The ONIOM calculation is unable to yield wavefunction as other tasks. So, if you want to perform wavefunction analysis, using ONIOM must be avoided.

Best regards,

Tian

]]>I am not sure if ORCA itself has this capacity (seemingly impossible for present version if I remembered correctly), but this can be easily realized by using Multiwfn program (http://sobereva.com/multiwfn) based on ORCA output file.

After loading .molden file generated by ORCA into Multiwfn, you will be able to study ground state electronic structure, various kinds of atomic charges and bond orders can be evaluated by main functions 7 and 9, and there are lots of examples in Section 4.7 and 4.9 of the Multiwfn maunal, respectively.

If you want to use Multiwfn to study excited state wavefunction, you should first generate .molden file containing nature orbitals of the excited state of your interest. You should first use ORCA to carry out a normal electron excitation calculation via keywords like below (see beginning of Section 3.21 of Multiwfn manual for detail):

! PBE0 def2-SVP nopop

%tddft

nroots 8

tprint 1E-8

endAssume that the output file is exc.out and the generated .molden file via orca_2mkl is exc.molden.input, then after boot up Multiwfn you should input:

exc.molden

18 // Electron excitation analysis

13 // Generate natural orbitals of specific excited states

exc.out

4 // Assume that the 4th excited state is the one you want to study

Now you will find NO_0004.molden has been generated in current folder. Using this file as input file of Multiwfn, the calculated quantities such as atomic charges and bond orders will correspond to the 4th excited state.Note that above mentioned way is strict for CIS or the TDDFT under TDA approximation. For TDHF and regular TDDFT, the result obtained in above way may or may not be very reliable (because current version of ORCA does not print excitation and de-excitation coefficients separately).

Sir,

When the RMSE appears on the screen, what is it's unit?Is it in a.u. as mentioned in page 277

https://i.postimg.cc/kDpF2rQt/Screenshot-20181022-154732.png

When no unit is explicitly given in the output, a.u. is used as default. Therefore, the RMSE of ESP is reported in a.u.

]]>If the charge transfer you mentioned does not come from electron excitation process but purely result from intermolecular interaction, you can study amount of charge transfer based on variation of fragment charge, which is defined as the sum of charges of the atoms in the fragment. Evidently, the fragment could be defined as adsorbate or adsorbent. The fragment charge could be directly outputted by Multiwfn, namely entering main function 7, using option -1 to define a fragment, and selecting one of methods to carry out atomic charge evaluation (the ADCH proposed by me is generally recommended), you will find fragment charge at the end of the output.

An alternative method is plotting density difference map between complex and all fragments, see Section 4.5.5 for example, the charge displacement can be vividly revealed. In addition, if you want to quantitatively represent charges transfer distance and direction during the adsorption, you can first calculate grid data of density difference, and then use subfunction 3 of main function 18 to transform/quantify the density difference (see the example in Section 4.18.3 of the latest version of manual. Although this method was originally proposed for studying charge transfer during electron excitation process, it can also be applied for other cases)

Finally, in certain case, plotting charge displacement curve is useful, see the example in Section 4.13.6.

We can visualize the molecular orbitals (MOs) of a molecule using Gaussview software, but how to visualize or generate the charge density plot of those MOs ?

I copy my reply here since some Multiwfn users may have interesting on this topic

You can use my program Multiwfn (http://sobereva.com/multiwfn) to do this, it is fairly easy. For Gaussian users, the .fch or .wfn or .wfx file generated by Gaussian could be used as input file. Assume that you want to plot density corresponding to MO 4,5,6, after loading input file into Multiwfn, you should first input below commands:

6 // Main function 6 (Modify & Check wavefunction)

0 // Select all orbitals

0 // Clean occupation of all orbitals

4-6 // Select MO 4,5,6

2 // Set occupation number of these MOs to 2.0 (assume that they are closed-shell MOs)

q // Return

1 // Return to main menuThen if you plot electron density in Multiwfn via usual way, what you obtained will correspond to density corresponding to MO 4,5,6. Note that electron density could be plotted in various ways, including curve map, plane map and isosurface map, they can be plotted by main function 3, 4 and 5 of Multiwfn, respectively; related examples can be found in Section 4.3, 4.4 and 4.5 of Multiwfn manual, respectively.

I optimized the ZnS nanotube and amino acid structure by DFT calculations(by DMOL3). i want to know how should i analyze that any bond formed between these 2 structures or not.

Since many Multiwfn users may have interesting on this topic, I copy my reply here:

The most straightforward way to prove formation of chemical bonds is calculating Mayer bond order. If the value is evidently larger than zero, then chemical bond should have formed. Mayer bond order can be easily calculated via Multiwfn (http://sobereva.com/multiwfn), example is given in Section 4.9.1 of Multiwfn manual. Multiwfn doesn't support Dmol3 because Multiwfn only supports Gauss type basis function, however you can use such as the freely available ORCA program to carry out a single point for the optimized geometry to yield .molden file, which could be used as input file of Multiwfn. More discussion about bond order can be found in my paper Phys. Chem. A, 117, 3100−3108 (2013), introduction of all kinds of bond orders supported by Multiwfn can be found in Section 3.11 of Multiwfn manual.

Other kinds of analyses, such as AIM analysis, ELF or LOL analysis, deformation map of electron density, are also quite useful for studying chemical bonding, all of them are fully supported by Multiwfn.

I have written a blog article devoted to discuss how to determine whether a chemical bond has formed, see http://sobereva.com/414 or http://bbs.keinsci.com/thread-9840-1-1.html, it should be very useful for you, but it was written in Chinese (however you could use Google translator to try to understand article content)

Currently wavefunction outputted by CRYSTAL is not supported, sorry!

Best regards,

Tian

]]>The ESP fitting charges based on wavefunction (including MK, CHELPG and RESP) can be calculated via main function 18 of Multiwfn. There is an example of calculating CHELPG charges in Section 4.7.1 of Multiwfn manual.

I just updated Multiwfn on official website today (the 3.6(dev) updated on 2018-Sep-18), this version is able to measure ESP reproducibility of given atomic charges at MK or CHELPG type of ESP fitting points in terms of RMSE and RRMSE. Please check Section 4.7.2 of the latest version of manual for example.

Regards,

Tian Lu

]]>Q:RESP charge by ORCA output

I am trying to get the RESP charges from ORCA calculations in a way similar than in the antechamber, but I am not finding any software that is able to do the fitting in the ORCA outputs. I have tried Multiwfn but the options are CHELPG, AIM, MK and HI.

My problem with the Multiwfn is the lack of equivalence on the atoms charges. I am using a dimer to get the charges, but one of the molecules is symmetrical and when I get the charges by CHELPG in Multiwfn there isn't a equivalence on the atoms. The atoms with the same atom type have different charges.Is there a way to restrain or constraint the charges to force all the atoms with the same atom type have the same atomic charge?

Does anyone know how to procedure?

A:

Fortunately, calculation of RESP charge has been *perfectly* supported by Multiwfn in its latest version. Please go to http://sobereva.com/multiwfn to download the latest version (the current latest version is the 3.6(dev) updated on 2018-Sep-12), and follow the examples given in Section 4.7.7 of the latest version of manual. Multiwfn makes calculation of RESP charge extemely easy. The .molden file outputted by ORCA can be directly used as input file. The RESP module of Multiwfn can not only calculate standard RESP charges, but can also calculate normal ESP fitting charges with customized penalty function, equivalence constraints, charge constraints and multi-conformation consideration.

The underlying reason that spatially equivalent atoms do not have equivalent charges is that the fitting points of CHELPG method are not distributed in accordance with molecular symmetry. If you do not intend to use the new RESP module of Multiwfn to manually impose equivalent constraint on that atoms, you can try to change the CHELPG method to MK method (subfunction 13 of main function 7), if the symmetry of atomic charges is still not satisifed well, you can then try to increase the density of fitting points (there are options used to set parameters of fitting points in the MK and CHELPG interfaces), this problem should be alleviated.

Q:

I saw that your program Multiwfn has a function to calculate the extent of the spatial overlap between two molecular orbitals (3.100.11 in your manual). I am currently looking into some organic polyradicals in which the overlap between the SOMOs is very important to determine the ground state multiplicity, using Gaussian 09 program, and I was wondering if you could guide me on how to use your program. Also, from a more technical point of view, I wonder how you actually perform the integral and how the phase of the orbitals is taken into account. Do you expand the MO in the basis of the atomic orbitals (expressed as gaussian orbitals) and then take the sum of each of the individual overlap?

A:

Proper way of choice of input file format for Multiwfn is described in Section 2.5 of the manual. As mentioned in Section 3.100.11, the needed information is GTF and atom coordinate, therefore according to the Table in Section 2.5, you can immediately know that you can use .wfn, .wfx or .fch generated by Gaussian as input file. Of course, the easiest way is directly using .fch file. After loading this file, enter main function 100 and select option 11, then input indices of the two orbitals you want to study, the overlap will be immediately outputted.

Technically, the overlap of absolutes of two orbitals is calculated in terms of Becke's multi-center integration method, detail can be found in JCP, 88, 2547 (1988). This is a numerical integration method, at each integration point, the program calculates psi_i and psi_j, and then get |psi_i|*|psi_j|, where psi is orbital wavefunction value and can be easily evaluated according to definition of basis functions and LCAO coefficients.