On 29 Jun = 2013, at 19:58, "Susi Lehtola susi.lehtola]_[alumni.helsinki.fi" <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

CHn groups have a much smaller dipole = component than OH and NH groups.

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

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.

=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
dr. = Marcel Swart

ICREA Research Professor at
Institut de Qu=EDmica = Computacional i Cat=E0lisi
Universitat de Girona

Facultat de = Ci=E8ncies
Campus Montilivi
17071 Girona
Catalunya = (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mailmarcel.swart#%#icrea.cat
marce= l.swart#%#udg.edu
web
http://www.marcelswart.eu
vCard

= --Apple-Mail=_AB973461-EA98-44B3-9388-5FB80A527EA8-- From owner-chemistry@ccl.net Sun Jun 30 09:59:00 2013 From: "sobereva .. sina.com" To: CCL Subject: CCL: Is there a tool to analyze hydrogen bonds like C-H...O Message-Id: <-48878-130630053209-28573-+ybpW+XdPKBbkNKIEMN4BA%x%server.ccl.net> X-Original-From: Content-Type: multipart/alternative; boundary="=-sinamail_alt_6cbcdc2b9789b1691a9a651b72478370" Date: Sun, 30 Jun 2013 17:31:55 +0800 MIME-Version: 1.0 Sent to CCL by: [sobereva{=}sina.com] --=-sinamail_alt_6cbcdc2b9789b1691a9a651b72478370 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: base64 Content-Disposition: inline RGVhciBXdSwNCiANClRoZSByZWR1Y2VkIGRlbnNpdHkgYW5hbHlzaXMgbWV0aG9kIGZvciBhbmFs eXppbmcgbm9uY292YWxlbnQgaW50ZXJhY3Rpb24gKEpBQ1MsIDEzMiwgNjQ5OOKAkzY1MDYpIGlz IGZ1bGx5IHN1cHBydGVkIGJ5IE11bHRpd2ZuIHByb2dyYW0gKGh0dHA6Ly9NdWx0aXdmbi5jb2Rl cGxleC5jb20pLCBzb21lIGV4YW1wbGVzIGFyZSBnaXZlbiBpbiBTZWN0aW9uIDQuMTAwLjEgb2Yg dGhlIG1hbnVhbCwgYW5kIG1vcmUgZGV0YWlsIGRpc2N1c3Npb25zIGFyZSBnaXZlbiBpbiBhIHBv c3QgKGh0dHA6Ly9oaS5iYWlkdS5jb20vc29iZXJldmEvaXRlbS9iYjExNjJkODgxYjhkNWVlM2Nj MmNiZGMsIGluIENoaW5lc2UpLiBBcyBNYXJjZWwgbWVudGlvbmVkLCB0aGlzIG1ldGhvZCBjb3Vs ZCBiZSB1c2VmdWwgZm9yIHN0dWR5aW5nIEMtSC4uLk8gaW50ZXJhY3Rpb24uDQpXb3J0aG5vdGlu Z2x5LCByZWNlbnRseSB0aGlzIGFuYWx5c2lzIG1ldGhvZCBoYXMgYmVlbiBleHRlbmRlZCB0byBz dHVkeSBub25jb3ZhbGVudCBpbnRlcmFjdGlvbiBpbiBmbHVjdHVhdGlvbiBlbnZpcm9ubWVudCAo ZS5nLiBpbnZlc3RpZ2F0aW5nIEgtYm9uZHMgYW5kIHZkVyBpbnRlcmFjdGlvbnMgYmFzZWQgb24g TUQgdHJhamVjdG9yeSksIHNlZSBKLiBDaGVtLiBUaGVvcnkgQ29tcHV0LiwgOSwgMjIyNuKAkzIy MzQuIFRoaXMgZXh0ZW5kZWQgbWV0aG9kIGhhcyBhbHNvIGJlZW4gc3VwcG9ydGVkIGJ5IE11bHRp d2ZuIHNpbmNlIHZlcnNpb24gMy4xLCBzZWUgU2VjdGlvbiAzLjIwMC4xIG9mIHRoZSBtYW51YWwu IEkgYWxzbyB3cm90ZSBhIHBvc3QgdG8gZGV0YWlsZWRseSBleGVtcGxpZnkgaG93IHRvIHV0aWxp emUgdGhpcyBtZXRob2QgaW4gTXVsdGl3Zm4gdG8gaW52ZXN0aWdhdGUgdGhlIG5vbmNvdmFsZW50 IGludGVyYWN0aW9uIGluIGJ1bGsgd2F0ZXIgc2ltdWxhdGlvbiwgc2VlIGh0dHA6Ly9oaS5iYWlk dS5jb20vc29iZXJldmEvaXRlbS9iZWY2YzUzMzE0ZDQwMGJlMTI0YjE0N2YgKGluIENoaW5lc2Up LgoNCkJlc3Qgd2lzaGVzLA0KIA0KVGlhbiBMdQoNCg0KLS0tLS0gT3JpZ2luYWwgTWVzc2FnZSAt LS0tLQpGcm9tOiAiV3VDaGFvZnUgeGlhb3d1NzU5Xl9eaG90bWFpbC5jb20iIDxvd25lci1jaGVt aXN0cnlAY2NsLm5ldD4KVG86ICJMdSwgVGlhbiAtaWQjM3BoLSIgPHNvYmVyZXZhQHNpbmEuY29t PgpTdWJqZWN0OiBDQ0w6IElzIHRoZXJlIGEgdG9vbCB0byBhbmFseXplIGh5ZHJvZ2VuIGJvbmRz IGxpa2UgQy1ILi4uTwpEYXRlOiAyMDEzLTA2LTI5IDIxOjU0CgoKU2VudCB0byBDQ0wgYnk6IFd1 Q2hhb2Z1IFt4aWFvd3U3NTkoKWhvdG1haWwuY29tXQpEZWFyIENDTGVycywKSSB0cnkgdG8gYW5h bHl6ZSB0aGUgaHlkcm9nZW4gYm9uZHMgKEhCcykgbGlrZSBDLUguLi5PIGluIG91ciBzeXN0ZW1z LiBIb3dldmVyLCBnZW5lcmFsIHRvb2xzIChpLmUuLCBnX2hib25kLCB2bWQpIGNhbm5vdCBhbmFs eXplIHN1Y2ggSEJzIGJ1dCBPLUguLi5PLCBOLUguLi5PLCBPLUguLi5OLCBOLUguLi5OLiBJcyB0 aGVyZSBzdWNoIGFuIGFsdGVybmF0aXZlIHRvb2wgdG8gcmVhbGl6ZSBpdC4gUGxlYXNlIGdpdmUg bWUgc29tZSBoaW50cy4gVGhhbmtzIGEgbG90IGZvciBhbnkgcmVwbGllcy4KWW91cnMgc2luY2Vy ZWx5LApDaGFvZnUgV3UKLT0gVGhpcyBpcyBhdXRvbWF0aWNhbGx5IGFkZGVkIHRvIGVhY2ggbWVz c2FnZSBieSB0aGUgbWFpbGluZyBzY3JpcHQgPS0KVG8gcmVjb3ZlciB0aGUgZW1haWwgYWRkcmVz cyBvZiB0aGUgYXV0aG9yIG9mIHRoZSBtZXNzYWdlLCBwbGVhc2UgY2hhbmdlCnRoZSBzdHJhbmdl IGNoYXJhY3RlcnMgb24gdGhlIHRvcCBsaW5lIHRvIHRoZSBAIHNpZ24uIFlvdSBjYW4gYWxzbwps b29rIHVwIHRoZSBYLU9yaWdpbmFsLUZyb206IGxpbmUgaW4gdGhlIG1haWwgaGVhZGVyLgpFLW1h aWwgdG8gc3Vic2NyaWJlcnM6IENIRU1JU1RSWUBjY2wubmV0IG9yIHVzZToKaHR0cDovL3d3dy5j Y2wubmV0L2NnaS1iaW4vY2NsL3NlbmRfY2NsX21lc3NhZ2UKRS1tYWlsIHRvIGFkbWluaXN0cmF0 b3JzOiBDSEVNSVNUUlktUkVRVUVTVEBjY2wubmV0IG9yIHVzZQpodHRwOi8vd3d3LmNjbC5uZXQv Y2dpLWJpbi9jY2wvc2VuZF9jY2xfbWVzc2FnZQpTdWJzY3JpYmUvVW5zdWJzY3JpYmU6IApodHRw Oi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L3N1Yl91bnN1Yi5zaHRtbApCZWZvcmUgcG9zdGluZywg Y2hlY2sgd2FpdCB0aW1lIGF0OiBodHRwOi8vd3d3LmNjbC5uZXQKSm9iOiBodHRwOi8vd3d3LmNj bC5uZXQvam9icyAKQ29uZmVyZW5jZXM6IGh0dHA6Ly9zZXJ2ZXIuY2NsLm5ldC9jaGVtaXN0cnkv YW5ub3VuY2VtZW50cy9jb25mZXJlbmNlcy8KU2VhcmNoIE1lc3NhZ2VzOiBodHRwOi8vd3d3LmNj bC5uZXQvY2hlbWlzdHJ5L3NlYXJjaGNjbC9pbmRleC5zaHRtbApJZiB5b3VyIG1haWwgYm91bmNl cyBmcm9tIENDTCB3aXRoIDUuNy4xIGVycm9yLCBjaGVjazoKaHR0cDovL3d3dy5jY2wubmV0L3Nw YW1tZXJzLnR4dApSVEZJOiBodHRwOi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L2Fib3V0Y2NsL2lu c3RydWN0aW9ucy8K --=-sinamail_alt_6cbcdc2b9789b1691a9a651b72478370 Content-Type: text/html; 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charset=UTF-8; format=flowed Date: Sun, 30 Jun 2013 14:19:11 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt::cosmologic.de] As I already mentioned recently with respect to the question oh sulfur hydrogen bonds: With the COSMO polarization charge densities you can quite generally analyze the strenze of almost any donor acceptor pair based on the sigmas of donor and acceptor, also for CH-donors. See for that our papers in PPCP Andreas Polarization charge densities provide a predictive quantification of hydrogen bond energies Phys. Chem. Chem. Phys., 2012,14, 955-963; DOI: 10.1039/C1CP22640A http://pubs.rsc.org/en/content/articlelanding/2012/cp/c1cp22640a Interpretation of experimental hydrogen-bond enthalpies and entropies > from COSMO polarisation charge densities Phys. Chem. Chem. Phys., 2013,15, 7147-7154; DOI: 10.1039/C3CP44611E http://pubs.rsc.org/en/content/articlelanding/2013/cp/c3cp44611e Am 29.06.2013 15:54, schrieb WuChaofu xiaowu759^_^hotmail.com: > 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> > > -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt::cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Sun Jun 30 11:38:00 2013 From: "Marc Baaden baaden]![smplinux.de" To: CCL Subject: CCL: Faraday Discussion on Molecular Simulation and Visualization - call for abstracts deadline 22 July 2013 Message-Id: <-48880-130630092448-16069-q/kzv6Gyr1fCdLMI0toqOg_._server.ccl.net> X-Original-From: Marc Baaden Content-Type: text/plain; charset=us-ascii Date: Sun, 30 Jun 2013 15:24:34 +0200 Mime-Version: 1.0 Sent to CCL by: Marc Baaden [baaden-x-smplinux.de] Dear Colleagues, Members of this list may be interested in the following event: Faraday Discussion #169 - Molecular Simulations and Visualization ** CALL for ABSTRACTS deadline 22.7.2013 ** http://www.rsc.org/ConferencesAndEvents/RSCConferences/FD/FD169/cfp.asp A few more details: Current biology, chemistry and materials science make extensive use of computational methods ranging from applications at the cellular level, e.g. in systems biology, to detailed atomistic simulations of molecular assemblies, materials or small molecules. 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