[QE-users] occupation in biological molecules and band gap

[Mahmoud Payami Shabestari]

Before any scf calculations one does not know about the levels distribution, 
so adding smearing may help in cases where the levels are too close near 
HOMO. Otherwise, it wont harm anything else.



Mahmoud









From: Kazume NISHIDATE <nisidate at iwate-u.ac.jp>
To: xavier neto <jxln_karate at yahoo.com.br>,  Quantum ESPRESSO users Forum 
<users at lists.quantum-espresso.org>
Date: Tue, 2 Nov 2021 10:56:28 +0900
Subject: Re: [QE-users] occupation in biological molecules and band gap




> I've watched/read some tutorials about QE, and some of these showed
> that the occupation of semiconductors should be "smearing", other
> ones that it should be "fixed",

The occupancies of metals and semiconductors should be "smeared" to
obtain a good convergence of the calculation.

In the plane-wave DFT calculation for the 'cyclic systems', we use
desecrate k-point mesh where the occupancies of electrons may have
decimal point if it cross the fermi-level (HOMO).

> What value should I use for the SCF and electronic calculations of
> the crystals that I'm going to work on (amino acids, hormones,
> neurotransmitters, and drugs)?

You should use the smearing method.

> *Are there any differences when the molecule has a metal, like the
   Heme group?

You also should use the smearing method in that case.

You also should perform the spin polarized calculation for the
molecule with a metal to check if there is no significant difference
with the no-spin polarized calculation.


> Besides, I would like to ask if there is a calculation that I could
> perform to obtain the bandgap of these molecules. Is it only
> possible if I create the band structure figure and calculate the
> difference between the peaks in VB and CB?

You can obtain a 'coarsely' estimated band gap by plotting the DOS
after the scf calculation with the dense k-point mesh.  If the value
is significantly differ from that at the gamma point, the VBM-CBM
(HOMO-LUMO) gap must be located at some k-point other than gamma.






best regards
kazume NISHIDATE
敬具　西館数芽

nisidate at iwate-u.ac.jp
kazume.nishidate at gmail.com
 
2021年11月2日(火) 9:05 xavier neto via users 
<users at lists.quantum-espresso.org>:
Dear Mahmoud Payami,
Thank you for your answer. It helps me a lot.
So, I can use the Fixed occupation and, if the energy levels show a small 
bandgap, I introduce the Smearing. Is it right?


About the second question. I've read that the result of HOMO - LUMO, 
obtained after the SCF calculation, can give the bandgap. Can I obtain the 
bandgap in that way? If yes, I just have to add the nbnd function in the 
input file?
On 11/1/21 02:04, Mahmoud Payami Shabestari wrote:
Dear José Xavier,
Hi.
Smearing for the occupations is used when the levels near HOMO are so close 
(commonly in metals near Fermi level) that in consecutive iterations they 
may exchange positions and lead to nonconvergence. For semiconductors with 
3-5 eV gap I think it won't help. 
Bests
Mahmoud Payami
NSTRI, AEOI, Tehran, Iran




From: José Xavier via users <users at lists.quantum-espresso.org>
To: "users at lists.quantum-espresso.org" <users at lists.quantum-espresso.org>
Date: Mon, 1 Nov 2021 00:18:55 +0000 (UTC)
Subject: [QE-users] occupation in biological molecules and band gap


Dear all,

I'm new in QE. The group that I'm working with usually calculates the 
properties of biologically relevant molecules, like amino acids, hormones, 
neurotransmitters, and drugs, and I would like to introduce the QE code to 
the group. Their previous papers have shown that the bandgap of these 
crystals is something between 3-5 eV, which I understand to be in the 
semiconductor range.

I've watched/read some tutorials about QE, and some of these showed that the 
occupation of semiconductors should be "smearing", other ones that it should 
be "fixed", but no one showed calculations with this kind of molecules. What 
value should I use for the SCF and electronic calculations of the crystals 
that I'm going to work on (amino acids, hormones, neurotransmitters, and 
drugs)?

*Are there any differences when the molecule has a metal, like the Heme 
group?

Besides, I would like to ask if there is a calculation that I could perform 
to obtain the bandgap of these molecules. Is it only possible if I create 
the band structure figure and calculate the difference between the peaks in 
VB and CB?

Thank you for your help,

Sincerely,
José Xavier

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