I'm new in computational chemistry. I'm doing molecular docking on organic compounds towards enzyme. basically, I'm using B3LYP/6-311G to optimize all the ligand structure. Is it generally accepted to use this basis set? if not, any suggestion? generally, I'm working with organic compounds such as phenolic derivatives and flavonoids.
6-311G should never be used, because it lacks of polarization functions, which is quite important for obtaining reasonable structure if the system contains heteroatoms (e.g. sulfur, oxygen, nitrogen). Commonly, I suggest using 6-311G* instead. When hydrogen plays an important role (e.g. studying H-bond, or bond characters that related to hydrogen), 6-311G** is suggested.
When optimizing very flexible systems, whose conformation/configuration is sensitive to dispersion effect, you should add dispersion correction (e.g. DFT-D3) to B3LYP, because it is well-known that B3LYP completely fails to represent dispersion interaction.
If your system shows widely conjugated character, B3LYP is not recommended, because it has strong tendency to optimize the system as a fully planar structure and the bond alternation character is usually underestimated. The failure of B3LYP in optimizing annulene systems is a typical example, see Angew. Chem. Int. Ed., 43, 4200 (2004) for discussion.
When B3LYP doesn't work well, I suggest using ωB97XD instead, which does not have the two aforementioned limitations and it is able to well represent various kinds of organic systems.
PS: Previously I wrote a blog article to extensively discuss when B3LYP is a reasonable choice of performing optimization, see http://sobereva.com/557 (in Chinese, you may use Google translate to understand the content.)
6-311G should never be used, because it lacks of polarization functions, which is quite important for obtaining reasonable structure if the system contains heteroatoms (e.g. sulfur, oxygen, nitrogen). Commonly, I suggest using 6-311G* instead. When hydrogen plays an important role (e.g. studying H-bond, or bond characters that related to hydrogen), 6-311G** is suggested.
When optimizing very flexible systems, whose conformation/configuration is sensitive to dispersion effect, you should add dispersion correction (e.g. DFT-D3) to B3LYP, because it is well-known that B3LYP completely fails to represent dispersion interaction.
If your system shows widely conjugated character, B3LYP is not recommended, because it has strong tendency to optimize the system as a fully planar structure and the bond alternation character is usually underestimated. The failure of B3LYP in optimizing annulene systems is a typical example, see Angew. Chem. Int. Ed., 43, 4200 (2004) for discussion.
When B3LYP doesn't work well, I suggest using ωB97XD instead, which does not have the two aforementioned limitations and it is able to well represent various kinds of organic systems.
PS: Previously I wrote a blog article to extensively discuss when B3LYP is a reasonable choice of performing optimization, see http://sobereva.com/557 (in Chinese, you may use Google translate to understand the content.)
Thank You Tian Lu . How about working with organometallic compound such as cisplatin (made up of platinum)? any suggestion?
Tian Lu So how about the basis set? should I use 6-311G* or 6-311G**?
I addition to lacking polarization functions, it doesn't take into account dispersion effects. Description of such effects is mandatory. You must add Grimme's dispersion (B3LYP-D3 or similar). With Gaussian program this is done withy the keyword EmpiricalDispersion=GD3
I agree with the preposters that you need polarizing functions. Instead of the Pople-type basis sets you could also use def2-TZVP; as soon as your molecule gets somewhat branched, the D3 dispersion correction Agusti Lledos mentioned gets pretty important.
Mohd Amir Asyraf Mohd Hamzah: As you have glimpsed from the responses thus far, asking a question like "which method is best?" will garner a wide variety of answers, depending upon the viewpoints of the advocates. The question needs to be more narrowly framed to obtain useful replies. From my perusal of your question, you are going to use the structures in a docking campaign. Docking is a low-fidelity operation that does not account for the induced fits that occur when ligands bind to the enzyme. As a result, fraction of an Angstrom differences in structures will not yield significant differences in your docking results. Therefore, you can probably get away with rather modest levels of theory. It wasn't that long ago that 6-31g* was the gold standard for structures. Now, 6-311++g** calculations are not not uncommon but drastically more expensive computationally.
My guess is that you are investigating decorating putative ligands with extra hydroxyl or methyl groups, or whatever, to see if that might improve the binding affinity. Given that none of your optimized structures will reflect the actual conformational changes that will take place in the enzyme, I suggest that a more modest basis level will be adequate. You can utilize either the Pople or def2-tvz
types, depending upon your particular tastes.
https://docs.google.com/forms/d/e/1FAIpQLSfNpiah9wUc--jA7V1_42J2M3Cjlgtvgj-vDEasBIPXbEs9MQ/viewform?usp=pp_url
Dear colleagues,
Department of Pharmacy, Universitas Muhammadiyah Palangkaraya openly inviting researchers with expertise in the field of Molecular Docking to join the new journal that will be released in early 2021, both as an editorial board and as peer-reviewers.
We will call this journal "Journal of Molecular Docking" or "J. Mol. Docking", with a very specific aim and scope, namely various research in the field of science and health using Molecular Docking as its main method.
Currently we are still preparing the journaling platform with OJS 3.1.1.2 and will start collecting articles as soon as the editorial board and peer-reviewer members are gathered. The link for this new journal is http://journal.umpalangkaraya.ac.id/index.php/jmd.
It should be noted that this position is voluntary, so all editors and reviewers will not receive any rewards in the form of funds. However, we will provide a certificate of appreciation for each manuscript handled, both as an editor and reviewer.
The target of this new journal is to be indexable by DOAJ after the first year and indexed by Scopus and/or ESCI WoS after the fifth year.
For this reason, we expect the willingness and participation of Molecular Docking researchers to be directly involved in the development of this new journal so that later it can become a publication benchmark for research with the molecular docking method.
Once again, we are grateful for the participation of all researchers and hope for their support to be able to create and grow this new journal.
Best regards,
Mohammad Rizki Fadhil Pratama
Assistant Professor of Medicinal Chemistry
Universitas Muhammadiyah Palangkaraya
http://orcid.org/0000-0002-0727-4392
Our gaussian does not have D3 dispersion correction. Is it ok to use wb97xd with basis 6-311++g** for my experiment?
Can someone suggest papers on wb97xd for further reference?
Thank you
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