[Pw_forum] Should we use a double bond or 2 H atoms to saturate the system?

O. Baris Malcioglu baris.malcioglu at gmail.com
Tue Apr 26 19:52:40 CEST 2011

Well, you literally add the coordinates of H atoms, and the definition
of H atom itself...

If you are asking how I do it, depending on the system, I either write
a simple script, or, if it is small enough, I extract the coordinates
to a standart from, and then use a freely available "geometry editor"
(I tend to use accelrys discovery studio viewer for such tasks, since
it is quite well equipped (the free version is available in accelrys
web site), with somewhat a guilty conscience because it is not GPL).

By the way, I beg to differ from "Hydrogen saturation is bad science".
Actually, I do fail to see your point in this generalisation.  Would
you, for a very simple example, consider studying the difference
between cyclohexane and benzene as bad science? I think this kind of
generalisations are quite dangerous to make without proper context,
after all, it all depends on what you want to study.

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