11.6. Regarding various parameters
11.6.1. Physical constants
The physical constants used in Winmostar are the 2018 CODATA recommended values [2018CODATA].
Tiesinga, P. J. Mohr, D. B. Newell, B. N. Taylor (2019), “The 2018 CODATA Recommended Values of the Fundamental Physical Constants” (Web Version 8.1). Database developed by J. Baker, M. Douma, S. Kotochigova. Available at http://physics.nist.gov/constants, National Institute of Standards and Technology, Gaithersburg, MD 20899.
11.6.2. Atomic data
The following are references for atomic data used in Winmostar.
Covalent radius (single bond) |
|
Covalent Radius (Multiple Coupling) |
|
van der Waals radius (typical elements) |
|
van der Waals radius (transition metal elements) |
|
Atomic mass |
Cordero, V. Gomez, A. E Platero-Prats, M. Reves, J. Echeverria, E. Cremades, F. Barragan, S. Alvarez, Dalton Trans., (2008) 2832-2838.
Pyykko, M. Atsumi, Chem. Eur. J., 15 (2009) 12770-12779.
Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, D. G. Truhlar, J. Phys. Chem. A, 113 (2009) 5806-5812.
Rahm, R. Hoffmann, N. W. Ashcroft, Chem. Eur. J., 22 (2016) 14625-14632.
Periodic Table: Atomic Properties of the Elements (Version 14), NIST SP 966. https://physics.nist.gov/pt/
Note that you can set the display radius of each element to any value by editing the third column of atoms1.wmx in .
11.6.3. Combining Criteria
11.6.3.1. single bond decision
If the distance between two atoms is shorter than the sum of the covalent bond radii (single bond) of each atom multiplied by the bonding coefficient, then it is determined to be a single bond. As an exception, H-H, O-O, and F-F bonds are determined by multiplying the values in the following table (unit: Å) by the bond coefficient. The H2, HOOH, and F2, respectively, were calculated using structural optimization calculations in B3LYP/6-31G*.
H-H |
0.74 |
O-O |
1.45 |
F-F |
1.40 |
11.6.3.2. Multiple join determination
For some two-atom combinations, if the distance between the two atoms is shorter than the sum of the covalent bond radii (multiple bonds) of the respective atoms times 1.03, it is determined to be a double or triple bond. If it is shorter than 1.03 times the sum of the averages of the single and double bonds, it is determined to be a 1.5-fold bond (aromatic bond). As an exception, N=N, O=O, and P=O double bonds are determined by multiplying the values in the following table (unit: Å) by 1.03. HNNH, O2, H3PO4, respectively, were calculated using structural optimization calculations in B3LYP/6-31G*.
N=N |
1.246 |
O=O |
1.215 |
P=O |
1.473 |
The following table shows the types of bonds that are being judged.
Binding type |
1.5 double bond |
double bond |
triple bond |
C-C |
✔ |
✔ |
✔ |
C-N |
✔ |
✔ |
✔ |
C-O |
✔ |
||
C-S |
✔ |
✔ |
|
N-N |
✔ |
✔ |
✔ |
N-O |
✔ |
✔ |
|
O-O |
✔ |
||
P-O |
✔ |
||
P-S |
✔ |
||
S-O |
✔ |