Xishi was a celebrated beautiful woman in Chinese history. It is said that each time when a school of fish in the river saw her washing yarn, they would feel ashamed of their ‘ugliness’ compared to the lady and swam to the bottom. Although she shone out with her speechless beauty, poor Xishi suffered from a weak heart that often left her knitting her brows as she agonized with pain. Read the rest of this entry »
ONIOM
June 28, 2007 at 3:46 pm (Computational chemistry, Gaussian)
I was curious to find the simple explanation about this word: ONIOM. You can believe me that (until I wrote this bog), the word ONION was not appeared in wikipedia. It comes in google but I beg you with already ‘advanced’ applications or uses. Sometimes, only some papers come with that word.
The basic meaning of ONIOM is computing the molecule with different level of theory simulataneously. The reason could be very simple, when you have a large molecule, it will spend a lot of time to calculate all parts with very precise method although you will get the ‘almost’ correct value. On the other hand, using low basis sets, you will produce untrustable result. So, in the middle, you can manage the important part of molecule, doing ‘more’ in term of calculation, and use the low level theory for other parts which don’t need to be very correct. As nowadays there are many basis sets for specific cases, the choice of that is the key of the correctness of the calculation. It requires many literature reviews before doing this case.
In ONION, you can split your molecule into three different levels of QC/MM or QC/QC. QC stands for quantum chemical while MM stands for molecular mechanical. You can find this definition in this blog or by googling I hope you will know it. The definition of these three levels of calculation will be mentioned after you defind the geometry of single atom in the input file of Gaussian. Most methods works with Oniom, e.g. optimisations and frequency calculations. However, SCRF does not work (it is not available for semiempirical or molecular mechanical methods). SCRF or self-consistent reaction field is usually used for the calcilation with solvation (solvent existence) or non gaseous-phase.
The example of ONIOM input in the Gaussian is:
#P Oniom(B3LYP/6-31G*:PM3:Amber) Opt Freq
A three-layer oniom calculation of CH3-CH2-CHO
0 1
h 1.303312051 0.000000000 1.949234062 High
c 0.375760127 0.000000000 1.351034669 High
o -0.718742386 0.000000000 1.904192435 High
c 0.583631613 0.000000000 -0.143478503 Medium H
h 1.171836119 -0.887154331 -0.398970957 Medium
h 1.171836119 0.887154331 -0.398970957 Medium
c -0.720914899 0.000000000 -0.916455389 Low H
h -1.320117994 0.884637788 -0.676628009 Low
h -1.320117994 -0.884637788 -0.676628009 Low
h -0.526482757 0.000000000 -1.993329341 Low
Multi-Coordinate Driven Reaction Path Search
June 28, 2007 at 3:34 pm (Computational chemistry, Gaussian)
Again, I found something that probably useful for you for computational chemist. I think this stuff not only interesting for theoritical chemist but also applied science and engineering, especially the ones who work in chemical kinetic. It is a software that helps you to find the transition structure between reactants and products. More information could be obtained in http://www.chem.elte.hu/departments/elmkem/berente/mcd/readme.htm. This program is made by Imre Berente and named as MCD 1.2. Published work is presented in J. Phys. Chem. A 110 (2006) 772. Here, I will put the Readme file of the sofware and I hope it will clear to you. Read the rest of this entry »
Spin contamination
June 21, 2007 at 12:40 pm (Computational chemistry, Gaussian, Physical chemistry)
Spin contamination is a major problem in computational chemistry science. It rises from the basic method how to calculate the existance of un-paired electrones. I found a good review about basic explanation of spin contamination, written by David Young and available online in http://www.ccl.net/cca/documents/dyoung/topics-orig/spin_cont.html Read the rest of this entry »
Geometry optimization
June 18, 2007 at 2:53 pm (Gaussian)
How much output is generated during geometry optimization (and actually all other types of Gaussian calculations as well) depends on the beginning of the keyword line:
#P will provide somewhat more detailed output
# will provide normal output
#T will provide somewhat less output
Geometry optimization can be performed in three different types of coordinate systems. Please observe that the way, the geometry is defined in the input file, is actually separate from deciding, in which coordinate system the optimization will be performed: Read the rest of this entry »
Catalyst software
June 17, 2007 at 6:35 pm (Computational chemistry, Physical chemistry)
This subject is also interesting to be modelized. The phenomena of diffusion, adsorption or desorption of gas on the surface of the catalyst, e.g. zeolite, is also challenging subject. Some softwares have been created to do MM/QM (Molecular-mechanic and Quantum-Mechanic) simulation to approch and study the phenomena. This is the list of that possible software: Read the rest of this entry »
Gaussian
June 14, 2007 at 9:41 pm (Gaussian)
GAUSSIAN adalah perangkat lunak atau program kimia komputasi yang dibuat pertama kali oleh John Pople [1] dan perangkat lunak paling populer saat ini. Nama dari perangkat lunak ini diambil dari penggunaan orbital Gaussian yang digunakan sebagai basis perhitungan komputer. GAUSSIAN memiliki kemampuan untuk melakukan perhitungan kimia kuantum secara ab initio maupun semi empiris. Versi terakhir dari GAUSSIAN adalah GAUSSIAN seri 03 (diambil dari dua angka terakhir tahun 2003) yang kemudian mengalami perbaikan dua kali, GAUSSIAN 03 c.01 dan GAUSSIAN 03 c.02. Hak cipta pertama GAUSSIAN dimiliki oleh Universitas Carnegie Mellon dan saat ini berpindah tangan ke Gaussian Inc.. Berkat pengembangan GAUSSIAN dan beberapa teori yang dihasilkannya, Pople kemudian memperoleh penghargaan Nobel pada tahun 1998. Read the rest of this entry »
Right or wrong using computational chemistry?
June 13, 2007 at 9:08 pm (Gaussian, Physical chemistry)
This question can be raised anytime when we use computational chemistry. Why? it is because computational chemisty contains ‘black’ parts of chemistry which probably not yet proofable or clearly correct. Easy example, the transition structure (TS). It is still controvercy whether it is really exist, exactly follows the way that we imagine or not? More than that, still many abundant questions on capability of what the computational chemistry is able to do or not possible to calculate. Read the rest of this entry »
Basic FAQ of Gaussian
June 13, 2007 at 2:59 pm (Gaussian)
Thise are some of Gaussian 98 tips that could be useful to start learning the software. In this stage, you are already able to use gaussian technically. This tips and manual is taken from the website of http://www.theorie.physik.uni-muenchen.de/~dahlke/computer/gaussianHowto.html
———————————————————–
1.How to write output file that can be visualized by MOLDEN?
Answer:
Add this line to the beginning of your input file:
#gfinput iop(6/7=3)
———————————————————– Read the rest of this entry »
SMILES
June 8, 2007 at 10:41 am (General chemistry)
Do you have porblem on naming the chemical structure that you find? I had it last time when i found 3-methyidene cyclopropene. And what is the relation with SMILES? Oke, may be you don’t need or there is no connection anymore. The most easies way to find the molecule is going to the chemical database. If you don’t have, there are some sources in the internet for example: eMolecules (http://www.emolecules.com) or PubChem (http://pubchem.ncbi.nlm.nih.gov). Those websites have the complete database of chemical molecules and referrer each others or to another site. The information is quite complete, for example the supplier, full name, brief property, mol structure, and the most important is IUPAC name. Read the rest of this entry »
