From owner-chemistry@ccl.net Fri May 14 19:31:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim%x%compchem.net" To: CCL Subject: CCL: Help with halogen bonding Message-Id: <-41861-100514110015-9652-mMhCc7zLGCfLZ0QczuOQMA ~~ server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016367fa7603a7f5a04868f2154 Date: Fri, 14 May 2010 16:00:01 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim . compchem.net] --0016367fa7603a7f5a04868f2154 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Mariya The distance between the two bonded atoms should equal to or less than the sum of the VDW radii of the atoms. NBO and AIM could be used as a further analysis to prove if there is a bond or not. Halogen bonds are weak bonds, you should use MP2 (better) or B3LYP (not recommended because of lacking of dispersion in DFT; but one paper shows a comparison between performance of these two methods regarding to halogen bonding, and proved that both of them are giving good results) with big basis set with diffuse functions, most of the papers done on halogen bonds used B3LYP/aug-cc-pVDZ. Your calculation shaw that the distance between the halogen atom and the Y atom is around VDW + 0.1, I think you didn't use a big basis set. If you ar= e studying Flourine or Chlorine atom (X), you should use 6-311+G** at least a= s a basis set. For Bromine or Iodine, you should use aug-cc-pVDZ basis set to include relativistic effect. There are many papers/reviews on this subject, you may like to have a look on the following: * Fourmigu=E9, M. "Halogen bonding: Recent advances." Current Opinion in So= lid State and Materials Science 13(3-4): 36-45. * Auffinger, P., F. A. Hays, et al. (2004). "Halogen bonds in biological molecules." Proceedings of the National Academy of Sciences of the United States of America 101(48): 16789-16794. Kov=E1cs, A. and Z. Varga (2006). "Halogen acceptors in hydrogen bonding." Coordination Chemistry Reviews 250(5-6): 710-727. * Politzer, P., P. Lane, et al. (2007). "An overview of halogen bonding." Journal of Molecular Modeling 13(2): 305-311. Sincerely; M. Ibrahim On Fri, May 14, 2010 at 8:28 AM, Mariya al-Rashida maria_al_rashida(!) hotmail.com wrote: > > Sent to CCL by: "Mariya al-Rashida" [maria_al_rashida~!~hotmail.com] > Hello everyone > > Im currently investigating crystal structures of some organic halogen > compounds. I'm pretty sure i've come across some "Halogen Bonds" [haolgen > bonds are non covalent interactions C-X...Y where X =3D halogen acting as > lewis acceptor and Y =3D N or O acting lewis base]. What i know from > literature, both exp and theoretical is that these interactions are found= at > distances equal to or slightly shorter than sum of van der wall radii. > Whereas i'm getting these interactions at distance which is equal to sum = of > van der wall radii + 0.1. Does this still count as a halogen bond ??? Or > should it be rather a weak type of haolgen bonding? > > Also does anyone know of any relavent theoretical literature for halogen > bonding > > Your comments will be highly apreciated > Mariiya > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim*o*compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016367fa7603a7f5a04868f2154 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Mariya
The distance between the two bonded atoms should equal to o= r less than the sum of the VDW radii of the atoms. NBO and AIM could be use= d as a further analysis to prove if there is a bond or not.
Halog= en bonds are weak bonds, you should use MP2 (better) or B3LYP (not recommen= ded=A0because=A0of lacking=A0of dispersion in DFT; but one paper shows a co= mparison between performance of these two methods=A0regarding=A0to halogen = bonding, and proved that both of them are giving good results) with big=A0b= asis=A0set with diffuse functions, most of the papers done on halogen bonds= used B3LYP/aug-cc-pVDZ.
Your calculation shaw that the distance between the halogen atom and t= he Y atom is around VDW + 0.1, I think you didn't use a big basis set. = If you are studying Flourine or Chlorine atom (X), you should use 6-311+G**= at least as a basis set. For Bromine or Iodine, you should use aug-cc-pVDZ= basis set to include=A0relativistic=A0effect.

There are many papers/reviews on this subject, you may like to have a = look on the following:

* Fourmigu=E9, M. "Hal= ogen bonding: Recent advances." Current Opinion in Solid State and Mat= erials Science 13(3-4): 36-45.
* Auffinger, P., F. A. Hays, et al. (2004). "Halogen bonds in bio= logical molecules." Proceedings of the National Academy of Sciences of= the United States of America 101(48): 16789-16794.
Kov=E1cs, A. = and Z. Varga (2006). "Halogen acceptors in hydrogen bonding." Coo= rdination Chemistry Reviews 250(5-6): 710-727.
* Politzer, P., P. Lane, et al. (2007). "An overview of halogen b= onding." Journal of Molecular Modeling 13(2): 305-311.
=A0
Sincerely;
M. Ibrahim=A0

On Fri, May 14, 2010 at 8:28 AM, Mariya al-Rashida maria_al_rashida(!)hotmail.com <owner-c= hemistry*o*ccl.net> wrote:

Sent to CCL by: "Mariya =A0al-Rashida" [maria_al_rashida~!~hotmail.com]
Hello everyone

Im currently investigating crystal structures of some organic halogen compo= unds. I'm pretty sure i've come across some "Halogen Bonds&quo= t; [haolgen bonds are non covalent interactions C-X...Y where X =3D halogen= acting as lewis acceptor and Y =3D N or O acting lewis base]. What i know = > from literature, both exp and theoretical is that these interactions are fo= und at distances equal to or slightly shorter than sum of van der wall radi= i. Whereas i'm getting these interactions at distance which is equal to= sum of van der wall radii + 0.1. Does this still count as a halogen bond ?= ?? Or should it be rather a weak type of haolgen bonding?

Also does anyone know of any relavent theoretical literature for halogen bo= nding

Your comments will be highly apreciated
Mariiya



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=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
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=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi= ty of Manchester,
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=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

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=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
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