Dear Lu= kman,

Your ques= tion is a tricky one and you will receive various responses. Let's start wi= th QTAIM first. QTAIM is a powerful and accurate theory but it's results ar= e not always straightforward to interpret. You may find 2 different cases i= n the literature criticizing QTAIM.

1- Cases in which a (= 3,-1) critical point (generally known as bond critical point or BCP) is mis= sing where a chemical bond is expected. In many cases of this type the main= problem is just neglecting the dynamics of molecular systems. For a very d= etailed discussion on these cases see Chem Eur J 2014, 20, 10140-10152. In = this paper we reviewed controversial cases. In general since (3,-1) CPs can= appear and disappear by dynamics of molecules my colleagues and I suggeste= d to rename BCP to Line Critical Point (LCP) in analogy with Ring and Cage = CPs because no one expect that a chemical bond appear/disappear just by vib= ration.

2- Cases with an unexpected (3, -1) CP like an additional= LCP between ortho hydrogens of byphenyl or hydrogens in bay region of phen= anthrene as Prof. Grimme mentioned. In these cases we already know that for= instance planar biphenyl is higher in energy compared to the tilt local mi= nimum structure. Matta, Hernandez and Bader demonstrated that the presence = of LCPs is accompanied with the presence of a (3, -1) CP in virial field th= at suggests a stabilization which is associated with this LCP (Chem Eur J, = 2003, 9, 1940-1951). But what does it mean? This stabilization as Matta et = al. originally suggested, is merely a "local stabilization" in hydrogen bas= ins that is compensated with "local destabilization" in carbon region. This= stabilizing interaction forms because if in an imaginary system it doesn't= , the energy of system can increase further! Indeed, molecular systems resp= ond towards any change. In case of H-H interaction, electrons shift from ne= ighboring carbon basins to the basin of hydrogens to reduce proton-proton r= epulsion. You "may" call it a bond as it looks like a bond with electron ac= cumulation between hydrogens or just a local electron redistribution. The c= ontroversial part is classification of this interaction which was unprecede= nted in chemistry before QTAIM era.

After all, I would li= ke to say that a simple topological AIM analysis is not enough to judge abo= ut the nature of bonding and convince chemical community. In my point of vi= ew, this is the same for other topological approaches like ELF or NCI, etc.= A robust theory that can help you in this case is the theory of Interactin= g Quantum Atoms (IQA) by Pendas et al. (JCP, 2004, 120, 4581-4592; JCTC, 20= 05, 1, 1096-1109; JCC, 2005, 26, 344-351 and many more).

Within t= he context of IQA you can recognize exact interaction energy between atoms.= This analysis is a bit expensive but worth doing!

I hope it helps.

All the best,

Cina

-------------------------------------------= --------------------------------

Cin= a Foroutan-Nejad, PhD

CEITEC, = Central European Institute of Technology,

Masaryk University, Brno, Czech Republic

https://muni.academia.edu/CinaForouta= nNejad

<= div style=3D"font-family:bookman old style, new york, times, serif;font-siz= e:16px;">

On Sat= urday, 14 February 2015, 0:38, Olasunkanmi Lukman Olawale walecomuk]~[yahoo= .co.uk <owner-chemistry-*-ccl.net> wrote:

Dear CClers,

Kindly assist.

I made DFT calculations on a = nitrogen heterocycle which was ordinarily expected to be a D2h molecule but= was found to be otherwise. It was found out that a pair of hydrogen atoms = in the molecule seems to exhibit intramolecular interaction. I have a vague= idea that QTAIM analysis could be used to justify whether the interaction = between the two hydrogen atoms is stabilizing (H-H attraction) or destabili= zing (repulsion) but I am not very sure of what (QTAIM) parameters will be = used for the findings. Your suggestions will be appreciated.

Thank you.

= ;

Lukman Olawale Olasunkanmi

Current Address= :
Department of C= hemistry,
Faculty of Agriculture, Science an= d Technology,
North West University (Mafiken= g Campus),
South Africa.
<= span>Cell: +27710156252 OR +27747614116

Pe= rmanent Address:
Department of Chemistry,Obafemi Awolowo University,
= Ile-Ife,
Nigeria.
Cell: +234 805 240 1564

------=_Part_5115931_1745450401.1423906978738-- From owner-chemistry@ccl.net Sat Feb 14 11:16:00 2015 From: "Mikael Johansson mikael.johansson+/-iki.fi" To: CCL Subject: CCL: QTAIM or else Message-Id: <-51033-150214062942-16629-zfssAWCNtI9yOb/sIkYOCA ~ server.ccl.net> X-Original-From: Mikael Johansson Content-Type: multipart/mixed; BOUNDARY="-696226883-1680503670-1423913374=:29555" Date: Sat, 14 Feb 2015 13:29:33 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson:iki.fi] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---696226883-1680503670-1423913374=:29555 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8BIT Hello Lukman and All, There is quite a debate on whether bond critical points always correspond to a stabilising interaction or not, and H...H bonds are an often discussed case in the literature. I doubt you will get an answer using QTAIM that would satisfy everyone ;-) You could try out the non-covalent interactions (NCI) analysis by Johnson and co-workers: http://pubs.acs.org/doi/abs/10.1021/ja100936w http://pubs.acs.org/doi/abs/10.1021/ct100641a It's, in my opinion, a rather beautiful method, and is already implemented in quite many programs. Look up NCIplot and Multiwfn, for example. Then there's of course a plethora of other analysis methods, like electron sharing numbers and various energy partititoning schemes that you could use, but I'd start out with the NCI analysis. Good luck, Mikael J. http://www.iki.fi/~mpjohans/ On Fri, 13 Feb 2015, Olasunkanmi Lukman Olawale walecomuk]~[yahoo.co.uk wrote: > Dear CClers, > Kindly assist. > > I made DFT calculations on a nitrogen heterocycle which was ordinarily > expected to be a D2h molecule but was found to be otherwise. It was > found out that a pair of hydrogen atoms in the molecule seems to exhibit > intramolecular interaction. I have a vague idea that QTAIM analysis > could be used to justify whether the interaction between the two > hydrogen atoms is stabilizing (H-H attraction) or destabilizing > (repulsion) but I am not very sure of what (QTAIM) parameters will be > used for the findings. Your suggestions will be appreciated. > > Thank you. > Â > Lukman Olawale Olasunkanmi > > Current Address: > Department of Chemistry, > Faculty of Agriculture, Science and Technology, > North West University (Mafikeng Campus), > South Africa. > Cell: +27710156252 OR +27747614116 > > Permanent Address: > Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, > Nigeria. > Cell: +234 805 240 1564 > > ---696226883-1680503670-1423913374=:29555-- From owner-chemistry@ccl.net Sat Feb 14 20:04:00 2015 From: "Nathan Houtz nhoutz^purdue.edu" To: CCL Subject: CCL: damped shifted force potential validation Message-Id: <-51034-150213230021-26932-FTT/jzTaM4V1Jhu/A8Neyw(!)server.ccl.net> X-Original-From: "Nathan Houtz" Date: Fri, 13 Feb 2015 23:00:20 -0500 Sent to CCL by: "Nathan Houtz" [nhoutz]^[purdue.edu] Hello everyone, I have been working for a while now to try and see if the damp shifted force potential is valid for my system. I am trying to study tetrolic acid in ethanol, and seperately tetrolic acid in chloroform. I have generated RDF's for hydrogen bonding atom pairs which agree very nicely with those predicted using the ewald summation. However when I compare the total potential energy of the two systems, I see that they disagree by about a factor of three. When I look at the output file lammps gave me, I see that this may be because the long range energy is still significant at a coulumbic cut off of 12nm for the DSF. How is it that the RDF's can agree so well, but the energies differ so much? I am currently using an alpha value of 0.2 and a coulombic cut off of 12.0 Angstroms. I am trying to follow the methodology in (Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation, by Zahn, Schilling, and Kast), where the found a cut off of 9.0 Angstroms worked very well for water, and found the potential energies to differ to within less than 5%. Is it possible the DSF potential will just not work for my system? Are there any suggestions for finding an optimal alpha and rcut value?