From owner-chemistry@ccl.net Sat Jun 29 23:12:01 2013 From: "Mark Zottola mzottola]=[gmail.com" To: CCL Subject: CCL: Is there a tool to analyze hydrogen bonds like C-H...O Message-Id: <-48875-130629161700-23767-ukOrfE634pdDSZJFcmoRgg{=}server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=089e01536e0640a23b04e050ad91 Date: Sat, 29 Jun 2013 16:16:55 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola_-_gmail.com] --089e01536e0640a23b04e050ad91 Content-Type: text/plain; charset=ISO-8859-1 I believe the IUPAC definition of a hydrogen bond does include those BH---HX, CH---X and other non-traditional hydrogen bonds. On Sat, Jun 29, 2013 at 1:58 PM, Susi Lehtola susi.lehtola]_[ alumni.helsinki.fi 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" 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 > ---------------------------------------------------------------> > > --089e01536e0640a23b04e050ad91 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
I believe the IUPAC definition of a hydrogen bond does inc= lude those BH---HX, CH---X and other non-traditional hydrogen bonds.
<= div class=3D"gmail_extra">

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 a= n
> 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 =A0 =A0 =A0 =A0 =A0 =A0 Postdoctoral researcher
susi.lehtola]~[alum= ni.helsinki.fi =A0 Department of Applied Physics
http://www.h= elsinki.fi/~jzlehtol =A0Aalto University
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Finland=
---------------------------------------------------------------
Susi Lehtola, FT =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Tutkijatohtori
susi.lehtola]~[alum= ni.helsinki.fi =A0 Fysiikan laitos
http://www.h= elsinki.fi/~jzlehtol =A0Aalto-yliopisto
---------------------------------------------------------------



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