简单量子化学问题答疑专帖

wzkchem5

moiumuio 发表于 2024-3-28 08:29
Hi prof.
Is it possible for me to downgrade the basis set when I optimize different structures?
M ...

If you are not doing even a single comparison between any of your monomer calculations and your polymer calculations, then yes you can. Otherwise you should re-optimize your monomers with B3LYP-D3BJ/6-31G*. Then, if the B3LYP-D3BJ/6-31G* and B3LYP-D3BJ/6-311G* structures are sufficiently similar, this proves that your monomer single point calculations can be done upon the B3LYP-D3BJ/6-31G* geometries without much problem (and your B3LYP-D3BJ/6-311G* calculations are not wasted, since you can include those results in your SI to support the validity of using B3LYP-D3BJ/6-31G*). If the structures are not similar, this would cast doubt on the quality of the B3LYP-D3BJ/6-31G* polymer results. You can then try to use some cheap method (e.g. gCP (J. Chem. Phys. 136, 154101 (2012); the method is available in ORCA and Turbomole)) to approximately correct the basis set deficiencies of 6-31G* without using larger basis sets.
Besides, unless you need to calculate the single point energy at the same level of theory for your polymer, you can afford to use much more accurate methods for the single point energies, such as DLPNO-CCSD(T)/cc-pVTZ, without significantly increasing your total computational cost.

moiumuio

wzkchem5 发表于 2024-3-28 16:56
If you are not doing even a single comparison between any of your monomer calculations and your po ...

The results of complexes' geometry are different between 6-31G* and 6-311G* in some cases, especially with difficult input structures. So I must also use 6-311G* for a polymer chain?
About other methods, ORCA is not familiar to me so it will cost lots of time to learn how to use it :(

wzkchem5

moiumuio 发表于 2024-3-28 10:23
The results of complexes' geometry are different between 6-31G* and 6-311G* in some cases, especia ...

If for some reason you have to use only e.g. Gaussian, then you'll probably have to use 6-311G* for the polymer. Since 6-311G* is not much larger than 6-31G*, such a calculation is probably not as difficult as it sounds.
While it indeed takes a lot of time to learn all functionalities of ORCA, it takes no more than half a day to learn how to do DLPNO-CCSD(T) and gCP calculations. There is a very nice ORCA tutorial for the most commonly used functionalities of ORCA (https://www.orcasoftware.de/tutorials_orca/), and you can see it's fairly short; if you only learn a subset of the functionalities it takes even less time. For details you can also refer to the ORCA manual (available in the Download section of the ORCA forum (https://orcaforum.kofo.mpg.de/index.php). Moreover, there are tools, e.g. Multiwfn (http://sobereva.com/multiwfn/) that can generate ORCA input files automatically, and the user merely needs to choose the desired level of theory out of a list, without needing to learn the ORCA input file grammar at all. Finally, not only is the basic functionalities of ORCA easy to learn and use, but also, in case the reviewer asks you to do an ORCA calculation, you can hardly find any excuse not to use it, because ORCA is free. You certainly cannot respond the reviewer with something like "I don't have time to learn ORCA" :)

moiumuio

wzkchem5 发表于 2024-3-28 17:56
If for some reason you have to use only e.g. Gaussian, then you'll probably have to use 6-311G* fo ...

Is the difference in the output between with and without polarization on Hydrogen small enough in order to not considered due to there are intermolecular interaction between monomers?
About ORCA, I used it before (on windows) but the output files were a lot and they don't have in-house GUI like gaussview so beginner like me confused for very first time. But, I will dive into it for the next project xD

wzkchem5

moiumuio 发表于 2024-3-28 13:30
Is the difference in the output between with and without polarization on Hydrogen small enough in  ...

Sorry I didn't see your extra "*". By 6-311G* I actually meant 6-311G**.

cokie

各位老师好，我在使用genmer+mopac做过二聚体构象筛选后，对能量最低的10个分子在gaussian16中进行优化，请问我采用wb97xd/6-311G**级别优化时，针对我的体系是否需要考虑BSSE呢？（酞菁环，面面堆积）

minhduy

Hi everyone,
I currently research on transition metal complex. I want to ask that there are many articles use BS1 (SDD, 6-31G**) and BS2 (SDD,6-311++G**) basis sets for optimization and SP calculation. For BS2, is it worth to add diffuse function on Hydrogen (considering there is participation of H in the formation of complex); and are there any better options that do not require much more resources?
Thank you all

moiumuio

moiumuio 发表于 2024-3-28 15:29
Hi prof.
Is it possible for me to downgrade the basis set when I optimize different structures?
M ...

BTW if I use B3LYP-D3(BJ)/ma-def2-TZVP(-f) to calculate binding energy, should I use it with BSSE. And should I change B3LYP-D3(BJ) to M06-2X?

junemu

sobereva 发表于 2024-3-28 00:21
这种一堆文字、有图有文件的情况不属于简单问题，应当单独发帖以引起更多人的关注

好的老师。我下次注意

15670538028

老师好，最近刚接触（一个钪取代氟化碳笼的一个C-F单元）的工作（145个原子左右），查阅文献发现了各种方法基组情况，想问老师直接用b3lyp-d3/6-31g(d,p)可以吗？需要对这一个钪单独设基组吗？如果需要设哪个基组更便宜好用？另外这个体系的自旋多重度为1吗？（搜索文献发现钪可能为+2价，也可能为+3价）

wzkchem5

15670538028 发表于 2024-3-29 09:15
老师好，最近刚接触（一个钪取代氟化碳笼的一个C-F单元）的工作（145个原子左右），查阅文献发现了各种方法 ...

由这些背景信息不足以回答。体系里面有没有单电子？带多少电荷？有单电子的情况可能需要HF exchange比较多的泛函，来减少SIE的影响；带比较多负电荷的情况，需要加弥散函数

wzkchem5

cokie 发表于 2024-3-29 02:36
各位老师好，我在使用genmer+mopac做过二聚体构象筛选后，对能量最低的10个分子在gaussian16中进行优化，请 ...

结构优化要考虑BSSE的话，基本只能用gCP，不能用counterpoise（因为没有解析梯度，计算量成百倍增加），所以高斯做不了，得用orca做。但gCP应该没有6-311G**的参数，所以需要换基组，具体参见orca说明书的gCP章节。

sobereva

15670538028 发表于 2024-3-29 16:15
老师好，最近刚接触（一个钪取代氟化碳笼的一个C-F单元）的工作（145个原子左右），查阅文献发现了各种方法 ...

当前计算级别没显著问题
自旋多重度拿不准就不同自旋态对比能量就完了

sobereva

cokie 发表于 2024-3-29 09:36
各位老师好，我在使用genmer+mopac做过二聚体构象筛选后，对能量最低的10个分子在gaussian16中进行优化，请 ...

这个档次基组对于结构优化一般不用特意考虑BSSE问题。但使用稍微更贵一点的def-TZVP会更好，BSSE还会更小

gyp

请问高斯如何建模这种带电体系并计算，小白刚学高斯，可以复现一些文献中不带电分子的HOMO LUMO轨道，但是遇到这种带电荷的就不知道怎么算了