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Once again, thank you very much for your kind consideration and willingness to assist.
Dear Mr. Tian Lu,
I am writing to express my admiration for the remarkable work being done on the Multiwfn forum in Chinese. It's evident that the forum is flourishing with an abundance of valuable information and engaging activities. One aspect that particularly stands out is the workshops you organize for Chinese students periodically.
I would like to inquire if there are any intentions or plans to organize workshops for a wider audience beyond the current scope. Your insights and teachings would be invaluable to us, and we are in dire need of such opportunities for growth and development.
Warm regards,
Mr. A.may
thanks rikaaardoss, it's helpful
Hello!, sorry to intrude, but no specific software is required to perform ASM calculations. It is only necessary to calculate the distortion energy (or also called preparation energy) and the interaction energy.
The former is calculated from the difference of the formed complex (independent of whether it is a local minimum or a transition state) and the free (i.e. optimized) fragments. Then, the interaction energy can be calculated through the difference of the energy of the complex and the fragments in the geometries they have in the complex (this is done through an SP calculation).
The ASM is also called the distortion/interaction model and was proposed by K. Houk, the studies of Houk's group emphasize mostly on the distortion energy, while bickelhaupt and the proponents of the ASM give more importance to the interaction energy and the energy decomposition analysis. But strictly speaking, that is already more EDA than ASM (or D-I model). Personally, what I have done with multiwfn by way of exploration is to perform a simple-EDA, however sometimes this analysis is somewhat incomplete or cumbersome to calculate (due to the need to calculate dispersion energies).
One suggestion for Multiwfn developers would be to be able to calculate the distortion and interaction energies through the IRC, I believe this would be relatively simple to implement, my programming skills are quite limited, however, I would like to be able to participate in the implementation through the application in a number of systems of interest.
Best regards and many thanks to developers
R.
Hi,
Does the "Activation Strain Model" Method exist in Multiwfn, or does it have one similar to it?
OK, thank you very much
thanks...but, it is D index in the Multiwfn screen output?
This index can be calculated both via hole-electron analysis and based on grid data of electron density difference (between ground and excited states). For the former case, see Section 4.18.1 of Multiwfn manual for example, for the latter case, see Section 4.18.3. The former is more convenient and usually more recommended.
Hello.
How can I use the multiwfn program to calculate the DCT index?
Thank you so much
OK, thanks a lot
well,
1/Do you have a study or reference dealing with this issue? (Organometallic solubility)?
2/Other than a G09 output file and the Multiwfn programme, what do I need to get the solubility value?
3/Is there a similarity between GIPF and COSMO-RS?
GIPF descriptors are suitable for any kind of system.
Hello,
Is it possible for GIPF descriptors to determine the solubility of a system containing metal atoms, such as Cu atom?
Thank you very much.
OK, thank you very much.
This is a very common and widely accepted practice, see my paper Computational and Theoretical Chemistry, 1200, 113249 (2021) DOI: 10.1016/j.comptc.2021.113249 for example, in the examples in Section 4 I used a relatively low level for geometry optimization while significantly better level for energy evaluation.
Hello,
I was aware that in a geometry optimization procedure, you encourage the usage of small basis sets. Are there any papers that support this suggestion...? Thank you so very much.
Thank you so much for your response, and please accept my apologies for the delay in responding because I only saw it now... In any case, thanks a lot
Hello,
the vmd program will do that for you as well in a very user friendly graphical environment. You will find the feature from the vmd main window under Extensions -> Analysis -> Symmetry Tool.
Regards,
Michael
AHHHH, My thanks and appreciation
Hello,
The following are the responses I received from the Orca Forum's leaders:
For the second question (ORCA outputted only the shielding tensor of the last real atom (94H) and has not shown up that of 95H (the ghost atom).) the answer is as follows:
One of the many idiosyncrasies of the EPRNMR module is that counting for the NUCLEI keyword starts at 1, unlike most of the program. This is noted in the manual. So 94H is the 95th atom in the molecule. You can ask for atom 96, but it's probably easiest to just let the program calculate all shieldings - as discussed, the calculation time is basically the same.
As for the basis set on the ghost atom: it is not wrong per se to use a regular basis like def2-TZVP - indeed, it gets the globally assigned basis for hydrogen (or whatever element the ghost atom is). However, it does introduce a basis set error if you compare multiple calculations which only differ in the position of the ghost atom (or lack thereof). Since def2-TZVP is probably not at the CBS limit for shieldings, this error may be significant.
In other words, the basis set of the ghost atom is added to the basis set of the system, but what you probably want is to probe different spatial positions of the system with its basis set unchanged. You can do that with a dummy atom (X) but then the problem is that the latter has no grid points, so for DFT at points just a couple of Angstrom away from real atoms, you get totally wrong results. Hence, the workaround of using ghost atoms (which do get grid points) but giving them a practically non-interacting basis of a single tight s-function (and corresponding aux functions, if necessary).
the answer on - although I asked the program to calculate the magnetic shielding tensor of one atom, the time spend to do that was not less than that it spend to calculate the magnetic shielding tensor of all the atoms of the molecule, Does this make sense?- the respond was:
Most of the time is spent in the CPSCF equations that are done for the x,y and z component of the magnetic field.
The shielding tensor is a second derivative, so one could formulate it to first take the derivative with respect to the nuclear magnetic moment and then wrt to the magnetic field. Then you would benefit greatly in performance if you have only one nucleus (see work by Ochsenfeld et al who report this "sublinear scaling") but as soon as you would have more than just a few nuclei (as you would typically for 1H NMR) you would need much (!) more time. This is why most codes first do the field derivative, and also why you hardly save any time if you only need few nuclei as the second derivative is comparably cheap after the CPSCF equations have been done.
well, thank you very much
I'll post my inquiry in the ORCA forum, then I'll share the reply here (If you don't mind).
I am not familiar with this feature of ORCA. What I can say is that multicenter bond order (also known as multi-center bond index) and AV1245 in Multiwfn are suitable for investigating aromaticity of porphyrin-like systems. The ICSS supported by Multiwfn is very useful in visually studying aromaticity of this system, though the cost is high.
Hello,
1/Which aromaticity index is appropriate for Porphyrin-like systems?
2/
I used ORCA and the corresponding input below to calculate the magnetic shielding tensor at a ghost atom H: 1 A° above the ring plan (-0.0676346525,0.0191628382,-0.8365329255). the order of the ghost atom is 95.
the structure of the input is:
%pal nprocs 10 end
%maxcore 3675
! B3LYP def2-TZVP def2/J def2/JK TightSCF NMR RijCosX GridX4
* xyz 0 1
C -2.82353463539941 -1.13724734028106 0.44846883140457
C -4.18974744461116 -0.69584407152261 0.53629948317338
.
.
.
H: -0.0676346525 0.0191628382 -0.8365329255 # This H atom is defined as a ghost atom
*
%EPRNMR
NUCLEI = 95 {SHIFT}
END
Somehow, ORCA outputted only the shielding tensor of the last real atom (94H) and has not shown up that of 95H (the ghost atom).
On the other hand, although I asked the program to calculate the magnetic shielding tensor of one atom, the time spend to do that was not less than that it spend to calculate the magnetic shielding tensor of all the atoms of the molecule, Does this make sense?
thank you very much
OK, thanks
Hello,
I’m using the ORCA output as an input for Multiwfn, and, when I want to view the Molecular structure and the orbitals ( option 0), I got the following message error: “Error: Data needed by this function is not presented! Check your input file!”
Which keywords should I add to my ORCA'input file to overcome this issue?
thank you very much.
Hello,
Follow the steps in the following reference:
thanks, I will
Have a look at SYVA code, which is freely available and can be downloaded at Computer Physics Communications 215 (2017) 156–164. SYVA is able to detect point group and can present symmetrized structure.
Hi,
I want to symmetrize it
Do you want to symmetrize your molecular structure? or simply detecting point group?
Hello,
I look for a free software, capable of imposing a point group symmetry to my molecule.
Thanks in advance.
Hello,
If necessary ... we will learn Chinese.
Ah!!! I thought, Really, that it was one of your useful programs... Anyway, thank you very much.
It is impossible.
This problem is irrelevant to Multiwfn, you should ask developer of AICD code.
Hello, Multiwfn users,
its possible for AICD to read the output of ORCA NMR calculation ?
thank you very much
good, thank you very much
well, thank you very much
The most rigorous way is performing molecular dynamics simulation of the substance in a given solvent environment, using such as GROMACS program.
From pure quantum chemistry perspective, you can calculate solvation free energy using SMD implicit solvation model, which is a key factor determining solubility, it is expected that the more negative the value, the higher the solubility. However, you should also consider vaporization free energy of the substance, which reflects the difficulty of scattering the substance from solid state to ideal gas state.
Hello,
It is possible, computationally, evaluate the molecule solubility, or, How do we know that the molecule x is more soluble than compound y?
Hello,
I respectfully request your assistance, to benefit from this experimental data (constant current mode, Tunneling current: 0.5 nA; bias voltage: 100 mV, scan rate: 40.7 Hz), to select the most appropriate Multiwfn sittings, to simulate the STM image.
HOMO=-3.872242 eV
LUMO=-3.903024 eV
HOMO-LUMO gap: -0.030782 eV
thank you in advance.