UserWiki:Meisam: Difference between revisions

Line 7:

*:It is hard to say. But AM1 results are fairly good and B3LYP results are mostly accurate for geometry of organic molecules.

*Why the molecular bonds/shapes look different than the [https://en.wikipedia.org/wiki/Skeletal_formula skeletal formula] representation?

*: Skeletal formula predictions for bonds/shapes are not accurate. My calculations find the geometry which have the least energy (therefore is the most stable one). These geometries may or may not be the same shape as their skeletal formula. ~~The visualization software that I use~~, ~~is guessing the bond-type based on~~ the ~~bond length and atomic type. (which may be a better estimation!) The correct way to find~~ the bond order is to perform a [https://en.wikipedia.org/wiki/Natural_bond_orbital NBO] analysis ~~to accurately determine the bond types~~. ~~(Unfortunately, I don't have enough free time to do that)~~

*: Skeletal formula predictions for bonds/shapes are not accurate. My calculations find the geometry which have the least energy (therefore is the most stable one). These geometries may or may not be the same shape as their skeletal formula. Also, the proper method for finding the bond order is to perform a [https://en.wikipedia.org/wiki/Natural_bond_orbital NBO] analysis.

*Are these geometries valid for molecules in water/SBF/blood/urine, etc?

*:No! All my calculations are done on isolated molecules (basically molecules in low pressure gas phase). The geometries depend on the environment and do change in presence of solvents. But based on the property you are interested in, they are generally a good approximation or a first guess.

@@ Line 7: / Line 7: @@
 *:It is hard to say. But AM1 results are fairly good and B3LYP results are mostly accurate for geometry of organic molecules.
 *Why the molecular bonds/shapes look different than the [https://en.wikipedia.org/wiki/Skeletal_formula skeletal formula] representation?
-*: Skeletal formula predictions for bonds/shapes are not accurate. My calculations find the geometry which have the least energy (therefore is the most stable one). These geometries may or may not be the same shape as their skeletal formula. The visualization software that I use, is guessing the bond-type based on the bond length and atomic type. (which may be a better estimation!) The correct way to find the bond order is to perform a [https://en.wikipedia.org/wiki/Natural_bond_orbital NBO] analysis to accurately determine the bond types. (Unfortunately, I don't have enough free time to do that)
+*: Skeletal formula predictions for bonds/shapes are not accurate. My calculations find the geometry which have the least energy (therefore is the most stable one). These geometries may or may not be the same shape as their skeletal formula. Also, the proper method for finding the bond order is to perform a [https://en.wikipedia.org/wiki/Natural_bond_orbital NBO] analysis.
 *Are these geometries valid for molecules in water/SBF/blood/urine, etc?
 *:No! All my calculations are done on isolated molecules (basically molecules in low pressure gas phase). The geometries depend on the environment and do change in presence of solvents. But based on the property you are interested in, they are generally a good approximation or a first guess.