CCL: Is there a tool to analyze hydrogen bonds like C-H...O

On Sat, Jun 29, 2013 at 1:58 PM, Susi Lehtola susi.lehtola]_[alumni.helsinki.fi <owner-chemistry*|*ccl.net> wrote:

Sent to CCL by: Susi Lehtola [susi.lehtola]![alumni.helsinki.fi]

On Sat, 29 Jun 2013 21:54:13 +0800
"WuChaofu xiaowu759^_^hotmail.com" <owner-chemistry]~[ccl.net> wrote:
> Sent to CCL by: WuChaofu [xiaowu759()hotmail.com]
> Dear CCLers,

> I try to analyze the hydrogen bonds (HBs) like C-H...O in our
> systems. However, general tools (i.e., g_hbond, vmd) cannot analyze

> such HBs but O-H...O, N-H...O, O-H...N, N-H...N. Is there such an

> alternative tool to realize it. Please give me some hints. Thanks a

> lot for any replies. Yours sincerely, Chaofu Wu

I'm not sure if that can be classifiable as a hydrogen bond, because
CHn groups have a much smaller dipole component than OH and NH groups.

Still, the determination is very simple to do if you use a geometric
criterion as in g_hbond and vmd. It should be pretty straightforward to
modify g_hbond to your needs.

Note that there are rather many geometric criteria also for the more
conventional OH..O hydrogen bonds, e.g. the criteria in references

M. Haughney, M. Ferrario and I. R. McDonald, J. Phys. Chem. 91 (1987), 4934.

P. Wernet et al., Science 304 (2004), 995.

B. Chen and J. I. Siepmann, J. Phys. Chem. B 110 (2006), 3555.

out of which AFAIK the Haughney criterion is most often used.
--
---------------------------------------------------------------
Mr. Susi Lehtola, PhD Postdoctoral researcher
susi.lehtola]~[alumni.helsinki.fi Department of Applied Physics
http://www.helsinki.fi/~jzlehtol Aalto University
Finland
---------------------------------------------------------------
Susi Lehtola, FT Tutkijatohtori
susi.lehtola]~[alumni.helsinki.fi Fysiikan laitos
http://www.helsinki.fi/~jzlehtol Aalto-yliopisto
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