Dear Cha= ofu,

Y= ou may analyze your H-bonds by studying the electron density of your system= , whatever it is, by quantum theory of atoms in molecules, QTAIM. First you= should have a normal wavefunction, *.wfn, file (many QM packages pro= duce .WFN files).

Then you can analyze the electron density by a QTAIM software. AIMPAC2 (http://qe-forge.= org/gf/project/aimpac2/)= , Multifn (http://multiwfn.codeplex.com/), AIMAll (http://aim.tkgr= istmill.com/), AIM2000 (http://www.aim2000.de/) are some examples of such softwa= res. First two are freely available; third and forth have free limited vers= ions.

Then look up in the literature to find a HUGE numb= er of papers on application of QTAIM for hydrogen bonding analysis.

Jus= t bear in your mind that QTAIM does not give you a clear-cut answer. You sh= ould cautiously "interpret" your outputs. Read as many paper as you can and= do your analysis.

Good luck,

Cina

=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D

Cina Foroutan-Nejad, Ph.D.

ht= tp://muni.academia.edu/CinaForoutanNejad

From: WuChaofu xiaowu759^_^hotmail.com <owner-chemistry~~c= cl.net>
To: "Forout= an-Nejad, Cina " <canyslopus~~yahoo.co.uk>
Sent: Saturday, 29 June 2013, 15:54
= Subject: CCL: Is there a t= ool to analyze hydrogen bonds like C-H...O

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 real= ize it. Please give me some hints. Thanks a lot for any replies.
Yours s= incerely,
Chaofu Wu

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---361436947-73119337-1372519664=:54193-- From owner-chemistry@ccl.net Sat Jun 29 14:58:01 2013 From: "Susi Lehtola susi.lehtola]_[alumni.helsinki.fi" To: CCL Subject: CCL: Is there a tool to analyze hydrogen bonds like C-H...O Message-Id: <-48874-130629135910-19326-ae/6tO0PX5kVwkFNoljqxg===server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Sat, 29 Jun 2013 20:58:58 +0300 Mime-Version: 1.0 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 --------------------------------------------------------------- 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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