Dear Mohammad,

There is no such thing called DFT code.

You have not achieved convergence since you are calculating three different molecules together. It is very hard for the program to reach global minimum for the three entities when no constrains is imposed.

In order to get convergence, you should at some stage to make constrains on the distances between the three molecules.

Hoping this will be helpful,

Rafik

As Rafik suggested this is a fairly complicated system. But it can be handled by several different methods. 

First, though, you say that DFT (B3LYP?) with 3-21G deforms it from the input structure. What's wrong with that? How did you get the input structure? And why do you presume that it should stay close to this geometry? If it's an experimental structure you have to make sure that you provide similar conditions (crystal - perdiodic boundaries or constraints; solution - solvent) before you make any judgement.

Going back to theory: there are many free DFT codes available - see e.g. Orca or Gamess. The thing is that their implementations of various DFT functionals are similar so I wouldn't expect different results than those obtained in gaussian. Since you don't have any metals you can try PM6 (in gaussian) or PM7 (in free mopac) which is much faster (should optimize in minutes) and quite good for organic systems. Also, any force-field based method that can handle simple organic molecules should also do fine, you can try the simplest UFF (or amber) in gaussian - but obviously the output will be basically limited to just the optimal geometry.

Dear Rafik and Bartosz,

First of all, many thanks for the kind comments expressed by both of you. the input file of this structure is obtained from a CIF using mercury + gaussview software an then I have tried an optimization. so you can see that I have not any interference or right to determine the distances of the molecules and a further notice is that the water molecule and citric acid are two intermediates between chlorhexidine (larger molecule) forming a network using hydrogen bonds (see attached file). 

Dear Bartosz,

I will take a look over the codes you mentioned and i hope  find a downloadable version.

Mr. Taghartapeh,

You can use ONIOM method, allowing you to treat different parts of a molecular ensemble for different levels of theory. Please pay attention to ref. 1 (below).

I am attaching you, too, files of MM2 optimized ensemble at one layer approach (RG-1.gjf) and a file (RG-Guan-ONIOM-1.gjf) with 2 layer ONIOM where the higher level involves DFT computations, while the medium level - UFF ones. You could replace these methods with any other ones in order to improve the accuracy of the energy as has been discussed by other participants. The acid, H2O and guanidinium fragment which participate in H-bonding are treated for DFT, while to the remaining part of the molecule is applied a force field (attachment).

I have received, however that H-bond scheme includes a charged guanidinium cation and R-COO- anion. The COO- and CH2 groups in the acid are almost perpendicular oriented, not as shown in your posting. But I can assume that you have not applied a preliminary MMX optimization. This is recommendable step, in order to reduce the computational time as well. So, your increased computational time, can be due to reason of such are character, too.

In addition, you may do a preliminary conformational analysis of the cation. Because of, if your initial conformation as given in your positing and used in attached herein files, does not correspond to most preferred geometry, this also increases the computational time. For flexible molecules there are possible set conformational states, so that it is better to use as starting geometry, this conformational state, which is most close to the corresponding one at the energy minimum.

You may reduce the number of optimization steps as well. In this context, GaussSum (http://gausssum.sourceforge.net/) is useful in order to monitor the geometry optimization. You do not need a large number optimization steps, and thus in your example (but this one!) of interacting ions/molecule, you can further reduce the computational time via iop(1/8=N) (DXMAXT=0.01.N) (http://www.gaussian.com/g_tech/g_iops/iops2.pdf)

Ref. 1. The ONIOM Method and Its Applications, L. Chung, W. Sameera, R. Ramozzi, A. Page, M. Hatanaka, G. Petrova, T. Harris, X. Li, Z. Ke, F. Liu, H. Li, L. Ding, K. Morokuma, Chem. Rev., 2015, 115, 5678–5796 (Review).

Dear Professor Ivanova,

Many thanks for your kind and helpful comment. I did not apply any preliminary optimization and/or conformational analysis over cation but i do believe it may has some conformations as well.

this is exactly a salt system between a cation and anion. I will try with GaussSum to see the results and attached you can see the .gjf files as well, as I have another crystal of this kind which is the same cation with different anion and it is greatly appreciated if you take a look over them and express your kind helpful comments on that.

please note that, there are two single Oxygen atoms next to Cl O4.

Mr. Taghartapeh,

 Please find *.gjf files of your crystal structures. There are given files associated with your initial crystallographic coordinates and these structures, which are optimized by MM2 before further optimization.

 Files of structure “p.b.”:

 -  Struct-1-cr-ONIOM.gjf data of “p.b.” in 2-layer ONIOM);

-   Struct-1-MM2.gjf (data of p.b. optimized by MM2)

-   Struct-1-MM2-ONIOM.gjf (data of :p.b.”, optimized by MM2 in 2-layer ONIOM)

 Files of structure “scr”:

-   Struct-2-cr-a.gjf (data of “scr”)

-   Struct-2-cr-1-ONIOM.gjf (data of “scr” in 2-layer ONIOM)

-   Struct-2-MM2-a.gjf (data of “scr”, optimized by MM2)

-   Struct-2-MM2-a-ONIOM.gjf (data of “scr”, optimized by MM2 in 2-layer ONIOM)

-   Struct-2-MM2-b.gjf (data of “scr”, optimized by MM2)

-   Struct-2-MM2-b-ONIOM.gjf (data of “scr”, optimized by MM2 in 2-layer ONIOM)

-   Struct-2-MM2-c.gjf (data of “scr”, optimized by MM2)

-   Struct-2-MM2-c-ONIOM.gjf (data of “scr”, optimized by MM2 in 2-layer ONIOM)

-   Struct-2-MM2-d.gjf (data of “scr”, optimized by MM2)

-   Struct-2-MM2-d-ONIOM.gjf (data of “scr”, optimized by MM2 in 2-layer ONIOM)

The difference between files shown as “a”–“d” consist in different initial position of the negative charge over {[ClO4]-} counterion. If you pay attention to your crystallographic file of “scr” and attachments “Struct-2-cr-a.gjf”  and “Struct-2-cr-1-ONIOM.gjf”, there are obtained following bond lengths of r(Cl-O) 2x(1.463), 1.464 and 1.451 A, respectively. As it is well known the negative charge of {[ClO4]-} is over the O-center. In this case there is only one position.

However the optimization of the crystal structure of “scr” by MM causes for an “almost equalization” of Cl-O distances (r(Cl-O) ca. 1.63 A). According to possible resonance structures (attachment) there should has only one position as well. But this should be accounted for an isolated state of the {[ClO4]-} ion. Because of, however, the environment around {[ClO4]-} ion in the nsemble “scr” is different and the electrostatic interactions are dominant between O- center of {[ClO4]-}, crystallohydrate (2H2O) molecules and guanidinium cation, there should have different energy terms depending on the position of negative charge over O-centers in {[ClO4]-} counterion. In this context you should optimize not only one structure, but 4-structural models with different initial positions of this negative charge in order to account for a correct energy of the interacting system of your model ensemble, which is different from the crystallographic one.    

Simply speaking, you shall obtain perturbation of the energy values, depending on the initial position of negative charge over different O-centers of {[ClO4]-} ion, due to different interaction modes with the environment (counter ions, H2Os; attachment).

NB! Depending on the combination of the theoretical methods using ONIOM {method1:method2:(method3)} there is possible to have different combination charge/multiplicity. There is needed to add in corresponding “charge/multiplicity” “window” of an opened file, ONLY the values as following: charge multiplicity “(high level, h)” charge multiplicity “(medium level, m)” charge multiplicity “(low level, l)” (eventually for 3-layer ONIOM) (attachment). 

Dear Professor Ivanova

What is the criterion of choosing the part of molecule for low, medium and high level calculation?

Thanks 

Mr. Alam,

I have already posted a reference (Ref. 1. The ONIOM method and its applications, L. Chung, W. Sameera, R. Ramozzi, A. Page, M. Hatanaka, G. Petrova, T. Harris, X. Li, Z. Ke, F. Liu, H. Li, L. Ding, K. Morokuma, Chem. Rev. 2015, 115, 5678-5796 (Review)).

There are explicitly written applicability criteria on the base on error contribution of the methods depending on the properties of interest. In ref. 1 the criteria are expressed in quantitative terms, using corresponding equations.

Professor Ivanova, Thank You