CarbonOxygen motif

• CarbonOxygen motif: CarbonOxygen motif represent a range of small C&O-containing compounds that are chained together by C-O/C=O bonds. The motif is developed for CTR modeling for the CO2 reduction project I am currently involving in. In princible, H atoms should also be present to make a complete C-containing compound, but H atoms are invisible to X-ray, they are not included for simplicity. Each subMotif is a specific C-O compound. The constituent atoms will be coplanar. The procedure to make such a compound is as follows.
  1. Determine which atom is the main anchor atom, which will serve as a reference for calculating directly or indirectly the positions of all the other atoms.
  2. Which atoms will lie down flat above the substrate surface plane? These atoms will have the same height as the anchor atom.
  3. Except for the main anchor atom, you need to specify the anchor atoms (can be the main anchor atom or other constituent atoms) for all the rest atoms. With anchor atoms being defined, the position of each atom can be calculated in a polar coordinate system that origin at the associated anchor atom by specifing the radial coordinate r and the angular coordinates φ, θ. We fix the angular coordinate φ (azimuth angle) to 0, and freely define the zenith angle as needed. In other words, all constituent atoms share one azimuth angle, and thus are coplanar. The orientation of the compound can be changed by rotating the whole compound molecule along x-axis, y-axis and z axis with each axis passing through the main anchor atom.
  4. Note by default, the initial zenith angles are all set to the same value. You should modify these values accordingly to create a C-O compound of expected structure.

• There are five predefined subMotifs available to choose, including OCCO, CCO, CO, CO3, CO2. The items in the setting tables are the same. Here only give one example for the case of OCCO.
  • sorbate: sorbate index, same definition as in BD_CASE_TP
  • motif: always OCCO
  • els: element symbols for the constituent atoms. The atom ids will be automatically generated.
  • anchor_index_list: a list of anchor index for each atom. The value for the main anchor atom should be set to None. First item 1 in an anchor_index_list [1, None, 1, 2] literally means the first atom will be achored to the atom with an index of 1 (second atom from left).
  • flat_down_index: A list of index of atoms,which have a 0 zenith angle in the polar coordinate system (the atom will lie flat above the substrate surface).
  • xyzu_oc_m: specify the information for the main anchor atom (first three items correspond to x, y, z fractional coordinates, 4th item is DWF, 5th the occupancy, 6th the multiplicatin factor [not used, but you need to feed this value for script compatability])
  • structure_pars_dict: structure parameters in a dictionary format {'r': 1.5, 'delta': 0}, r is the initial value for radial coordinate (equivalent to the bond length of C-O), delta is the aforementioned zenith angle.
  • binding_mode: always OS.