calculation of aggregates

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RickV
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calculation of aggregates

Post by RickV » 06 Jan 2015, 10:02

Hello all,

I have done some measurements on a small, rod-like, rigid molecule and I'm thinking the molecule switches over time from h-aggregates to j-aggregates. I was wondering if it is possible to confirm this hypothesis with some calculations using Dalton?

Thanks!

taylor
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First name(s): Peter
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Re: calculation of aggregates

Post by taylor » 06 Jan 2015, 10:30

So as I read it your post is "I've been doing some calculations on some molecules that for whatever reason I don't identify, and I'm wondering if Dalton can help me answer a couple questions that to anyone else are completely meaningless". Well, my answer, at least, is RTFM. And stop wasting the time of people who have a lot of work to do with such an embarrassingly inadequate posting.

If you tell us what you want to do, most of us, including me (no matter how aggressive this posting reads!), will try to help. There are literally years of evidence of our willingness to help, and megabytes of responses. But your posting deserves nothing in the way of assistance.

Pete

RickV
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Country: Belgium

Re: calculation of aggregates

Post by RickV » 06 Jan 2015, 10:59

Firstly, sorry, my post was not meant to be aggressive, or to waste someones time. My mistake. I will give some more information:
I didn't do some calculations on some molecules that for whatever reason I don't identify. I did some real life experimental Faraday rotation measurements in my setup on 1-propoxy-4-{[(trifluoromethyl)-phenyl]-ethynyl}-benzene (this is a linear molecule, consisting of 2 benzenerings, joined via a triple bond, with on one side of the molecule a CF3 group and on the other side an -OC3H7 group).

Now, in my experiment, I see a time-dependent variation of the Faradaysignal (t=0h gives a lot of signal, t = 24h gives almost no signal). My hypothesis is, that at t=0h, the molecule has formed h-aggregates, but at a later moment, t=24h, those aggregates are rearranged to j-aggregates. This should mean the H-aggregates are the kineticly formed structure, but the J-aggregates are the thermodynamic stable structure.

Now, I was wondering if I could test this hypothesis via computational measurements. My own thought is to calculate a molecule on its own, then calculate 2 molecules arranged as H-aggregate and calculate 2 molecules as J-aggregate. Now i was wondering, how can I put two molecules in an inputfile? Do I just add another set of atoms? How will the program know that there are 2 molecules in the file, and not one big molecule?

I hope this is a more satisfying and less aggressive post?

bast
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Re: calculation of aggregates

Post by bast » 06 Jan 2015, 17:31

hi Rick,
your post was not aggressive, it was just information-minimalist :-)
to calculate two molecules just put the second set of atoms behind the first.
unless the second molecule is "environment" of some sort (embedding calculations),
Dalton will not see them as two molecules but as one system. but does it matter?
Dalton just sees nuclear charges and does not even care so much about
atom labels so you can give the centers different labels.
good luck!

taylor
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Re: calculation of aggregates

Post by taylor » 07 Jan 2015, 04:08

Having said I would be willing to respond to a more detailed posting, I will. First, Radovan states exactly what you need to do for a dimer (or trimer or higher): you just list all the atoms in the input file. Yes, this effectively constructing a very large molecule, or supermolecule, if you like, but the program doesn't care about that, and neither does the quantum mechanics. You can put two helium atoms twenty kilometres apart and even though the program will see this as an He_2 "molecule" the energy calculated will (for most of the methods programmed in Dalton, because most of them are size-extensive) be exactly twice the energy of a single He atom.

But a couple of further points. You do not speculate on the nature of the interactions that lead to aggregation. Your molecule looks a bit polar, but perhaps not a lot? Are you of the opinion that the binding comes from a dipole-dipole term, and if so is that from permanent dipoles or induced dipoles (that is, dispersion)? The answers to these questions are critical for deciding what sort of calculation it makes sense to do. Weak interactions are difficult to describe because they are dominated by electron correlation effects that are absent from Hartree-Fock calculations and poorly described by almost all functionals used in DFT calculations. (I would suggest that CAMB3LYP makes the most sense if you are doing DFT, but I am not a DFT expert and would defer to those who are on this.) Probably best for a system of this size would be MP2, but it is going to get expensive.

My other point is an operational one. You have a system where the monomer appears to have no symmetry. Of course, one can obtain a symmetric dimer in many ways from an asymmetric monomer. Nevertheless, if whatever calculations you decide to do can be performed with LSDalton as well as Dalton, I strongly suggest you use LSDalton. (Disclaimer --- I have used LSDalton extensively but I am not a developer of LSDalton, only Dalton.) LSDalton does not treat symmetry explicitly in any way, and for symmetric systems there can be very good reasons to exploit the symmetry and to use Dalton. But most of LSDalton was written relatively recently, compared to much of Dalton, and particularly much of the "basic functionality" in Dalton. As a result the performance of LSDalton is almost always far superior: it has excellent parallelization, at both the OpenMP/thread level and the coarse-grained MPI level. If you have access to a parallel system, even only a small cluster, and if whatever calculation you want to do (SCF, DFT, at least with some functionals, MP2, all in the 2013 release, plus some coupled-cluster)functionality) can be handled with LSDalton, then you should consider that. The input files to Dalton and LSDalton are almost interchangeable, and although the LSDalton documentation does not have the "War and Peace" length of the Dalton documentation it is more than adequate. We have run energy calculations for systems with thousands of atoms --- we prefer to build the program to use Scalapack as the coarse-grained parallel level, but this is up to you.

I hope some of this is useful to you in planning your calculations!

Best regards
Pete

RickV
Posts: 37
Joined: 20 Feb 2014, 14:47
First name(s): Rick
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Re: calculation of aggregates

Post by RickV » 07 Jan 2015, 10:03

Thank you both for your answers! This definetly helps me.
I have a colleague who is used to doing dft calculations, so I will ask him about the dft part. I am by far no specialist on computational chemistry.

Thank you for your help.

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