get that? And guess what they found? The valence electrons were occupying a space the shape of a molecular orbital also derived from computation!! Amazing.

The aerial view of the facility is shown below. Despite the ring being situated on bedrock, the alignment of the magnets in the storage ring is so precise that the moon’s tidal forces can have a measurable impact on the ring’s performance.

The experimental work in question is that of Takeshi Hara, Masatoshi Hasebe, Takao Tsuneda, Toshio Naito, Yuiga Nakamura, Naoyuki Katayama, Tetsuya Taketsugu, and Hiroshi Sawa*, “Unveiling the Nature of Chemical Bonds in Real Space”, Journal of the American Chemical Society, accepted July 10, 2024. https://doi.org/10.1021/jacs.4c05673. As of this writing the full journal citation was not available.

Density Function Theory (DFT) calculations were performed with Gaussian 16, revision A.03.

Below is an illustration by a Riken artist comparing the theoretical valence level molecular orbital (MO) of glycine by DFT calculations and the experimental valence electron density distribution, or VED, collected by synchrotron x-ray diffraction at SPring-8.

If you’ve been through college chemistry, then no doubt you are familiar with atomic orbital theory beginning with Linear Combination of Atomic Orbitals, LCAO. Beyond LCAO is MO theory which goes on to help in the understanding of optical, electronic, magnetic and bonding properties of molecules. In the 1980’s and 90’s commercial software became available (and affordable)

Experimental details from the JACS paper-

Single Crystal XRD Experiments and Structure Analysis.
Single crystal XRD experiments were conducted at BL02B1 beamline in SPring-8, using the quarter-circle diffractometer (Rigaku Co., Japan), with diffraction reflections detected by a two-dimensional semiconductor detector, PILATUS3 X CdTe (DECTRIS Ltd., Switzerland). X-ray energies of 40 and 37 keV were used for Glycine and Cytidine, respectively. Temperature variation was achieved using a helium-gas-blowing device (Japan Thermal Engineering Co., Ltd., Japan). The intensities of Bragg reflections were collected by CrysAlisPro program. Diffraction reflection averaging and crystal structure analysis were performed using SORTAV program and JANA2006 program, respectively. VESTA program was employed for drawing the crystal structure and electron density. The structural analyses of Glycine and Cytidine were performed at 45 and 35 K, respectively. In the present XRD experiments, the
resolution limit of Glycine was d_min = 0.28 Å [(sin θ/λ)max = 1.786 Å⁻¹] and that of Cytidine was d_min = 0.30 Å [(sin θ/λ)max = 1.6565 Å⁻¹]. Accurate determination of structure factor F_cal(K) is crucial for the VED analysis using the CDFS method to obtain phase terms of crystal structure factors. To achieve this requirement, we refined the structure parameters using only high-angle data, a technique known as “high-angle refinement” (Section S1).

VED Analysis Using the CDFS Method. The CDFS method, a technique for directly observing a 3D VED in crystals, employs single crystal X-ray diffraction data obtained from synchrotron radiation. A detailed explanation can be found in previous papers. In this method, the experimental VED distribution is derived by subtracting the calculated core electron density from the experimental total electron density. In both cases, Glycine (C₂H₃NO₃) and Cytidine (C₅H₉N₂O₃), the core electron density corresponds to 1s² orbital density of C, N, and O atoms. Therefore, the phase relationship and distribution of the hybridized orbitals by 2s and 2p should be visible.
DFT Calculation. Theoretical valence orbital calculations were performed using DFT with LC-BLYP functional (μ = 0.47)36 and ccpVTZ basis set by Gaussian 16 Revision A.03 program. The structure parameters determined in the present XRD experiments were used for the calculations (Tables S2 and S5). The structures, orbitals, and electron densities are illustrated using ChemCraft program, while the contour plots are drawn using the VESTA program.

Source: The Sawa paper cited above. The experiment was a single crystal X-ray Diffraction (XRD) study using the very narrow x-ray beam available from the synchrotron ring. The underlined text above reveals that the 1s² orbital electron density was subtracted from the total experimental electron density. This would leave the partially filled 2s and 2p valence level MOs in isolation.

While structural determination by x-ray diffraction has been around for a very long time, what makes this work notable is the detection and imaging of electron density in valence level MOs and the close correlation to computational modeling.

For more information about the SPring-8 synchrotron storage ring, visit their website. The name stems from “Super Photon ring–8 GeV”.