Hi Shaumik, This will be a time consuming process and I don't think you can simply draw it in gaussview (although I am not certain of this). As far I can tell there are two options:

1 A crystal structure for the molecule from the reference you gave me, exists in the Cambridge structural database (CSD) already. If you can I strongly recommend you download this, then make the modification you wish to make to the structure in that file. The refcode to search the CSD for is GEHRIV.

2 As the paper gives you all of the crystallographic information in it you can write your own .cif, .res .dat or any other crystallographic format you wish to write it in. Gaussview can read .cif files I believe.

Gaussian 09 is not really a code for carrying out calculations on crystal structures. Gaussian 09 is good for gas phase and some solution phase calculations. If you are keen on using Gaussian for this calculation you need to use periodic boundary conditions, here is a link to a good guide (http://scuseria.rice.edu/gau/PBC-Guide.pdf). There are specialized codes for carrying out crystal structure/solid state calculations, which allow supercells with periodic boundary conditions to effectively model an infinite crystal, based on specifying a single unit / asymmetric cell. If you want to remain in the realms of quantum chemistry I would suggest CASTEP which is a plane wave DFT code or CRYSTAL09 which uses the more familiar Gaussian type basis sets with Hartree Fock and DFT methods available. I believe these codes can calculate the IR frequencies for you. URL's for their web pages are below.

CASTEP http://www.castep.org/

CRYSTAL 09 http://www.crystal.unito.it/

Hope that's helpful.

Good luck.

You can definitely use it to draw a single molecule from a unit/asymmetric cell, but in terms of drawing a crystal structure what do you mean exactly? Do you have an experimental crystal structure which you wish to visualise? If so I would recommend something like Mercury, Gdis, VMD, Jmol or Avagadro depending on the format you have the crystal structure in and what it is a crystal structure of. If you don't know the structure are you trying to predict it? If so using what code are you using for this?

Hi James. Thanks for your reply. I actually want to draw what is given in the Fig 2 of the attachment and such similar structures with other molecules as well. So for doing the simulations do I have to write some codes in Gaussian09 or can I straightway draw the structures in GaussView?

I am starting off with Gaussian so a little help would be very much appreciated.

Hi Shaumik, This will be a time consuming process and I don't think you can simply draw it in gaussview (although I am not certain of this). As far I can tell there are two options:

1 A crystal structure for the molecule from the reference you gave me, exists in the Cambridge structural database (CSD) already. If you can I strongly recommend you download this, then make the modification you wish to make to the structure in that file. The refcode to search the CSD for is GEHRIV.

2 As the paper gives you all of the crystallographic information in it you can write your own .cif, .res .dat or any other crystallographic format you wish to write it in. Gaussview can read .cif files I believe.

Gaussian 09 is not really a code for carrying out calculations on crystal structures. Gaussian 09 is good for gas phase and some solution phase calculations. If you are keen on using Gaussian for this calculation you need to use periodic boundary conditions, here is a link to a good guide (http://scuseria.rice.edu/gau/PBC-Guide.pdf). There are specialized codes for carrying out crystal structure/solid state calculations, which allow supercells with periodic boundary conditions to effectively model an infinite crystal, based on specifying a single unit / asymmetric cell. If you want to remain in the realms of quantum chemistry I would suggest CASTEP which is a plane wave DFT code or CRYSTAL09 which uses the more familiar Gaussian type basis sets with Hartree Fock and DFT methods available. I believe these codes can calculate the IR frequencies for you. URL's for their web pages are below.

CASTEP http://www.castep.org/

CRYSTAL 09 http://www.crystal.unito.it/

Hope that's helpful.

Good luck.

Hi James, Thanks a lot for such an informative response. I will go through them is great detail and keep your suggestions in mind. It will be of great help to me.

If you have the Gaussian code, I suggest to use Gabedit (http://gabedit.sourceforge.net/). For solids, independent of the code that you use to obtain their structural properties as well as some important wavefunctions, I suggest Vesta (http://jp-minerals.org/vesta/en/) which draws nice pictures and can use the crystallographic information file (cif) as a input as well.

That great Horacio. Thanks a lot for this information.

Hi Shaumik,

two other solid state codes to consider are VASP and SIESTA I have very little experience with these but maybe worth a look.

Thanks a lot once again James. I will go through these softwares as well and start off asap..

Dear Shaumik, you are in a specific case of studing molecular crystals. You have the big advantage of crystal periodicity, when choosing and using a simulating program (regarding computing resources). CRYSTAL09, CASTEP - are very good, but commercial. Anyway, for all simulating codes you need in input more than the cell parameters and the group symmetry (given in the article attached by you), you need as well the fractional coordinates. I've attached the .cif regarding 2-Formylbenzonitrile (found on http://www.crystallography.net/search.html database). VESTA is a good free software (both Win and Linux) for read, drawing, export .cif, .xyz (text files!). All the structure information you need for further calculations input is in the text (open with notepad or gedit), the visualisation program... is for the picture.

A good free code for properties calculations (including IR spectra) is QuantumEspresso, with well implemented parallel routines; runs only on linux environment.

Well, the previos original cif was non standard, I attached the standardized one (with Vesta) - if you will open as a text file, you'll see modifications on cell parameters, but the picture is OK :)

Good luck!

Gaussian is mainly use for gas phase structure optimization and other calculations such as IR, NMR, energy, TS. Gaussian 09 have much more advantage to solid state calculations. Gauss View can be use for draw molecular structures. However, it may represent most stable structure. But, when we going to calculate isomeric molecules, better to use z-metrix as input method. However, you can use gaussian 09 for your calculations, but I'm not sure it will give most accurate results for that. May be you can try this with applying periodic boundary conditions (PBC), if you know the correct crystal structure for your molecules.

However, for your calculation, it is better to use CRYSTAL software fore for obtain correct structure and then do IR calculation. Sometime you have to develop force field for your system (like Fig 2) with hydrogen bonds (Inter molecular interactions). Best for your studies.

Thanks James once again. I will go through the VASP and SIESTA sites.

Thanks a lot Adrian, regarding your suggestions and sharing the CIF file. I will go through VESTA.

Thanks Lakmal for your advise. Actually I have the Gaussian 09 version and starting off. I will go through the periodic boundary conditions. As suggested earlier, CRYSTAL 09 seems to be the best suited for my studies. Unfortunately, I dont have the CRSYAL09 software.

Unfortunately, I dont have it. There are some free software available in here. You can try with it. If you ok to give some details about your molecule, I try to draw it with gaussian and will send input file. All the best your study.

Dear researchers,

I do have a query regarding DFT run. I want to optimize my metal oxide which has a perovskite structure and its interaction with an fatty acid.

I have already optimized the fatty acid structure using gauss view. Now, how would I do it with metal oxide.

Suggest me.