How to run beta calculation for ionic species

Find answers or ask questions regarding Dalton calculations.
Please upload an output file showing the problem, if applicable.
(It is not necessary to upload input files, they can be found in the output file.)

Post Reply
varuniitr
Posts: 69
Joined: 26 Mar 2014, 10:28
First name(s): Varun
Last name(s): Kundi
Affiliation: IIT Roorkee
Country: India

How to run beta calculation for ionic species

Post by varuniitr » 08 Sep 2015, 13:50

Dear DALTON Users,
I am posting very elementary question. Suppose we have cationic species e.g. ammonium ion, how can we incorporate that positive charge in input file? where do we need to specify it? i.e. in .dal file or mol file? The same is the question if we want to optimize the geometry of ammonium ion.

Is this file ammonium.mol correct ?
BASIS
6-31+G*
LINE2
LINE3
Atomtypes=2 Angstrom Nosymmetry
Charge=6.0 Atoms=1
N x y z
Charge=1.0 Atoms=4
H x y z
H x y z
H x y z
H x y z

Thanks in advance !!!!

arnfinn
Posts: 231
Joined: 28 Aug 2013, 08:02
First name(s): Arnfinn
Middle name(s): Hykkerud
Last name(s): Steindal
Affiliation: UiT
Country: Norway
Location: UiT The Arctic University of Norway

Re: How to run beta calculation for ionic species

Post by arnfinn » 08 Sep 2015, 13:53

add Charge=1 to this line:

Code: Select all

Atomtypes=2 Angstrom Nosymmetry Charge=1

varuniitr
Posts: 69
Joined: 26 Mar 2014, 10:28
First name(s): Varun
Last name(s): Kundi
Affiliation: IIT Roorkee
Country: India

Re: How to run beta calculation for ionic species

Post by varuniitr » 08 Sep 2015, 13:56

Dear Arfinn,
Thanks for such a fast reply. If we have one negative charge, then also we need to specify the same?

is this file correct now?
BASIS
6-31+G*
LINE2
LINE3
Atomtypes=2 Angstrom Nosymmetry Charge=1
Charge=7.0 Atoms=1
N x y z
Charge=1.0 Atoms=4
H x y z
H x y z
H x y z
H x y z

arnfinn
Posts: 231
Joined: 28 Aug 2013, 08:02
First name(s): Arnfinn
Middle name(s): Hykkerud
Last name(s): Steindal
Affiliation: UiT
Country: Norway
Location: UiT The Arctic University of Norway

Re: How to run beta calculation for ionic species

Post by arnfinn » 08 Sep 2015, 14:03

Your welcome:)

I am not sure I understood your last question, but I will try to answer it anyway.

The charge you specify in line 5 is the total charge of your system. Thus, if you system consist of one molecule with a positive charge and one molecule with a negative charge, the total charge is zero. Then you have to run either with "charge=0" or not specify the charge at all. If you run a calculation with one molecule with a negative charge (your total QM system you have specified in your mol-file have a negative charge), you have to write "charge=-1".

arnfinn
Posts: 231
Joined: 28 Aug 2013, 08:02
First name(s): Arnfinn
Middle name(s): Hykkerud
Last name(s): Steindal
Affiliation: UiT
Country: Norway
Location: UiT The Arctic University of Norway

Re: How to run beta calculation for ionic species

Post by arnfinn » 08 Sep 2015, 14:07

By the way, in all calculations you have to run with "Charge=7" for the Nitrogen! Otherwise, Dalton will treat it as Carbon. I am no chemist, so did not notice the mistake:)

varuniitr
Posts: 69
Joined: 26 Mar 2014, 10:28
First name(s): Varun
Last name(s): Kundi
Affiliation: IIT Roorkee
Country: India

Re: How to run beta calculation for ionic species

Post by varuniitr » 08 Sep 2015, 14:11

Again, Thank you very much. I got the point.

taylor
Posts: 595
Joined: 15 Oct 2013, 05:37
First name(s): Peter
Middle name(s): Robert
Last name(s): Taylor
Affiliation: Tianjin University
Country: China

Re: How to run beta calculation for ionic species

Post by taylor » 08 Sep 2015, 18:25

Can I caution you that if you want an ammonium ion that displays the "proper" symmetry, that is, Td, you need to be very careful as to how you enter the coordinates. I do not know why you turn symmetry off explicitly: this has nothing but disadvantages for such a small symmetric system, by the way. From a symmetry perspective you would be best advised to specify the symmetry explicitly with

Code: Select all

Generators= 2 XZ YZ
to indicate C2 axes around y and x, respectively: their product will then give C2z. In this case you need specify only one hydrogen, and assuming the N is at the origin the hydrogen coordinates should be

Code: Select all

H  a.bcde  a.bcde  a.bcde
that is, the x, y and z coordinates should have identical values. The program will generate the three symmetry-equivalent hydrogens, and trivial application of symmetry analysis will tell you that the occupation pattern for the ion should be

Code: Select all

.DOUBLY OCCUPIED
  2  1  1  1
and there is then no need to specify the molecular charge in the input file. And your calculation will run considerably faster...

Best regards
Pete

Post Reply

Who is online

Users browsing this forum: No registered users and 7 guests