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- How to choose sigma and epsilon value for carbon to calculate the bond . . .
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- What are the types of bond orders? - Matter Modeling Stack Exchange
For a fixed bond length and spin multiplet (e g , triplet spin state at 200 pm bond length), the SZ=S and SZ=0 molecules are almost energy degenerate (except for a tiny spin-orbit coupling energy), have nearly identical electron density distributions, and therefore should have similar computed bond orders
- molecular modeling - Bond length from infrared spectra? - Matter . . .
$\begingroup$ You can get some estimates on bond strengths (in simple cases), which might be useful for ordering bond orders strengths (the "classical" literature on metal-carbonyl complexes has used that extensively) This does not, however, assign a bond length, but might be used to estimate it from other known compounds based on the bond
- How may I estimate the bond energy of a molecule?
Can I estimate the bond energy by running a single Gaussian calculation of the fragments at very long separation (say, 40 angstroms)? Or do I have to calculate each fragment without the other? quantum-chemistry
- Scanning two bond lengths G-16 - Matter Modeling Stack Exchange
For example, consider the case where you are scanning the bond lengths of C-Cl and C-H in chloromethane The code will first increment the bond length of C-Cl, and will then scan the C-H bond while keeping C-Cl bond constant This will result in a 2D scan, with one axis corresponding to C-Cl bond and other corresponding to C-H bond
- Maximum bond length in Vesta - Matter Modeling Stack Exchange
Bond length is calculated by using atomic positions and lattice parameters Ionic or covalent size do not matter, the distance will be always the same because it is between the centers of the atoms, not between their surfaces To determine the coordination number, you must look at your structure and play with it
- computational chemistry - An algorithm for implicit bond order and . . .
Step 2: Use the SDF to get the bond order and formal charge information using Python + rdkit Below is a fully reproducible example of both steps using Methanol as a sample compound All of the following can be run in a Google Colab notebook:
- My CHARMM IC table generation has caused hydrogen to bond to two . . .
You can clearly see that the hydrogens are oriented along the C-C bond axis, which in turn causes the extra bonds that OP complained about Now, the structure that I generated using the input provided below The hydrogens are oriented properly now Conclusion: VMD was not the problem, instead the coordinates generated by OP was the problem
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